On Oct 17 2004, SourceForge.net wrote:
Bugs item #1048504, was opened at 2004-10-17 01:25 Message generated for change (Comment added) made by migueljmol You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=1048504&group_id=23629
Category: File Input/Output Group: None >Status: Closed >Resolution: Fixed Priority: 5 Submitted By: Nobody/Anonymous (nobody) Assigned to: Miguel (migueljmol) Summary: Jmol doesn't read CIF file
Initial Comment: I tried opening a file Peter suggested from http://journals.iucr.org/e/issues/2004/10/00/EAtxtisscontsbdy.html (inorganic compounds-- Acta Cryst. (2004). E60, i120-i123) (checkCIF/PLATON results: No syntax errors found) But nonetheless, Jmol does not read
http://scripts.iucr.org/cgi-bin/sendcif?hb6095sup1
We have initially a problem identifying this as a CIF file, because there are too many comments:
I think this is a valid CIF
FileManager.openFile(t.cif)
java.lang.ArrayIndexOutOfBoundsException: 2048
at org.jmol.adapter.smarter.LimitedLineReader.readLineWithNewline(ModelResolver.java:221)
at org.jmol.adapter.smarter.ModelResolver.determineModelReader(ModelResolver.java:70)
at
org.jmol.adapter.smarter.ModelResolver.resolveModel(ModelResolver.java:37)
at org.jmol.adapter.smarter.SmarterModelAdapter.openBufferedReader(SmarterModelAdapter.java:55)
at org.openscience.jmol.viewer.managers.FileManager$FileOpenThread.openReader(FileManager.java:409)
at org.openscience.jmol.viewer.managers.FileManager$FileOpenThread.openInputStream(FileManager.java:402)
at org.openscience.jmol.viewer.managers.FileManager$FileOpenThread.run(FileManager.java:379)
at org.openscience.jmol.viewer.managers.FileManager.openFile(FileManager.java:100)
at
org.openscience.jmol.viewer.JmolViewer.openFile(JmolViewer.java:945)
at
org.openscience.jmol.viewer.script.Eval.load(Eval.java:1606)
at org.openscience.jmol.viewer.script.Eval.instructionDispatchLoop(Eval.java:348)
at
org.openscience.jmol.viewer.script.Eval.run(Eval.java:290)
at java.lang.Thread.run(Unknown Source)
error opening file:/D:/js/jmol/docs/examples/t.cif java.lang.ArrayIndexOutOfBoundsException: 2048
---------------------- after removal of 4 top header lines we have a successful identification but still can't read data:
FileManager.openFile(t.cif) SmarterModelAdapter:The model resolver thinks:Cif
java.lang.NullPointerException
at
org.jmol.adapter.smarter.ModelReader.parseFloat(ModelReader.java:45)
at org.jmol.adapter.smarter.CifReader.processAtomSiteLoopBlock(CifReader.java:306)
at
org.jmol.adapter.smarter.CifReader.processLoopBlock(CifReader.java:144)
at
org.jmol.adapter.smarter.CifReader.readModel(CifReader.java:65)
at
org.jmol.adapter.smarter.ModelResolver.resolveModel(ModelResolver.java:57)
at org.jmol.adapter.smarter.SmarterModelAdapter.openBufferedReader(SmarterModelAdapter.java:55)
at org.openscience.jmol.viewer.managers.FileManager$FileOpenThread.openReader(FileManager.java:409)
at org.openscience.jmol.viewer.managers.FileManager$FileOpenThread.openInputStream(FileManager.java:402)
at org.openscience.jmol.viewer.managers.FileManager$FileOpenThread.run(FileManager.java:379)
at org.openscience.jmol.viewer.managers.FileManager.openFile(FileManager.java:100)
at
org.openscience.jmol.viewer.JmolViewer.openFile(JmolViewer.java:945)
at
org.openscience.jmol.viewer.script.Eval.load(Eval.java:1606)
at org.openscience.jmol.viewer.script.Eval.instructionDispatchLoop(Eval.java:348)
at
org.openscience.jmol.viewer.script.Eval.run(Eval.java:290)
at java.lang.Thread.run(Unknown Source)
error opening file:/D:/js/jmol/docs/examples/t.cif
-------------------------------------- after adding #END in atom block loop, we have a successful read:
FileManager.openFile(t.cif) SmarterModelAdapter:The model resolver thinks:Cif openFile(t.cif) 0 ms
[model displays properly]
This #END is at:
loop_ _atom_site_label _atom_site_fract_x _atom_site_fract_y _atom_site_fract_z _atom_site_U_iso_or_equiv _atom_site_adp_type _atom_site_calc_flag _atom_site_refinement_flags _atom_site_occupancy _atom_site_disorder_assembly _atom_site_disorder_group _atom_site_type_symbol Sr 0.3333 0.6667 0.1667 0.0145(3) Uani d S 1 . . Sr N 0.0000 0.0000 0.0820(3) 0.0182(10) Uani d S 1 . . N C 0.0000 0.0000 0.0000 0.0126(14) Uani d S 1 . . C #END
this is NOT a keyword in CIF. There is no endLoop token. A loop is ended either by the end of file or by a loop_ or data_ or _foo. The only way to read CIFs reliably is to read the CIF spec and implement it! There are no half measures - it will break somewhere else. It is like trying to write an XML reader on the assumption there is a newline after every tag. CIF, like XML need not have any newlines at all
P.
loop_ _atom_site_aniso_label _atom_site_aniso_U_11 _atom_site_aniso_U_22 _atom_site_aniso_U_33 _atom_site_aniso_U_12 _atom_site_aniso_U_13 _atom_site_aniso_U_23 Sr 0.0131(3) 0.0131(3) 0.0172(4) 0.00654(15) 0.000 0.000 N 0.0179(16) 0.0179(16) 0.019(2) 0.0089(8) 0.000 0.000 C 0.009(2) 0.009(2) 0.020(4) 0.0044(10) 0.000 0.000 _geom_special_details
P.
Bob Hanson
----------------------------------------------------------------------
>Comment By: Miguel (migueljmol) Date: 2004-10-17 16:47
Message:
Logged In: YES user_id=1050060
OK, the 'lots of comments' problem was certainly my bug. It
is now fixed.
It is not clear to me that this is a valid .cif file. There
is no clear indication of loop_ termination. I will post a
message for Peter.
Miguel
----------------------------------------------------------------------
You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=1048504&group_id=23629
------------------------------------------------------- This SF.net email is sponsored by: IT Product Guide on ITManagersJournal Use IT products in your business? Tell us what you think of them. Give us Your Opinions, Get Free ThinkGeek Gift Certificates! Click to find out more http://productguide.itmanagersjournal.com/guidepromo.tmpl _______________________________________________ Jmol-developers mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-developers
------------------------------------------------------- This SF.net email is sponsored by: IT Product Guide on ITManagersJournal Use IT products in your business? Tell us what you think of them. Give us Your Opinions, Get Free ThinkGeek Gift Certificates! Click to find out more http://productguide.itmanagersjournal.com/guidepromo.tmpl _______________________________________________ Jmol-developers mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-developers
