[Jmol-developers] [ jmol-Bugs-1048504 ] Jmol doesn't read CIF file

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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:

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
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



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