Re: [PyMOL] dcd trajectories in PyMOL

2012-02-29 Thread Thomas Holder
Hi Andreas,

I forgot one step, sorry. The update.py script does not copy the header 
files from the include directory, so you need:

cd $VMD/plugins/include
cp vmdconio.h molfile_plugin.h $PYMOL/contrib/uiuc/plugins/include

Here I put $VMD and $PYMOL as the respective source tree roots.

Hopefully these were all steps now...

Cheers,
   Thomas

On 02/28/2012 07:39 PM, Andreas Förster wrote:
 Thanks for your help, Thomas, but this didn't do the trick for me. I can
 run the python update.py and get a list of available plugins, but python
 setup.py build install (after patching) still crashes at the point of
 compiling the VMD plugins.

 gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall
 -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
 --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC
 -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
 -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic
 -D_GNU_SOURCE -fPIC -fwrapv -fPIC -D_PYMOL_MODULE -D_PYMOL_INLINE
 -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_OPENGL_SHADERS
 -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_CGO_DRAWARRAYS
 -D_PYMOL_GL_CALLLISTS -DOPENGL_ES_2 -D_PYMOL_VMD_PLUGINS -Iov/src
 -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5
 -I/usr/include/freetype2 -Imodules/cealign/src -Imodules/cealign/src/tnt
 -Igenerated/include -Igenerated/src -Icontrib/uiuc/plugins/include
 -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/include/python2.6 -c
 contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c -o
 build/temp.linux-x86_64-2.6/contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.o
 -ffast-math -funroll-loops -O3 -g
 In file included from
 contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c:43:
 contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h: In function
 ‘init_qmdata’:
 contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:442: error:
 ‘MOLFILE_QMSTATUS_UNKNOWN’ undeclared (first use in this function)
 contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:442: error: (Each
 undeclared identifier is reported only once
 contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:442: error: for each
 function it appears in.)
 contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h: In function ‘eatline’:
 contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:835: warning:
 ignoring return value of ‘fgets’, declared with attribute
 warn_unused_result
 contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c: In function
 ‘read_basis_rundata’:
 contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c:262: error:
 ‘molfile_qm_basis_t’ has no member named ‘shell_types’
 error: command 'gcc' failed with exit status 1

 Looks like I'm tied to VMD.


 Andreas



 On 28/02/2012 3:02, Thomas Holder wrote:
 Hi Andreas,

 this error was introduced in the open-source tree with the updates from
 PyMOL 1.5. I'm not sure what the easiest fix would be, but here is how I
 got it to work:

 Download the latest VMD source code and unpack it:
 http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD

 In the PyMOL source tree, edit the file
 contrib/uiuc/plugins/molfile_plugin/update.py
 and point molfile_src_path to the correct path in the VMD source tree.
 Then run python update.py.

 In setup.py, comment out cpmdlogplugin.c, cpmdplugin.c and
 gaussianplugin.c (they are commented out in update.py as well). You
 may use the attached patch.

 Cheers,
 Thomas

 On 02/28/2012 11:36 AM, Andreas Förster wrote:
 Dear all,

 driven beyond the reach of sanity by VMD, I've tried to enable the
 loading of DCD trajectories (from NAMD2 molecular dynamics simulations)
 in PyMOL. I followed the instructions given on this mailing list a few
 weeks back, specifically (setup.py):

 - uncommenting contrib/uiuc/plugins/include,
 contrib/uiuc/plugins/molfile_plugin/src,
 (_PYMOL_VMD_PLUGINS,None),
 - changing the line underneath
 # VMD plugin support
 # switch the 0 to 1 to activate the additional source code
 from ] + 0 * [
 to ] + 1 * [

 Compilation (python setup.py build install) crashes because of an error
 in the molfile plugin:

 contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c: In function
 ‘read_basis_metadata’:
 contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c:208: error:
 ‘molfile_qm_metadata_t’ has no member named ‘have_esp’
 contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c:209: error:
 ‘molfile_qm_metadata_t’ has no member named ‘have_npa’
 contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c:211: error:
 ‘molfile_qm_metadata_t’ has no member named ‘have_internals’
 error: command 'gcc' failed with exit status 1


 Have others encountered that? Is there a solution or work-around?

 Thanks.


 Andreas


-- 
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen

--
Virtualization  Cloud Management Using Capacity Planning
Cloud computing makes use of virtualization - but cloud 

Re: [PyMOL] dcd trajectories in PyMOL

2012-02-28 Thread Thomas Holder

Hi Andreas,

this error was introduced in the open-source tree with the updates from 
PyMOL 1.5. I'm not sure what the easiest fix would be, but here is how I 
got it to work:


Download the latest VMD source code and unpack it:
http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD

In the PyMOL source tree, edit the file
contrib/uiuc/plugins/molfile_plugin/update.py
and point molfile_src_path to the correct path in the VMD source tree. 
Then run python update.py.


In setup.py, comment out cpmdlogplugin.c, cpmdplugin.c and 
gaussianplugin.c (they are commented out in update.py as well). You 
may use the attached patch.


Cheers,
  Thomas

On 02/28/2012 11:36 AM, Andreas Förster wrote:

Dear all,

driven beyond the reach of sanity by VMD, I've tried to enable the
loading of DCD trajectories (from NAMD2 molecular dynamics simulations)
in PyMOL.  I followed the instructions given on this mailing list a few
weeks back, specifically (setup.py):

- uncommenting contrib/uiuc/plugins/include,
 contrib/uiuc/plugins/molfile_plugin/src,
(_PYMOL_VMD_PLUGINS,None),
- changing the line underneath
 # VMD plugin support
 # switch the 0 to 1 to activate the additional source code
from] + 0 * [
to  ] + 1 * [

Compilation (python setup.py build install) crashes because of an error
in the molfile plugin:

contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c: In function
‘read_basis_metadata’:
contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c:208: error:
‘molfile_qm_metadata_t’ has no member named ‘have_esp’
contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c:209: error:
‘molfile_qm_metadata_t’ has no member named ‘have_npa’
contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c:211: error:
‘molfile_qm_metadata_t’ has no member named ‘have_internals’
error: command 'gcc' failed with exit status 1


Have others encountered that?  Is there a solution or work-around?

Thanks.


Andreas


--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen
Index: setup.py
===
--- setup.py	(revision 3983)
+++ setup.py	(working copy)
@@ -9,6 +9,8 @@
 from distutils.core import setup, Extension
 import sys, os
 
+with_vmd_plugins = 0
+
 #
 if sys.platform=='win32': 
 # NOTE: this branch not tested in years and may not work...
@@ -265,6 +267,11 @@
   -g ]
 ext_link_args = []
 
+with_vmd_plugins = 1
+if with_vmd_plugins:
+inc_dirs += [ contrib/uiuc/plugins/include,
+  contrib/uiuc/plugins/molfile_plugin/src]
+def_macros += [ (_PYMOL_VMD_PLUGINS, None) ]
 
 distribution = setup ( # Distribution meta-data
 name  = pymol,
@@ -420,7 +427,7 @@
 layer5/main.c
 # VMD plugin support
 # switch the 0 to 1 to activate the additional source code
-] + 0 * [
+] + (1 if with_vmd_plugins else 0) * [
 # (incomplete support -- only TRJ, TRR, XTC, DCD so far...)
 'contrib/uiuc/plugins/molfile_plugin/src/PlugIOManagerInit.c',
 'contrib/uiuc/plugins/molfile_plugin/src/avsplugin.cpp',
@@ -432,8 +439,8 @@
 'contrib/uiuc/plugins/molfile_plugin/src/carplugin.c',
 'contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.cpp',
 'contrib/uiuc/plugins/molfile_plugin/src/corplugin.c',
-'contrib/uiuc/plugins/molfile_plugin/src/cpmdlogplugin.c',
-'contrib/uiuc/plugins/molfile_plugin/src/cpmdplugin.c',
+#'contrib/uiuc/plugins/molfile_plugin/src/cpmdlogplugin.c',
+#'contrib/uiuc/plugins/molfile_plugin/src/cpmdplugin.c',
 'contrib/uiuc/plugins/molfile_plugin/src/crdplugin.c',
 'contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp',
 'contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c',
@@ -444,7 +451,7 @@
 'contrib/uiuc/plugins/molfile_plugin/src/edmplugin.cpp',
 'contrib/uiuc/plugins/molfile_plugin/src/fs4plugin.cpp',
 'contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c',
-'contrib/uiuc/plugins/molfile_plugin/src/gaussianplugin.c',
+#'contrib/uiuc/plugins/molfile_plugin/src/gaussianplugin.c',
 'contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp',
 'contrib/uiuc/plugins/molfile_plugin/src/grdplugin.cpp',
 'contrib/uiuc/plugins/molfile_plugin/src/gridplugin.cpp',
--
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