[Cdk-devel] [ cdk-Patches-3209130 ] PDBReader and PDBWriter improvements

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Patches item #3209130, was opened at 2011-03-13 15:46
Message generated for change (Comment added) made by rajarshi
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Category: cdk-1.4.x
Group: Needs Review
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: gilleain maclean torrance (gilleain)
Assigned to: Egon Willighagen (egonw)
Summary: PDBReader and PDBWriter improvements

Initial Comment:
https://github.com/gilleain/cdk/tree/pdbreadwrite

A number of changes to PDBReader and PDBWriter. Mainly to get small-molecule "PDB" files to read and write properly.

CONECT:
- Make CONNECT records work with non-protein PDB files 
- Rewrote CONNECT parsing
- Do not write CONECT records for atoms that have no bonds

Element Symbols:
- Read element symbol from columns 76-78

Atom Types:
- Explicit types on atom number map and bonding of small molecules
- Type map for PDB HETatoms created from RCSB compound dictionary
    
PDBWriter :
-  Upgrade of PDBWriter to latest specifications
-  More IOSettings for PDBWriter

Tests:
- Updated tests for PDBWriter
- Roundtrip test for PDBReader/Writer
- Charge test
- Test for groups that are not in the amino acid dictionary (eg UNK)
- Test for old format vs new format pdb files
- Simplification of tests by factoring out duplicate tests of PDB object counts

Odd PDB files:    
- Deal with HETATM only files, with test case
- Deal with files with ATOM lines padded to 80 with spaces, but with old format


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>Comment By: Rajarshi Guha (rajarshi)
Date: 2011-05-15 08:35

Message:
I took a look at this and it seems clean to me. I'd say it's OK to merge

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Comment By: gilleain maclean torrance (gilleain)
Date: 2011-03-23 09:42

Message:
Author info added.

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Comment By: Egon Willighagen (egonw)
Date: 2011-03-13 16:18

Message:
Quick note... since you made such extensive rewrites, make sure to add
proper entries in the copyright header :)

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