Re: [Jmol-developers] [ jmol-Bugs-1418722 ] CIF bonding block being misread

[Bob H. <ha...@st...>]

Excellent! Thanks.

Questions:

How do I run the latest version after a "commit"?
Where do I get the compiled JmolApplet<n>.jar files?

Bob


SourceForge.net wrote:

> Bugs item #1418722, was opened at 2006-01-30 16:57
> Message generated for change (Comment added) made by nicove
> You can respond by visiting: 
> https://sourceforge.net/tracker/?func=detail&atid=379133&aid=1418722&group_id=23629
> 
> Please note that this message will contain a full copy of the comment thread,
> including the initial issue submission, for this request,
> not just the latest update.
> Category: File Input/Output
> Group: None
> 
>>Status: Closed
>>Resolution: Fixed
> 
> Priority: 5
> Submitted By: Bob Hanson (hansonr)
> 
>>Assigned to: Nicolas (nicove)
> 
> Summary: CIF bonding block being misread
> 
> Initial Comment:
> JmolApplet 10.00.47
> 
> In the attached CIF file, also found at 
> http://www.stolaf.edu/people/hansonr/jmol/docs/
> examples/mc2.cif
> 
> the block
> 
> loop_
>  _geom_bond_atom_site_label_1
>  _geom_bond_site_symmetry_1
>  _geom_bond_atom_site_label_2
>  _geom_bond_site_symmetry_2
>  _geom_bond_distance
>  _geom_bond_publ_flag
> Cu1 . S1 . 2.2466(15)    yes
> ...
> 
> is being misread, resulting in file load failure. The 
> reader is not properly recognizing that the two labels 
> aren't the first two fields and instead trying to read 
> the second label from the symmetry_1 field, resulting 
> in an error.
> 
> When I remove this block or change this block to
> 
> loop_
>  _geom_bond_atom_site_label_1
>  _geom_bond_atom_site_label_2
>  _geom_bond_site_symmetry_2
>  _geom_bond_distance
>  _geom_bond_publ_flag
> Cu1 S1 . 2.2466(15)    yes
> ...
> 
> the modified file is read properly, so I'm sure this
> is all it is.
> 
> Bob Hanson
> 
> 
> ----------------------------------------------------------------------
> 
> 
>>Comment By: Nicolas (nicove)
> 
> Date: 2006-01-31 19:18
> 
> Message:
> Logged In: YES 
> user_id=1096197
> 
> I have just committed the modification to the CIF Reader.
> Your file is now being read without problems.
> You can check if the result is ok.
> 
> ----------------------------------------------------------------------
> 
> Comment By: Nicolas (nicove)
> Date: 2006-01-31 01:07
> 
> Message:
> Logged In: YES 
> user_id=1096197
> 
> Forget my first analysis: the problem is quite simple in fact.
> 
> The method processGeomBondLoopBlock() never checks for the
> end of the loop (for example for a loop_ line). It should do
> something like the processAtomSiteLoopBlock().
> 
> It crashes in your case because after the first _geom_bond
> loop, there's a whitespace at the beginning of the lines.
> The crash is happening only because there's no test to check
> the end of the loop.
> 
> I can't fix right now, the CVS problem is blocking me (and
> probably everyone else) to do an update or a commit.
> 
> ----------------------------------------------------------------------
> 
> Comment By: Nicolas (nicove)
> Date: 2006-01-30 22:22
> 
> Message:
> Logged In: YES 
> user_id=1096197
> 
> Bob, I am trying to commit modifications to the Cif reader
> in CVS but I have a big problem with CVS. The commit failed
> and now there's a lock I can't get rid of
> (https://sourceforge.net/tracker/index.php?func=detail&aid=1419160&group_id=1&atid=200001)
> 
> 
> Could you test the modification with a few Cif files ?
> 
> To Miguel: I think the Cif reader works only in some
> situations (probably the most common). It requires that the
> known fields are present and at the beginning: for example,
> if _geom_bond_distance is put before one of the three
> others, it won't work.
> 
> The modification has to be made from line 399 in
> CifReader.java. The text up to the comment about helix and
> turn structure data has to be replaced by:
>   final static byte GEOM_BOND_ATOM_SITE_LABEL_1 = 1;
>   final static byte GEOM_BOND_ATOM_SITE_LABEL_2 = 2;
>   final static byte GEOM_BOND_SITE_SYMMETRY_1   = 3;
>   final static byte GEOM_BOND_SITE_SYMMETRY_2   = 4;
>   //  final static byte GEOM_BOND_DISTANCE          = 5;
>   
>   final static byte GEOM_BOND_PROPERTY_MAX      = 5;
> 
>   final static String[] geomBondFields = {
>     "_geom_bond_atom_site_label_1",
>     "_geom_bond_atom_site_label_2",
>     "_geom_bond_site_symmetry_1",
>     "_geom_bond_site_symmetry_2",
>     //    "_geom_bond_distance",
>   };
> 
>   final static byte[] geomBondFieldMap = {
>     GEOM_BOND_ATOM_SITE_LABEL_1,
>     GEOM_BOND_ATOM_SITE_LABEL_2,
>     GEOM_BOND_SITE_SYMMETRY_1,
>     GEOM_BOND_SITE_SYMMETRY_2,
>     //    GEOM_BOND_DISTANCE,
>   };
> 
>   final static boolean[] geomBondFieldRequired = {
>     true,
>     true,
>     false,
>     true,
>   };
>   
>   void processGeomBondLoopBlock() throws Exception {
>     int[] fieldTypes = new int[100]; // should be enough
>     boolean[] propertyReferenced = new
> boolean[GEOM_BOND_PROPERTY_MAX];
>     int fieldCount = parseLoopParameters(geomBondFields,
>                                          geomBondFieldMap,
>                                          fieldTypes,
>                                          propertyReferenced);
>     for (int i = GEOM_BOND_PROPERTY_MAX; --i > 0; ) // only
> 
>>0, not >= 0
> 
>       if (! propertyReferenced[i] && geomBondFieldRequired[i]) {
>         logger.log("?que? missing _geom_bond property:" + i);
>         skipLoopData();
>         return;
>       }
> 
>     for (; line != null &&
>            (line = line.trim()).length() > 0 &&
>            line.charAt(0) != '#';
>          line = reader.readLine()) {
>       tokenizer.setString(line);
>       int atomIndex1 = -1;
>       int atomIndex2 = -1;
>       String symmetry1 = null;
>       String symmetry2 = null;
>       for (int i = 0; i < fieldCount; ++i) {
>         if (! tokenizer.hasMoreTokens())
>           tokenizer.setString(reader.readLine());
>         String field = tokenizer.nextToken();
>         switch (fieldTypes[i]) {
>         case NONE:
>           break;
>         case GEOM_BOND_ATOM_SITE_LABEL_1:
>           atomIndex1 =
> atomSetCollection.getAtomNameIndex(field);
>           break;
>         case GEOM_BOND_ATOM_SITE_LABEL_2:
>           atomIndex2 =
> atomSetCollection.getAtomNameIndex(field);
>           break;
>         case GEOM_BOND_SITE_SYMMETRY_1:
>           if (field.charAt(0) != '.')
>             symmetry1 = field;
>           break;
>         case GEOM_BOND_SITE_SYMMETRY_2:
>           if (field.charAt(0) != '.')
>             symmetry2 = field;
>           break;
>         }
>       }
>       if (atomIndex1 >= 0 && atomIndex2 >= 0) {
>         //TODO
>         // miguel 2004 11 19
>         // for now, do not deal with symmetry
>         if ((symmetry1 == null) && (symmetry2 == null)) {
>           Bond bond = new Bond();
>           bond.atomIndex1 = atomIndex1;
>           bond.atomIndex2 = atomIndex2;
>           atomSetCollection.addBond(bond);
>         }
>       }
>     }
>   }
> 
> 
> ----------------------------------------------------------------------
> 
> Comment By: Nicolas (nicove)
> Date: 2006-01-30 20:27
> 
> Message:
> Logged In: YES 
> user_id=1096197
> 
> In the CIF reader, there's no code for handling
> "_geom_bond_site_symmetry_1" (not even parsing)
> 
> The handling of "_geom_bond_site_symmetry_2" only consists
> of parsing the value, not using it.
> 
> Would it be ok to deal with symmetry_1 the same way as
> symmetry_2: parsing it but not using it ?
> 
> ----------------------------------------------------------------------
> 
> You can respond by visiting: 
> https://sourceforge.net/tracker/?func=detail&atid=379133&aid=1418722&group_id=23629
> 
> 
> -------------------------------------------------------
> This SF.net email is sponsored by: Splunk Inc. Do you grep through log files
> for problems?  Stop!  Download the new AJAX search engine that makes
> searching your log files as easy as surfing the  web.  DOWNLOAD SPLUNK!
> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=103432&bid=230486&dat=121642
> _______________________________________________
> Jmol-developers mailing list
> Jmo...@li...
> https://lists.sourceforge.net/lists/listinfo/jmol-developers

-- 

Robert M. Hanson, ha...@st..., 507-646-3107
Professor of Chemistry, St. Olaf College
1520 St. Olaf Ave., Northfield, MN 55057
mailto:ha...@st...
http://www.stolaf.edu/people/hansonr

"Imagination is more important than knowledge."  - Albert Einstein