r28307 - in /trunk/test_suite/shared_data/frame_order/cam: ./ double_rotor/ double_rotor_large_angle/ free_rotor/ free_rotor...
Author: bugman Date: Sun Nov 20 10:45:42 2016 New Revision: 28307 URL: http://svn.gna.org/viewcvs/relax?rev=28307=rev Log: Updates to many frame order test suite shared data relax scripts. These scripts are used for data generation and display, and are not part of the test suite. The updates are for the frame_order.pdb_model and pymol.frame_order user functions which no longer support the 'dist' keyword argument (this functionality was shifted into the frame_order.simulate user function). Modified: trunk/test_suite/shared_data/frame_order/cam/double_rotor/frame_order.py trunk/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/frame_order.py trunk/test_suite/shared_data/frame_order/cam/free_rotor/frame_order.py trunk/test_suite/shared_data/frame_order/cam/free_rotor2/frame_order.py trunk/test_suite/shared_data/frame_order/cam/free_rotor_missing_data/frame_order.py trunk/test_suite/shared_data/frame_order/cam/iso_cone/frame_order.py trunk/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor/frame_order.py trunk/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor2/frame_order.py trunk/test_suite/shared_data/frame_order/cam/iso_cone_torsionless/frame_order.py trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse/frame_order.py trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse2/frame_order.py trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order.py trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order.py trunk/test_suite/shared_data/frame_order/cam/represent_frame_order.py trunk/test_suite/shared_data/frame_order/cam/rigid/frame_order.py trunk/test_suite/shared_data/frame_order/cam/rigid/rotor_analysis/frame_order.py trunk/test_suite/shared_data/frame_order/cam/rotor/frame_order.py trunk/test_suite/shared_data/frame_order/cam/rotor/frame_order_free_start.py trunk/test_suite/shared_data/frame_order/cam/rotor/perm_iso_cone_torsionless_xy_le_z/iso_cone.py trunk/test_suite/shared_data/frame_order/cam/rotor/perm_iso_cone_torsionless_xy_le_z/pymol_display.py trunk/test_suite/shared_data/frame_order/cam/rotor/perm_iso_cone_xy_le_z/iso_cone.py trunk/test_suite/shared_data/frame_order/cam/rotor/perm_iso_cone_xy_le_z/pymol_display.py trunk/test_suite/shared_data/frame_order/cam/rotor/perm_iso_cone_z_le_xy/iso_cone.py trunk/test_suite/shared_data/frame_order/cam/rotor/perm_iso_cone_z_le_xy/pymol_display.py trunk/test_suite/shared_data/frame_order/cam/rotor/perm_pseudo_ellipse_x_le_y_le_z/pseudo-ellipse.py trunk/test_suite/shared_data/frame_order/cam/rotor/perm_pseudo_ellipse_x_le_y_le_z/pymol_display.py trunk/test_suite/shared_data/frame_order/cam/rotor/perm_pseudo_ellipse_x_le_z_le_y/pseudo-ellipse.py trunk/test_suite/shared_data/frame_order/cam/rotor/perm_pseudo_ellipse_x_le_z_le_y/pymol_display.py trunk/test_suite/shared_data/frame_order/cam/rotor/perm_pseudo_ellipse_z_le_x_le_y/pseudo-ellipse.py trunk/test_suite/shared_data/frame_order/cam/rotor/perm_pseudo_ellipse_z_le_x_le_y/pymol_display.py trunk/test_suite/shared_data/frame_order/cam/rotor/perm_pseudo_ellipse_z_le_x_le_y_alt/pseudo-ellipse.py trunk/test_suite/shared_data/frame_order/cam/rotor/perm_pseudo_ellipse_z_le_x_le_y_alt/pymol_display.py trunk/test_suite/shared_data/frame_order/cam/rotor2/frame_order.py trunk/test_suite/shared_data/frame_order/cam/rotor_2_state/frame_order.py trunk/test_suite/shared_data/frame_order/cam/rotor_small_angle/frame_order.py [This mail would be too long, it was shortened to contain the URLs only.] Modified: trunk/test_suite/shared_data/frame_order/cam/double_rotor/frame_order.py URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/double_rotor/frame_order.py?rev=28307=28306=28307=diff Modified: trunk/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/frame_order.py URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/frame_order.py?rev=28307=28306=28307=diff Modified: trunk/test_suite/shared_data/frame_order/cam/free_rotor/frame_order.py URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/free_rotor/frame_order.py?rev=28307=28306=28307=diff Modified: trunk/test_suite/shared_data/frame_order/cam/free_rotor2/frame_order.py URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/free_rotor2/frame_order.py?rev=28307=28306=28307=diff Modified: trunk/test_suite/shared_data/frame_order/cam/free_rotor_missing_data/frame_order.py URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/free_rotor_missing_data/frame_order.py?rev=28307=28306=28307=diff Modified: trunk/test_suite/shared_data/frame_order/cam/iso_cone/frame_order.py URL:
r28306 - /trunk/docs/devel/Release_Checklist
Author: bugman Date: Thu Nov 17 18:00:39 2016 New Revision: 28306 URL: http://svn.gna.org/viewcvs/relax?rev=28306=rev Log: Expanded the release checklist instructions for creating the README.rst files. Modified: trunk/docs/devel/Release_Checklist Modified: trunk/docs/devel/Release_Checklist URL: http://svn.gna.org/viewcvs/relax/trunk/docs/devel/Release_Checklist?rev=28306=28305=28306=diff == --- trunk/docs/devel/Release_Checklist (original) +++ trunk/docs/devel/Release_Checklist Thu Nov 17 18:00:39 2016 @@ -295,4 +295,4 @@ $ html2rest --no-wrap --embedded-uri http://wiki.nmr-relax.com/Relax_4.0.3 $RELAX_DOWNLOAD_PATH/4.0.3/README.rst -And rerun the upload commands as above. +Delete all the wiki text under the main title, and everything after "Retrieved from". Then rerun the upload commands as above. ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
r28305 - /trunk/docs/devel/Release_Checklist
Author: bugman
Date: Thu Nov 17 14:37:45 2016
New Revision: 28305
URL: http://svn.gna.org/viewcvs/relax?rev=28305=rev
Log:
Added release instructions for creating the README.rst files for the download
area.
This is for using the custom html2rest at
ttps://sourceforge.net/p/nmr-relax/code-python-html2rest
to automatically generate the reStructuredText file from the wiki release notes.
Modified:
trunk/docs/devel/Release_Checklist
Modified: trunk/docs/devel/Release_Checklist
URL:
http://svn.gna.org/viewcvs/relax/trunk/docs/devel/Release_Checklist?rev=28305=28304=28305=diff
==
--- trunk/docs/devel/Release_Checklist (original)
+++ trunk/docs/devel/Release_Checklist Thu Nov 17 14:37:45 2016
@@ -286,3 +286,13 @@
"""
Not all of these links may work, as the email archives are not 100% perfect.
For the wiki, transclude the softpedia page http://wiki.nmr-relax.com/Softpedia
using {{:Softpedia}}, and add a section to the table at
http://wiki.nmr-relax.com/Category:Release_Notes for the release. For the news
item, reply to the item with the subject "Links to the other release
announcements.".
+
+
+README file
+---
+
+For the Gna! and SourceForge download area, a reStructuredText formatted
README.rst file should be created. This is automatically generated from the
wiki page using html2rest. To have access to the --no-wrap and --embedded-uri
options for 100% accurate links, install a copy of python-html2rest from
https://sourceforge.net/p/nmr-relax/code-python-html2rest/. Then type:
+
+$ html2rest --no-wrap --embedded-uri http://wiki.nmr-relax.com/Relax_4.0.3
$RELAX_DOWNLOAD_PATH/4.0.3/README.rst
+
+And rerun the upload commands as above.
___
relax (http://www.nmr-relax.com)
This is the relax-commits mailing list
relax-commits@gna.org
To unsubscribe from this list, get a password
reminder, or change your subscription options,
visit the list information page at
https://mail.gna.org/listinfo/relax-commits
r28304 - /website/links.html
Author: bugman Date: Wed Nov 16 19:51:36 2016 New Revision: 28304 URL: http://svn.gna.org/viewcvs/relax?rev=28304=rev Log: Even more div box fixes. Modified: website/links.html Modified: website/links.html URL: http://svn.gna.org/viewcvs/relax/website/links.html?rev=28304=28303=28304=diff == --- website/links.html (original) +++ website/links.html Wed Nov 16 19:51:36 2016 @@ -211,8 +211,7 @@ - - + Protein dynamics @@ -232,7 +231,6 @@ - relax libraries ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
r28303 - /website/links.html
Author: bugman Date: Wed Nov 16 18:44:50 2016 New Revision: 28303 URL: http://svn.gna.org/viewcvs/relax?rev=28303=rev Log: The "Protein dynamics" and "relax libraries" sections have been split into a "main_box" div box. Modified: website/links.html Modified: website/links.html URL: http://svn.gna.org/viewcvs/relax/website/links.html?rev=28303=28302=28303=diff == --- website/links.html (original) +++ website/links.html Wed Nov 16 18:44:50 2016 @@ -210,6 +210,8 @@ + + Protein dynamics ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
r28302 - /website/links.html
Author: bugman Date: Wed Nov 16 18:03:15 2016 New Revision: 28302 URL: http://svn.gna.org/viewcvs/relax?rev=28302=rev Log: More div box fixes for http://www.nmr-relax.com/links.html. Modified: website/links.html Modified: website/links.html URL: http://svn.gna.org/viewcvs/relax/website/links.html?rev=28302=28301=28302=diff == --- website/links.html (original) +++ website/links.html Wed Nov 16 18:03:15 2016 @@ -109,8 +109,7 @@ - - + Mailing list archives @@ -144,8 +143,8 @@ - - + + Web resources ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
r28301 - /website/download.html
Author: bugman Date: Wed Nov 16 16:48:38 2016 New Revision: 28301 URL: http://svn.gna.org/viewcvs/relax?rev=28301=rev Log: The 4.0.0 and 4.0.1 download links now point to http://www.nmr-relax.com/download_request.html. These releases are no longer in the download area. Modified: website/download.html Modified: website/download.html URL: http://svn.gna.org/viewcvs/relax/website/download.html?rev=28301=28300=28301=diff == --- website/download.html (original) +++ website/download.html Wed Nov 16 16:48:38 2016 @@ -455,77 +455,77 @@ http://wiki.nmr-relax.com/Relax_4.0.1;>Version 4.0.1 (2015-12-14) - http://download.gna.org/relax/4.0.1/relax-4.0.1.GNU-Linux.i686.tar.bz2; title="relax">relax-4.0.1.GNU-Linux.i686.tar.bz2 + relax-4.0.1.GNU-Linux.i686.tar.bz2 463a0e914cff318bb5b25da65fcc41c5 - http://download.gna.org/relax/4.0.1/relax-4.0.1.GNU-Linux.i686.tar.bz2.sig; title="relax GPG signature">signature + signature 105,787,595 - http://download.gna.org/relax/4.0.1/relax-4.0.1.GNU-Linux.x86_64.tar.bz2; title="relax">relax-4.0.1.GNU-Linux.x86_64.tar.bz2 + relax-4.0.1.GNU-Linux.x86_64.tar.bz2 9c09da031e0346a1f46c78a8aa4c2265 - http://download.gna.org/relax/4.0.1/relax-4.0.1.GNU-Linux.x86_64.tar.bz2.sig; title="relax GPG signature">signature + signature 106,000,392 - http://download.gna.org/relax/4.0.1/relax-4.0.1.Win32.zip; title="relax">relax-4.0.1.Win32.zip + relax-4.0.1.Win32.zip 1322eaa493fc8d6af79044de3e3e7789 - http://download.gna.org/relax/4.0.1/relax-4.0.1.Win32.zip.sig; title="relax GPG signature">signature + signature 111,856,780 - http://download.gna.org/relax/4.0.1/relax-4.0.1.Darwin.dmg; title="relax">relax-4.0.1.Darwin.dmg + relax-4.0.1.Darwin.dmg ff282d948816f3bbedc650642b00b288 - http://download.gna.org/relax/4.0.1/relax-4.0.1.Darwin.dmg.sig; title="relax GPG signature">signature + signature 333,632,768 - http://download.gna.org/relax/4.0.1/relax-4.0.1.src.tar.bz2; title="relax">relax-4.0.1.src.tar.bz2 + relax-4.0.1.src.tar.bz2 7c07917f22169f4afc76b5e362bb2112 - http://download.gna.org/relax/4.0.1/relax-4.0.1.src.tar.bz2.sig; title="relax GPG signature">signature + signature 105,985,056 - http://download.gna.org/relax/4.0.1/relax-4.0.1.src.zip; title="relax">relax-4.0.1.src.zip + relax-4.0.1.src.zip 8d942c8de7415f56ba35948129144f3c - http://download.gna.org/relax/4.0.1/relax-4.0.1.src.zip.sig; title="relax GPG signature">signature + signature 111,977,790 http://wiki.nmr-relax.com/Relax_4.0.0;>Version 4.0.0 (2015-10-07) - http://download.gna.org/relax/4.0.0/relax-4.0.0.GNU-Linux.i686.tar.bz2; title="relax">relax-4.0.0.GNU-Linux.i686.tar.bz2 + relax-4.0.0.GNU-Linux.i686.tar.bz2 79de39ad88175deb13e6893d6b43d170 - http://download.gna.org/relax/4.0.0/relax-4.0.0.GNU-Linux.i686.tar.bz2.sig; title="relax GPG signature">signature + signature 105,515,294 - http://download.gna.org/relax/4.0.0/relax-4.0.0.GNU-Linux.x86_64.tar.bz2; title="relax">relax-4.0.0.GNU-Linux.x86_64.tar.bz2 + relax-4.0.0.GNU-Linux.x86_64.tar.bz2 88e583699725277b280c82eefdf15c34 - http://download.gna.org/relax/4.0.0/relax-4.0.0.GNU-Linux.x86_64.tar.bz2.sig; title="relax GPG signature">signature + signature 105,655,707 - http://download.gna.org/relax/4.0.0/relax-4.0.0.Win32.zip; title="relax">relax-4.0.0.Win32.zip + relax-4.0.0.Win32.zip 0fb40b9164361ee37cc0981bc896f043 - http://download.gna.org/relax/4.0.0/relax-4.0.0.Win32.zip.sig; title="relax GPG signature">signature + signature 111,557,167 - http://download.gna.org/relax/4.0.0/relax-4.0.0.Darwin.dmg; title="relax">relax-4.0.0.Darwin.dmg + relax-4.0.0.Darwin.dmg d894c25abc73a6ac175cb1bf191d5cea - http://download.gna.org/relax/4.0.0/relax-4.0.0.Darwin.dmg.sig; title="relax GPG signature">signature + signature 334,077,536 - http://download.gna.org/relax/4.0.0/relax-4.0.0.src.tar.bz2; title="relax">relax-4.0.0.src.tar.bz2 + relax-4.0.0.src.tar.bz2 8820a6deb987017b072e49378b5f6f92 - http://download.gna.org/relax/4.0.0/relax-4.0.0.src.tar.bz2.sig; title="relax GPG signature">signature + signature 105,659,752 - http://download.gna.org/relax/4.0.0/relax-4.0.0.src.zip; title="relax">relax-4.0.0.src.zip + relax-4.0.0.src.zip 3ce9533638cd09305bc156c843448c48 - http://download.gna.org/relax/4.0.0/relax-4.0.0.src.zip.sig; title="relax GPG signature">signature + signature 111,676,490
r28299 - /website/links.html
Author: bugman Date: Wed Nov 16 16:32:07 2016 New Revision: 28299 URL: http://svn.gna.org/viewcvs/relax?rev=28299=rev Log: Div box fixes for the http://www.nmr-relax.com/links.html page. Modified: website/links.html Modified: website/links.html URL: http://svn.gna.org/viewcvs/relax/website/links.html?rev=28299=28298=28299=diff == --- website/links.html (original) +++ website/links.html Wed Nov 16 16:32:07 2016 @@ -109,6 +109,7 @@ + Mailing list archives @@ -143,6 +144,7 @@ + Web resources @@ -208,6 +210,7 @@ + Protein dynamics ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
r28298 - in /website: ./ images/
Author: bugman Date: Wed Nov 16 16:05:58 2016 New Revision: 28298 URL: http://svn.gna.org/viewcvs/relax?rev=28298=rev Log: Added links to the SourceForge, GitLab, and GitHub nmr-relax infrastructure sites. This is for http://www.nmr-relax.com/links.html. The public domain or CC BY-SA 4.0 licenced logos from Wikipedia have been added and modified. Added: website/images/GitLab_logo.png (with props) website/images/Octocats.zip (with props) website/images/gh_logo.png (with props) website/images/gl_logo.png (with props) website/images/sf_logo.png (with props) Modified: website/links.html Added: website/images/GitLab_logo.png URL: http://svn.gna.org/viewcvs/relax/website/images/GitLab_logo.png?rev=28298=auto == Binary file - no diff available. Propchange: website/images/GitLab_logo.png -- svn:mime-type = image/png Added: website/images/Octocats.zip URL: http://svn.gna.org/viewcvs/relax/website/images/Octocats.zip?rev=28298=auto == Binary file - no diff available. Propchange: website/images/Octocats.zip -- svn:mime-type = application/octet-stream Added: website/images/gh_logo.png URL: http://svn.gna.org/viewcvs/relax/website/images/gh_logo.png?rev=28298=auto == Binary file - no diff available. Propchange: website/images/gh_logo.png -- svn:mime-type = image/png Added: website/images/gl_logo.png URL: http://svn.gna.org/viewcvs/relax/website/images/gl_logo.png?rev=28298=auto == Binary file - no diff available. Propchange: website/images/gl_logo.png -- svn:mime-type = image/png Added: website/images/sf_logo.png URL: http://svn.gna.org/viewcvs/relax/website/images/sf_logo.png?rev=28298=auto == Binary file - no diff available. Propchange: website/images/sf_logo.png -- svn:mime-type = image/png Modified: website/links.html URL: http://svn.gna.org/viewcvs/relax/website/links.html?rev=28298=28297=28298=diff == --- website/links.html (original) +++ website/links.html Wed Nov 16 16:05:58 2016 @@ -31,6 +31,9 @@ relax on the web Gna! + SourceForge + GitLab + GitHub relax on the web @@ -83,6 +86,25 @@ Gna! is a central point for the development, distribution and maintenance of Libre Software (Free Software) projects. The relax project page is https://gna.org/projects/relax;>https://gna.org/projects/relax. The relax developer Gna! pages are (in alphabetical order): http://gna.org/users/bugman;>Edward dAuvergne, http://gna.org/users/michaelbieri;>Michael Bieri, http://gna.org/users/macraild;>Chris MacRaild, http://gna.org/users/semor;>Sbastien Morin, http://gna.org/users/pansapiens;>Andrew Perry, http://gna.org/users/han87;>Han Sun, http://gna.org/users/varioustoxins;>Gary Thompson. + + + https://sourceforge.net/projects/nmr-relax;> + SourceForge is an Open Source community resource dedicated to helping open source projects be as successful as possible. + This is a backup infrastructure site. The relax project page is https://sourceforge.net/projects/nmr-relax;>https://sourceforge.net/projects/nmr-relax. + + + + https://gitlab.com/nmr-relax;> + Open source software to collaborate on code. + This is a backup infrastructure site. The relax project page is https://gitlab.com/nmr-relax;>https://gitlab.com/nmr-relax. + + + + https://github.com/nmr-relax;> + GitHub is how people build software. + This is a backup infrastructure site. The relax project page is https://github.com/nmr-relax;>https://github.com/nmr-relax. + + ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
r28297 - /website/links.html
Author: bugman Date: Wed Nov 16 15:48:47 2016 New Revision: 28297 URL: http://svn.gna.org/viewcvs/relax?rev=28297=rev Log: More sectioning for the links at http://www.nmr-relax.com/links.html. This includes a section for relax infrastructure, mailing list archives, and web resources. Modified: website/links.html Modified: website/links.html URL: http://svn.gna.org/viewcvs/relax/website/links.html?rev=28297=28296=28297=diff == --- website/links.html (original) +++ website/links.html Wed Nov 16 15:48:47 2016 @@ -28,12 +28,20 @@ Links -relax on the web +relax on the web Gna! + + +relax on the web + The Mail Archive MARC + + +relax on the web + Free Software Directory DMOZ open directory project Linuxlinks.com @@ -59,20 +67,35 @@ - - relax on the web - - - - - Site - Description - Where to find relax - + + relax infrastructure + + + + + Site + Description + Links + + http://gna.org/projects/relax;> Gna! is a central point for the development, distribution and maintenance of Libre Software (Free Software) projects. The relax project page is https://gna.org/projects/relax;>https://gna.org/projects/relax. The relax developer Gna! pages are (in alphabetical order): http://gna.org/users/bugman;>Edward dAuvergne, http://gna.org/users/michaelbieri;>Michael Bieri, http://gna.org/users/macraild;>Chris MacRaild, http://gna.org/users/semor;>Sbastien Morin, http://gna.org/users/pansapiens;>Andrew Perry, http://gna.org/users/han87;>Han Sun, http://gna.org/users/varioustoxins;>Gary Thompson. + + + + + + + Mailing list archives + + + + + Site + Description + Links
r28296 - /website/download.html
Author: bugman Date: Wed Nov 16 15:37:22 2016 New Revision: 28296 URL: http://svn.gna.org/viewcvs/relax?rev=28296=rev Log: The 3.3.6 to 3.3.8 download links now point to http://www.nmr-relax.com/download_request.html. These releases were removed from the download area a long time ago. Modified: website/download.html Modified: website/download.html URL: http://svn.gna.org/viewcvs/relax/website/download.html?rev=28296=28295=28296=diff == --- website/download.html (original) +++ website/download.html Wed Nov 16 15:37:22 2016 @@ -587,115 +587,115 @@ http://wiki.nmr-relax.com/Relax_3.3.8;>Version 3.3.8 (2015-04-02) - http://download.gna.org/relax/relax-3.3.8.GNU-Linux.i686.tar.bz2; title="relax">relax-3.3.8.GNU-Linux.i686.tar.bz2 + relax-3.3.8.GNU-Linux.i686.tar.bz2 ced0f46c08d19891d54c860437c521b9 - http://download.gna.org/relax/relax-3.3.8.GNU-Linux.i686.tar.bz2.sig; title="relax GPG signature">signature + signature 90,148,435 - http://download.gna.org/relax/relax-3.3.8.GNU-Linux.x86_64.tar.bz2; title="relax">relax-3.3.8.GNU-Linux.x86_64.tar.bz2 + relax-3.3.8.GNU-Linux.x86_64.tar.bz2 0f303dfa45bb93d2b3fcb21573a85313 - http://download.gna.org/relax/relax-3.3.8.GNU-Linux.x86_64.tar.bz2.sig; title="relax GPG signature">signature + signature 90,288,284 - http://download.gna.org/relax/relax-3.3.8.Win32.zip; title="relax">relax-3.3.8.Win32.zip + relax-3.3.8.Win32.zip a45f597f97608199783fdc8c659c6f8d - http://download.gna.org/relax/relax-3.3.8.Win32.zip.sig; title="relax GPG signature">signature + signature 95,481,119 - http://download.gna.org/relax/relax-3.3.8.Darwin.dmg; title="relax">relax-3.3.8.Darwin.dmg + relax-3.3.8.Darwin.dmg cbb02dfd35bc200d7b4ce1e725c45ddf - http://download.gna.org/relax/relax-3.3.8.Darwin.dmg.sig; title="relax GPG signature">signature + signature 301,462,611 - http://download.gna.org/relax/relax-3.3.8.src.tar.bz2; title="relax">relax-3.3.8.src.tar.bz2 + relax-3.3.8.src.tar.bz2 5c189d4070bc746b57f55292877a070c - http://download.gna.org/relax/relax-3.3.8.src.tar.bz2.sig; title="relax GPG signature">signature + signature 90,271,667 - http://download.gna.org/relax/relax-3.3.8.src.zip; title="relax">relax-3.3.8.src.zip + relax-3.3.8.src.zip aacce935366969f3a16f9d7bbdc18712 - http://download.gna.org/relax/relax-3.3.8.src.zip.sig; title="relax GPG signature">signature + signature 95,600,160 http://wiki.nmr-relax.com/Relax_3.3.7;>Version 3.3.7 (2015-03-13) - http://download.gna.org/relax/relax-3.3.7.GNU-Linux.i686.tar.bz2; title="relax">relax-3.3.7.GNU-Linux.i686.tar.bz2 + relax-3.3.7.GNU-Linux.i686.tar.bz2 27bf8c6a183d53fc773e5f1722090c57 - http://download.gna.org/relax/relax-3.3.7.GNU-Linux.i686.tar.bz2.sig; title="relax GPG signature">signature + signature 90,148,136 - http://download.gna.org/relax/relax-3.3.7.GNU-Linux.x86_64.tar.bz2; title="relax">relax-3.3.7.GNU-Linux.x86_64.tar.bz2 + relax-3.3.7.GNU-Linux.x86_64.tar.bz2 d84657eb772670dbdbe54f34fd769941 - http://download.gna.org/relax/relax-3.3.7.GNU-Linux.x86_64.tar.bz2.sig; title="relax GPG signature">signature + signature 90,285,547 - http://download.gna.org/relax/relax-3.3.7.Win32.zip; title="relax">relax-3.3.7.Win32.zip + relax-3.3.7.Win32.zip 19c7059cfd584a3d1c0ddf53d4175550 - http://download.gna.org/relax/relax-3.3.7.Win32.zip.sig; title="relax GPG signature">signature + signature 95,479,591 - http://download.gna.org/relax/relax-3.3.7.Darwin.dmg; title="relax">relax-3.3.7.Darwin.dmg + relax-3.3.7.Darwin.dmg 8d28113d40010e6de798b279235fef70 - http://download.gna.org/relax/relax-3.3.7.Darwin.dmg.sig; title="relax GPG signature">signature + signature 285,999,780 - http://download.gna.org/relax/relax-3.3.7.src.tar.bz2; title="relax">relax-3.3.7.src.tar.bz2 + relax-3.3.7.src.tar.bz2 ee31e6acb50ce3679cc6f7dc619c4c65 - http://download.gna.org/relax/relax-3.3.7.src.tar.bz2.sig; title="relax GPG signature">signature + signature 90,268,061 - http://download.gna.org/relax/relax-3.3.7.src.zip; title="relax">relax-3.3.7.src.zip + relax-3.3.7.src.zip b83ada904edb7e1c5a8d60fc05276e7f - http://download.gna.org/relax/relax-3.3.7.src.zip.sig; title="relax GPG signature">signature + signature 95,598,632 http://wiki.nmr-relax.com/Relax_3.3.6;>Version 3.3.6 (2015-02-04) - http://download.gna.org/relax/relax-3.3.6.GNU-Linux.i686.tar.bz2;
r28295 - /website/download.html
Author: bugman Date: Wed Nov 16 15:34:02 2016 New Revision: 28295 URL: http://svn.gna.org/viewcvs/relax?rev=28295=rev Log: Changed all the relax download links to point to the new release subdirectories. This is for http://www.nmr-relax.com/download.html. Modified: website/download.html [This mail would be too long, it was shortened to contain the URLs only.] Modified: website/download.html URL: http://svn.gna.org/viewcvs/relax/website/download.html?rev=28295=28294=28295=diff ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
r28294 - /trunk/docs/devel/Release_Checklist
Author: bugman Date: Wed Nov 16 14:10:32 2016 New Revision: 28294 URL: http://svn.gna.org/viewcvs/relax?rev=28294=rev Log: Updates to the upload section of the release checklist document for sending files to SourceForge. Modified: trunk/docs/devel/Release_Checklist Modified: trunk/docs/devel/Release_Checklist URL: http://svn.gna.org/viewcvs/relax/trunk/docs/devel/Release_Checklist?rev=28294=28293=28294=diff == --- trunk/docs/devel/Release_Checklist (original) +++ trunk/docs/devel/Release_Checklist Wed Nov 16 14:10:32 2016 @@ -125,13 +125,21 @@ $ rsync -av --progress --no-perms --rsh="ssh" bug...@download.gna.org:/upload/relax/ . -Then rsync the entire directory contents to download.gna.org/upload/relax/ using the command: - -$ rsync --delete -av --progress --no-perms --partial --rsh="ssh" . bug...@download.gna.org:/upload/relax/ +Change "bugman" to your user name. Then rsync the entire directory contents to download.gna.org/upload/relax/ using the command: + +$ rsync --delete -rlptoDvP --progress --partial --no-perms --rsh="ssh" --numeric-ids . bug...@download.gna.org:/upload/relax/ The upload script simplifies the upload process: -$ ./upload +$ ./upload bugman + +Upload copies to the relax SourceForge file area as well: + +$ rsync --delete -rlptoDvP --progress --partial --no-perms -e ssh --numeric-ids . bug...@frs.sourceforge.net:/home/frs/project/nmr-relax/ + +Or: + +$ ./upload bugman sf ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
r28293 - /website/links.html
Author: bugman Date: Wed Nov 16 12:25:00 2016 New Revision: 28293 URL: http://svn.gna.org/viewcvs/relax?rev=28293=rev Log: Commented out the Gmane links at http://www.nmr-relax.com/links.html. This is at least until Gmane is back up. Modified: website/links.html Modified: website/links.html URL: http://svn.gna.org/viewcvs/relax/website/links.html?rev=28293=28292=28293=diff == --- website/links.html (original) +++ website/links.html Wed Nov 16 12:25:00 2016 @@ -3,7 +3,7 @@ http://www.w3.org/1999/xhtml;> The Mail Archive MARC Free Software Directory @@ -75,12 +75,14 @@ The relax project page is https://gna.org/projects/relax;>https://gna.org/projects/relax. The relax developer Gna! pages are (in alphabetical order): http://gna.org/users/bugman;>Edward dAuvergne, http://gna.org/users/michaelbieri;>Michael Bieri, http://gna.org/users/macraild;>Chris MacRaild, http://gna.org/users/semor;>Sbastien Morin, http://gna.org/users/pansapiens;>Andrew Perry, http://gna.org/users/han87;>Han Sun, http://gna.org/users/varioustoxins;>Gary Thompson. + - http://www.mail-archive.com;> An easy-to-use archiving service for electronic mailing lists. ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
r28292 - /trunk/test_suite/gui_tests/rx.py
Author: bugman Date: Wed Nov 16 12:07:50 2016 New Revision: 28292 URL: http://svn.gna.org/viewcvs/relax?rev=28292=rev Log: More precision decreases in the Rx.test_r1_analysis GUI test. This is to allow the test to pass on wxPython-Phoenix and Python 3. Modified: trunk/test_suite/gui_tests/rx.py Modified: trunk/test_suite/gui_tests/rx.py URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/gui_tests/rx.py?rev=28292=28291=28292=diff == --- trunk/test_suite/gui_tests/rx.py(original) +++ trunk/test_suite/gui_tests/rx.pyWed Nov 16 12:07:50 2016 @@ -73,8 +73,8 @@ # Check the errors. for key in cdp.sigma_I: -self.assertEqual(cdp.sigma_I[key], 10578.039482421433) -self.assertEqual(cdp.var_I[key], 111894919.2919) +self.assertAlmostEqual(cdp.sigma_I[key], 10578.039482421433) +self.assertAlmostEqual(cdp.var_I[key], 111894919.2919) # Spin data check. i = 0 ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
r28291 - in /trunk/graphics/misc: relaxGUI_splash.png relaxGUI_splash.xcf
Author: bugman Date: Tue Nov 15 21:28:19 2016 New Revision: 28291 URL: http://svn.gna.org/viewcvs/relax?rev=28291=rev Log: Updated the copyright notice in the GUI splash screen to 2001-2016. Modified: trunk/graphics/misc/relaxGUI_splash.png trunk/graphics/misc/relaxGUI_splash.xcf Modified: trunk/graphics/misc/relaxGUI_splash.png URL: http://svn.gna.org/viewcvs/relax/trunk/graphics/misc/relaxGUI_splash.png?rev=28291=28290=28291=diff == Binary files - no diff available. Modified: trunk/graphics/misc/relaxGUI_splash.xcf URL: http://svn.gna.org/viewcvs/relax/trunk/graphics/misc/relaxGUI_splash.xcf?rev=28291=28290=28291=diff == Binary files - no diff available. ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
r28290 - /trunk/docs/bash_completion.sh
Author: bugman
Date: Tue Nov 15 20:56:10 2016
New Revision: 28290
URL: http://svn.gna.org/viewcvs/relax?rev=28290=rev
Log:
Removal of unused variables from the bash completion relax script.
Modified:
trunk/docs/bash_completion.sh
Modified: trunk/docs/bash_completion.sh
URL:
http://svn.gna.org/viewcvs/relax/trunk/docs/bash_completion.sh?rev=28290=28289=28290=diff
==
--- trunk/docs/bash_completion.sh (original)
+++ trunk/docs/bash_completion.sh Tue Nov 15 20:56:10 2016
@@ -25,7 +25,7 @@
_relax() {
# Define the variables.
-local cur prev dir py_scripts opts
+local cur prev opts
# Initialise the COMPREPLY array.
COMPREPLY=()
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r28289 - /trunk/docs/bash_completion.sh
Author: bugman Date: Tue Nov 15 20:50:27 2016 New Revision: 28289 URL: http://svn.gna.org/viewcvs/relax?rev=28289=rev Log: Fine tuning of the bash completion relax script. The option "-o nospace" for "complete" has been removed as spaces are not added for directories anyway. This means that a space is added after all options and scripts. Modified: trunk/docs/bash_completion.sh Modified: trunk/docs/bash_completion.sh URL: http://svn.gna.org/viewcvs/relax/trunk/docs/bash_completion.sh?rev=28289=28288=28289=diff == --- trunk/docs/bash_completion.sh (original) +++ trunk/docs/bash_completion.sh Tue Nov 15 20:50:27 2016 @@ -96,5 +96,5 @@ return 0 } -# Set up the completion for relax, avoiding trailing spaces for better subdirectory completion. -complete -o nospace -F _relax relax +# Set up the completion for relax. +complete -F _relax relax ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
r28288 - /trunk/docs/bash_completion.sh
Author: bugman
Date: Tue Nov 15 20:34:48 2016
New Revision: 28288
URL: http://svn.gna.org/viewcvs/relax?rev=28288=rev
Log:
Improvements for the bash completion relax script.
Directories and relax scripts are now much better handled.
Modified:
trunk/docs/bash_completion.sh
Modified: trunk/docs/bash_completion.sh
URL:
http://svn.gna.org/viewcvs/relax/trunk/docs/bash_completion.sh?rev=28288=28287=28288=diff
==
--- trunk/docs/bash_completion.sh (original)
+++ trunk/docs/bash_completion.sh Tue Nov 15 20:34:48 2016
@@ -34,20 +34,6 @@
cur="${COMP_WORDS[COMP_CWORD]}"
prev="${COMP_WORDS[COMP_CWORD-1]}"
-# Multi-processor option values.
-case "${prev}" in
---multi)
-COMPREPLY=( $(compgen -W "mpi4py" -- ${cur}) )
-return 0
-;;
---processors)
-COMPREPLY=( $(compgen -W "$(seq 2 257)" -- ${cur}) )
-return 0
-;;
-*)
-;;
-esac
-
# Handle options.
if [[ ${cur} == -* ]] ; then
# The help options.
@@ -73,20 +59,42 @@
# Success.
return 0
+fi
-# Handle scripts.
-else [[ ${cur} == * ]]
-# Directories and Python scripts.
-dir=$(echo .*/ */ 2> /dev/null)
-py_scripts=$(/bin/ls *.py 2> /dev/null)
+# Multi-processor option values.
+case "${prev}" in
+--multi)
+COMPREPLY=( $(compgen -W "mpi4py" -- ${cur}) )
+return 0
+;;
+--processors)
+COMPREPLY=( $(compgen -W "$(seq 2 257)" -- ${cur}) )
+return 0
+;;
+*)
+;;
+esac
-# Set COMPREPLY.
-COMPREPLY=( $(compgen -W "${dir} ${py_scripts}" -- ${cur}) )
+# Handle relax scripts which must end in *.py.
+COMPREPLY=( $(compgen -f -X '!*.py' -- ${cur}) )
-# Success.
+# Defer to _filedir for directory completion.
+if [[ -z "${CDPATH:-}" || "$cur" == ?(.)?(.)/* ]]; then
+_filedir -d
return 0
+fi
+# Append a trailing '/' for unique directory names, if missing.
+if [[ ${#COMPREPLY[@]} -eq 1 ]]; then
+i=${COMPREPLY[0]}
+if [[ "$i" == "${cur}" && $i != "*/" ]]; then
+COMPREPLY[0]="${i}/"
+fi
+return 0
fi
+
+return 0
}
-complete -F _relax relax
+# Set up the completion for relax, avoiding trailing spaces for better
subdirectory completion.
+complete -o nospace -F _relax relax
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r28287 - /trunk/docs/bash_completion.sh
Author: bugman
Date: Tue Nov 15 18:48:08 2016
New Revision: 28287
URL: http://svn.gna.org/viewcvs/relax?rev=28287=rev
Log:
Creation of an initial bash script for enabling bash completion.
Added:
trunk/docs/bash_completion.sh (with props)
Added: trunk/docs/bash_completion.sh
URL:
http://svn.gna.org/viewcvs/relax/trunk/docs/bash_completion.sh?rev=28287=auto
==
--- trunk/docs/bash_completion.sh (added)
+++ trunk/docs/bash_completion.sh Tue Nov 15 18:48:08 2016
@@ -0,0 +1,92 @@
+###
+# #
+# Copyright (C) 2016 Edward d'Auvergne#
+# #
+# This file is part of the program relax (http://www.nmr-relax.com). #
+# #
+# This program is free software: you can redistribute it and/or modify#
+# it under the terms of the GNU General Public License as published by#
+# the Free Software Foundation, either version 3 of the License, or #
+# (at your option) any later version. #
+# #
+# This program is distributed in the hope that it will be useful, #
+# but WITHOUT ANY WARRANTY; without even the implied warranty of #
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
+# GNU General Public License for more details.#
+# #
+# You should have received a copy of the GNU General Public License #
+# along with this program. If not, see <http://www.gnu.org/licenses/>. #
+# #
+###
+
+# Bash completion support for relax.
+#
+# To use this script, copy it to /etc/bash_completion.d/relax.
+
+_relax() {
+# Define the variables.
+local cur prev dir py_scripts opts
+
+# Initialise the COMPREPLY array.
+COMPREPLY=()
+
+# Set the current and previous comp words.
+cur="${COMP_WORDS[COMP_CWORD]}"
+prev="${COMP_WORDS[COMP_CWORD-1]}"
+
+# Multi-processor option values.
+case "${prev}" in
+--multi)
+COMPREPLY=( $(compgen -W "mpi4py" -- ${cur}) )
+return 0
+;;
+--processors)
+COMPREPLY=( $(compgen -W "$(seq 2 257)" -- ${cur}) )
+return 0
+;;
+*)
+;;
+esac
+
+# Handle options.
+if [[ ${cur} == -* ]] ; then
+# The help options.
+opts="--help"
+
+# UI options.
+opts="${opts} --prompt --gui --info --version --licence --test"
+
+# Multi-processor options.
+opts="${opts} --multi --processors"
+
+# IO redirection options.
+opts="${opts} --log --tee"
+
+# Test suite options.
+opts="${opts} --test-suite --system-tests --unit-tests --gui-tests
--verification-tests --time --no-skip"
+
+# Debugging options.
+opts="${opts} --debug --error-state --traceback --escalate
--numpy-raise"
+
+# Set COMPREPLY.
+COMPREPLY=( $(compgen -W "${opts}" -- ${cur}) )
+
+# Success.
+return 0
+
+# Handle scripts.
+else [[ ${cur} == * ]]
+# Directories and Python scripts.
+dir=$(echo .*/ */ 2> /dev/null)
+py_scripts=$(/bin/ls *.py 2> /dev/null)
+
+# Set COMPREPLY.
+COMPREPLY=( $(compgen -W "${dir} ${py_scripts}" -- ${cur}) )
+
+# Success.
+return 0
+
+fi
+}
+
+complete -F _relax relax
Propchange: trunk/docs/bash_completion.sh
--
svn:eol-style = native
Propchange: trunk/docs/bash_completion.sh
--
svn:executable = *
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r28286 - /trunk/gui/components/spectrum.py
Author: bugman
Date: Tue Nov 15 16:39:40 2016
New Revision: 28286
URL: http://svn.gna.org/viewcvs/relax?rev=28286=rev
Log:
Replacement of a wx.ListCtrl.DeleteAllColumns() function call from the spectrum
GUI element.
This function does not exist in wxPython-Phoenix. Instead the columns are
looped over and
wx.ListCtrl.DeleteColumn() is called instead.
Modified:
trunk/gui/components/spectrum.py
Modified: trunk/gui/components/spectrum.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/gui/components/spectrum.py?rev=28286=28285=28286=diff
==
--- trunk/gui/components/spectrum.py(original)
+++ trunk/gui/components/spectrum.pyTue Nov 15 16:39:40 2016
@@ -1,7 +1,7 @@
###
# #
# Copyright (C) 2009-2011 Michael Bieri #
-# Copyright (C) 2010-2014 Edward d'Auvergne #
+# Copyright (C) 2010-2016 Edward d'Auvergne #
# #
# This file is part of the program relax (http://www.nmr-relax.com). #
# #
@@ -784,7 +784,8 @@
# Delete the rows and columns.
self.element.DeleteAllItems()
-self.element.DeleteAllColumns()
+for i in reversed(range(self.element.GetColumnCount())):
+self.element.DeleteColumn(i)
# Initialise to a single column.
self.element.InsertColumn(0, str_to_gui("Spectrum ID"))
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r28285 - /trunk/gui/components/spectrum.py
Author: bugman
Date: Tue Nov 15 16:27:52 2016
New Revision: 28285
URL: http://svn.gna.org/viewcvs/relax?rev=28285=rev
Log:
Reverted r28283 as this change broke the spectrum list GUI element.
The command used was:
svn merge -r28283:r28282 .
.
r28283 | bugman | 2016-11-15 15:44:48 +0100 (Tue, 15 Nov 2016) | 4 lines
Changed paths:
M /trunk/gui/components/spectrum.py
Removal of a wx.ListCtrl.DeleteAllColumns() function call from the spectrum
GUI element.
This function does not exist in wxPython-Phoenix and is redundant anyway due
to the DeleteAllItems()
function call on the line before.
.
Modified:
trunk/gui/components/spectrum.py
Modified: trunk/gui/components/spectrum.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/gui/components/spectrum.py?rev=28285=28284=28285=diff
==
--- trunk/gui/components/spectrum.py(original)
+++ trunk/gui/components/spectrum.pyTue Nov 15 16:27:52 2016
@@ -1,7 +1,7 @@
###
# #
# Copyright (C) 2009-2011 Michael Bieri #
-# Copyright (C) 2010-2016 Edward d'Auvergne #
+# Copyright (C) 2010-2014 Edward d'Auvergne #
# #
# This file is part of the program relax (http://www.nmr-relax.com). #
# #
@@ -784,6 +784,7 @@
# Delete the rows and columns.
self.element.DeleteAllItems()
+self.element.DeleteAllColumns()
# Initialise to a single column.
self.element.InsertColumn(0, str_to_gui("Spectrum ID"))
___
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r28284 - /trunk/gui/spin_viewer/containers.py
Author: bugman Date: Tue Nov 15 16:10:00 2016 New Revision: 28284 URL: http://svn.gna.org/viewcvs/relax?rev=28284=rev Log: Keyword to positional argument conversion for the GUI wx.Font() calls. A number of these were being called with keyword arguments, however the old wxPython and Phoenix documentation say that these are not keyword arguments (this must have been for backwards compatibility with very old wxPython versions). Modified: trunk/gui/spin_viewer/containers.py Modified: trunk/gui/spin_viewer/containers.py URL: http://svn.gna.org/viewcvs/relax/trunk/gui/spin_viewer/containers.py?rev=28284=28283=28284=diff == --- trunk/gui/spin_viewer/containers.py (original) +++ trunk/gui/spin_viewer/containers.py Tue Nov 15 16:10:00 2016 @@ -139,7 +139,7 @@ obj = wx.StaticText(self.parent, -1, text) # Formatting. -obj.SetFont(wx.Font(pointSize=12, family=wx.FONTFAMILY_ROMAN, style=wx.ITALIC, weight=wx.NORMAL, face='Times')) +obj.SetFont(wx.Font(12, wx.FONTFAMILY_ROMAN, wx.ITALIC, wx.NORMAL, False, 'Times')) # Return the object. return obj @@ -164,7 +164,7 @@ obj = wx.StaticText(self.parent, -1, text) # Formatting. -obj.SetFont(wx.Font(pointSize=16, family=wx.FONTFAMILY_ROMAN, style=wx.ITALIC, weight=wx.NORMAL, face='Times')) +obj.SetFont(wx.Font(16, wx.FONTFAMILY_ROMAN, wx.ITALIC, wx.NORMAL, False, 'Times')) # Return the object. return obj @@ -183,7 +183,7 @@ title = wx.StaticText(self.parent, -1, text) # Formatting. -title.SetFont(wx.Font(pointSize=32, family=wx.FONTFAMILY_ROMAN, style=wx.ITALIC, weight=wx.NORMAL, face='Times')) +title.SetFont(wx.Font(32, wx.FONTFAMILY_ROMAN, wx.ITALIC, wx.NORMAL, False, 'Times')) # Return the object. return title ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
r28283 - /trunk/gui/components/spectrum.py
Author: bugman
Date: Tue Nov 15 15:44:48 2016
New Revision: 28283
URL: http://svn.gna.org/viewcvs/relax?rev=28283=rev
Log:
Removal of a wx.ListCtrl.DeleteAllColumns() function call from the spectrum GUI
element.
This function does not exist in wxPython-Phoenix and is redundant anyway due to
the DeleteAllItems()
function call on the line before.
Modified:
trunk/gui/components/spectrum.py
Modified: trunk/gui/components/spectrum.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/gui/components/spectrum.py?rev=28283=28282=28283=diff
==
--- trunk/gui/components/spectrum.py(original)
+++ trunk/gui/components/spectrum.pyTue Nov 15 15:44:48 2016
@@ -1,7 +1,7 @@
###
# #
# Copyright (C) 2009-2011 Michael Bieri #
-# Copyright (C) 2010-2014 Edward d'Auvergne #
+# Copyright (C) 2010-2016 Edward d'Auvergne #
# #
# This file is part of the program relax (http://www.nmr-relax.com). #
# #
@@ -784,7 +784,6 @@
# Delete the rows and columns.
self.element.DeleteAllItems()
-self.element.DeleteAllColumns()
# Initialise to a single column.
self.element.InsertColumn(0, str_to_gui("Spectrum ID"))
___
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r28280 - in /trunk/gui: about.py analyses/auto_model_free.py
Author: bugman Date: Tue Nov 15 15:44:42 2016 New Revision: 28280 URL: http://svn.gna.org/viewcvs/relax?rev=28280=rev Log: Keyword to positional argument conversion for the GUI wx.ScrolledWindow.EnableScrolling() calls. These function calls were using keyword arguments, however the old wxPython and Phoenix documentation say that these are not keyword arguments (this must have been for backwards compatibility with very old wxPython versions). Modified: trunk/gui/about.py trunk/gui/analyses/auto_model_free.py Modified: trunk/gui/about.py URL: http://svn.gna.org/viewcvs/relax/trunk/gui/about.py?rev=28280=28279=28280=diff == --- trunk/gui/about.py (original) +++ trunk/gui/about.py Tue Nov 15 15:44:42 2016 @@ -526,7 +526,7 @@ dim_y = self.offset() + self.border self.SetSize((dim_x, dim_y)) self.window.SetVirtualSize((dim_x, dim_y)) -self.window.EnableScrolling(x_scrolling=False, y_scrolling=False) +self.window.EnableScrolling(False, False) # Add space to the bottom. self.offset(self.border) Modified: trunk/gui/analyses/auto_model_free.py URL: http://svn.gna.org/viewcvs/relax/trunk/gui/analyses/auto_model_free.py?rev=28280=28279=28280=diff == --- trunk/gui/analyses/auto_model_free.py (original) +++ trunk/gui/analyses/auto_model_free.py Tue Nov 15 15:44:42 2016 @@ -144,7 +144,7 @@ virt_y = self.offset() self.SetSize((dim_x, self.dim_y)) self.window.SetVirtualSize((dim_x, virt_y)) -self.window.EnableScrolling(x_scrolling=False, y_scrolling=True) +self.window.EnableScrolling(False, True) ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
r28281 - /trunk/gui/spin_viewer/containers.py
Author: bugman Date: Tue Nov 15 15:44:45 2016 New Revision: 28281 URL: http://svn.gna.org/viewcvs/relax?rev=28281=rev Log: Keyword to positional argument conversion for a GUI wx.BoxSizer.Clear() call. This is for the spin containers in the spin viewer window. The keyword argument in wxPython classic is deleteWindows however in Phoenix it is delete_windows. Modified: trunk/gui/spin_viewer/containers.py Modified: trunk/gui/spin_viewer/containers.py URL: http://svn.gna.org/viewcvs/relax/trunk/gui/spin_viewer/containers.py?rev=28281=28280=28281=diff == --- trunk/gui/spin_viewer/containers.py (original) +++ trunk/gui/spin_viewer/containers.py Tue Nov 15 15:44:45 2016 @@ -1,6 +1,6 @@ ### # # -# Copyright (C) 2010-2013 Edward d'Auvergne # +# Copyright (C) 2010-2016 Edward d'Auvergne # # # # This file is part of the program relax (http://www.nmr-relax.com). # # # @@ -90,7 +90,7 @@ """ # Destroy all the original contents. -self.main_sizer.Clear(deleteWindows=True) +self.main_sizer.Clear(True) # The root window display. if info == 'root' or info == None: ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
r28282 - /trunk/test_suite/gui_tests/rx.py
Author: bugman Date: Tue Nov 15 15:44:47 2016 New Revision: 28282 URL: http://svn.gna.org/viewcvs/relax?rev=28282=rev Log: Decreased the precision of a check in the Rx.test_r1_analysis GUI test. This is to allow the test to pass on wxPython-Phoenix and Python 3. Modified: trunk/test_suite/gui_tests/rx.py Modified: trunk/test_suite/gui_tests/rx.py URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/gui_tests/rx.py?rev=28282=28281=28282=diff == --- trunk/test_suite/gui_tests/rx.py(original) +++ trunk/test_suite/gui_tests/rx.pyTue Nov 15 15:44:47 2016 @@ -1,6 +1,6 @@ ### # # -# Copyright (C) 2006-2014 Edward d'Auvergne # +# Copyright (C) 2006-2016 Edward d'Auvergne # # # # This file is part of the program relax (http://www.nmr-relax.com). # # # @@ -69,7 +69,7 @@ self.assertEqual(len(cdp.relax_times), 10) cdp_relax_times = sorted(cdp.relax_times.values()) for i in range(10): -self.assertEqual(cdp_relax_times[i], relax_times[i]) +self.assertAlmostEqual(cdp_relax_times[i], relax_times[i]) # Check the errors. for key in cdp.sigma_I: ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
r28279 - in /trunk: devel_scripts/memory_management/ gui/input_elements/ test_suite/gui_tests/
Author: bugman
Date: Tue Nov 15 14:36:02 2016
New Revision: 28279
URL: http://svn.gna.org/viewcvs/relax?rev=28279=rev
Log:
Keyword to positional argument conversion for the GUI
wx.ListCtrl.SetStringItem() function calls.
The keyword arguments for this function must exist for backwards compatibility
with ancient wxPython
versions. The current documentation lists them as positional arguments, and
keyword arguments are
not accepted by wxPython-Phoenix.
Modified:
trunk/devel_scripts/memory_management/GUI_uf_align_tensor_init.py
trunk/gui/input_elements/sequence.py
trunk/test_suite/gui_tests/test_user_functions.py
Modified: trunk/devel_scripts/memory_management/GUI_uf_align_tensor_init.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/devel_scripts/memory_management/GUI_uf_align_tensor_init.py?rev=28279=28278=28279=diff
==
--- trunk/devel_scripts/memory_management/GUI_uf_align_tensor_init.py
(original)
+++ trunk/devel_scripts/memory_management/GUI_uf_align_tensor_init.py Tue Nov
15 14:36:02 2016
@@ -1,6 +1,6 @@
###
# #
-# Copyright (C) 2015 Edward d'Auvergne#
+# Copyright (C) 2015-2016 Edward d'Auvergne #
# #
# This file is part of the program relax (http://www.nmr-relax.com). #
# #
@@ -58,7 +58,7 @@
# Set the parameters.
uf.page.uf_args['params'].SetValue(str_to_gui('(0.0, -0.00017,
0.00016, 0.00060, -0.00019)'))
uf.page.uf_args['params'].selection_win_show()
-uf.page.uf_args['params'].sel_win.sequence.SetStringItem(index=0,
col=1, label=float_to_gui(0.00037))
+uf.page.uf_args['params'].sel_win.sequence.SetStringItem(0, 1,
float_to_gui(0.00037))
uf.page.uf_args['params'].selection_win_data()
# Set up the other tensor data.
Modified: trunk/gui/input_elements/sequence.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/gui/input_elements/sequence.py?rev=28279=28278=28279=diff
==
--- trunk/gui/input_elements/sequence.py(original)
+++ trunk/gui/input_elements/sequence.pyTue Nov 15 14:36:02 2016
@@ -611,7 +611,7 @@
for i in range(len(values)):
# Fixed dimension sequences - set the values of the pre-created
list.
if not self.variable_length:
-self.sequence.SetStringItem(index=i, col=1,
label=self.convert_to_gui(values[i]))
+self.sequence.SetStringItem(i, 1,
self.convert_to_gui(values[i]))
# Variable dimension sequences - append the item to the end of the
blank list.
else:
@@ -621,7 +621,7 @@
self.sequence.InsertStringItem(i, int_to_gui(i+1))
# Then set the value.
-self.sequence.SetStringItem(index=i, col=1,
label=self.convert_to_gui(values[i]))
+self.sequence.SetStringItem(i, 1,
self.convert_to_gui(values[i]))
def add_buttons(self, sizer):
Modified: trunk/test_suite/gui_tests/test_user_functions.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/gui_tests/test_user_functions.py?rev=28279=28278=28279=diff
==
--- trunk/test_suite/gui_tests/test_user_functions.py (original)
+++ trunk/test_suite/gui_tests/test_user_functions.py Tue Nov 15 14:36:02 2016
@@ -1,6 +1,6 @@
###
# #
-# Copyright (C) 2012-2014 Edward d'Auvergne #
+# Copyright (C) 2012-2016 Edward d'Auvergne #
# #
# This file is part of the program relax (http://www.nmr-relax.com). #
# #
@@ -70,7 +70,7 @@
# Set the y-value of a single point, and check.
uf.page.uf_args['point'].selection_win_show()
-uf.page.uf_args['point'].sel_win.sequence.SetStringItem(index=0,
col=2, label=int_to_gui(2))
+uf.page.uf_args['point'].sel_win.sequence.SetStringItem(0, 2,
int_to_gui(2))
uf.page.uf_args['point'].selection_win_data()
points = uf.page.uf_args['point'].GetValue()
print("Points: %s" % points)
@@ -133,8 +133,8 @@
for val in ['x']:
uf.page.uf_args['point'].SetValue(
r28278 - /trunk/gui/menu.py
Author: bugman Date: Tue Nov 15 11:33:19 2016 New Revision: 28278 URL: http://svn.gna.org/viewcvs/relax?rev=28278=rev Log: Bug fix for "Tools->System information" GUI menu item. The user function has been renamed from sys_info to system.sys_info. Modified: trunk/gui/menu.py Modified: trunk/gui/menu.py URL: http://svn.gna.org/viewcvs/relax/trunk/gui/menu.py?rev=28278=28277=28278=diff == --- trunk/gui/menu.py (original) +++ trunk/gui/menu.py Tue Nov 15 11:33:19 2016 @@ -1,7 +1,7 @@ ### # # # Copyright (C) 2009 Michael Bieri# -# Copyright (C) 2010-2014 Edward d'Auvergne # +# Copyright (C) 2010-2016 Edward d'Auvergne # # # # This file is part of the program relax (http://www.nmr-relax.com). # # # @@ -235,7 +235,7 @@ """ # Launch the user function. -uf_store['sys_info']() +uf_store['system.sys_info']() def update_menus(self, event): ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
r28277 - /trunk/gui/input_elements/sequence.py
Author: bugman Date: Mon Nov 14 23:16:52 2016 New Revision: 28277 URL: http://svn.gna.org/viewcvs/relax?rev=28277=rev Log: Python 3 fix for the combo list sequence elements. Comparison of integers to values of None are not allowed. Modified: trunk/gui/input_elements/sequence.py Modified: trunk/gui/input_elements/sequence.py URL: http://svn.gna.org/viewcvs/relax/trunk/gui/input_elements/sequence.py?rev=28277=28276=28277=diff == --- trunk/gui/input_elements/sequence.py(original) +++ trunk/gui/input_elements/sequence.pyMon Nov 14 23:16:52 2016 @@ -212,6 +212,10 @@ if read_only == None: read_only = False +# Correct the min_length argument. +if combo_list_min == None: +combo_list_min = 1 + # Set up the Combo_list object. self._field = Combo_list(parent, sizer, desc, value_type=value_type, min_length=combo_list_min, choices=combo_choices, data=combo_data, default=default, tooltip=tooltip, read_only=read_only, can_be_none=can_be_none) ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
r28276 - /trunk/gui/misc.py
Author: bugman Date: Mon Nov 14 23:02:28 2016 New Revision: 28276 URL: http://svn.gna.org/viewcvs/relax?rev=28276=rev Log: Python 3 fixes for the gui.misc module. This is for text formatting using the "x"*num logic. In Python 3, num is often a float so this does not work and an explicit int() function call is required. Modified: trunk/gui/misc.py Modified: trunk/gui/misc.py URL: http://svn.gna.org/viewcvs/relax/trunk/gui/misc.py?rev=28276=28275=28276=diff == --- trunk/gui/misc.py (original) +++ trunk/gui/misc.py Mon Nov 14 23:02:28 2016 @@ -1,7 +1,7 @@ ### # # # Copyright (C) 2009 Michael Bieri# -# Copyright (C) 2010-2013 Edward d'Auvergne # +# Copyright (C) 2010-2016 Edward d'Auvergne # # # # This file is part of the program relax (http://www.nmr-relax.com). # # # @@ -212,7 +212,7 @@ total_width = sum(new_widths) + used # The header. -text += " " + "_" * (total_width - 2) + "\n\n"# Top rule and black line. +text += " " + "_" * int(total_width - 2) + "\n\n"# Top rule and black line. text += table_line(text=table.headings, widths=new_widths)# The headings. text += table_line(widths=new_widths, bottom=True)# Middle rule. @@ -353,16 +353,16 @@ # A bottom line. if bottom: -line += "_" * widths[i] +line += "_" * int(widths[i]) # Empty line. elif text == None: -line += " " * widths[i] +line += " " * int(widths[i]) # The text. else: line += text[i] -line += " " * (widths[i] - len(text[i])) +line += " " * int(widths[i] - len(text[i])) # Close the line. if bottom: ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
r28275 - in /trunk/gui: icons.py relax_gui.py
Author: bugman Date: Mon Nov 14 21:22:01 2016 New Revision: 28275 URL: http://svn.gna.org/viewcvs/relax?rev=28275=rev Log: Removal of the Mac OS X taskbar icon functionality. This code has been disabled since its deletion back in Jun 2012 (r16772), as it does not work with wxPython 2.8 or 2.9. However with wxPython Phoenix, the disabled code fails as there is no wx.TaskBarIcon. Modified: trunk/gui/icons.py trunk/gui/relax_gui.py Modified: trunk/gui/icons.py URL: http://svn.gna.org/viewcvs/relax/trunk/gui/icons.py?rev=28275=28274=28275=diff == --- trunk/gui/icons.py (original) +++ trunk/gui/icons.py Mon Nov 14 21:22:01 2016 @@ -42,84 +42,5 @@ self.AddIconFromFile(status.install_path + sep + 'graphics' + sep + 'ulysses.ico', wx.BITMAP_TYPE_ANY) -class Relax_task_bar_icon(wx.TaskBarIcon): -"""The icon for the Mac OS X task bar.""" - -# Set up some ID numbers for the menu entries. -TBMENU_RESTORE = wx.NewId() -TBMENU_CLOSE = wx.NewId() - -def __init__(self, gui): -"""Set up the task bar icon. - -@param gui: The GUI object. -@type gui: wx.Frame instance -""" - -# Store the args. -self.gui = gui - -# Initilise the base class. -wx.TaskBarIcon.__init__(self) - -# Set the task bar icon. -self.SetIcon(wx.Icon(status.install_path + sep + 'graphics' + sep + 'ulysses_shadowless_trans_128x128.png', wx.BITMAP_TYPE_ANY)) - -# Bind mouse events. -self.Bind(wx.EVT_TASKBAR_LEFT_DCLICK, self.restore) - - -def CreatePopupMenu(self): -"""Create and return the task bar menu. - -@return:The pop up menu. -@rtype: wx.Menu instance -""" - -# Initialise the menu. -popup = wx.Menu() - -# Add some menu entries. -popup.Append(self.TBMENU_RESTORE, "Restore relax") -popup.Append(self.TBMENU_CLOSE, "Exit relax") - -# Bind the menu events. -self.Bind(wx.EVT_MENU, self.restore, id=self.TBMENU_RESTORE) -self.Bind(wx.EVT_MENU, self.exit, id=self.TBMENU_CLOSE) - -# Return the menu. -return popup - - -def exit(self, event): -"""Exit relax from the task bar. - -@param event: The wx event. -@type event:wx event -""" - -# Exit relax. -wx.CallAfter(self.gui.exit_gui) - - -def restore(self, event): -"""Restore relax from the task bar. - -@param event: The wx event. -@type event:wx event -""" - -# Show relax. -if status.show_gui and not self.gui.IsShown(): -self.gui.Show(True) - -# De-iconise relax. -if self.gui.IsIconized(): -self.gui.Iconize(False) - -# Raise relax to the top of the window hierarchy. -self.gui.Raise() - - # Set up the main set of icons for relax. relax_icons = Relax_icons() Modified: trunk/gui/relax_gui.py URL: http://svn.gna.org/viewcvs/relax/trunk/gui/relax_gui.py?rev=28275=28274=28275=diff == --- trunk/gui/relax_gui.py (original) +++ trunk/gui/relax_gui.py Mon Nov 14 21:22:01 2016 @@ -131,10 +131,6 @@ relax_icons.setup() self.SetIcons(relax_icons) -# Set up the Mac OS X task bar icon. -#if status.wx_info["os"] == 'darwin' and status.wx_info["build"] != 'gtk': -#self.taskbar_icon = Relax_task_bar_icon(self) - # Initialise some variables for the GUI. self.launch_dir = getcwd() ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
r28274 - /trunk/test_suite/system_tests/scripts/relax_disp/r2eff_missing_data.py
Author: bugman Date: Mon Nov 14 20:23:03 2016 New Revision: 28274 URL: http://svn.gna.org/viewcvs/relax?rev=28274=rev Log: Python 3 bugfix for the Relax_disp.test_bug_24601_r2eff_missing_data system test. Tab characters rather than spaces made the system test script unloadable in Python 3. Modified: trunk/test_suite/system_tests/scripts/relax_disp/r2eff_missing_data.py Modified: trunk/test_suite/system_tests/scripts/relax_disp/r2eff_missing_data.py URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/scripts/relax_disp/r2eff_missing_data.py?rev=28274=28273=28274=diff == --- trunk/test_suite/system_tests/scripts/relax_disp/r2eff_missing_data.py (original) +++ trunk/test_suite/system_tests/scripts/relax_disp/r2eff_missing_data.py Mon Nov 14 20:23:03 2016 @@ -187,9 +187,9 @@ # set each spectrum noise RMSD if ndat == 1: - spectrum.baseplane_rmsd(error=24000, spectrum_id=id, spin_id=None) +spectrum.baseplane_rmsd(error=24000, spectrum_id=id, spin_id=None) elif ndat == 6: - spectrum.baseplane_rmsd(error=65000, spectrum_id=id, spin_id=None) +spectrum.baseplane_rmsd(error=65000, spectrum_id=id, spin_id=None) # Peak intensity error analysis. spectrum.error_analysis_per_field() ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
r28273 - /trunk/docs/devel/Release_Checklist
Author: bugman Date: Mon Nov 14 19:12:06 2016 New Revision: 28273 URL: http://svn.gna.org/viewcvs/relax?rev=28273=rev Log: Clarifications and minor expansion of the release checklist document. Modified: trunk/docs/devel/Release_Checklist Modified: trunk/docs/devel/Release_Checklist URL: http://svn.gna.org/viewcvs/relax/trunk/docs/devel/Release_Checklist?rev=28273=28272=28273=diff == --- trunk/docs/devel/Release_Checklist (original) +++ trunk/docs/devel/Release_Checklist Mon Nov 14 19:12:06 2016 @@ -151,7 +151,9 @@ $ scons user_manual_html -Replace the old manual with the new in the http://www.nmr-relax.com/manual SVN repository (http://svn.gna.org/viewcvs/relax/website) and commit the new manual. +Replace the old manual with the new in the http://www.nmr-relax.com/manual SVN repository (http://svn.gna.org/viewcvs/relax/website) and commit the new manual. To restore any missing redirects, in the website repository checkout run: + +$ python .setup_redirects.py API documentation @@ -202,8 +204,8 @@ - For all bugs, support requests, and tasks, make links to the trackers including the full description in the link. (for vim, go to the start of the text and use the register: "3dwr[/)^Mi ^[pxr]"). - Make links to the relax manual for all user functions: -- Vim register: "v/[ ,\r\n]^M<80>kl<80>kDi[http://www.nmr-relax.com/manual/^[pa.html ^[pa]^[/user function^M", -- Vim register: "v/[ ,\r\n]^M<80>kl<80>kDi[http://www.nmr-relax.com/manual/^[pa.html ^[p/user function^M2cwuser function]^[", +- Vim register: "v/[ ,\r\n] hxi[http://www.nmr-relax.com/manual/pa.html pa]/user function ", +- Vim register: "v/[ ,\r\n] hxi[http://www.nmr-relax.com/manual/pa.html p/user function 2cwuser function]", - Then search for "www.nmr-relax.com\/manual\/[a-z0-9_]*\.\|html" and replace all '.'. - Make internal links for all relax versions (vi search for "[1-3]\.[0-9]*\.[0-9]*"). - Convert all symbols to use wiki formatting. ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
r28272 - in /trunk: pipe_control/pcs.py test_suite/system_tests/pcs.py
Author: bugman
Date: Mon Nov 14 17:00:33 2016
New Revision: 28272
URL: http://svn.gna.org/viewcvs/relax?rev=28272=rev
Log:
Bug fix for the pcs.structural_error user function.
The user function now uses a real multivariate normal distribution for sampling
atomic positions.
The previous random unit vector + univariate Gaussian sampling does not
correctly reproduce the
multivariate normal distribution.
Modified:
trunk/pipe_control/pcs.py
trunk/test_suite/system_tests/pcs.py
Modified: trunk/pipe_control/pcs.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/pipe_control/pcs.py?rev=28272=28271=28272=diff
==
--- trunk/pipe_control/pcs.py (original)
+++ trunk/pipe_control/pcs.py Mon Nov 14 17:00:33 2016
@@ -1,6 +1,6 @@
###
# #
-# Copyright (C) 2003-2015 Edward d'Auvergne #
+# Copyright (C) 2003-2016 Edward d'Auvergne #
# #
# This file is part of the program relax (http://www.nmr-relax.com). #
# #
@@ -25,9 +25,9 @@
# Python module imports.
from copy import deepcopy
from math import ceil, floor, pi, sqrt
-from numpy import array, float64, int32, ones, std, zeros
+from numpy import array, eye, float64, int32, ones, std, zeros
from numpy.linalg import norm
-from random import gauss
+from numpy.random import multivariate_normal
import sys
from warnings import warn
@@ -35,7 +35,6 @@
from lib.alignment.pcs import ave_pcs_tensor, pcs_tensor
from lib.check_types import is_float
from lib.errors import RelaxError, RelaxNoAlignError, RelaxNoPdbError,
RelaxNoPCSError, RelaxNoSequenceError
-from lib.geometry.vectors import random_unit_vector
from lib.io import open_write_file, write_data
from lib.periodic_table import periodic_table
from lib.physical_constants import pcs_constant
@@ -1090,7 +1089,7 @@
The protocol for the simulation is as follows:
- The lanthanide or paramagnetic centre position will be fixed. Its
motion is assumed to be on the femto- to pico- and nanosecond timescales.
Hence the motion is averaged over the evolution of the PCS and can be ignored.
-- The positions of the nuclear spins will be randomised N times. For
each simulation a random unit vector will be generated. Then a random distance
along the unit vector will be generated by sampling from a Gaussian
distribution centered at zero, the original spin position, with a standard
deviation set to the given RMSD. Both positive and negative displacements will
be used.
+- The positions of the nuclear spins will be randomised N times using
a multivariate normal distribution.
- The PCS for the randomised position will be back calculated.
- The PCS standard deviation will be calculated from the N randomised
PCS values.
@@ -1130,6 +1129,9 @@
grace_data.append([])
pcs[id] = zeros(sim_num, float64)
+# Pre-calculate the covariance matrix as the spherical covariance.
+cov = rmsd**2 * eye(3)
+
# Print out.
print("Executing %i simulations for each spin system." % sim_num)
@@ -1161,19 +1163,13 @@
orig_vect = pos - cdp.paramagnetic_centre
orig_r = norm(orig_vect)
+# Sample from the multivariate normal distribution.
+new_pos = multivariate_normal(pos, cov, sim_num)
+
# Loop over the N randomisations.
for i in range(sim_num):
-# The random unit vector.
-random_unit_vector(unit_vect)
-
-# The random displacement (in Angstrom).
-disp = gauss(0, rmsd)
-
-# Move the atom.
-new_pos = pos + disp*unit_vect
-
# The vector and length.
-vect = new_pos - cdp.paramagnetic_centre
+vect = new_pos[i] - cdp.paramagnetic_centre
r = norm(vect)
vect = vect / r
Modified: trunk/test_suite/system_tests/pcs.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/pcs.py?rev=28272=28271=28272=diff
==
--- trunk/test_suite/system_tests/pcs.py(original)
+++ trunk/test_suite/system_tests/pcs.pyMon Nov 14 17:00:33 2016
@@ -1,6 +1,6 @@
###
# #
-# Copyright (C) 2011-2015 Edward d'Auvergne #
+# Copyright (C) 2011-2016 Edward
r28271 - /website/api/index.html
Author: bugman Date: Fri Oct 28 15:44:54 2016 New Revision: 28271 URL: http://svn.gna.org/viewcvs/relax?rev=28271=rev Log: Updated the relax version number to 4.0.3 on the http://www.nmr-relax.com/api/index.html webpage. Modified: website/api/index.html Modified: website/api/index.html URL: http://svn.gna.org/viewcvs/relax/website/api/index.html?rev=28271=28270=28271=diff == --- website/api/index.html (original) +++ website/api/index.html Fri Oct 28 15:44:54 2016 @@ -30,7 +30,7 @@ The most recent version of the documentation is: - http://www.nmr-relax.com/api/4.0/;>relax 4.0.2 API documentation + http://www.nmr-relax.com/api/4.0/;>relax 4.0.3 API documentation The relax library @@ -42,7 +42,7 @@ The automatically generated API documentation is also available for earlier relax versions: - http://www.nmr-relax.com/api/4.0/;>relax 4.0.2 API documentation + http://www.nmr-relax.com/api/4.0/;>relax 4.0.3 API documentation http://www.nmr-relax.com/api/3.3/;>relax 3.3.9 API documentation http://www.nmr-relax.com/api/3.2/;>relax 3.2.3 API documentation http://www.nmr-relax.com/api/3.1/;>relax 3.1.7 API documentation ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
r28270 - /website/api/4.0/
Author: bugman Date: Fri Oct 28 15:42:03 2016 New Revision: 28270 URL: http://svn.gna.org/viewcvs/relax?rev=28270=rev Log: Updated the relax API documentation at http://www.nmr-relax.com/api/4.0/ to version 4.0.3. Removed: website/api/4.0/target_functions.relax_fit-module.html website/api/4.0/toc-target_functions.relax_fit-module.html Modified: website/api/4.0/abc.ABCMeta-class.html website/api/4.0/api-objects.txt website/api/4.0/auto_analyses-module.html website/api/4.0/auto_analyses-pysrc.html website/api/4.0/auto_analyses.dauvergne_protocol-module.html website/api/4.0/auto_analyses.dauvergne_protocol-pysrc.html website/api/4.0/auto_analyses.dauvergne_protocol.Container-class.html website/api/4.0/auto_analyses.dauvergne_protocol.dAuvergne_protocol-class.html website/api/4.0/auto_analyses.frame_order-module.html website/api/4.0/auto_analyses.frame_order-pysrc.html website/api/4.0/auto_analyses.frame_order.Frame_order_analysis-class.html website/api/4.0/auto_analyses.frame_order.Optimisation_settings-class.html website/api/4.0/auto_analyses.noe-module.html website/api/4.0/auto_analyses.noe-pysrc.html website/api/4.0/auto_analyses.noe.NOE_calc-class.html website/api/4.0/auto_analyses.relax_disp-module.html website/api/4.0/auto_analyses.relax_disp-pysrc.html website/api/4.0/auto_analyses.relax_disp.Relax_disp-class.html website/api/4.0/auto_analyses.relax_disp_repeat_cpmg-module.html website/api/4.0/auto_analyses.relax_disp_repeat_cpmg-pysrc.html website/api/4.0/auto_analyses.relax_disp_repeat_cpmg.Relax_disp_rep-class.html website/api/4.0/auto_analyses.relax_fit-module.html website/api/4.0/auto_analyses.relax_fit-pysrc.html website/api/4.0/auto_analyses.relax_fit.Relax_fit-class.html website/api/4.0/auto_analyses.stereochem_analysis-module.html website/api/4.0/auto_analyses.stereochem_analysis-pysrc.html website/api/4.0/auto_analyses.stereochem_analysis.Stereochem_analysis-class.html website/api/4.0/bmrblib-module.html website/api/4.0/bmrblib-pysrc.html website/api/4.0/bmrblib.NMR_parameters-module.html website/api/4.0/bmrblib.NMR_parameters-pysrc.html website/api/4.0/bmrblib.NMR_parameters.chem_shift_anisotropy-module.html website/api/4.0/bmrblib.NMR_parameters.chem_shift_anisotropy-pysrc.html website/api/4.0/bmrblib.NMR_parameters.chem_shift_anisotropy.CSAnisotropy-class.html website/api/4.0/bmrblib.NMR_parameters.chem_shift_anisotropy.CSAnisotropyExperiment-class.html website/api/4.0/bmrblib.NMR_parameters.chem_shift_anisotropy.CSAnisotropySoftware-class.html website/api/4.0/bmrblib.NMR_parameters.chem_shift_anisotropy.ChemShiftAnisotropy-class.html website/api/4.0/bmrblib.NMR_parameters.chem_shift_anisotropy.ChemShiftAnisotropySaveframe-class.html website/api/4.0/bmrblib.NMR_parameters.chem_shift_anisotropy_v3_1-module.html website/api/4.0/bmrblib.NMR_parameters.chem_shift_anisotropy_v3_1-pysrc.html website/api/4.0/bmrblib.NMR_parameters.chem_shift_anisotropy_v3_1.CSAnisotropyExperiment_v3_1-class.html website/api/4.0/bmrblib.NMR_parameters.chem_shift_anisotropy_v3_1.CSAnisotropySoftware_v3_1-class.html website/api/4.0/bmrblib.NMR_parameters.chem_shift_anisotropy_v3_1.CSAnisotropy_v3_1-class.html website/api/4.0/bmrblib.NMR_parameters.chem_shift_anisotropy_v3_1.ChemShiftAnisotropySaveframe_v3_1-class.html website/api/4.0/bmrblib.NMR_parameters.chem_shift_anisotropy_v3_1.ChemShiftAnisotropy_v3_1-class.html website/api/4.0/bmrblib.assembly_supercategory-module.html website/api/4.0/bmrblib.assembly_supercategory-pysrc.html website/api/4.0/bmrblib.assembly_supercategory.entity-module.html website/api/4.0/bmrblib.assembly_supercategory.entity-pysrc.html website/api/4.0/bmrblib.assembly_supercategory.entity.Entity-class.html website/api/4.0/bmrblib.assembly_supercategory.entity.EntityCompIndex-class.html website/api/4.0/bmrblib.assembly_supercategory.entity.EntitySaveframe-class.html website/api/4.0/bmrblib.assembly_supercategory.entity_v2_1-module.html website/api/4.0/bmrblib.assembly_supercategory.entity_v2_1-pysrc.html website/api/4.0/bmrblib.assembly_supercategory.entity_v2_1.EntityCompIndex_v2_1-class.html website/api/4.0/bmrblib.assembly_supercategory.entity_v2_1.EntitySaveframe_v2_1-class.html website/api/4.0/bmrblib.assembly_supercategory.entity_v2_1.Entity_v2_1-class.html website/api/4.0/bmrblib.assembly_supercategory.entity_v3_1-module.html website/api/4.0/bmrblib.assembly_supercategory.entity_v3_1-pysrc.html website/api/4.0/bmrblib.assembly_supercategory.entity_v3_1.EntityCompIndex_v3_1-class.html website/api/4.0/bmrblib.assembly_supercategory.entity_v3_1.EntitySaveframe_v3_1-class.html website/api/4.0/bmrblib.assembly_supercategory.entity_v3_1.Entity_v3_1-class.html website/api/4.0/bmrblib.base_classes-module.html
r28268 - /website/download.html
Author: bugman Date: Fri Oct 28 15:26:27 2016 New Revision: 28268 URL: http://svn.gna.org/viewcvs/relax?rev=28268=rev Log: Updated the http://www.nmr-relax.com/download.html webpage for the relax 4.0.3 release. Modified: website/download.html [This mail would be too long, it was shortened to contain the URLs only.] Modified: website/download.html URL: http://svn.gna.org/viewcvs/relax/website/download.html?rev=28268=28267=28268=diff ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
r28267 - /trunk/docs/CHANGES
Author: bugman Date: Fri Oct 28 12:34:05 2016 New Revision: 28267 URL: http://svn.gna.org/viewcvs/relax?rev=28267=rev Log: Backported the relax 4.0.3 CHANGES file changes to trunk. The command used was: svn merge -r28265:28266 svn+ssh://bug...@svn.gna.org/svn/relax/tags/4.0.3 . Modified: trunk/docs/CHANGES Modified: trunk/docs/CHANGES URL: http://svn.gna.org/viewcvs/relax/trunk/docs/CHANGES?rev=28267=28266=28267=diff == --- trunk/docs/CHANGES (original) +++ trunk/docs/CHANGES Fri Oct 28 12:34:05 2016 @@ -1,10 +1,64 @@ +Version 4.0.3 +(28 October 2016, from /trunk) +http://svn.gna.org/svn/relax/tags/4.0.3 + +Features: +* Per-atom RMSD calculation by the structure.rmsd user function. +* Much faster superimposition of structures. +* More relax deployment scripts for Google Cloud for different GNU/Linux distributions. +* Addition of OpenMPI testing scripts. +* Improved relax information printout. + + +Changes: +* Addition of the atomic boolean argument to the structure.rmsd user function front end. This will be used to enable the calculation of per-atom RMSDs. +* Created the Structure.test_rmsd_spins system test for checking the per-atom RMSD calculation. This is for the new option in the structure.rmsd user function. +* Implemented the per-atom RMSD calculation for the structure.rmsd user function. +* Fixes for the Relax_fit.test_inversion_recovery system test. The wrong equation was used in the calc.py Python script used to calculate the peak intensities in the test_suite/shared_data/curve_fitting/inversion_recovery/*.list files. The script and Sparky files have been updated. And the I0 value in the script and system test has been changed from 30 to -30, so that the curves start as negative. +* Huge speed up for the superimposition of a large number of structures. The internal structural object validate_models() method was being called once for each structure via the selection() method prior performing the translations, and once prior to performing the rotations, for creating the atomic selection object. This resulted in the _translate() internal structural object method, which converts all input data to formatted strings, being called hundreds of millions of times. Therefore selection() method no longer calls validate_models(). This may speed up quite a number of internal structure object methods when large numbers of structures are present. +* Copying deployment script of Ubuntu to a Fedora version. This is a response to bug #25084 (https://gna.org/bugs/?25084). +* Moving fedora to redhat. Google Cloud does not offer fedora images. +* Adding deploy script for RHEL 6. +* Added initial script for testing OpenMPI. +* Making a redhat 6 deploy script, which will upgrade Python from 2.6 to 2.7 The normal installation through yum will have Python 2.6 and only numpy 2.4. This is not good. +* Moved deploy scripts. There would probably have to be a deploy script for each system. +* Renamed the Ubuntu deploy script. +* Adding scripts to test OpenMPI installation and deploy in redhat. +* Change to pip install command, to source Python first. +* Adding installation of matplotlib to Redhat 6, Python 2.7. +* More changing to deploy scripts. +* Small change to deploy script to build wxPython. +* More changing to deployment scripts. +* Moving test script of OpenMPI to bash version. +* Made a copy of OpenMPI test script for tcsh shell. +* Again small changes to deployment scripts. +* Changed more to OpenMPI script. +* Altering test OpenMPI script to an alias function. +* Change to bash OpenMPI test script. +* Last changes to testing of OpenMPI. +* Small change to test OpenMPI script for bash +* Back to function in bash script for OpenMPI. +* Made a deployment script for CentOS 6. +* Scons on CentOS finds python2.6 instead of python2.7 +* Try to make the script for tcsh and OpenMPI working on all versions of tcsh. +* Added the MPI version information to the mpi4py information printout. +* Windows scons C module compilation now defaults to 32-bit. This is because the default Python downloads are 32-bit. And many libraries (e.g. numpy and scipy) are only pre-compiled as 32-bit. Hence a 64-bit relax build on Windows will require a lot of custom compilation that most users will never do. +* Added support in the information printout for Windows versions of the 'file' program. This enables the C modules to be identified as 32 or 64-bit, if the 'file' program is installed. + + +Bugfixes: +* Fix for bug #24723 (https://gna.org/bugs/?24723). This is the bug that the mean RMSD
r28266 - /tags/4.0.3/docs/CHANGES
Author: bugman Date: Fri Oct 28 12:32:26 2016 New Revision: 28266 URL: http://svn.gna.org/viewcvs/relax?rev=28266=rev Log: Updated the CHANGES file for relax 4.0.3. Modified: tags/4.0.3/docs/CHANGES Modified: tags/4.0.3/docs/CHANGES URL: http://svn.gna.org/viewcvs/relax/tags/4.0.3/docs/CHANGES?rev=28266=28265=28266=diff == --- tags/4.0.3/docs/CHANGES (original) +++ tags/4.0.3/docs/CHANGES Fri Oct 28 12:32:26 2016 @@ -1,10 +1,64 @@ +Version 4.0.3 +(28 October 2016, from /trunk) +http://svn.gna.org/svn/relax/tags/4.0.3 + +Features: +* Per-atom RMSD calculation by the structure.rmsd user function. +* Much faster superimposition of structures. +* More relax deployment scripts for Google Cloud for different GNU/Linux distributions. +* Addition of OpenMPI testing scripts. +* Improved relax information printout. + + +Changes: +* Addition of the atomic boolean argument to the structure.rmsd user function front end. This will be used to enable the calculation of per-atom RMSDs. +* Created the Structure.test_rmsd_spins system test for checking the per-atom RMSD calculation. This is for the new option in the structure.rmsd user function. +* Implemented the per-atom RMSD calculation for the structure.rmsd user function. +* Fixes for the Relax_fit.test_inversion_recovery system test. The wrong equation was used in the calc.py Python script used to calculate the peak intensities in the test_suite/shared_data/curve_fitting/inversion_recovery/*.list files. The script and Sparky files have been updated. And the I0 value in the script and system test has been changed from 30 to -30, so that the curves start as negative. +* Huge speed up for the superimposition of a large number of structures. The internal structural object validate_models() method was being called once for each structure via the selection() method prior performing the translations, and once prior to performing the rotations, for creating the atomic selection object. This resulted in the _translate() internal structural object method, which converts all input data to formatted strings, being called hundreds of millions of times. Therefore selection() method no longer calls validate_models(). This may speed up quite a number of internal structure object methods when large numbers of structures are present. +* Copying deployment script of Ubuntu to a Fedora version. This is a response to bug #25084 (https://gna.org/bugs/?25084). +* Moving fedora to redhat. Google Cloud does not offer fedora images. +* Adding deploy script for RHEL 6. +* Added initial script for testing OpenMPI. +* Making a redhat 6 deploy script, which will upgrade Python from 2.6 to 2.7 The normal installation through yum will have Python 2.6 and only numpy 2.4. This is not good. +* Moved deploy scripts. There would probably have to be a deploy script for each system. +* Renamed the Ubuntu deploy script. +* Adding scripts to test OpenMPI installation and deploy in redhat. +* Change to pip install command, to source Python first. +* Adding installation of matplotlib to Redhat 6, Python 2.7. +* More changing to deploy scripts. +* Small change to deploy script to build wxPython. +* More changing to deployment scripts. +* Moving test script of OpenMPI to bash version. +* Made a copy of OpenMPI test script for tcsh shell. +* Again small changes to deployment scripts. +* Changed more to OpenMPI script. +* Altering test OpenMPI script to an alias function. +* Change to bash OpenMPI test script. +* Last changes to testing of OpenMPI. +* Small change to test OpenMPI script for bash +* Back to function in bash script for OpenMPI. +* Made a deployment script for CentOS 6. +* Scons on CentOS finds python2.6 instead of python2.7 +* Try to make the script for tcsh and OpenMPI working on all versions of tcsh. +* Added the MPI version information to the mpi4py information printout. +* Windows scons C module compilation now defaults to 32-bit. This is because the default Python downloads are 32-bit. And many libraries (e.g. numpy and scipy) are only pre-compiled as 32-bit. Hence a 64-bit relax build on Windows will require a lot of custom compilation that most users will never do. +* Added support in the information printout for Windows versions of the 'file' program. This enables the C modules to be identified as 32 or 64-bit, if the 'file' program is installed. + + +Bugfixes: +* Fix for bug #24723 (https://gna.org/bugs/?24723). This is the bug that the mean RMSD from the structure.rmsd user function is incorrectly calculated - it should be a
r28265 - /tags/4.0.3/docs/relax.pdf
Author: bugman Date: Fri Oct 28 11:04:29 2016 New Revision: 28265 URL: http://svn.gna.org/viewcvs/relax?rev=28265=rev Log: Added the relax 4.0.3 manual to the repository. Added: tags/4.0.3/docs/relax.pdf (with props) Added: tags/4.0.3/docs/relax.pdf URL: http://svn.gna.org/viewcvs/relax/tags/4.0.3/docs/relax.pdf?rev=28265=auto == Binary file - no diff available. Propchange: tags/4.0.3/docs/relax.pdf -- svn:mime-type = application/octet-stream ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
r28264 - /tags/4.0.3/version.py
Author: bugman Date: Fri Oct 28 10:53:49 2016 New Revision: 28264 URL: http://svn.gna.org/viewcvs/relax?rev=28264=rev Log: Updated the version number to relax 4.0.3. Modified: tags/4.0.3/version.py Modified: tags/4.0.3/version.py URL: http://svn.gna.org/viewcvs/relax/tags/4.0.3/version.py?rev=28264=28263=28264=diff == --- tags/4.0.3/version.py (original) +++ tags/4.0.3/version.py Fri Oct 28 10:53:49 2016 @@ -34,7 +34,7 @@ from status import Status; status = Status() -version = "repository checkout" +version = "4.0.3" repo_revision = None repo_url = None ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
r28263 - /tags/4.0.3/
Author: bugman Date: Fri Oct 28 10:42:19 2016 New Revision: 28263 URL: http://svn.gna.org/viewcvs/relax?rev=28263=rev Log: relax version 4.0.3. This is a minor feature and bugfix release. The structure.rmsd user function can now calculate per-atom RMSDs, structure superimposition is now orders of magnitude faster, the relax deployment scripts have been improved and expanded to cover other GNU/Linux systems, OpenMPI system testing scripts have been added, and the relax information printout has been improved. Bugfixes include that the structure.rmsd user function now correctly calculates the RMSD value, and the inversion recovery relaxation curve-fitting equations are now correct. Added: tags/4.0.3/ - copied from r28262, trunk/ ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
r28262 - /trunk/info.py
Author: bugman
Date: Thu Oct 27 12:48:18 2016
New Revision: 28262
URL: http://svn.gna.org/viewcvs/relax?rev=28262=rev
Log:
Added support in the information printout for Windows versions of the 'file'
program.
This enables the C modules to be identified as 32 or 64-bit, if the 'file'
program is installed.
Modified:
trunk/info.py
Modified: trunk/info.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/info.py?rev=28262=28261=28262=diff
==
--- trunk/info.py (original)
+++ trunk/info.py Thu Oct 27 12:48:18 2016
@@ -176,8 +176,10 @@
if Popen == None:
return ''
-# MS Windows (has no 'file' command or libmagic, so return nothing).
-if hasattr(ctypes, 'windll'):
+# Test if the 'file' program is installed.
+pipe = Popen('file --help', shell=True, stdout=PIPE, stderr=PIPE,
close_fds=False)
+err = pipe.stderr.readlines()
+if err:
return ''
# The command.
@@ -185,7 +187,8 @@
# Execute.
pipe = Popen(cmd, shell=True, stdout=PIPE, close_fds=False)
-waitpid(pipe.pid, 0)
+if not hasattr(ctypes, 'windll'):
+waitpid(pipe.pid, 0)
# The STDOUT data.
data = pipe.stdout.readlines()
@@ -240,7 +243,9 @@
arch[i] = row[1][:-1]
file_type += " %s" % arch
-# Return the string.
+# Return a string value.
+if file_type == None:
+return ''
return file_type
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r28261 - /trunk/sconstruct
Author: bugman Date: Thu Oct 27 12:35:53 2016 New Revision: 28261 URL: http://svn.gna.org/viewcvs/relax?rev=28261=rev Log: Windows scons C module compilation now defaults to 32-bit. This is because the default Python downloads are 32-bit. And many libraries (e.g. numpy and scipy) are only pre-compiled as 32-bit. Hence a 64-bit relax build on Windows will require a lot of custom compilation that most users will never do. Modified: trunk/sconstruct Modified: trunk/sconstruct URL: http://svn.gna.org/viewcvs/relax/trunk/sconstruct?rev=28261=28260=28261=diff == --- trunk/sconstruct(original) +++ trunk/sconstructThu Oct 27 12:35:53 2016 @@ -59,6 +59,10 @@ # Symbolic link flag. SYMLINK_FLAG = 1 +# Force a different target archictecture for MS Windows, if set (as the default Python download is 32-bit). +WIN_TARGET_OVERRIDE = True +TARGET_ARCH = None + # GNU/Linux. if SYSTEM == 'Linux': # System specific string. @@ -73,20 +77,27 @@ # Set the system to 'Windows' no matter what. SYSTEM = 'Windows' -# Architecture. -arch = platform.architecture()[0] - -# 32 bit. -if arch == '32bit': +# Force a default of 32-bit. +if WIN_TARGET_OVERRIDE: +TARGET_ARCH = 'x86' SYS = 'Win32' -# 64 bit. -elif arch == '64bit': -SYS = 'Win64' - -# Unknown. +# Determine the architecture. else: -SYS = 'Win' +# Architecture. +arch = platform.architecture()[0] + +# 32 bit. +if arch == '32bit': +SYS = 'Win32' + +# 64 bit. +elif arch == '64bit': +SYS = 'Win64' + +# Unknown. +else: +SYS = 'Win' # Windows installation path. INSTALL_PATH = 'C:\\' @@ -601,7 +612,7 @@ py_bin_fullpath = py_bin_minpath + path.sep + 'python' + `sys.version_info[0]` + '.' + `sys.version_info[1]` # Relaxation curve fitting build environment. -env = Environment() +env = Environment(TARGET_ARCH=TARGET_ARCH) # Determine the cross-compilation architectures for Mac systems. if env['PLATFORM'] == 'darwin': ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
r28260 - /trunk/info.py
Author: bugman
Date: Thu Oct 27 10:15:06 2016
New Revision: 28260
URL: http://svn.gna.org/viewcvs/relax?rev=28260=rev
Log:
Added the MPI version information to the mpi4py information printout.
Modified:
trunk/info.py
Modified: trunk/info.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/info.py?rev=28260=28259=28260=diff
==
--- trunk/info.py (original)
+++ trunk/info.py Thu Oct 27 10:15:06 2016
@@ -418,6 +418,15 @@
try:
version.append(dep_check.mpi4py.__version__)
path.append(dep_check.mpi4py.__path__[0])
+
+# MPI version.
+try:
+import mpi4py.MPI
+vendor = mpi4py.MPI.get_vendor()
+version[-1] += (" (%s %s.%s.%s)" % (vendor[0], vendor[1][0],
vendor[1][1], vendor[1][2]))
+except:
+pass
+
except:
version.append('')
path.append('')
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r28259 - in /trunk/devel_scripts: openmpi_test_install_bash.sh openmpi_test_install_tcsh.sh
Author: bugman Date: Tue Oct 4 16:35:02 2016 New Revision: 28259 URL: http://svn.gna.org/viewcvs/relax?rev=28259=rev Log: Set the svn:executable property on the OpenMPI installation testing scripts. Modified: trunk/devel_scripts/openmpi_test_install_bash.sh (props changed) trunk/devel_scripts/openmpi_test_install_tcsh.sh (props changed) Propchange: trunk/devel_scripts/openmpi_test_install_bash.sh -- svn:executable = * Propchange: trunk/devel_scripts/openmpi_test_install_tcsh.sh -- svn:executable = * ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
r28228 - /trunk/test_suite/system_tests/relax_disp.py
Author: bugman Date: Thu Aug 11 19:16:23 2016 New Revision: 28228 URL: http://svn.gna.org/viewcvs/relax?rev=28228=rev Log: Removed a debugging printout statement. Modified: trunk/test_suite/system_tests/relax_disp.py Modified: trunk/test_suite/system_tests/relax_disp.py URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/relax_disp.py?rev=28228=28227=28228=diff == --- trunk/test_suite/system_tests/relax_disp.py (original) +++ trunk/test_suite/system_tests/relax_disp.py Thu Aug 11 19:16:23 2016 @@ -6409,7 +6409,6 @@ self.assertEqual(len(cdp.mol[0].res), 2) self.assertEqual(cdp.spectrometer_frq_count, 2) -print cdp.spectrometer_frq_list self.assertEqual(cdp.spectrometer_frq_list, [6.0, 95000.0]) self.assertEqual(cdp.exp_type_list, ['R1rho']) ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
r28227 - /trunk/lib/plotting/grace.py
Author: bugman Date: Thu Aug 11 16:56:55 2016 New Revision: 28227 URL: http://svn.gna.org/viewcvs/relax?rev=28227=rev Log: Removed a debugging statement introduced at r28204 which breaks Python3 support. Modified: trunk/lib/plotting/grace.py Modified: trunk/lib/plotting/grace.py URL: http://svn.gna.org/viewcvs/relax/trunk/lib/plotting/grace.py?rev=28227=28226=28227=diff == --- trunk/lib/plotting/grace.py (original) +++ trunk/lib/plotting/grace.py Thu Aug 11 16:56:55 2016 @@ -176,7 +176,6 @@ norm_fact = 1.0 if norm[gi]: if norm_type == 'first': -print `data[gi][si]` norm_fact = data[gi][si][0][1] elif norm_type == 'last': norm_fact = data[gi][si][-1][1] ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
r28226 - /trunk/lib/structure/internal/object.py
Author: bugman Date: Tue Jun 7 17:27:04 2016 New Revision: 28226 URL: http://svn.gna.org/viewcvs/relax?rev=28226=rev Log: Huge speed up for the superimposition of a large number of structures. The internal structural object validate_models() method was being called once for each structure via the selection() method prior performing the translations, and once prior to performing the rotations, for creating the atomic selection object. This resulted in the _translate() internal structural object method, which converts all input data to formatted strings, being called hundreds of millions of times. Therefore selection() method no longer calls validate_models(). This may speed up quite a number of internal structure object methods when large numbers of structures are present. Modified: trunk/lib/structure/internal/object.py Modified: trunk/lib/structure/internal/object.py URL: http://svn.gna.org/viewcvs/relax/trunk/lib/structure/internal/object.py?rev=28226=28225=28226=diff == --- trunk/lib/structure/internal/object.py (original) +++ trunk/lib/structure/internal/object.py Tue Jun 7 17:27:04 2016 @@ -2668,9 +2668,6 @@ if atom_id: sel_obj = Selection(atom_id) -# Validate the models. -self.validate_models(verbosity=0) - # Obtain all data from the first model (except the position data). model = self.structural_data[0] ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
r28224 - /trunk/target_functions/exponential_inv.c
Author: bugman
Date: Fri Jun 3 11:03:54 2016
New Revision: 28224
URL: http://svn.gna.org/viewcvs/relax?rev=28224=rev
Log:
Bug fix for the inversion recovery equations (sr #3345).
The inversion recovery experiment was incorrectly implemented as I(t) = Iinf -
I0 * exp(-R1 * t)
whereas it should be I(t) = Iinf - (Iinf - I0) * exp(-R1 * t).
Modified:
trunk/target_functions/exponential_inv.c
Modified: trunk/target_functions/exponential_inv.c
URL:
http://svn.gna.org/viewcvs/relax/trunk/target_functions/exponential_inv.c?rev=28224=28223=28224=diff
==
--- trunk/target_functions/exponential_inv.c(original)
+++ trunk/target_functions/exponential_inv.cFri Jun 3 11:03:54 2016
@@ -1,5 +1,5 @@
/*
- * Copyright (C) 2006-2014 Edward d'Auvergne
+ * Copyright (C) 2006-2016 Edward d'Auvergne
*
* This file is part of the program relax (http://www.nmr-relax.com).
*
@@ -30,21 +30,21 @@
*
* The function used is::
*
- * I = Iinf - I0 * exp(-R.t)
-*/
-
-/* Declarations. */
-int i;
-
-/* Loop over the time points. */
-for (i = 0; i < num_times; i++) {
-/* Zero Rx value. */
-if (R == 0.0)
-back_calc[i] = Iinf - I0;
+ * I = Iinf - (Iinf - I0) * exp(-R.t)
+*/
+
+/* Declarations. */
+int i;
+
+/* Loop over the time points. */
+for (i = 0; i < num_times; i++) {
+/* Zero Rx value. */
+if (R == 0.0)
+back_calc[i] = I0;
/* Back calculate. */
else
-back_calc[i] = Iinf - I0 * exp(-relax_times[i] * R);
+back_calc[i] = Iinf - (Iinf - I0) * exp(-relax_times[i] * R);
}
}
@@ -61,11 +61,11 @@
for (i = 0; i < num_times; i++) {
/* Zero Rx value. */
if (R == 0.0)
-back_calc_grad[param_index][i] = -1.0;
-
-/* The partial derivate. */
-else
-back_calc_grad[param_index][i] = -exp(-relax_times[i] * R);
+back_calc_grad[param_index][i] = 1.0;
+
+/* The partial derivate. */
+else
+back_calc_grad[param_index][i] = exp(-relax_times[i] * R);
}
}
@@ -79,7 +79,13 @@
/* Everything is one. */
for (i = 0; i < num_times; i++) {
-back_calc_grad[param_index][i] = 1.0;
+/* Zero Rx value. */
+if (R == 0.0)
+back_calc_grad[param_index][i] = 0.0;
+
+/* The partial derivate. */
+else
+back_calc_grad[param_index][i] = 1.0 - exp(-relax_times[i] * R);
}
}
@@ -95,11 +101,11 @@
for (i = 0; i < num_times; i++) {
/* Zero Rx value. */
if (R == 0.0)
-back_calc_grad[param_index][i] = I0 * relax_times[i];
-
-/* The partial derivate. */
-else
-back_calc_grad[param_index][i] = I0 * relax_times[i] *
exp(-relax_times[i] * R);
+back_calc_grad[param_index][i] = (Iinf - I0) * relax_times[i];
+
+/* The partial derivate. */
+else
+back_calc_grad[param_index][i] = (Iinf - I0) * relax_times[i] *
exp(-relax_times[i] * R);
}
}
@@ -158,11 +164,11 @@
for (i = 0; i < num_times; i++) {
/* Zero Rx value. */
if (R == 0.0)
-back_calc_hess[I0_index][R_index][i] = relax_times[i];
+back_calc_hess[I0_index][R_index][i] = -relax_times[i];
/* The second partial derivate. */
else
-back_calc_hess[I0_index][R_index][i] = relax_times[i] *
exp(-relax_times[i] * R);
+back_calc_hess[I0_index][R_index][i] = -relax_times[i] *
exp(-relax_times[i] * R);
/* Hessian symmetry. */
back_calc_hess[R_index][I0_index][i] =
back_calc_hess[I0_index][R_index][i];
@@ -177,10 +183,18 @@
/* Declarations. */
int i;
-/* Everything is zero. */
-for (i = 0; i < num_times; i++) {
-back_calc_hess[R_index][Iinf_index][i] = 0.0;
-back_calc_hess[Iinf_index][R_index][i] = 0.0;
+/* Loop over the time points. */
+for (i = 0; i < num_times; i++) {
+/* Zero Rx value. */
+if (R == 0.0)
+back_calc_hess[Iinf_index][R_index][i] = relax_times[i];
+
+/* The second partial derivate. */
+else
+back_calc_hess[Iinf_index][R_index][i] = relax_times[i] *
exp(-relax_times[i] * R);
+
+/* Hessian symmetry. */
+back_calc_hess[R_index][Iinf_index][i] =
back_calc_hess[Iinf_index][R_index][i];
}
}
@@ -196,10 +210,10 @@
for (i = 0; i < num_times; i++) {
/* Zero Rx value. */
if (R == 0.0)
-back_calc_hess[R_index][R_index][i] = -I0 * square(relax_times[i]);
-
-/* The partial derivate. */
-else
-back_calc_hess[R_index][R_index][i] = -I0 * square(relax_times[i])
* exp(-relax_times[i] * R);
-}
-}
+back_calc_hess[R_index][R_index][i] = -(Iinf -
r28225 - in /trunk/test_suite: shared_data/curve_fitting/inversion_recovery/ system_tests/
==
--- trunk/test_suite/system_tests/relax_fit.py (original)
+++ trunk/test_suite/system_tests/relax_fit.py Fri Jun 3 11:03:56 2016
@@ -1,6 +1,6 @@
###
# #
-# Copyright (C) 2006-2015 Edward d'Auvergne #
+# Copyright (C) 2006-2016 Edward d'Auvergne #
# Copyright (C) 2014 Troels E. Linnet #
# #
# This file is part of the program relax (http://www.nmr-relax.com). #
@@ -480,7 +480,7 @@
# Check the curve-fitting results.
spin = return_spin(":4@N")
self.assertAlmostEqual(spin.rx, 1.2)
-self.assertAlmostEqual(spin.i0, 30.0)
+self.assertAlmostEqual(spin.i0, -30.0)
self.assertAlmostEqual(spin.iinf, 22.0)
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r28220 - /trunk/user_functions/structure.py
Author: bugman
Date: Thu Jun 2 19:09:34 2016
New Revision: 28220
URL: http://svn.gna.org/viewcvs/relax?rev=28220=rev
Log:
Addition of the atomic boolean argument to the structure.rmsd user function
front end.
This will be used to enable the calculation of per-atom RMSDs.
Modified:
trunk/user_functions/structure.py
Modified: trunk/user_functions/structure.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/user_functions/structure.py?rev=28220=28219=28220=diff
==
--- trunk/user_functions/structure.py (original)
+++ trunk/user_functions/structure.py Thu Jun 2 19:09:34 2016
@@ -1284,15 +1284,26 @@
desc = "The atom identification string of the coordinates of interest.",
can_be_none = True
)
-# Description.
-uf.desc.append(Desc_container())
-uf.desc[-1].add_paragraph("This allows the root mean squared deviation (RMSD)
between all structures to be calculated. The RMSDs for individual structures
to the mean structure will be calculated and reported, and then these values
averaged for the global RMSD. This will be stored in the structural object of
the current data pipe.")
+uf.add_keyarg(
+name = "atomic",
+default = False,
+py_type = "bool",
+desc_short = "atomic-level RMSD flag",
+desc = "A flag which if if True will allow for per-atom RMSDs to be
additionally calculated."
+)
+# Description.
+uf.desc.append(Desc_container())
+uf.desc[-1].add_paragraph("This allows the root mean squared deviation (RMSD)
between all structures to be calculated. The RMSDs for individual structures
to the mean structure will be calculated and reported. These values averaged
to produce a global RMSD stored in the structural object of the current data
pipe. If the 'atomic' argument is set, per-atom RMSDs will additionally be
calculated stored in spin containers.")
uf.desc[-1].add_paragraph(paragraph_multi_struct)
uf.desc[-1].add_paragraph(paragraph_atom_id)
# Prompt examples.
uf.desc.append(Desc_container("Prompt examples"))
uf.desc[-1].add_paragraph("To determine the RMSD of all models in the current
data pipe, simply type:")
uf.desc[-1].add_prompt("relax> structure.rmsd()")
+uf.desc[-1].add_paragraph("For the backbone heavy atom RMSD of all models in
the current data pipe, simply type:")
+uf.desc[-1].add_prompt("relax> structure.rmsd(atom_id='@N,C,CA,O')")
+uf.desc[-1].add_paragraph("To calculate the C-alpha backbone RMSDs of all
models in the current data pipe, type:")
+uf.desc[-1].add_prompt("relax> structure.rmsd(atom_id='CA', atomic=True)")
uf.backend = pipe_control.structure.main.rmsd
uf.menu_text = ""
uf.wizard_height_desc = 400
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r28221 - /trunk/test_suite/system_tests/structure.py
Author: bugman Date: Thu Jun 2 19:09:36 2016 New Revision: 28221 URL: http://svn.gna.org/viewcvs/relax?rev=28221=rev Log: Created the Structure.test_rmsd_spins system test for checking the per-atom RMSD calculation. This is for the new option in the structure.rmsd user function. Modified: trunk/test_suite/system_tests/structure.py Modified: trunk/test_suite/system_tests/structure.py URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/structure.py?rev=28221=28220=28221=diff == --- trunk/test_suite/system_tests/structure.py (original) +++ trunk/test_suite/system_tests/structure.py Thu Jun 2 19:09:36 2016 @@ -5098,6 +5098,47 @@ self.assertAlmostEqual(cdp.structure.rmsd, 2./3*sqrt(2)) +def test_rmsd_spins(self): +"""Test the structure.rmsd user function for per-atom RMSDs.""" + +# Set up 3 models. +self.interpreter.structure.add_model(model_num=1) +self.interpreter.structure.add_model(model_num=2) +self.interpreter.structure.add_model(model_num=4) + +# Check that the models were correctly created. +self.assert_(hasattr(cdp, 'structure')) +self.assert_(hasattr(cdp.structure, 'structural_data')) +self.assertEqual(len(cdp.structure.structural_data), 3) + +# Create a structure with some atoms. +self.interpreter.structure.add_atom(atom_name='CA', res_name='UNK', res_num=1, pos=[[1., 0., -1.], [0., 0., 0.], [-1., 0., 1.]], element='S') +self.interpreter.structure.add_atom(atom_name='CA', res_name='UNK', res_num=2, pos=[[1., 2., -1.], [0., 2., 0.], [-1., 2., 1.]], element='S') +self.interpreter.structure.add_atom(atom_name='CA', res_name='UNK', res_num=3, pos=[[1., 20., -1.], [0., 20., 0.], [-1., 20., 1.]], element='S') + +# Check the internal atomic info. +self.assertEqual(cdp.structure.structural_data[0].mol[0].x, [1., 1., 1.]) +self.assertEqual(cdp.structure.structural_data[0].mol[0].y, [0., 2., 20.]) +self.assertEqual(cdp.structure.structural_data[0].mol[0].z, [-1., -1., -1.]) +self.assertEqual(cdp.structure.structural_data[1].mol[0].x, [0., 0., 0.]) +self.assertEqual(cdp.structure.structural_data[1].mol[0].y, [0., 2., 20.]) +self.assertEqual(cdp.structure.structural_data[1].mol[0].z, [0., 0., 0.]) +self.assertEqual(cdp.structure.structural_data[2].mol[0].x, [-1., -1., -1.]) +self.assertEqual(cdp.structure.structural_data[2].mol[0].y, [0., 2., 20.]) +self.assertEqual(cdp.structure.structural_data[2].mol[0].z, [1., 1., 1.]) + +# Create the spins from the structural data. +self.interpreter.structure.load_spins(ave_pos=False) + +# Calculate the RMSD. +self.interpreter.structure.rmsd(atomic=True) + +# Checks. +self.assertAlmostEqual(cdp.mol[0].res[0].spin[0].pos_rmsd, sqrt(4.0/3.0)) +self.assertAlmostEqual(cdp.mol[0].res[1].spin[0].pos_rmsd, sqrt(4.0/3.0)) +self.assertAlmostEqual(cdp.mol[0].res[2].spin[0].pos_rmsd, sqrt(4.0/3.0)) + + def test_rmsd_ubi(self): """Test the structure.rmsd user function on the truncated ubiquitin ensemble.""" ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
r28222 - in /trunk: lib/structure/statistics.py pipe_control/structure/main.py
Author: bugman
Date: Thu Jun 2 19:09:39 2016
New Revision: 28222
URL: http://svn.gna.org/viewcvs/relax?rev=28222=rev
Log:
Implemented the per-atom RMSD calculation for the structure.rmsd user function.
Modified:
trunk/lib/structure/statistics.py
trunk/pipe_control/structure/main.py
Modified: trunk/lib/structure/statistics.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/structure/statistics.py?rev=28222=28221=28222=diff
==
--- trunk/lib/structure/statistics.py (original)
+++ trunk/lib/structure/statistics.py Thu Jun 2 19:09:39 2016
@@ -1,6 +1,6 @@
###
# #
-# Copyright (C) 2011-2015 Edward d'Auvergne #
+# Copyright (C) 2011-2016 Edward d'Auvergne #
# #
# This file is part of the program relax (http://www.nmr-relax.com). #
# #
@@ -115,3 +115,42 @@
# Average.
mean[i] = mean[i] / weights.sum()
+
+
+def per_atom_rmsd(coord, verbosity=0):
+"""Determine the per-atom RMSDs for the given atomic coordinates.
+
+This is the per atom RMSD to the mean structure.
+
+
+@keyword coord: The array of molecular coordinates. The first
dimension corresponds to the model, the second the atom, the third the
coordinate.
+@type coord:rank-3 numpy array
+@return:The list of RMSD values for each atom.
+@rtype: rank-1 numpy float64 array
+"""
+
+# Init.
+M = len(coord)
+N = len(coord[0])
+model_rmsd = zeros(M, float64)
+mean_str = zeros((N, 3), float64)
+rmsd = zeros(N, float64)
+
+# Calculate the mean structure.
+calc_mean_structure(coord, mean_str)
+
+# Loop over the atoms.
+for j in range(N):
+# Loop over the models.
+for i in range(M):
+# The vector connecting the mean to model atom.
+vect = mean_str[j] - coord[i][j]
+
+# The atomic RMSD.
+rmsd[j] += norm(vect)**2
+
+# Normalise, and sqrt.
+rmsd[j] = sqrt(rmsd[j] / M)
+
+# Return the RMSDs.
+return rmsd
Modified: trunk/pipe_control/structure/main.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/pipe_control/structure/main.py?rev=28222=28221=28222=diff
==
--- trunk/pipe_control/structure/main.py(original)
+++ trunk/pipe_control/structure/main.pyThu Jun 2 19:09:39 2016
@@ -44,7 +44,7 @@
from lib.structure.internal.object import Internal
from lib.structure.pca import pca_analysis
from lib.structure.represent.diffusion_tensor import diffusion_tensor
-from lib.structure.statistics import atomic_rmsd
+from lib.structure.statistics import atomic_rmsd, per_atom_rmsd
from lib.structure.superimpose import fit_to_first, fit_to_mean
from lib.warnings import RelaxWarning, RelaxNoPDBFileWarning,
RelaxZeroVectorWarning
from pipe_control import molmol, pipes
@@ -1308,7 +1308,7 @@
cdp.structure.load_xyz(file_path, read_mol=read_mol,
set_mol_name=set_mol_name, read_model=read_model, set_model_num=set_model_num,
verbosity=verbosity)
-def rmsd(pipes=None, models=None, molecules=None, atom_id=None):
+def rmsd(pipes=None, models=None, molecules=None, atom_id=None, atomic=False):
"""Calculate the RMSD between the loaded models.
The RMSD value will be placed into the current data pipe
cdp.structure.rmsd data structure.
@@ -1322,6 +1322,8 @@
@type molecules:None or list of lists of str
@keyword atom_id: The atom identification string of the coordinates of
interest. This matches the spin ID string format.
@type atom_id: str or None
+@keyword atomic:A flag which if True will allow for per-atom RMSDs to
be additionally calculated.
+@type atomic: bool
@return:The RMSD value.
@rtype: float
"""
@@ -1332,10 +1334,34 @@
# Assemble the structural coordinates.
coord, ids, mol_names, res_names, res_nums, atom_names, elements =
assemble_structural_coordinates(pipes=pipes, models=models,
molecules=molecules, atom_id=atom_id)
+# Per-atom RMSDs.
+if atomic:
+# Printout.
+print("\nCalculating the atomic-level RMSDs.")
+
+# Calculate the per-atom RMSDs.
+rmsd = per_atom_rmsd(coord, verbosity=0)
+
+# Loop over the atoms.
+for i in range(len(res_nums)):
+# The spin identification string.
+id = generate_spin_id_unique(mol_name=mol_names[i],
res_num=res_nums[i], res_name=r
r28223 - in /trunk: lib/structure/statistics.py test_suite/system_tests/structure.py
Author: bugman
Date: Thu Jun 2 19:09:40 2016
New Revision: 28223
URL: http://svn.gna.org/viewcvs/relax?rev=28223=rev
Log:
Fix for bug #24723 (https://gna.org/bugs/?24723).
This is the bug that the mean RMSD from the structure.rmsd user function is
incorrectly
calculated - it should be a quadratic mean.
The quadratic mean and quadratic standard deviation are now correctly
calculated, and the
structure.test_rmsd, structure.test_rmsd_molecules, and structure.test_rmsd_ubi
system tests have
been updated for the fix.
Modified:
trunk/lib/structure/statistics.py
trunk/test_suite/system_tests/structure.py
Modified: trunk/lib/structure/statistics.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/structure/statistics.py?rev=28223=28222=28223=diff
==
--- trunk/lib/structure/statistics.py (original)
+++ trunk/lib/structure/statistics.py Thu Jun 2 19:09:40 2016
@@ -65,16 +65,16 @@
if verbosity:
print("Model %2s RMSD: %s" % (i, model_rmsd[i]))
-# Calculate the mean.
-rmsd_mean = mean(model_rmsd)
+# Calculate the quadratic mean.
+rmsd_mean = sqrt(mean(model_rmsd**2))
-# Calculate the normal non-biased standard deviation.
+# Calculate the normal non-biased quadratic standard deviation.
try:
-rmsd_sd = std(model_rmsd, ddof=1)
+rmsd_sd = sqrt(std(model_rmsd**2, ddof=1))
# Handle old numpy versions not having the ddof argument.
except TypeError:
-rmsd_sd = std(model_rmsd) * sqrt(M / (M - 1.0))
+rmsd_sd = sqrt(std(model_rmsd**2) * sqrt(M / (M - 1.0)))
# Printout.
if verbosity:
Modified: trunk/test_suite/system_tests/structure.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/structure.py?rev=28223=28222=28223=diff
==
--- trunk/test_suite/system_tests/structure.py (original)
+++ trunk/test_suite/system_tests/structure.py Thu Jun 2 19:09:40 2016
@@ -21,7 +21,7 @@
# Python module imports.
from math import sqrt
-from numpy import array, average, dot, float64, sign, std, zeros
+from numpy import array, average, dot, float64, mean, sign, std, zeros
from numpy.linalg import norm
from os import sep
from re import search
@@ -5070,7 +5070,7 @@
# Checks.
self.assert_(hasattr(cdp.structure, 'rmsd'))
-self.assertAlmostEqual(cdp.structure.rmsd, 2./3*sqrt(2))
+self.assertAlmostEqual(cdp.structure.rmsd, sqrt(4.0/3.0))
def test_rmsd_molecules(self):
@@ -5095,7 +5095,7 @@
# Checks.
self.assert_(hasattr(cdp.structure, 'rmsd'))
-self.assertAlmostEqual(cdp.structure.rmsd, 2./3*sqrt(2))
+self.assertAlmostEqual(cdp.structure.rmsd, sqrt(4.0/3.0))
def test_rmsd_spins(self):
@@ -5149,9 +5149,13 @@
# Calculate the RMSD.
self.interpreter.structure.rmsd()
+# The per-structure RMSDs, and their quadratic average.
+all_rmsd = array([1.06994466835, 0.411387603119, 0.647768214719,
0.522216519591, 0.274450954939, 0.979817275482, 0.752817901842, 1.28956426491,
1.12979370978, 0.650514765397], float64)
+rmsd = sqrt(mean(all_rmsd**2))
+
# Checks (the values match the VMD 1.9.1 RMSD numbers).
self.assert_(hasattr(cdp.structure, 'rmsd'))
-self.assertAlmostEqual(cdp.structure.rmsd, 0.77282758781333061)
+self.assertAlmostEqual(cdp.structure.rmsd, rmsd)
def test_sequence_alignment_central_star_nw70_blosum62(self):
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r28219 - /trunk/docs/CHANGES
Author: bugman Date: Fri May 13 19:11:54 2016 New Revision: 28219 URL: http://svn.gna.org/viewcvs/relax?rev=28219=rev Log: Small edits for the CHANGES file. Modified: trunk/docs/CHANGES Modified: trunk/docs/CHANGES URL: http://svn.gna.org/viewcvs/relax/trunk/docs/CHANGES?rev=28219=28218=28219=diff == --- trunk/docs/CHANGES (original) +++ trunk/docs/CHANGES Fri May 13 19:11:54 2016 @@ -21,7 +21,7 @@ * Added the spin_num boolean argument to the structure.load_spins user function. Setting this flag to False will cause the spin number information to be ignored when creating the spin containers. This allows for better support of homologous structures but with different PDB atom numbering. The default flag value is True, preserving the old behaviour. * Added support for concatenating atomic positions in the structure.load_spins user function. Together with the spin_num flag set to False, this allows for atomic positions to be read from multiple homologous structures with different PDB atomic numbering. The spin containers will be created from the first structure, in which the spin is defined, and the atomic position from subsequent structures will be appended to the list of current atomic positions. * Fix for the Structure.test_read_pdb_internal3 system test. With the new atomic position concatenation support, when called sequentially the structure.load_spins user function should always use the same value for the ave_pos argument. -* In the GUI the userfunctions sys_info() and time() are now grouped into a "system" subclass. This is to prepare for other system related functions. +* In the GUI the user functions sys_info and time are now grouped into a "system" subclass. This is to prepare for other system related functions. * Added a new 16x16 icon for the oxygen folder-favorites icon. * Adding a new file at lib/system.py. This file will contain different functions related to python os and system related functions. For example changing directory or printing working directory. * In /lib/__init__.py, adding the filename for system.py. @@ -51,7 +51,7 @@ * Fix for GUI prompt bug, where ANSI escape characters should not be printed when interpreter is inherited from wxPython. * Added a newline character after printing the script. * Optimising the width of the statusbar. -* When the user function script is called, a notification of pipe_alteration is made. This will force the GUI to update, and make sure that it is up to-date. +* When the user function script is called, a notification of pipe_alteration is made. This will force the GUI to update, and make sure that it is up to date. * Updated the frame order auto-analysis for the time -> system.time user function change. * Fix for the GUI status bar element widths. Fixed widths in pixels causes text truncation on many systems, depending on the width of the main relax window. Instead variable widths should be used to allow wxPython to more elegantly present the text while minimising truncation. * Created a system test for catching bug #24601. This is the failure of the optimisation of the 'R2eff' dispersion model when peaks are missing from one spectrum, as reported by Petr Padrta at https://gna.org/bugs/?24601. The test uses his data and script to trigger the bug. ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
r28218 - /website/api/index.html
Author: bugman Date: Fri May 13 17:44:47 2016 New Revision: 28218 URL: http://svn.gna.org/viewcvs/relax?rev=28218=rev Log: Updated the relax version number to 4.0.2 on the http://www.nmr-relax.com/api/index.html webpage. Modified: website/api/index.html Modified: website/api/index.html URL: http://svn.gna.org/viewcvs/relax/website/api/index.html?rev=28218=28217=28218=diff == --- website/api/index.html (original) +++ website/api/index.html Fri May 13 17:44:47 2016 @@ -30,7 +30,7 @@ The most recent version of the documentation is: - http://www.nmr-relax.com/api/4.0/;>relax 4.0.1 API documentation + http://www.nmr-relax.com/api/4.0/;>relax 4.0.2 API documentation The relax library @@ -42,7 +42,7 @@ The automatically generated API documentation is also available for earlier relax versions: - http://www.nmr-relax.com/api/4.0/;>relax 4.0.1 API documentation + http://www.nmr-relax.com/api/4.0/;>relax 4.0.2 API documentation http://www.nmr-relax.com/api/3.3/;>relax 3.3.9 API documentation http://www.nmr-relax.com/api/3.2/;>relax 3.2.3 API documentation http://www.nmr-relax.com/api/3.1/;>relax 3.1.7 API documentation ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
r28217 - /website/api/4.0/
Author: bugman Date: Fri May 13 17:34:28 2016 New Revision: 28217 URL: http://svn.gna.org/viewcvs/relax?rev=28217=rev Log: Updated the relax API documentation at http://www.nmr-relax.com/api/4.0/ to version 4.0.2. Added: website/api/4.0/pipe_control.system-module.html website/api/4.0/pipe_control.system-pysrc.html website/api/4.0/toc-pipe_control.system-module.html Modified: website/api/4.0/abc.ABCMeta-class.html website/api/4.0/api-objects.txt website/api/4.0/auto_analyses-module.html website/api/4.0/auto_analyses-pysrc.html website/api/4.0/auto_analyses.dauvergne_protocol-module.html website/api/4.0/auto_analyses.dauvergne_protocol-pysrc.html website/api/4.0/auto_analyses.dauvergne_protocol.Container-class.html website/api/4.0/auto_analyses.dauvergne_protocol.dAuvergne_protocol-class.html website/api/4.0/auto_analyses.frame_order-module.html website/api/4.0/auto_analyses.frame_order-pysrc.html website/api/4.0/auto_analyses.frame_order.Frame_order_analysis-class.html website/api/4.0/auto_analyses.frame_order.Optimisation_settings-class.html website/api/4.0/auto_analyses.noe-module.html website/api/4.0/auto_analyses.noe-pysrc.html website/api/4.0/auto_analyses.noe.NOE_calc-class.html website/api/4.0/auto_analyses.relax_disp-module.html website/api/4.0/auto_analyses.relax_disp-pysrc.html website/api/4.0/auto_analyses.relax_disp.Relax_disp-class.html website/api/4.0/auto_analyses.relax_disp_repeat_cpmg-module.html website/api/4.0/auto_analyses.relax_disp_repeat_cpmg-pysrc.html website/api/4.0/auto_analyses.relax_disp_repeat_cpmg.Relax_disp_rep-class.html website/api/4.0/auto_analyses.relax_fit-module.html website/api/4.0/auto_analyses.relax_fit-pysrc.html website/api/4.0/auto_analyses.relax_fit.Relax_fit-class.html website/api/4.0/auto_analyses.stereochem_analysis-module.html website/api/4.0/auto_analyses.stereochem_analysis-pysrc.html website/api/4.0/auto_analyses.stereochem_analysis.Stereochem_analysis-class.html website/api/4.0/bmrblib-module.html website/api/4.0/bmrblib-pysrc.html website/api/4.0/bmrblib.NMR_parameters-module.html website/api/4.0/bmrblib.NMR_parameters-pysrc.html website/api/4.0/bmrblib.NMR_parameters.chem_shift_anisotropy-module.html website/api/4.0/bmrblib.NMR_parameters.chem_shift_anisotropy-pysrc.html website/api/4.0/bmrblib.NMR_parameters.chem_shift_anisotropy.CSAnisotropy-class.html website/api/4.0/bmrblib.NMR_parameters.chem_shift_anisotropy.CSAnisotropyExperiment-class.html website/api/4.0/bmrblib.NMR_parameters.chem_shift_anisotropy.CSAnisotropySoftware-class.html website/api/4.0/bmrblib.NMR_parameters.chem_shift_anisotropy.ChemShiftAnisotropy-class.html website/api/4.0/bmrblib.NMR_parameters.chem_shift_anisotropy.ChemShiftAnisotropySaveframe-class.html website/api/4.0/bmrblib.NMR_parameters.chem_shift_anisotropy_v3_1-module.html website/api/4.0/bmrblib.NMR_parameters.chem_shift_anisotropy_v3_1-pysrc.html website/api/4.0/bmrblib.NMR_parameters.chem_shift_anisotropy_v3_1.CSAnisotropyExperiment_v3_1-class.html website/api/4.0/bmrblib.NMR_parameters.chem_shift_anisotropy_v3_1.CSAnisotropySoftware_v3_1-class.html website/api/4.0/bmrblib.NMR_parameters.chem_shift_anisotropy_v3_1.CSAnisotropy_v3_1-class.html website/api/4.0/bmrblib.NMR_parameters.chem_shift_anisotropy_v3_1.ChemShiftAnisotropySaveframe_v3_1-class.html website/api/4.0/bmrblib.NMR_parameters.chem_shift_anisotropy_v3_1.ChemShiftAnisotropy_v3_1-class.html website/api/4.0/bmrblib.assembly_supercategory-module.html website/api/4.0/bmrblib.assembly_supercategory-pysrc.html website/api/4.0/bmrblib.assembly_supercategory.entity-module.html website/api/4.0/bmrblib.assembly_supercategory.entity-pysrc.html website/api/4.0/bmrblib.assembly_supercategory.entity.Entity-class.html website/api/4.0/bmrblib.assembly_supercategory.entity.EntityCompIndex-class.html website/api/4.0/bmrblib.assembly_supercategory.entity.EntitySaveframe-class.html website/api/4.0/bmrblib.assembly_supercategory.entity_v2_1-module.html website/api/4.0/bmrblib.assembly_supercategory.entity_v2_1-pysrc.html website/api/4.0/bmrblib.assembly_supercategory.entity_v2_1.EntityCompIndex_v2_1-class.html website/api/4.0/bmrblib.assembly_supercategory.entity_v2_1.EntitySaveframe_v2_1-class.html website/api/4.0/bmrblib.assembly_supercategory.entity_v2_1.Entity_v2_1-class.html website/api/4.0/bmrblib.assembly_supercategory.entity_v3_1-module.html website/api/4.0/bmrblib.assembly_supercategory.entity_v3_1-pysrc.html website/api/4.0/bmrblib.assembly_supercategory.entity_v3_1.EntityCompIndex_v3_1-class.html website/api/4.0/bmrblib.assembly_supercategory.entity_v3_1.EntitySaveframe_v3_1-class.html website/api/4.0/bmrblib.assembly_supercategory.entity_v3_1.Entity_v3_1-class.html
r28216 - /website/.setup_redirects.py
Author: bugman Date: Fri May 13 17:29:16 2016 New Revision: 28216 URL: http://svn.gna.org/viewcvs/relax?rev=28216=rev Log: Added some more user function renaming redirects. Modified: website/.setup_redirects.py Modified: website/.setup_redirects.py URL: http://svn.gna.org/viewcvs/relax/website/.setup_redirects.py?rev=28216=28215=28216=diff == --- website/.setup_redirects.py (original) +++ website/.setup_redirects.py Fri May 13 17:29:16 2016 @@ -128,7 +128,9 @@ ['manual/relax_fit_read.html', '%s/manual/spectrum_read_intensities.html'%url], ['manual/structure_vectors.html', '%s/manual/interatom_unit_vectors.html'%url], ['manual/structure_align.html', '%s/manual/structure_superimpose.html'%url], -['manual/temperature.html', '%s/manual/spectrometer_temperature.html'%url] +['manual/sys_info.html', '%s/manual/system_sys_info.html'%url], +['manual/temperature.html', '%s/manual/spectrometer_temperature.html'%url], +['manual/time.html', '%s/manual/system_time.html'%url] ] # HTML manual user function link mistakes. ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
r28215 - /website/manual/
Author: bugman Date: Fri May 13 17:28:07 2016 New Revision: 28215 URL: http://svn.gna.org/viewcvs/relax?rev=28215=rev Log: Updated the relax HTML manual at http://www.nmr-relax.com/manual/index.html to version 4.0.2. Added: website/manual/folder-development.png (with props) website/manual/folder-favorites.png (with props) website/manual/structure_delete_ss.html website/manual/system_cd.html website/manual/system_pwd.html website/manual/system_sys_info.html website/manual/system_time.html Modified: website/manual/A_warning_about_the_formatting.html website/manual/Abbreviations.html website/manual/About_this_document.html website/manual/Access_to_the_internals_of_relax.html website/manual/Advanced_topics.html website/manual/All_model_free_models_script_mode_explanation.html website/manual/All_model_free_models_script_mode_the_sample_script.html website/manual/Alphabetical_listing_of_user_functions.html website/manual/Analysing_dispersion_in_the_prompt_script_UI_mode.html website/manual/Assigning_an_issue_to_yourself.html website/manual/Becoming_a_committer.html website/manual/Bibliography.html website/manual/Branch_creation.html website/manual/Branches.html website/manual/Brownian_rotational_diffusion.html website/manual/C_module_compilation.html website/manual/Calculating_the_NOE.html website/manual/Calculation_of_the_NOE_in_the_prompt_script_UI_mode.html website/manual/Cleaning_up.html website/manual/Closing_an_issue.html website/manual/Coding_conventions.html website/manual/Comments.html website/manual/Committers.html website/manual/Comparison_of_dispersion_analysis_software.html website/manual/Compilation_of_the_API_documentation_HTML_version.html website/manual/Compilation_of_the_user_manual_HTML_version.html website/manual/Compilation_of_the_user_manual_PDF_version.html website/manual/Components_of_the_Ri_theta_equations.html website/manual/Computation_time_and_the_numerical_integration_of_the_PCS.html website/manual/Computation_times.html website/manual/Conjugate_gradient_methods.html website/manual/Consistency_testing.html website/manual/Consistency_testing_analysis_references.html website/manual/Consistency_testing_in_the_prompt_script_UI_mode.html website/manual/Consistency_testing_script_mode_calculation_and_error_propagation.html website/manual/Consistency_testing_script_mode_data_pipe_and_spin_system_setup.html website/manual/Consistency_testing_script_mode_relaxation_data_loading.html website/manual/Consistency_testing_script_mode_relaxation_interactions.html website/manual/Consistency_testing_script_mode_the_sample_script.html website/manual/Consistency_testing_script_mode_visualisation_and_data_output.html website/manual/Constraint_algorithms.html website/manual/Construction_of_the_Hessian.html website/manual/Construction_of_the_gradient.html website/manual/Construction_of_the_values_gradients_and_Hessians.html website/manual/Contents.html website/manual/Copying_modification_sublicencing_and_distribution_of_relax.html website/manual/Dasha.html website/manual/Data_analysis_tools.html website/manual/Data_visualisation.html website/manual/Defaults.html website/manual/Dependencies.html website/manual/Derivation_of_a_2D_trigonometric_function_the_pseudo_elliptic_cosine.html website/manual/Determining_stereochemistry_in_dynamic_molecules.html website/manual/Diagonal_scaling.html website/manual/Discussing_major_changes.html website/manual/Dispersion_GUI_mode_choosing_the_models_to_optimise.html website/manual/Dispersion_GUI_mode_comparing_models.html website/manual/Dispersion_GUI_mode_comparison_of_the_analyses.html website/manual/Dispersion_GUI_mode_computation_time.html website/manual/Dispersion_GUI_mode_dispersion_setup.html website/manual/Dispersion_GUI_mode_execution_of_the_non_clustered_analysis.html website/manual/Dispersion_GUI_mode_general_setup.html website/manual/Dispersion_GUI_mode_initialisation_of_the_data_pipe.html website/manual/Dispersion_GUI_mode_inspection_of_the_results.html website/manual/Dispersion_GUI_mode_loading_the_data.html website/manual/Dispersion_GUI_mode_optimisation_settings.html website/manual/Dispersion_GUI_mode_setting_up_the_spin_systems.html website/manual/Dispersion_GUI_mode_the_clustered_analysis.html website/manual/Dispersion_GUI_mode_two_analyses.html website/manual/Dispersion_GUI_mode_unresolved_spins.html website/manual/Dispersion_curve_insignificance.html website/manual/Dispersion_model_summary.html website/manual/Dispersion_parameter_grid_search.html website/manual/Dispersion_parameter_optimisation.html website/manual/Dispersion_script_mode_analysis_variables.html
r28214 - /website/download.html
Author: bugman Date: Fri May 13 17:22:43 2016 New Revision: 28214 URL: http://svn.gna.org/viewcvs/relax?rev=28214=rev Log: Updated the http://www.nmr-relax.com/download.html webpage for the relax 4.0.2 release. Modified: website/download.html [This mail would be too long, it was shortened to contain the URLs only.] Modified: website/download.html URL: http://svn.gna.org/viewcvs/relax/website/download.html?rev=28214=28213=28214=diff ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
r28213 - /trunk/docs/CHANGES
Author: bugman Date: Fri May 13 16:43:15 2016 New Revision: 28213 URL: http://svn.gna.org/viewcvs/relax?rev=28213=rev Log: Backported the relax 4.0.2 CHANGES file changes to trunk. The command used was: svn merge -r28211:28212 svn+ssh://bug...@svn.gna.org/svn/relax/tags/4.0.2 . Modified: trunk/docs/CHANGES Modified: trunk/docs/CHANGES URL: http://svn.gna.org/viewcvs/relax/trunk/docs/CHANGES?rev=28213=28212=28213=diff == --- trunk/docs/CHANGES (original) +++ trunk/docs/CHANGES Fri May 13 16:43:15 2016 @@ -1,3 +1,74 @@ +Version 4.0.2 +(13 May 2016, from /trunk) +http://svn.gna.org/svn/relax/tags/4.0.2 + +Features: +* Addition of the new user functions system.cd and system.pwd to allow the working directory to be changed and displayed. +* Addition of the structure.delete_ss user function to remove the helix and sheet information from the internal structural object. + + +Changes: +* Improved formatting for the \yes LaTeX command for the HTML manual (www.nmr-relax.com/manual/). This now inputs the raw HTML character for a tick. +* The replicate title finding script now processes short titles as well. This shows that the Frame_order.html file will be conflicting and overwritten. +* Avoidance of a replicated title in the frame order chapter of the manual. +* Added some unicode characters for improved formatting of the CHANGES file. +* A number of updates for the release checklist document. This should make it easier to replicate the full release process. +* Update the release checklist document. The version number at http://wiki.nmr-relax.com/Template:Current_version_relax also needs to be updated for each release. +* Added a check for the total argument for the frame_order.distribute user function. The maximum value is , as the PDB format cannot accept more models. +* Creation of the structure.delete_ss user function. This simply resets the helices and sheets data structures in the internal structural object to []. +* Updated the copyright notices for 2016. +* Created a short Info_box copyright string for displaying in the main GUI window. This shows the full range of copyright dates. +* Added the spin_num boolean argument to the structure.load_spins user function. Setting this flag to False will cause the spin number information to be ignored when creating the spin containers. This allows for better support of homologous structures but with different PDB atom numbering. The default flag value is True, preserving the old behaviour. +* Added support for concatenating atomic positions in the structure.load_spins user function. Together with the spin_num flag set to False, this allows for atomic positions to be read from multiple homologous structures with different PDB atomic numbering. The spin containers will be created from the first structure, in which the spin is defined, and the atomic position from subsequent structures will be appended to the list of current atomic positions. +* Fix for the Structure.test_read_pdb_internal3 system test. With the new atomic position concatenation support, when called sequentially the structure.load_spins user function should always use the same value for the ave_pos argument. +* In the GUI the userfunctions sys_info() and time() are now grouped into a "system" subclass. This is to prepare for other system related functions. +* Added a new 16x16 icon for the oxygen folder-favorites icon. +* Adding a new file at lib/system.py. This file will contain different functions related to python os and system related functions. For example changing directory or printing working directory. +* In /lib/__init__.py, adding the filename for system.py. +* Renaming the folder-favorites icon. +* Deleting the old folder-favorites icon. +* Adding a new graphics variable: WIZARD_OXYGEN_PATH, to use oxygen icons with size of 200px. +* Adding the new user function system.cd. This is to change the current working directory. +* Adding a new 200px of oxygen folder-favorites icon. This is to be used in the wizard image. +* Adding a user function translation for: This is to catch the new naming of these functions. +* Adding a new lib.system.pwd() function, to print and return the current working directory. +* Adding a new user function system.pwd() to print/display the current working directory. +* Adding new 16x16 px and 200px of the oxygen icon folder-development. This icon is used for displaying the current working directory. +* Adding a relax GUI menu for changing the current working directory. +* Adding a menu item for changing the current working directory. +* Adding a verbose True/False for the
r28212 - /tags/4.0.2/docs/CHANGES
Author: bugman Date: Fri May 13 16:42:06 2016 New Revision: 28212 URL: http://svn.gna.org/viewcvs/relax?rev=28212=rev Log: Updated the CHANGES file for relax 4.0.2. Modified: tags/4.0.2/docs/CHANGES Modified: tags/4.0.2/docs/CHANGES URL: http://svn.gna.org/viewcvs/relax/tags/4.0.2/docs/CHANGES?rev=28212=28211=28212=diff == --- tags/4.0.2/docs/CHANGES (original) +++ tags/4.0.2/docs/CHANGES Fri May 13 16:42:06 2016 @@ -1,3 +1,74 @@ +Version 4.0.2 +(13 May 2016, from /trunk) +http://svn.gna.org/svn/relax/tags/4.0.2 + +Features: +* Addition of the new user functions system.cd and system.pwd to allow the working directory to be changed and displayed. +* Addition of the structure.delete_ss user function to remove the helix and sheet information from the internal structural object. + + +Changes: +* Improved formatting for the \yes LaTeX command for the HTML manual (www.nmr-relax.com/manual/). This now inputs the raw HTML character for a tick. +* The replicate title finding script now processes short titles as well. This shows that the Frame_order.html file will be conflicting and overwritten. +* Avoidance of a replicated title in the frame order chapter of the manual. +* Added some unicode characters for improved formatting of the CHANGES file. +* A number of updates for the release checklist document. This should make it easier to replicate the full release process. +* Update the release checklist document. The version number at http://wiki.nmr-relax.com/Template:Current_version_relax also needs to be updated for each release. +* Added a check for the total argument for the frame_order.distribute user function. The maximum value is , as the PDB format cannot accept more models. +* Creation of the structure.delete_ss user function. This simply resets the helices and sheets data structures in the internal structural object to []. +* Updated the copyright notices for 2016. +* Created a short Info_box copyright string for displaying in the main GUI window. This shows the full range of copyright dates. +* Added the spin_num boolean argument to the structure.load_spins user function. Setting this flag to False will cause the spin number information to be ignored when creating the spin containers. This allows for better support of homologous structures but with different PDB atom numbering. The default flag value is True, preserving the old behaviour. +* Added support for concatenating atomic positions in the structure.load_spins user function. Together with the spin_num flag set to False, this allows for atomic positions to be read from multiple homologous structures with different PDB atomic numbering. The spin containers will be created from the first structure, in which the spin is defined, and the atomic position from subsequent structures will be appended to the list of current atomic positions. +* Fix for the Structure.test_read_pdb_internal3 system test. With the new atomic position concatenation support, when called sequentially the structure.load_spins user function should always use the same value for the ave_pos argument. +* In the GUI the userfunctions sys_info() and time() are now grouped into a "system" subclass. This is to prepare for other system related functions. +* Added a new 16x16 icon for the oxygen folder-favorites icon. +* Adding a new file at lib/system.py. This file will contain different functions related to python os and system related functions. For example changing directory or printing working directory. +* In /lib/__init__.py, adding the filename for system.py. +* Renaming the folder-favorites icon. +* Deleting the old folder-favorites icon. +* Adding a new graphics variable: WIZARD_OXYGEN_PATH, to use oxygen icons with size of 200px. +* Adding the new user function system.cd. This is to change the current working directory. +* Adding a new 200px of oxygen folder-favorites icon. This is to be used in the wizard image. +* Adding a user function translation for: This is to catch the new naming of these functions. +* Adding a new lib.system.pwd() function, to print and return the current working directory. +* Adding a new user function system.pwd() to print/display the current working directory. +* Adding new 16x16 px and 200px of the oxygen icon folder-development. This icon is used for displaying the current working directory. +* Adding a relax GUI menu for changing the current working directory. +* Adding a menu item for changing the current working directory. +* Adding a verbose True/False for the lib.system.pwd() function. +* Storing the current working directory as a GUI
r28209 - /tags/4.0.2/
Author: bugman Date: Fri May 13 16:06:22 2016 New Revision: 28209 URL: http://svn.gna.org/viewcvs/relax?rev=28209=rev Log: relax version 4.0.2. This is a minor feature and bugfix release. The new user functions system.cd and system.pwd have been added to allow the working directory to be changed and displayed. The time and sys_info user functions have been renamed to system.time and system.sys_info. The structure.delete_ss user function has been created to remove the helix and sheet information from the internal structural object. For bugs, the 'R2eff' dispersion model can now handle missing peaks in subsets of spectra, and the structure.read_pdb can now handle multiple structures and multiple models with the merge flag set. Added: tags/4.0.2/ - copied from r28208, trunk/ ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
r28211 - /tags/4.0.2/docs/relax.pdf
Author: bugman Date: Fri May 13 16:21:23 2016 New Revision: 28211 URL: http://svn.gna.org/viewcvs/relax?rev=28211=rev Log: Added the relax 4.0.2 manual to the repository. Added: tags/4.0.2/docs/relax.pdf (with props) Added: tags/4.0.2/docs/relax.pdf URL: http://svn.gna.org/viewcvs/relax/tags/4.0.2/docs/relax.pdf?rev=28211=auto == Binary file - no diff available. Propchange: tags/4.0.2/docs/relax.pdf -- svn:mime-type = application/octet-stream ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
r28210 - /tags/4.0.2/version.py
Author: bugman Date: Fri May 13 16:11:34 2016 New Revision: 28210 URL: http://svn.gna.org/viewcvs/relax?rev=28210=rev Log: Updated the version number to relax 4.0.2. Modified: tags/4.0.2/version.py Modified: tags/4.0.2/version.py URL: http://svn.gna.org/viewcvs/relax/tags/4.0.2/version.py?rev=28210=28209=28210=diff == --- tags/4.0.2/version.py (original) +++ tags/4.0.2/version.py Fri May 13 16:11:34 2016 @@ -34,7 +34,7 @@ from status import Status; status = Status() -version = "repository checkout" +version = "4.0.2" repo_revision = None repo_url = None ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
r28208 - /trunk/test_suite/system_tests/structure.py
Author: bugman Date: Thu May 12 11:46:15 2016 New Revision: 28208 URL: http://svn.gna.org/viewcvs/relax?rev=28208=rev Log: Mac OS X fixes for the Structure.test_pca and Structure.test_pca_observers system tests. The eigenvectors on this OS are sometimes inverted. As the sign of the eigenvector is irrelevant, the vectors hardcoded into the system tests are now inverted as required. Modified: trunk/test_suite/system_tests/structure.py Modified: trunk/test_suite/system_tests/structure.py URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/structure.py?rev=28208=28207=28208=diff == --- trunk/test_suite/system_tests/structure.py (original) +++ trunk/test_suite/system_tests/structure.py Thu May 12 11:46:15 2016 @@ -21,7 +21,7 @@ # Python module imports. from math import sqrt -from numpy import array, average, dot, float64, std, zeros +from numpy import array, average, dot, float64, sign, std, zeros from numpy.linalg import norm from os import sep from re import search @@ -4150,6 +4150,11 @@ proj[:, 2] = -proj[:, 2] proj[:, 3] = -proj[:, 3] +# Are more inversion necessary? +for mode in range(4): +if sign(cdp.structure.pca_proj[mode][0]) != sign(proj[0][mode]): +proj[:, mode] = -proj[:, mode] + # Checks. self.assert_(hasattr(cdp.structure, 'pca_values')) self.assert_(hasattr(cdp.structure, 'pca_vectors')) @@ -4180,6 +4185,11 @@ # Invert the 3rd and 4th Gromacs eigenvectors to match. proj[:, 2] = -proj[:, 2] proj[:, 3] = -proj[:, 3] + +# Are more inversion necessary? +for mode in range(4): +if sign(cdp.structure.pca_proj[mode][0]) != sign(proj[0][mode]): +proj[:, mode] = -proj[:, mode] # Checks. self.assert_(hasattr(cdp.structure, 'pca_values')) ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
r28207 - /trunk/graphics/README
Author: bugman Date: Thu May 12 10:14:40 2016 New Revision: 28207 URL: http://svn.gna.org/viewcvs/relax?rev=28207=rev Log: Some more details for the *.eps.gz icon creation process. Modified: trunk/graphics/README Modified: trunk/graphics/README URL: http://svn.gna.org/viewcvs/relax/trunk/graphics/README?rev=28207=28206=28207=diff == --- trunk/graphics/README (original) +++ trunk/graphics/README Thu May 12 10:14:40 2016 @@ -7,3 +7,7 @@ - Export to EPS. - Set the width and height to 6 mm each, and the offsets to 0.0. - Use Gzip to compress the EPS file. + +The final *.eps.gz file must contain the following header line: + +%%BoundingBox: 0 0 18 18 ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
r28206 - in /trunk/graphics: ./ oxygen_icons/ oxygen_icons/128x128/places/ oxygen_icons/32x32/places/ oxygen_icons/48x48/pla...
Author: bugman Date: Thu May 12 10:12:29 2016 New Revision: 28206 URL: http://svn.gna.org/viewcvs/relax?rev=28206=rev Log: Added some missing oxygen icons to allow the relax manual to compile. These are the 128x128 EPS versions of the places/folder-development.png and places/folder-favorites.png Oxygen icons recently introduced. For completeness the 32x32, 48x48, and 128x128 PNG versions of the icons have also been added. To help create these EPS icons in the future, the graphics/README file has been added with a description of the *.eps.gz file creation. Added: trunk/graphics/README trunk/graphics/oxygen_icons/128x128/places/ trunk/graphics/oxygen_icons/128x128/places/folder-development.eps.gz (with props) trunk/graphics/oxygen_icons/128x128/places/folder-development.png (with props) trunk/graphics/oxygen_icons/128x128/places/folder-favorites.eps.gz (with props) trunk/graphics/oxygen_icons/128x128/places/folder-favorites.png (with props) trunk/graphics/oxygen_icons/32x32/places/ trunk/graphics/oxygen_icons/32x32/places/folder-development.png (with props) trunk/graphics/oxygen_icons/32x32/places/folder-favorites.png (with props) trunk/graphics/oxygen_icons/48x48/places/ trunk/graphics/oxygen_icons/48x48/places/folder-development.png (with props) trunk/graphics/oxygen_icons/48x48/places/folder-favorites.png (with props) Modified: trunk/graphics/oxygen_icons/README Added: trunk/graphics/README URL: http://svn.gna.org/viewcvs/relax/trunk/graphics/README?rev=28206=auto == --- trunk/graphics/README (added) +++ trunk/graphics/README Thu May 12 10:12:29 2016 @@ -0,0 +1,9 @@ += User function icons in the manual = + +For the compilation of the manual, 128x128 versions of the icons for user functions must be added. The steps are: + +- Firstly copy or create the 128x128 PNG version of the icon. +- Open the file in the Gimp. +- Export to EPS. +- Set the width and height to 6 mm each, and the offsets to 0.0. +- Use Gzip to compress the EPS file. Added: trunk/graphics/oxygen_icons/128x128/places/folder-development.eps.gz URL: http://svn.gna.org/viewcvs/relax/trunk/graphics/oxygen_icons/128x128/places/folder-development.eps.gz?rev=28206=auto == Binary file - no diff available. Propchange: trunk/graphics/oxygen_icons/128x128/places/folder-development.eps.gz -- svn:mime-type = application/octet-stream Added: trunk/graphics/oxygen_icons/128x128/places/folder-development.png URL: http://svn.gna.org/viewcvs/relax/trunk/graphics/oxygen_icons/128x128/places/folder-development.png?rev=28206=auto == Binary file - no diff available. Propchange: trunk/graphics/oxygen_icons/128x128/places/folder-development.png -- svn:mime-type = image/png Added: trunk/graphics/oxygen_icons/128x128/places/folder-favorites.eps.gz URL: http://svn.gna.org/viewcvs/relax/trunk/graphics/oxygen_icons/128x128/places/folder-favorites.eps.gz?rev=28206=auto == Binary file - no diff available. Propchange: trunk/graphics/oxygen_icons/128x128/places/folder-favorites.eps.gz -- svn:mime-type = application/octet-stream Added: trunk/graphics/oxygen_icons/128x128/places/folder-favorites.png URL: http://svn.gna.org/viewcvs/relax/trunk/graphics/oxygen_icons/128x128/places/folder-favorites.png?rev=28206=auto == Binary file - no diff available. Propchange: trunk/graphics/oxygen_icons/128x128/places/folder-favorites.png -- svn:mime-type = image/png Added: trunk/graphics/oxygen_icons/32x32/places/folder-development.png URL: http://svn.gna.org/viewcvs/relax/trunk/graphics/oxygen_icons/32x32/places/folder-development.png?rev=28206=auto == Binary file - no diff available. Propchange: trunk/graphics/oxygen_icons/32x32/places/folder-development.png -- svn:mime-type = image/png Added: trunk/graphics/oxygen_icons/32x32/places/folder-favorites.png URL: http://svn.gna.org/viewcvs/relax/trunk/graphics/oxygen_icons/32x32/places/folder-favorites.png?rev=28206=auto == Binary file - no diff available. Propchange:
r28205 - in /trunk: gui/ lib/ pipe_control/ user_functions/
Author: bugman Date: Thu May 12 10:04:01 2016 New Revision: 28205 URL: http://svn.gna.org/viewcvs/relax?rev=28205=rev Log: Fix for the independence of the relax library. As lib.system was using the status object, the library independence was broken. To work around this, the module has simply been shifted into the pipe_control package. Added: trunk/pipe_control/system.py - copied unchanged from r28204, trunk/lib/system.py Removed: trunk/lib/system.py Modified: trunk/gui/relax_gui.py trunk/lib/__init__.py trunk/pipe_control/__init__.py trunk/user_functions/sys_info.py Modified: trunk/gui/relax_gui.py URL: http://svn.gna.org/viewcvs/relax/trunk/gui/relax_gui.py?rev=28205=28204=28205=diff == --- trunk/gui/relax_gui.py (original) +++ trunk/gui/relax_gui.py Thu May 12 10:04:01 2016 @@ -2,6 +2,7 @@ # # # Copyright (C) 2009 Michael Bieri# # Copyright (C) 2010-2016 Edward d'Auvergne # +# Copyright (C) 2016 Troels Schwartz-Linnet # # # # This file is part of the program relax (http://www.nmr-relax.com). # # # @@ -58,10 +59,10 @@ from info import Info_box from lib.errors import RelaxNoPipeError from lib.io import io_streams_restore -from lib.system import pwd from pipe_control import state from pipe_control.pipes import cdp_name from pipe_control.reset import reset +from pipe_control.system import pwd from status import Status; status = Status() from version import version Modified: trunk/lib/__init__.py URL: http://svn.gna.org/viewcvs/relax/trunk/lib/__init__.py?rev=28205=28204=28205=diff == --- trunk/lib/__init__.py (original) +++ trunk/lib/__init__.py Thu May 12 10:04:01 2016 @@ -58,7 +58,6 @@ 'spectrum', 'statistics', 'structure', -'system', 'text', 'timing', 'warnings', Removed: trunk/lib/system.py URL: http://svn.gna.org/viewcvs/relax/trunk/lib/system.py?rev=28204=auto == --- trunk/lib/system.py (original) +++ trunk/lib/system.py (removed) @@ -1,78 +0,0 @@ -### -# # -# Copyright (C) 2016 Troels Schwartz-Linnet # -# # -# This file is part of the program relax (http://www.nmr-relax.com). # -# # -# This program is free software: you can redistribute it and/or modify# -# it under the terms of the GNU General Public License as published by# -# the Free Software Foundation, either version 3 of the License, or # -# (at your option) any later version. # -# # -# This program is distributed in the hope that it will be useful, # -# but WITHOUT ANY WARRANTY; without even the implied warranty of # -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # -# GNU General Public License for more details.# -# # -# You should have received a copy of the GNU General Public License # -# along with this program. If not, see <http://www.gnu.org/licenses/>. # -# # -### - -# Module docstring. -"""Module for various os and sys python module purposes.""" - -# Python module imports. -from os import chdir, getcwd - -# relax module imports. -import lib.arg_check -from status import Status; status = Status() - - -def cd(path, verbose=False): -"""The equivalent of python module os.chdir(path). Change the current working directory to the specified path. - -@keyword verbose: A flag which if True will cause the previous directory to be printed. -@type verbose: bool -@param path: The path to the directory for the current working directory. -@type path: str -""" - -# Check that the path is a string. -lib.arg_check.is_str(path, name="pa
r28204 - in /trunk: lib/plotting/grace.py specific_analyses/relax_disp/api.py specific_analyses/relax_disp/optimisation.py
Author: bugman
Date: Wed Apr 27 11:13:48 2016
New Revision: 28204
URL: http://svn.gna.org/viewcvs/relax?rev=28204=rev
Log:
Fix for bug #24601.
This is the failure of the optimisation of the 'R2eff' dispersion model when
peaks are missing from
one spectrum, as reported by Petr Padrta at https://gna.org/bugs/?24601.
To handle the missing data, the peak intensity keys are now checked for in the
spin container
peak_intensities data structure. This is both for the R2eff model optimisation
as well as the data
back-calculation. A warning is given when the key is missing. The relaxation
dispersion
base_data_loop() method has been modified to now yield the spin ID string, as
this is used in the
warnings.
In addition, the Grace plotting code in the relax library was also modified.
When peak intensity
keys are missing, some of the Grace plots will have no data. The code will now
generate a plot for
that data set, but detect the missing data and allow an empty plot to be
created.
Modified:
trunk/lib/plotting/grace.py
trunk/specific_analyses/relax_disp/api.py
trunk/specific_analyses/relax_disp/optimisation.py
Modified: trunk/lib/plotting/grace.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/plotting/grace.py?rev=28204=28203=28204=diff
==
--- trunk/lib/plotting/grace.py (original)
+++ trunk/lib/plotting/grace.py Wed Apr 27 11:13:48 2016
@@ -1,6 +1,6 @@
###
# #
-# Copyright (C) 2003-2015 Edward d'Auvergne #
+# Copyright (C) 2003-2016 Edward d'Auvergne #
# Copyright (C) 2013-2014 Troels E. Linnet#
# #
# This file is part of the program relax (http://www.nmr-relax.com). #
@@ -167,10 +167,16 @@
file.write("@target G%s.S%s\n" % (gi, si))
file.write("@type %s\n" % graph_type)
+# Catch missing data sets.
+if len(data[gi][si]) == 0:
+file.write("&\n")
+continue
+
# Normalisation (to the first data point y value!).
norm_fact = 1.0
if norm[gi]:
if norm_type == 'first':
+print `data[gi][si]`
norm_fact = data[gi][si][0][1]
elif norm_type == 'last':
norm_fact = data[gi][si][-1][1]
Modified: trunk/specific_analyses/relax_disp/api.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/relax_disp/api.py?rev=28204=28203=28204=diff
==
--- trunk/specific_analyses/relax_disp/api.py (original)
+++ trunk/specific_analyses/relax_disp/api.py Wed Apr 27 11:13:48 2016
@@ -1,6 +1,6 @@
###
# #
-# Copyright (C) 2004-2014 Edward d'Auvergne #
+# Copyright (C) 2004-2016 Edward d'Auvergne #
# Copyright (C) 2009 Sebastien Morin #
# Copyright (C) 2013-2014 Troels E. Linnet#
# #
@@ -86,7 +86,7 @@
# The R2eff model data (the base data is peak intensities).
if cdp.model_type == MODEL_R2EFF:
# Loop over the sequence.
-for spin in spin_loop():
+for spin, spin_id in spin_loop(return_id=True):
# Skip deselected spins.
if not spin.select:
continue
@@ -97,7 +97,7 @@
# Loop over each spectrometer frequency and dispersion point.
for exp_type, frq, offset, point in
loop_exp_frq_offset_point():
-yield spin, exp_type, frq, offset, point
+yield spin, spin_id, exp_type, frq, offset, point
# All other models (the base data is the R2eff/R1rho values).
else:
@@ -318,10 +318,10 @@
# The R2eff model (with peak intensity base data).
if cdp.model_type == MODEL_R2EFF:
# Unpack the data.
-spin, exp_type, frq, offset, point = data_id
+spin, spin_id, exp_type, frq, offset, point = data_id
# Back calculate the peak intensities.
-values = back_calc_peak_intensities(spin=spin, exp_type=exp_type,
frq=frq, offset=offset, point=point)
+values = back_calc_peak_intensities(spin=spin, spin_id=spin_id,
exp_type=exp_type, f
r28203 - /trunk/test_suite/system_tests/scripts/relax_disp/r2eff_missing_data.py
Author: bugman Date: Wed Apr 27 11:08:35 2016 New Revision: 28203 URL: http://svn.gna.org/viewcvs/relax?rev=28203=rev Log: Simplified the Relax_disp.test_bug_24601_r2eff_missing_data system test. This is to allow the test to catch bug #24601 to complete in a reasonable time (2 seconds on one system). Modified: trunk/test_suite/system_tests/scripts/relax_disp/r2eff_missing_data.py Modified: trunk/test_suite/system_tests/scripts/relax_disp/r2eff_missing_data.py URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/scripts/relax_disp/r2eff_missing_data.py?rev=28203=28202=28203=diff == --- trunk/test_suite/system_tests/scripts/relax_disp/r2eff_missing_data.py (original) +++ trunk/test_suite/system_tests/scripts/relax_disp/r2eff_missing_data.py Wed Apr 27 11:08:35 2016 @@ -39,14 +39,12 @@ # # The dispersion models. -MODELS = ['R2eff', 'LM63', 'CR72'] +MODELS = ['R2eff'] # The grid search size (the number of increments per dimension). -GRID_INC = 11 -#GRID_INC = None +GRID_INC = 3 # The number of Monte Carlo simulations to be used for error analysis at the end of the analysis. -MC_NUM = 1000 MC_NUM = 3 # A flag which if True will activate Monte Carlo simulations for all models. Note this will hugely increase the computation time. ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
r28202 - in /trunk/test_suite: shared_data/dispersion/bug_24601_R2eff_missing_data/ shared_data/dispersion/bug_24601_R2eff_m...
Author: bugman Date: Wed Apr 27 08:48:14 2016 New Revision: 28202 URL: http://svn.gna.org/viewcvs/relax?rev=28202=rev Log: Created a system test for catching bug #24601. This is the failure of the optimisation of the 'R2eff' dispersion model when peaks are missing from one spectrum, as reported by Petr Padrta at https://gna.org/bugs/?24601. The test uses his data and script to trigger the bug. Added: trunk/test_suite/shared_data/dispersion/bug_24601_R2eff_missing_data/ trunk/test_suite/shared_data/dispersion/bug_24601_R2eff_missing_data/60/ trunk/test_suite/shared_data/dispersion/bug_24601_R2eff_missing_data/60/60_1000_0.024_1.in trunk/test_suite/shared_data/dispersion/bug_24601_R2eff_missing_data/60/60_1000_0.036_1.in trunk/test_suite/shared_data/dispersion/bug_24601_R2eff_missing_data/60/60_1000_0_1.in trunk/test_suite/shared_data/dispersion/bug_24601_R2eff_missing_data/60/60_111.11_0.018_1.in trunk/test_suite/shared_data/dispersion/bug_24601_R2eff_missing_data/60/60_111.11_0.036_1.in trunk/test_suite/shared_data/dispersion/bug_24601_R2eff_missing_data/60/60_111.11_0_1.in trunk/test_suite/shared_data/dispersion/bug_24601_R2eff_missing_data/60/60_166.67_0.024_1.in trunk/test_suite/shared_data/dispersion/bug_24601_R2eff_missing_data/60/60_166.67_0.036_1.in trunk/test_suite/shared_data/dispersion/bug_24601_R2eff_missing_data/60/60_166.67_0_1.in trunk/test_suite/shared_data/dispersion/bug_24601_R2eff_missing_data/60/60_222.22_0.027_1.in trunk/test_suite/shared_data/dispersion/bug_24601_R2eff_missing_data/60/60_222.22_0.036_1.in trunk/test_suite/shared_data/dispersion/bug_24601_R2eff_missing_data/60/60_222.22_0_1.in trunk/test_suite/shared_data/dispersion/bug_24601_R2eff_missing_data/60/60_277.78_0.0216_1.in trunk/test_suite/shared_data/dispersion/bug_24601_R2eff_missing_data/60/60_277.78_0.036_1.in trunk/test_suite/shared_data/dispersion/bug_24601_R2eff_missing_data/60/60_277.78_0_1.in trunk/test_suite/shared_data/dispersion/bug_24601_R2eff_missing_data/60/60_333.33_0.024_1.in trunk/test_suite/shared_data/dispersion/bug_24601_R2eff_missing_data/60/60_333.33_0.036_1.in trunk/test_suite/shared_data/dispersion/bug_24601_R2eff_missing_data/60/60_333.33_0_1.in trunk/test_suite/shared_data/dispersion/bug_24601_R2eff_missing_data/60/60_388.89_0.0205714_1.in trunk/test_suite/shared_data/dispersion/bug_24601_R2eff_missing_data/60/60_388.89_0.036_1.in trunk/test_suite/shared_data/dispersion/bug_24601_R2eff_missing_data/60/60_388.89_0_1.in trunk/test_suite/shared_data/dispersion/bug_24601_R2eff_missing_data/60/60_444.44_0.0225_1.in trunk/test_suite/shared_data/dispersion/bug_24601_R2eff_missing_data/60/60_444.44_0.036_1.in trunk/test_suite/shared_data/dispersion/bug_24601_R2eff_missing_data/60/60_444.44_0_1.in trunk/test_suite/shared_data/dispersion/bug_24601_R2eff_missing_data/60/60_500_0.024_1.in trunk/test_suite/shared_data/dispersion/bug_24601_R2eff_missing_data/60/60_500_0.036_1.in trunk/test_suite/shared_data/dispersion/bug_24601_R2eff_missing_data/60/60_500_0_1.in trunk/test_suite/shared_data/dispersion/bug_24601_R2eff_missing_data/60/60_555.56_0.0216_1.in trunk/test_suite/shared_data/dispersion/bug_24601_R2eff_missing_data/60/60_555.56_0.036_1.in trunk/test_suite/shared_data/dispersion/bug_24601_R2eff_missing_data/60/60_555.56_0_1.in trunk/test_suite/shared_data/dispersion/bug_24601_R2eff_missing_data/60/60_611.11_0.0229091_1.in trunk/test_suite/shared_data/dispersion/bug_24601_R2eff_missing_data/60/60_611.11_0.036_1.in trunk/test_suite/shared_data/dispersion/bug_24601_R2eff_missing_data/60/60_611.11_0_1.in trunk/test_suite/shared_data/dispersion/bug_24601_R2eff_missing_data/60/60_666.67_0.024_1.in trunk/test_suite/shared_data/dispersion/bug_24601_R2eff_missing_data/60/60_666.67_0.036_1.in trunk/test_suite/shared_data/dispersion/bug_24601_R2eff_missing_data/60/60_666.67_0_1.in trunk/test_suite/shared_data/dispersion/bug_24601_R2eff_missing_data/60/60_722.22_0.0249231_1.in trunk/test_suite/shared_data/dispersion/bug_24601_R2eff_missing_data/60/60_722.22_0.036_1.in trunk/test_suite/shared_data/dispersion/bug_24601_R2eff_missing_data/60/60_722.22_0_1.in trunk/test_suite/shared_data/dispersion/bug_24601_R2eff_missing_data/60/60_777.78_0.0231429_1.in trunk/test_suite/shared_data/dispersion/bug_24601_R2eff_missing_data/60/60_777.78_0.036_1.in trunk/test_suite/shared_data/dispersion/bug_24601_R2eff_missing_data/60/60_777.78_0_1.in trunk/test_suite/shared_data/dispersion/bug_24601_R2eff_missing_data/60/60_833.33_0.024_1.in trunk/test_suite/shared_data/dispersion/bug_24601_R2eff_missing_data/60/60_833.33_0.036_1.in trunk/test_suite/shared_data/dispersion/bug_24601_R2eff_missing_data/60/60_833.33_0_1.in
r28201 - /trunk/gui/relax_gui.py
Author: bugman Date: Wed Apr 20 10:33:29 2016 New Revision: 28201 URL: http://svn.gna.org/viewcvs/relax?rev=28201=rev Log: Fix for the GUI status bar element widths. Fixed widths in pixels causes text truncation on many systems, depending on the width of the main relax window. Instead variable widths should be used to allow wxPython to more elegantly present the text while minimising truncation. Modified: trunk/gui/relax_gui.py Modified: trunk/gui/relax_gui.py URL: http://svn.gna.org/viewcvs/relax/trunk/gui/relax_gui.py?rev=28201=28200=28201=diff == --- trunk/gui/relax_gui.py (original) +++ trunk/gui/relax_gui.py Wed Apr 20 10:33:29 2016 @@ -166,7 +166,7 @@ # Set up the status bar. self.status_bar = self.CreateStatusBar(4, 0) -self.status_bar.SetStatusWidths([292, -1, 59, 250]) +self.status_bar.SetStatusWidths([-4, -4, -1, -2]) self.update_status_bar() # Add the start screen. ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
r28200 - /trunk/auto_analyses/frame_order.py
Author: bugman Date: Wed Apr 20 10:00:46 2016 New Revision: 28200 URL: http://svn.gna.org/viewcvs/relax?rev=28200=rev Log: Updated the frame order auto-analysis for the time -> system.time user function change. Modified: trunk/auto_analyses/frame_order.py Modified: trunk/auto_analyses/frame_order.py URL: http://svn.gna.org/viewcvs/relax/trunk/auto_analyses/frame_order.py?rev=28200=28199=28200=diff == --- trunk/auto_analyses/frame_order.py (original) +++ trunk/auto_analyses/frame_order.py Wed Apr 20 10:00:46 2016 @@ -1,6 +1,6 @@ ### # # -# Copyright (C) 2011-2015 Edward d'Auvergne # +# Copyright (C) 2011-2016 Edward d'Auvergne # # # # This file is part of the program relax (http://www.nmr-relax.com). # # # @@ -485,7 +485,7 @@ self.interpreter.on(verbose=False) # Output the starting time. -self.interpreter.time() +self.interpreter.system.time() # The nested model optimisation protocol. self.nested_models() @@ -519,7 +519,7 @@ self.results_output(model='final', dir=self.results_dir+'final', results_file=False) # Output the finishing time. -self.interpreter.time() +self.interpreter.system.time() # Final title printout. subtitle(file=sys.stdout, text="Summaries") @@ -571,7 +571,7 @@ subtitle(file=sys.stdout, text=text, prespace=5) # Output the model staring time. -self.interpreter.time() +self.interpreter.system.time() # A new model name. perm_model = "%s permutation %s" % (model, perm) @@ -930,7 +930,7 @@ subtitle(file=sys.stdout, text="%s frame order model"%title, prespace=5) # Output the model staring time. -self.interpreter.time() +self.interpreter.system.time() # The data pipe name. self.pipe_name_dict[model] = '%s - %s' % (title, self.pipe_bundle) @@ -1104,7 +1104,7 @@ subtitle(file=sys.stdout, text="%s frame order model"%title, prespace=5) # Output the model staring time. -self.interpreter.time() +self.interpreter.system.time() # The data pipe name. self.pipe_name_dict[model] = '%s - %s' % (title, self.pipe_bundle) ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
r28166 - /trunk/test_suite/system_tests/structure.py
Author: bugman Date: Tue Jan 12 09:43:10 2016 New Revision: 28166 URL: http://svn.gna.org/viewcvs/relax?rev=28166=rev Log: Fix for the Structure.test_read_pdb_internal3 system test. With the new atomic position concatenation support, when called sequentially the structure.load_spins user function should always use the same value for the ave_pos argument. Modified: trunk/test_suite/system_tests/structure.py Modified: trunk/test_suite/system_tests/structure.py URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/structure.py?rev=28166=28165=28166=diff == --- trunk/test_suite/system_tests/structure.py (original) +++ trunk/test_suite/system_tests/structure.py Tue Jan 12 09:43:10 2016 @@ -1,6 +1,6 @@ ### # # -# Copyright (C) 2008-2015 Edward d'Auvergne # +# Copyright (C) 2008-2016 Edward d'Auvergne # # # # This file is part of the program relax (http://www.nmr-relax.com). # # # @@ -4498,7 +4498,7 @@ self.assertEqual(len(cdp.mol[0].res[0].spin[0].pos), 2) # And now all the rest of the atoms. -self.interpreter.structure.load_spins() +self.interpreter.structure.load_spins(ave_pos=False) def test_read_pdb_internal4(self): ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
r28164 - in /trunk: pipe_control/structure/main.py user_functions/structure.py
Author: bugman
Date: Tue Jan 12 09:38:10 2016
New Revision: 28164
URL: http://svn.gna.org/viewcvs/relax?rev=28164=rev
Log:
Added the spin_num boolean argument to the structure.load_spins user function.
Setting this flag to False will cause the spin number information to be ignored
when creating the
spin containers. This allows for better support of homologous structures but
with different PDB
atom numbering. The default flag value is True, preserving the old behaviour.
Modified:
trunk/pipe_control/structure/main.py
trunk/user_functions/structure.py
Modified: trunk/pipe_control/structure/main.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/pipe_control/structure/main.py?rev=28164=28163=28164=diff
==
--- trunk/pipe_control/structure/main.py(original)
+++ trunk/pipe_control/structure/main.pyTue Jan 12 09:38:10 2016
@@ -1,6 +1,6 @@
###
# #
-# Copyright (C) 2003-2015 Edward d'Auvergne #
+# Copyright (C) 2003-2016 Edward d'Auvergne #
# #
# This file is part of the program relax (http://www.nmr-relax.com). #
# #
@@ -816,7 +816,7 @@
write_data(out=sys.stdout, headings=["Spin_ID", "Position"], data=data)
-def load_spins(spin_id=None, str_id=None, from_mols=None,
mol_name_target=None, ave_pos=False):
+def load_spins(spin_id=None, str_id=None, from_mols=None,
mol_name_target=None, ave_pos=False, spin_num=True):
"""Load the spins from the structural object into the relax data store.
@keyword spin_id: The molecule, residue, and spin identifier
string.
@@ -829,11 +829,13 @@
@type mol_name_target: str or None
@keyword ave_pos: A flag specifying if the average atom position
or the atom position from all loaded structures is loaded into the
SpinContainer.
@type ave_pos: bool
+@keyword spin_num: A flag specifying if the spin number should be
loaded.
+@type spin_num: bool
"""
# The multi-molecule case.
if from_mols != None:
-load_spins_multi_mol(spin_id=spin_id, str_id=str_id,
from_mols=from_mols, mol_name_target=mol_name_target, ave_pos=ave_pos)
+load_spins_multi_mol(spin_id=spin_id, str_id=str_id,
from_mols=from_mols, mol_name_target=mol_name_target, ave_pos=ave_pos,
spin_num=spin_num)
return
# Checks.
@@ -856,6 +858,10 @@
# Override the molecule name.
if mol_name_target:
mol_name = mol_name_target
+
+# No spin number.
+if not spin_num:
+atom_num = None
# Remove the '+' regular expression character from the mol, res, and
spin names!
if mol_name and search('\+', mol_name):
@@ -904,7 +910,7 @@
cdp.N = cdp.structure.num_models()
-def load_spins_multi_mol(spin_id=None, str_id=None, from_mols=None,
mol_name_target=None, ave_pos=False):
+def load_spins_multi_mol(spin_id=None, str_id=None, from_mols=None,
mol_name_target=None, ave_pos=False, spin_num=True):
"""Load the spins from the structural object into the relax data store.
@keyword spin_id: The molecule, residue, and spin identifier
string.
@@ -917,6 +923,8 @@
@type mol_name_target: str or None
@keyword ave_pos: A flag specifying if the average atom position
or the atom position from all loaded structures is loaded into the
SpinContainer.
@type ave_pos: bool
+@keyword spin_num: A flag specifying if the spin number should be
loaded.
+@type spin_num: bool
"""
# Checks.
@@ -966,6 +974,10 @@
res_name = res_name.replace('+', '')
if atom_name and search('\+', atom_name):
atom_name = atom_name.replace('+', '')
+
+# No spin number.
+if not spin_num:
+atom_num = None
# Generate a spin ID for the current atom.
id = generate_spin_id_unique(mol_name=mol_name_target,
res_num=res_num, res_name=res_name, spin_name=atom_name)
Modified: trunk/user_functions/structure.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/user_functions/structure.py?rev=28164=28163=28164=diff
==
--- trunk/user_functions/structure.py (origina
r28165 - /trunk/pipe_control/structure/main.py
Author: bugman
Date: Tue Jan 12 09:41:21 2016
New Revision: 28165
URL: http://svn.gna.org/viewcvs/relax?rev=28165=rev
Log:
Added support for concatenating atomic positions in the structure.load_spins
user function.
Together with the spin_num flag set to False, this allows for atomic positions
to be read from
multiple homologous structures with different PDB atomic numbering. The spin
containers will be
created from the first structure, in which the spin is defined, and the atomic
position from
subsequent structures will be appended to the list of current atomic positions.
Modified:
trunk/pipe_control/structure/main.py
Modified: trunk/pipe_control/structure/main.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/pipe_control/structure/main.py?rev=28165=28164=28165=diff
==
--- trunk/pipe_control/structure/main.py(original)
+++ trunk/pipe_control/structure/main.pyTue Jan 12 09:41:21 2016
@@ -21,7 +21,7 @@
# Python module imports.
from minfx.generic import generic_minimise
-from numpy import array, average, dot, float64, mean, ones, std, zeros
+from numpy import array, average, concatenate, dot, float64, mean, ones, std,
zeros
from numpy.linalg import norm
from os import F_OK, access, getcwd
from re import search
@@ -893,7 +893,11 @@
spin_names.append(atom_name)
# Position vector.
-spin_cont.pos = pos
+if hasattr(spin_cont, 'pos') and spin_cont.pos != None and
(spin_cont.pos.shape != pos.shape or (spin_cont.pos != pos).any()):
+warn(RelaxWarning("Positional information already exists for the
spin %s, appending the new positions." % id))
+spin_cont.pos = concatenate((spin_cont.pos, pos))
+else:
+spin_cont.pos = pos
# Add the element.
spin_cont.element = element
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r28160 - /trunk/lib/structure/internal/object.py
Author: bugman
Date: Mon Jan 11 09:37:45 2016
New Revision: 28160
URL: http://svn.gna.org/viewcvs/relax?rev=28160=rev
Log:
Bug fix for the structure.read_pdb user function (bug #24300,
https://gna.org/bugs/?24300).
When the merge flag is True, and both multiple structures and multiple models
are present, the
structure.read_pdb user function would fail with a RelaxError. The problem was
that the molecule
index was simply not being updated correctly.
Modified:
trunk/lib/structure/internal/object.py
Modified: trunk/lib/structure/internal/object.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/structure/internal/object.py?rev=28160=28159=28160=diff
==
--- trunk/lib/structure/internal/object.py (original)
+++ trunk/lib/structure/internal/object.py Mon Jan 11 09:37:45 2016
@@ -2506,6 +2506,7 @@
for k in range(len(model.mol)):
if model.mol[k].mol_name == set_mol_name[j]:
found = True
+index = k
if not found:
merge_new = False
@@ -2530,9 +2531,8 @@
print("Adding molecule '%s'%s (from the original
molecule number %s%s)." % (set_mol_name[j], new_model_text, orig_mol_num[i][j],
orig_model_text))
# The index of the new molecule to add or merge.
-index = len(model.mol)
-if merge_new:
-index -= 1
+if not merge_new:
+index = len(model.mol)
# Store the index+1 as the new molecule number, and store the
original molecule number.
store_mol_num_new[i].append(index+1)
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r28161 - /trunk/lib/structure/internal/object.py
Author: bugman Date: Mon Jan 11 16:17:34 2016 New Revision: 28161 URL: http://svn.gna.org/viewcvs/relax?rev=28161=rev Log: Copyright update for the previous commit. Modified: trunk/lib/structure/internal/object.py Modified: trunk/lib/structure/internal/object.py URL: http://svn.gna.org/viewcvs/relax/trunk/lib/structure/internal/object.py?rev=28161=28160=28161=diff == --- trunk/lib/structure/internal/object.py (original) +++ trunk/lib/structure/internal/object.py Mon Jan 11 16:17:34 2016 @@ -1,6 +1,6 @@ ### # # -# Copyright (C) 2003-2015 Edward d'Auvergne # +# Copyright (C) 2003-2016 Edward d'Auvergne # # # # This file is part of the program relax (http://www.nmr-relax.com). # # # ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
r28162 - in /trunk: info.py relax.py
Author: bugman
Date: Mon Jan 11 16:23:44 2016
New Revision: 28162
URL: http://svn.gna.org/viewcvs/relax?rev=28162=rev
Log:
Updated the copyright notices for 2016.
Modified:
trunk/info.py
trunk/relax.py
Modified: trunk/info.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/info.py?rev=28162=28161=28162=diff
==
--- trunk/info.py (original)
+++ trunk/info.py Mon Jan 11 16:23:44 2016
@@ -1,6 +1,6 @@
###
# #
-# Copyright (C) 2003-2015 Edward d'Auvergne #
+# Copyright (C) 2003-2016 Edward d'Auvergne #
# #
# This file is part of the program relax (http://www.nmr-relax.com). #
# #
@@ -95,7 +95,7 @@
# Copyright printout.
self.copyright = []
self.copyright.append("Copyright (C) 2001-2006 Edward d'Auvergne")
-self.copyright.append("Copyright (C) 2006-2015 the relax development
team")
+self.copyright.append("Copyright (C) 2006-2016 the relax development
team")
# Program licence and help.
self.licence = "This is free software which you are welcome to modify
and redistribute under the conditions of the GNU General Public License (GPL).
This program, including all modules, is licensed under the GPL and comes with
absolutely no warranty. For details type 'GPL' within the relax prompt."
Modified: trunk/relax.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/relax.py?rev=28162=28161=28162=diff
==
--- trunk/relax.py (original)
+++ trunk/relax.py Mon Jan 11 16:23:44 2016
@@ -13,7 +13,7 @@
# relax, a program for relaxation data analysis. #
# #
# Copyright (C) 2001-2006 Edward d'Auvergne #
-# Copyright (C) 2006-2015 the relax development team #
+# Copyright (C) 2006-2016 the relax development team #
# #
# This program is free software; you can redistribute it and/or modify#
# it under the terms of the GNU General Public License as published by#
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r28163 - in /trunk: gui/relax_gui.py info.py
Author: bugman
Date: Mon Jan 11 16:25:25 2016
New Revision: 28163
URL: http://svn.gna.org/viewcvs/relax?rev=28163=rev
Log:
Created a short Info_box copyright string for displaying in the main GUI window.
This shows the full range of copyright dates.
Modified:
trunk/gui/relax_gui.py
trunk/info.py
Modified: trunk/gui/relax_gui.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/gui/relax_gui.py?rev=28163=28162=28163=diff
==
--- trunk/gui/relax_gui.py (original)
+++ trunk/gui/relax_gui.py Mon Jan 11 16:25:25 2016
@@ -1,7 +1,7 @@
###
# #
# Copyright (C) 2009 Michael Bieri#
-# Copyright (C) 2010-2015 Edward d'Auvergne #
+# Copyright (C) 2010-2016 Edward d'Auvergne #
# #
# This file is part of the program relax (http://www.nmr-relax.com). #
# #
@@ -924,6 +924,6 @@
info = Info_box()
# Set the status.
-wx.CallAfter(self.status_bar.SetStatusText, info.copyright[1], 0)
+wx.CallAfter(self.status_bar.SetStatusText, info.copyright_short, 0)
wx.CallAfter(self.status_bar.SetStatusText, "Current data pipe:", 1)
wx.CallAfter(self.status_bar.SetStatusText, pipe, 2)
Modified: trunk/info.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/info.py?rev=28163=28162=28163=diff
==
--- trunk/info.py (original)
+++ trunk/info.py Mon Jan 11 16:25:25 2016
@@ -96,6 +96,7 @@
self.copyright = []
self.copyright.append("Copyright (C) 2001-2006 Edward d'Auvergne")
self.copyright.append("Copyright (C) 2006-2016 the relax development
team")
+self.copyright_short = "Copyright (C) 2001-2016 the relax development
team"
# Program licence and help.
self.licence = "This is free software which you are welcome to modify
and redistribute under the conditions of the GNU General Public License (GPL).
This program, including all modules, is licensed under the GPL and comes with
absolutely no warranty. For details type 'GPL' within the relax prompt."
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r28158 - /trunk/specific_analyses/frame_order/uf.py
Author: bugman
Date: Wed Dec 23 11:21:46 2015
New Revision: 28158
URL: http://svn.gna.org/viewcvs/relax?rev=28158=rev
Log:
Added a check for the total argument for the frame_order.distribute user
function.
The maximum value is , as the PDB format cannot accept more models.
Modified:
trunk/specific_analyses/frame_order/uf.py
Modified: trunk/specific_analyses/frame_order/uf.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/frame_order/uf.py?rev=28158=28157=28158=diff
==
--- trunk/specific_analyses/frame_order/uf.py (original)
+++ trunk/specific_analyses/frame_order/uf.py Wed Dec 23 11:21:46 2015
@@ -68,6 +68,10 @@
# Printout.
print("Uniform distribution of structures representing the frame order
motions.")
+# Check the total.
+if total > :
+raise RelaxError("A maximum of models is allowed in the PDB
format.")
+
# Checks.
check_pipe()
check_model()
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r28157 - /trunk/pipe_control/align_tensor.py
Author: bugman Date: Mon Dec 21 11:14:30 2015 New Revision: 28157 URL: http://svn.gna.org/viewcvs/relax?rev=28157=rev Log: Fix for bug #24218 (https://gna.org/bugs/?24218). This is the incorrect labelling of alignment tensors by the align_tensor.matrix_angles user function when a subset of tensors is specified. The logic for the labels was expanded from being only for all tensors to handling subsets. Modified: trunk/pipe_control/align_tensor.py Modified: trunk/pipe_control/align_tensor.py URL: http://svn.gna.org/viewcvs/relax/trunk/pipe_control/align_tensor.py?rev=28157=28156=28157=diff == --- trunk/pipe_control/align_tensor.py (original) +++ trunk/pipe_control/align_tensor.py Mon Dec 21 11:14:30 2015 @@ -1055,18 +1055,27 @@ # The table header. table.append(['']) for i in range(tensor_num): -if cdp.align_tensors[i].name == None: -table[0].append(repr(i)) +# All tensors. +if not tensors: +if cdp.align_tensors[i].name == None: +table[0].append(repr(i)) +else: +table[0].append(cdp.align_tensors[i].name) + +# Subset. else: -table[0].append(cdp.align_tensors[i].name) +table[0].append(tensors[i]) # First loop over the rows. for i in range(tensor_num): # Add the tensor name. -if cdp.align_tensors[i].name == None: -table.append([repr(i)]) +if not tensors: +if cdp.align_tensors[i].name == None: +table.append([repr(i)]) +else: +table.append([cdp.align_tensors[i].name]) else: -table.append([cdp.align_tensors[i].name]) +table.append([tensors[i]]) # Second loop over the columns. for j in range(tensor_num): ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
r28156 - /trunk/docs/devel/Release_Checklist
Author: bugman Date: Wed Dec 16 13:45:55 2015 New Revision: 28156 URL: http://svn.gna.org/viewcvs/relax?rev=28156=rev Log: Update the release checklist document. The version number at http://wiki.nmr-relax.com/Template:Current_version_relax also needs to be updated for each release. Modified: trunk/docs/devel/Release_Checklist Modified: trunk/docs/devel/Release_Checklist URL: http://svn.gna.org/viewcvs/relax/trunk/docs/devel/Release_Checklist?rev=28156=28155=28156=diff == --- trunk/docs/devel/Release_Checklist (original) +++ trunk/docs/devel/Release_Checklist Wed Dec 16 13:45:55 2015 @@ -213,7 +213,10 @@ - Add tags for better formatting of certain elements (file and directory names, code elements, console output, GUI element, etc). - To avoid dead links, perform a final proof that all the links in the wiki article are correct by following the links. -Update all of the release note links for the new version (http://wiki.nmr-relax.com/Category:Release_Notes). +Also: + +- Update all of the release note links for the new version (http://wiki.nmr-relax.com/Category:Release_Notes). +- Update the version number at http://wiki.nmr-relax.com/Template:Current_version_relax. Mailing list ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
r28149 - /trunk/docs/latex/relax.tex
Author: bugman
Date: Tue Dec 15 11:51:59 2015
New Revision: 28149
URL: http://svn.gna.org/viewcvs/relax?rev=28149=rev
Log:
Improved formatting for the \yes LaTeX command for the HTML manual
(www.nmr-relax.com/manual/).
This now inputs the raw HTML character for a tick.
Modified:
trunk/docs/latex/relax.tex
Modified: trunk/docs/latex/relax.tex
URL:
http://svn.gna.org/viewcvs/relax/trunk/docs/latex/relax.tex?rev=28149=28148=28149=diff
==
--- trunk/docs/latex/relax.tex (original)
+++ trunk/docs/latex/relax.tex Tue Dec 15 11:51:59 2015
@@ -331,7 +331,7 @@
% Redefine some commands to be prettier in HTML.
\newcommand{\no}{-}
- \newcommand{\yes}{y}
+ \newcommand{\yes}{\begin{rawhtml}\end{rawhtml}}
\newcommand{\FO}{\textrm{Daeg}}
\newcommand{\FOn}{\textrm{Daeg}^{(n)}}
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r28150 - /trunk/docs/latex/find_replicate_titles.py
Author: bugman
Date: Tue Dec 15 12:01:21 2015
New Revision: 28150
URL: http://svn.gna.org/viewcvs/relax?rev=28150=rev
Log:
The replicate title finding script now processes short titles as well.
This shows that the Frame_order.html file will be conflicting and overwritten.
Modified:
trunk/docs/latex/find_replicate_titles.py
Modified: trunk/docs/latex/find_replicate_titles.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/docs/latex/find_replicate_titles.py?rev=28150=28149=28150=diff
==
--- trunk/docs/latex/find_replicate_titles.py (original)
+++ trunk/docs/latex/find_replicate_titles.py Tue Dec 15 12:01:21 2015
@@ -67,7 +67,7 @@
# Loop over the file contents.
for line in lines:
# Skip everything that is not a chapter or section.
-if not (search("chapter{", line) or
search("section{", line) or search("subsection{", line)):
+if not (search("chapter", line) or
search("section", line) or search("subsection", line)):
continue
# Strip off the newline character.
@@ -77,8 +77,13 @@
if search(' label', line):
line = line[:line.index(' \label')]
-# Extract the title string by finding the first '{' and
chop off the final '}'.
-title = line[line.index('{')+1:-1]
+# Extract the short title string, if it exists.
+if '[' in line:
+title = line[line.index('[')+1:line.index(']')]
+
+# Extract the full title string by finding the first '{'
and chop off the final '}'.
+else:
+title = line[line.index('{')+1:-1]
# Is the title new?
if not title in self.titles:
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r28152 - in /tags/4.0.1/docs: devel/Release_Checklist latex/find_replicate_titles.py latex/frame_order/theory.tex
Author: bugman
Date: Tue Dec 15 12:06:54 2015
New Revision: 28152
URL: http://svn.gna.org/viewcvs/relax?rev=28152=rev
Log:
Ported r28149 to r28151 from the trunk to improve the HTML manual.
The command used was:
svn log -r28149:r28151 svn+ssh://bug...@svn.gna.org/svn/relax/trunk .
Modified:
tags/4.0.1/docs/devel/Release_Checklist
tags/4.0.1/docs/latex/find_replicate_titles.py
tags/4.0.1/docs/latex/frame_order/theory.tex
Modified: tags/4.0.1/docs/devel/Release_Checklist
URL:
http://svn.gna.org/viewcvs/relax/tags/4.0.1/docs/devel/Release_Checklist?rev=28152=28151=28152=diff
==
--- tags/4.0.1/docs/devel/Release_Checklist (original)
+++ tags/4.0.1/docs/devel/Release_Checklist Tue Dec 15 12:06:54 2015
@@ -205,8 +205,9 @@
- Vim register: "v/[
,\r\n]^M<80>kl<80>kDi[http://www.nmr-relax.com/manual/^[pa.html ^[pa]^[/user
function^M",
- Vim register: "v/[
,\r\n]^M<80>kl<80>kDi[http://www.nmr-relax.com/manual/^[pa.html ^[p/user
function^M2cwuser function]^[",
- Then search for "www.nmr-relax.com\/manual\/[a-z0-9_]*\.\|html" and
replace all '.'.
-- Make internal links for all relax versions (search for
"[1-3]\.[0-9]*\.[0-9]*").
-- Convert all symbols/parameters to use wiki formatting.
+- Make internal links for all relax versions (vi search for
"[1-3]\.[0-9]*\.[0-9]*").
+- Convert all symbols to use wiki formatting.
+- Convert all model parameters to use the {{:xyz}} parameter template
infrastructure.
- Convert all model names to internal wiki links (vi search
"\\|\\|No Rex\|R2eff\|LM63\|LM63 3-site\|CR72\|CR72
full\|IT99\|TSMFK01\|B14\|B14 full\|NS CPMG\|MMQ CR72\|NS
MMQ\|M61\|DPL94\|TP02\|TAP03\|MP05\|NS R1rho\|BK13").
- Add as many links as possible to the API documentation (to help users
dive into the relax code and to help with search engine indexing). Mediawiki
syntax highlighting is a significant aid (see
https://en.wikipedia.org/wiki/Wikipedia:Text_editor_support#Vim).
- To avoid dead links, perform a final proof that all the links in the
wiki article are correct by following the links.
@@ -238,6 +239,7 @@
- Convert internal [[xyz]] wiki links into proper
[http://wiki.nmr-relax.com/xyz] links.
- Item references such as bug #7641, task #3122, etc. are automatically
converted into links. Savane will replace the links as formatted for the wiki
to these links, so nothing needs to be done.
- Remove all symbol formatting ('&', ';', '', '', etc.).
+- Remove all parameter templates.
Cross-linking
Modified: tags/4.0.1/docs/latex/find_replicate_titles.py
URL:
http://svn.gna.org/viewcvs/relax/tags/4.0.1/docs/latex/find_replicate_titles.py?rev=28152=28151=28152=diff
==
--- tags/4.0.1/docs/latex/find_replicate_titles.py (original)
+++ tags/4.0.1/docs/latex/find_replicate_titles.py Tue Dec 15 12:06:54 2015
@@ -67,7 +67,7 @@
# Loop over the file contents.
for line in lines:
# Skip everything that is not a chapter or section.
-if not (search("chapter{", line) or
search("section{", line) or search("subsection{", line)):
+if not (search("chapter", line) or
search("section", line) or search("subsection", line)):
continue
# Strip off the newline character.
@@ -77,8 +77,13 @@
if search(' label', line):
line = line[:line.index(' \label')]
-# Extract the title string by finding the first '{' and
chop off the final '}'.
-title = line[line.index('{')+1:-1]
+# Extract the short title string, if it exists.
+if '[' in line:
+title = line[line.index('[')+1:line.index(']')]
+
+# Extract the full title string by finding the first '{'
and chop off the final '}'.
+else:
+title = line[line.index('{')+1:-1]
# Is the title new?
if not title in self.titles:
Modified: tags/4.0.1/docs/latex/frame_order/theory.tex
URL:
http://svn.gna.org/viewcvs/relax/tags/4.0.1/docs/latex/frame_order/theory.tex?rev=28152=28151=28152=diff
==
--- tags/4.0.1/docs/latex/frame_order/theory.tex(original)
+++ tags/4.0.1/docs/latex/frame_order/theory.texTue Dec 15 12:06:54 2015
@@ -6,10 +6,10 @@
-% Frame order.
-%~
-
-\subsection{Frame order}
+% Frame order introduction.
+%~~
+
+\subsection{Frame order introduction}
___
relax
r28151 - /trunk/docs/latex/frame_order/theory.tex
Author: bugman
Date: Tue Dec 15 12:05:03 2015
New Revision: 28151
URL: http://svn.gna.org/viewcvs/relax?rev=28151=rev
Log:
Avoidance of a replicated title in the frame order chapter of the manual.
Modified:
trunk/docs/latex/frame_order/theory.tex
Modified: trunk/docs/latex/frame_order/theory.tex
URL:
http://svn.gna.org/viewcvs/relax/trunk/docs/latex/frame_order/theory.tex?rev=28151=28150=28151=diff
==
--- trunk/docs/latex/frame_order/theory.tex (original)
+++ trunk/docs/latex/frame_order/theory.tex Tue Dec 15 12:05:03 2015
@@ -6,10 +6,10 @@
-% Frame order.
-%~
-
-\subsection{Frame order}
+% Frame order introduction.
+%~~
+
+\subsection{Frame order introduction}
___
relax (http://www.nmr-relax.com)
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relax-commits@gna.org
To unsubscribe from this list, get a password
reminder, or change your subscription options,
visit the list information page at
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r28155 - /trunk/docs/devel/Release_Checklist
Author: bugman
Date: Tue Dec 15 14:50:27 2015
New Revision: 28155
URL: http://svn.gna.org/viewcvs/relax?rev=28155=rev
Log:
A number of updates for the release checklist document.
This should make it easier to replicate the full release process.
Modified:
trunk/docs/devel/Release_Checklist
Modified: trunk/docs/devel/Release_Checklist
URL:
http://svn.gna.org/viewcvs/relax/trunk/docs/devel/Release_Checklist?rev=28155=28154=28155=diff
==
--- trunk/docs/devel/Release_Checklist (original)
+++ trunk/docs/devel/Release_Checklist Tue Dec 15 14:50:27 2015
@@ -188,7 +188,7 @@
Wiki
-Create a new release page at the URL http://wiki.nmr-relax.com/Relax_x.y.z.
Use, for example, http://wiki.nmr-relax.com/Relax_3.3.0 as a guide. The basic
page structure is as follows:
+Create a new release page at the URL http://wiki.nmr-relax.com/Relax_x.y.z.
Use, for example, http://wiki.nmr-relax.com/Relax_4.0.1 as a guide. The basic
page structure is as follows:
{{lowercase title}} - Start with this to allow the title to be in
lowercase. The URL on a wiki always starts with a capital, but the title can
be changed to lowercase in this way.
= Description = - Create this section by writing a detailed and full
description of the release. Add internal wiki links and external links, for
example to the relax manual web pages for the user functions.
@@ -205,10 +205,12 @@
- Vim register: "v/[
,\r\n]^M<80>kl<80>kDi[http://www.nmr-relax.com/manual/^[pa.html ^[pa]^[/user
function^M",
- Vim register: "v/[
,\r\n]^M<80>kl<80>kDi[http://www.nmr-relax.com/manual/^[pa.html ^[p/user
function^M2cwuser function]^[",
- Then search for "www.nmr-relax.com\/manual\/[a-z0-9_]*\.\|html" and
replace all '.'.
-- Make internal links for all relax versions (search for
"[1-3]\.[0-9]*\.[0-9]*").
-- Convert all symbols/parameters to use wiki formatting.
+- Make internal links for all relax versions (vi search for
"[1-3]\.[0-9]*\.[0-9]*").
+- Convert all symbols to use wiki formatting.
+- Convert all model parameters to use the {{:xyz}} parameter template
infrastructure.
- Convert all model names to internal wiki links (vi search
"\\|\\|No Rex\|R2eff\|LM63\|LM63 3-site\|CR72\|CR72
full\|IT99\|TSMFK01\|B14\|B14 full\|NS CPMG\|MMQ CR72\|NS
MMQ\|M61\|DPL94\|TP02\|TAP03\|MP05\|NS R1rho\|BK13").
- Add as many links as possible to the API documentation (to help users
dive into the relax code and to help with search engine indexing). Mediawiki
syntax highlighting is a significant aid (see
https://en.wikipedia.org/wiki/Wikipedia:Text_editor_support#Vim).
+- Add tags for better formatting of certain elements (file and
directory names, code elements, console output, GUI element, etc).
- To avoid dead links, perform a final proof that all the links in the
wiki article are correct by following the links.
Update all of the release note links for the new version
(http://wiki.nmr-relax.com/Category:Release_Notes).
@@ -220,7 +222,7 @@
On the relax-announce mailing list (relax-announce att gna.org), write the
release announcement by:
- Copy the 'Description' and 'Download' text from the wiki. Do not
include the section titles and remove any wiki markup.
-- Add a paragraph before the 'Download' paragraph with the text 'For the
official, easy to navigate release notes, please see
http://wiki.nmr-relax.com/Relax_3.3.1 .'. This is to direct both users and
search engines to the wiki page (the users via the release email and the search
engines via the multiple archives).
+- Add a paragraph before the 'Download' paragraph with the text 'For the
official, easy to navigate release notes, please see
http://wiki.nmr-relax.com/Relax_4.0.1 .'. This is to direct both users and
search engines to the wiki page (the users via the release email and the search
engines via the multiple archives).
- At the end, add a section titled 'The full list of changes is:' and cut
and paste the part of the CHANGES file for this release. Do not use the wiki
text for this.
- Include links to the trackers in the full list of changes, if not
already present.
@@ -231,13 +233,21 @@
The steps are:
- Log into Gna! and go to https://gna.org/news/submit.php?group=relax.
-- Cut and paste all of the wiki text. Delete the initial lower case title
formatting text, the final 'Links', 'Announcements' and 'See also' sections,
and any wiki markup.
-- Add a paragraph before the 'Download' paragraph with the text 'For the
official, easy to navigate release notes, please see
http://wiki.nmr-relax.com/Relax_3.3.1.'.
+- Cut and paste all of the wiki text. Delete the initial lower case title
formatting text and infobox, the final 'Links', 'Announcements' and 'See also'
sections, and any wiki markup.
+- Add a paragraph before the
r28154 - /trunk/docs/CHANGES
Author: bugman
Date: Tue Dec 15 14:37:59 2015
New Revision: 28154
URL: http://svn.gna.org/viewcvs/relax?rev=28154=rev
Log:
Added some unicode characters for improved formatting of the CHANGES file.
Modified:
trunk/docs/CHANGES
Modified: trunk/docs/CHANGES
URL:
http://svn.gna.org/viewcvs/relax/trunk/docs/CHANGES?rev=28154=28153=28154=diff
==
--- trunk/docs/CHANGES (original)
+++ trunk/docs/CHANGES Tue Dec 15 14:37:59 2015
@@ -4,7 +4,7 @@
Features:
* Many improvements for the compilation of the HTML version of the
relax manual (http://www.nmr-relax.com/manual/index.html).
-* Updated relax to eliminate all FutureWarnings from numpy >= 1.9, to
future-proof relax against upcoming numpy behaviour changes.
+* Updated relax to eliminate all FutureWarnings from numpy ⥠1.9, to
future-proof relax against upcoming numpy behaviour changes.
* Ability to handle replicated R2eff data points by the
relax_disp.r2eff_read user function, but adding 0.001 to the frequency value
for the replicated point.
* A new sample script for loading a model-free results file and
back-calculating relaxation data.
* Improvements for the handling of PDB structural data.
@@ -15,12 +15,12 @@
Changes:
* Fix for the rigid frame order model 2nd degree frame order matrix in
the manual. The wrong symbol was being used.
* Removed the newparagraph and newsubparagraph definitions from the
LaTeX manual. These were causing conflicts with latex2html, preventing the
HTML version of the manual at http://www.nmr-relax.com/manual/index.html from
being compiled. These definitions are unnecessary for the current set up of
the sectioning in the manual.
-* Modified the short captions in the new frame models chapter of the
manual. The runic Daeg character has been replaced simply by 'Daeg'. This is
due to incompatibilities with latex2html which prevents the HTML manual at
http://www.nmr-relax.com/manual/index.html from being compiled.
+* Modified the short captions in the new frame models chapter of the
manual. The runic á character has been replaced simply by 'Daeg'. This is
due to incompatibilities with latex2html which prevents the HTML manual at
http://www.nmr-relax.com/manual/index.html from being compiled.
* Removal of the definition of a fixed-width table column from the
LaTeX manual preamble. This is required as the definition breaks latex2html
compatibility, causing a corruption in the figure numbering resulting in the
images in the HTML to be essentially randomised.
* Removal of the accents package to allow the HTML manual to be
compiled. The 'accents' LaTeX package is not compatible with latex2html, so
the easiest fix is to eliminate the package.
* Manually rotated the frame order matrix element EPS manual figures,
for latex2html compatibility. The '90 rotate' command has been deleted and the
bounding box permuted as 'a b c d' -> 'b -c d -a'. This allows the angle
argument in the \includegraphics{} command to be dropped, as latex2html does
not recognise this. It allows the figures to be visible in the HTML version of
the manual at http://www.nmr-relax.com/manual/index.html .
* Redesign of the frame order parameter nesting table in the manual
for latex2html compatibility. The table uses the tikz package, which is fatal
for latex2html, even if not used. Therefore the table in the
docs/latex/frame_order/parameter_nesting.tex file has been converted into a
standalone LaTeX document to create a cropped postscript version of the tikz
formatted table. A compilation script has been added as well. The resultant
*.ps file is now included into the PCS numerical integration section, rather
than this section creating the tikz table. All tikz preamble text has been
removed to allow latex2html to run.
-* Workaround for latex2html not being able to handle the allrunes
package or associated font. In the preamble 'htmlonly' environment, the frame
order symbols are redefined using the text 'Daeg' instead of the runic
character.
+* Workaround for latex2html not being able to handle the allrunes
package or associated font. In the preamble 'htmlonly' environment, the frame
order symbols are redefined using the text 'Daeg' instead of the runic
character á.
* Fixes for sub and superscripts throughout the manual. This
introduces {} around all sub and superscripted \textrm{} instances. This is
not needed for the PDF version of the manual as the missing bracket problem is
avoided, but it affects the HTML version of the manual compiled by latex2html,
which requires the correct notation. The fixes are for both the new frame
order chapter as well as the relaxation dispersion chapter.
* Editing and fixes for the relax 4.0.0 part of the CHANGES file.
r28142 - /tags/4.0.1/docs/relax.pdf
Author: bugman Date: Mon Dec 14 11:53:53 2015 New Revision: 28142 URL: http://svn.gna.org/viewcvs/relax?rev=28142=rev Log: Added the relax 4.0.1 PDF manual to the repository. Added: tags/4.0.1/docs/relax.pdf (with props) Added: tags/4.0.1/docs/relax.pdf URL: http://svn.gna.org/viewcvs/relax/tags/4.0.1/docs/relax.pdf?rev=28142=auto == Binary file - no diff available. Propchange: tags/4.0.1/docs/relax.pdf -- svn:mime-type = application/octet-stream ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
r28147 - /website/api/4.0/
Author: bugman Date: Mon Dec 14 17:14:37 2015 New Revision: 28147 URL: http://svn.gna.org/viewcvs/relax?rev=28147=rev Log: Updated the relax API documentation at http://www.nmr-relax.com/api/4.0/ to version 4.0.1. Added: website/api/4.0/docs.latex.find_replicate_titles-module.html website/api/4.0/docs.latex.find_replicate_titles-pysrc.html website/api/4.0/docs.latex.find_replicate_titles.Replicated_titles-class.html website/api/4.0/lib.structure.pca-module.html website/api/4.0/lib.structure.pca-pysrc.html website/api/4.0/toc-docs.latex.find_replicate_titles-module.html website/api/4.0/toc-lib.structure.pca-module.html Modified: website/api/4.0/abc.ABCMeta-class.html website/api/4.0/api-objects.txt website/api/4.0/auto_analyses-module.html website/api/4.0/auto_analyses-pysrc.html website/api/4.0/auto_analyses.dauvergne_protocol-module.html website/api/4.0/auto_analyses.dauvergne_protocol-pysrc.html website/api/4.0/auto_analyses.dauvergne_protocol.Container-class.html website/api/4.0/auto_analyses.dauvergne_protocol.dAuvergne_protocol-class.html website/api/4.0/auto_analyses.frame_order-module.html website/api/4.0/auto_analyses.frame_order-pysrc.html website/api/4.0/auto_analyses.frame_order.Frame_order_analysis-class.html website/api/4.0/auto_analyses.frame_order.Optimisation_settings-class.html website/api/4.0/auto_analyses.noe-module.html website/api/4.0/auto_analyses.noe-pysrc.html website/api/4.0/auto_analyses.noe.NOE_calc-class.html website/api/4.0/auto_analyses.relax_disp-module.html website/api/4.0/auto_analyses.relax_disp-pysrc.html website/api/4.0/auto_analyses.relax_disp.Relax_disp-class.html website/api/4.0/auto_analyses.relax_disp_repeat_cpmg-module.html website/api/4.0/auto_analyses.relax_disp_repeat_cpmg-pysrc.html website/api/4.0/auto_analyses.relax_disp_repeat_cpmg.Relax_disp_rep-class.html website/api/4.0/auto_analyses.relax_fit-module.html website/api/4.0/auto_analyses.relax_fit-pysrc.html website/api/4.0/auto_analyses.relax_fit.Relax_fit-class.html website/api/4.0/auto_analyses.stereochem_analysis-module.html website/api/4.0/auto_analyses.stereochem_analysis-pysrc.html website/api/4.0/auto_analyses.stereochem_analysis.Stereochem_analysis-class.html website/api/4.0/bmrblib-module.html website/api/4.0/bmrblib-pysrc.html website/api/4.0/bmrblib.NMR_parameters-module.html website/api/4.0/bmrblib.NMR_parameters-pysrc.html website/api/4.0/bmrblib.NMR_parameters.chem_shift_anisotropy-module.html website/api/4.0/bmrblib.NMR_parameters.chem_shift_anisotropy-pysrc.html website/api/4.0/bmrblib.NMR_parameters.chem_shift_anisotropy.CSAnisotropy-class.html website/api/4.0/bmrblib.NMR_parameters.chem_shift_anisotropy.CSAnisotropyExperiment-class.html website/api/4.0/bmrblib.NMR_parameters.chem_shift_anisotropy.CSAnisotropySoftware-class.html website/api/4.0/bmrblib.NMR_parameters.chem_shift_anisotropy.ChemShiftAnisotropy-class.html website/api/4.0/bmrblib.NMR_parameters.chem_shift_anisotropy.ChemShiftAnisotropySaveframe-class.html website/api/4.0/bmrblib.NMR_parameters.chem_shift_anisotropy_v3_1-module.html website/api/4.0/bmrblib.NMR_parameters.chem_shift_anisotropy_v3_1-pysrc.html website/api/4.0/bmrblib.NMR_parameters.chem_shift_anisotropy_v3_1.CSAnisotropyExperiment_v3_1-class.html website/api/4.0/bmrblib.NMR_parameters.chem_shift_anisotropy_v3_1.CSAnisotropySoftware_v3_1-class.html website/api/4.0/bmrblib.NMR_parameters.chem_shift_anisotropy_v3_1.CSAnisotropy_v3_1-class.html website/api/4.0/bmrblib.NMR_parameters.chem_shift_anisotropy_v3_1.ChemShiftAnisotropySaveframe_v3_1-class.html website/api/4.0/bmrblib.NMR_parameters.chem_shift_anisotropy_v3_1.ChemShiftAnisotropy_v3_1-class.html website/api/4.0/bmrblib.assembly_supercategory-module.html website/api/4.0/bmrblib.assembly_supercategory-pysrc.html website/api/4.0/bmrblib.assembly_supercategory.entity-module.html website/api/4.0/bmrblib.assembly_supercategory.entity-pysrc.html website/api/4.0/bmrblib.assembly_supercategory.entity.Entity-class.html website/api/4.0/bmrblib.assembly_supercategory.entity.EntityCompIndex-class.html website/api/4.0/bmrblib.assembly_supercategory.entity.EntitySaveframe-class.html website/api/4.0/bmrblib.assembly_supercategory.entity_v2_1-module.html website/api/4.0/bmrblib.assembly_supercategory.entity_v2_1-pysrc.html website/api/4.0/bmrblib.assembly_supercategory.entity_v2_1.EntityCompIndex_v2_1-class.html website/api/4.0/bmrblib.assembly_supercategory.entity_v2_1.EntitySaveframe_v2_1-class.html website/api/4.0/bmrblib.assembly_supercategory.entity_v2_1.Entity_v2_1-class.html website/api/4.0/bmrblib.assembly_supercategory.entity_v3_1-module.html website/api/4.0/bmrblib.assembly_supercategory.entity_v3_1-pysrc.html
r28140 - /tags/4.0.1/
Author: bugman Date: Mon Dec 14 10:36:17 2015 New Revision: 28140 URL: http://svn.gna.org/viewcvs/relax?rev=28140=rev Log: relax version 4.0.1. This is a major feature and bugfix release. Features include the new structure.pca user function for performing a principle component analysis (PCA) of a set of structures, handling of replicated R2eff data points in the dispersion analysis, improvements in the handling of PDB structures, the protection against numpy >= 1.9 FutureWarnings for a number of soon to change behaviours in numpy, and addition of a deployment script for the Google Cloud Computing. Bugfixes include an error when loading relaxation data, the CSA constant equation in the manual, missing information in the relax state and results files, loading of certain state files in the GUI, running relax with no graphical display and using matplotlib, BMRB export failure when a spin container is missing data or parameters. Added: tags/4.0.1/ - copied from r28139, trunk/ ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
r28145 - /website/download.html
Author: bugman Date: Mon Dec 14 16:35:17 2015 New Revision: 28145 URL: http://svn.gna.org/viewcvs/relax?rev=28145=rev Log: Updated the http://www.nmr-relax.com/download.html webpage for the relax 4.0.1 release. Modified: website/download.html [This mail would be too long, it was shortened to contain the URLs only.] Modified: website/download.html URL: http://svn.gna.org/viewcvs/relax/website/download.html?rev=28145=28144=28145=diff ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
r28146 - /website/manual/
Author: bugman Date: Mon Dec 14 16:59:24 2015 New Revision: 28146 URL: http://svn.gna.org/viewcvs/relax?rev=28146=rev Log: Updated the relax HTML manual at http://www.nmr-relax.com/manual/index.html to version 4.0.1. Added: website/manual/structure_pca.html Modified: website/manual/A_warning_about_the_formatting.html website/manual/Abbreviations.html website/manual/About_this_document.html website/manual/Access_to_the_internals_of_relax.html website/manual/Advanced_topics.html website/manual/All_model_free_models_script_mode_explanation.html website/manual/All_model_free_models_script_mode_the_sample_script.html website/manual/Alphabetical_listing_of_user_functions.html website/manual/Analysing_dispersion_in_the_prompt_script_UI_mode.html website/manual/Assigning_an_issue_to_yourself.html website/manual/Becoming_a_committer.html website/manual/Bibliography.html website/manual/Branch_creation.html website/manual/Branches.html website/manual/Brownian_rotational_diffusion.html website/manual/C_module_compilation.html website/manual/Calculating_the_NOE.html website/manual/Calculation_of_the_NOE_in_the_prompt_script_UI_mode.html website/manual/Cleaning_up.html website/manual/Closing_an_issue.html website/manual/Coding_conventions.html website/manual/Comments.html website/manual/Committers.html website/manual/Comparison_of_dispersion_analysis_software.html website/manual/Compilation_of_the_API_documentation_HTML_version.html website/manual/Compilation_of_the_user_manual_HTML_version.html website/manual/Compilation_of_the_user_manual_PDF_version.html website/manual/Components_of_the_Ri_theta_equations.html website/manual/Computation_time_and_the_numerical_integration_of_the_PCS.html website/manual/Computation_times.html website/manual/Conjugate_gradient_methods.html website/manual/Consistency_testing.html website/manual/Consistency_testing_analysis_references.html website/manual/Consistency_testing_in_the_prompt_script_UI_mode.html website/manual/Consistency_testing_script_mode_calculation_and_error_propagation.html website/manual/Consistency_testing_script_mode_data_pipe_and_spin_system_setup.html website/manual/Consistency_testing_script_mode_relaxation_data_loading.html website/manual/Consistency_testing_script_mode_relaxation_interactions.html website/manual/Consistency_testing_script_mode_the_sample_script.html website/manual/Consistency_testing_script_mode_visualisation_and_data_output.html website/manual/Constraint_algorithms.html website/manual/Construction_of_the_Hessian.html website/manual/Construction_of_the_gradient.html website/manual/Construction_of_the_values_gradients_and_Hessians.html website/manual/Contents.html website/manual/Copying_modification_sublicencing_and_distribution_of_relax.html website/manual/Dasha.html website/manual/Data_analysis_tools.html website/manual/Data_visualisation.html website/manual/Defaults.html website/manual/Dependencies.html website/manual/Derivation_of_a_2D_trigonometric_function_the_pseudo_elliptic_cosine.html website/manual/Determining_stereochemistry_in_dynamic_molecules.html website/manual/Diagonal_scaling.html website/manual/Discussing_major_changes.html website/manual/Dispersion_GUI_mode_choosing_the_models_to_optimise.html website/manual/Dispersion_GUI_mode_comparing_models.html website/manual/Dispersion_GUI_mode_comparison_of_the_analyses.html website/manual/Dispersion_GUI_mode_computation_time.html website/manual/Dispersion_GUI_mode_dispersion_setup.html website/manual/Dispersion_GUI_mode_execution_of_the_non_clustered_analysis.html website/manual/Dispersion_GUI_mode_general_setup.html website/manual/Dispersion_GUI_mode_initialisation_of_the_data_pipe.html website/manual/Dispersion_GUI_mode_inspection_of_the_results.html website/manual/Dispersion_GUI_mode_loading_the_data.html website/manual/Dispersion_GUI_mode_optimisation_settings.html website/manual/Dispersion_GUI_mode_setting_up_the_spin_systems.html website/manual/Dispersion_GUI_mode_the_clustered_analysis.html website/manual/Dispersion_GUI_mode_two_analyses.html website/manual/Dispersion_GUI_mode_unresolved_spins.html website/manual/Dispersion_curve_insignificance.html website/manual/Dispersion_model_summary.html website/manual/Dispersion_parameter_grid_search.html website/manual/Dispersion_parameter_optimisation.html website/manual/Dispersion_script_mode_analysis_variables.html website/manual/Dispersion_script_mode_execution.html website/manual/Dispersion_script_mode_imports.html website/manual/Dispersion_script_mode_initialisation_of_the_data_pipe.html website/manual/Dispersion_script_mode_loading_the_data.html
r28143 - /tags/4.0.1/docs/CHANGES
Author: bugman Date: Mon Dec 14 14:39:06 2015 New Revision: 28143 URL: http://svn.gna.org/viewcvs/relax?rev=28143=rev Log: Updated the CHANGES file for relax 4.0.1. Modified: tags/4.0.1/docs/CHANGES [This mail would be too long, it was shortened to contain the URLs only.] Modified: tags/4.0.1/docs/CHANGES URL: http://svn.gna.org/viewcvs/relax/tags/4.0.1/docs/CHANGES?rev=28143=28142=28143=diff ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
r28144 - /trunk/docs/CHANGES
Author: bugman Date: Mon Dec 14 14:40:24 2015 New Revision: 28144 URL: http://svn.gna.org/viewcvs/relax?rev=28144=rev Log: Backported the relax 4.0.1 CHANGES file changes to trunk. The command used was: svn merge -r28142:28143 svn+ssh://bug...@svn.gna.org/svn/relax/tags/4.0.1 . Modified: trunk/docs/CHANGES [This mail would be too long, it was shortened to contain the URLs only.] Modified: trunk/docs/CHANGES URL: http://svn.gna.org/viewcvs/relax/trunk/docs/CHANGES?rev=28144=28143=28144=diff ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
r28148 - /website/api/index.html
Author: bugman Date: Mon Dec 14 17:55:08 2015 New Revision: 28148 URL: http://svn.gna.org/viewcvs/relax?rev=28148=rev Log: Updated the relax version number to 4.0.1 on the http://www.nmr-relax.com/api/index.html webpage. Modified: website/api/index.html Modified: website/api/index.html URL: http://svn.gna.org/viewcvs/relax/website/api/index.html?rev=28148=28147=28148=diff == --- website/api/index.html (original) +++ website/api/index.html Mon Dec 14 17:55:08 2015 @@ -30,7 +30,7 @@ The most recent version of the documentation is: - http://www.nmr-relax.com/api/4.0/;>relax 4.0.0 API documentation + http://www.nmr-relax.com/api/4.0/;>relax 4.0.1 API documentation The relax library @@ -42,7 +42,7 @@ The automatically generated API documentation is also available for earlier relax versions: - http://www.nmr-relax.com/api/4.0/;>relax 4.0.0 API documentation + http://www.nmr-relax.com/api/4.0/;>relax 4.0.1 API documentation http://www.nmr-relax.com/api/3.3/;>relax 3.3.9 API documentation http://www.nmr-relax.com/api/3.2/;>relax 3.2.3 API documentation http://www.nmr-relax.com/api/3.1/;>relax 3.1.7 API documentation ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
