Revision 137 - Directory Listing
Modified Mon May 14 14:53:09 2007 UTC (17 years, 5 months ago) by stehr

Made chain field in PDB class public

Revision 136 - Directory Listing
Modified Mon May 14 14:50:44 2007 UTC (17 years, 5 months ago) by duarte

FIXED BUG: pdb data load from msdsd wasn't working for NULL chaincodes

Revision 135 - Directory Listing
Modified Mon May 14 09:49:04 2007 UTC (17 years, 5 months ago) by duarte

NEW FUNCTIONALITY: reading of graph from db is fully implemented for all cases

New chain member variable in the Info classes, read in get_asym_id (Pdbase) and in get_chain_id (Msdsd)
Reading chain also in Pdb in read_pdb_data_from_file
Not reading chain anymore in read_atomData of PdbaseInfo
Added oneletter2threeletter and getoneletter2threeletter to AA class
Changes in Graph:
- added db static vars and getUserName method
- new member variables graphid and sm_id
- new method read_graph_from_db to read contacts, nodes (and sequence from nodes) from db
- new method getgraphid
New Exception class GraphIdNotFoundError

Revision 134 - Directory Listing
Modified Mon May 14 07:52:10 2007 UTC (17 years, 5 months ago) by duarte

Implemented basic reading contacts from file

Revision 133 - Directory Listing
Modified Fri May 11 09:37:38 2007 UTC (17 years, 5 months ago) by duarte

New functionality: now can create a Pdb object passing a model serial for NMR structures. Not implemented when reading from pdb files!

Revision 131 - Directory Listing
Modified Thu May 10 15:53:14 2007 UTC (17 years, 5 months ago) by duarte

2 new convenience methods: getBoolMatrix and getIntMatrix
Got rid of method to print constraint equations, was useless

Revision 130 - Directory Listing
Modified Thu May 10 15:52:24 2007 UTC (17 years, 5 months ago) by duarte

NEW FEATURE: reading pdb data from msdsd
New classes MsdsdInfo and its exception classes
FIXED BUG in dump2pdbfile in Pdb: was not sorting the atom lines

Revision 129 - Directory Listing
Modified Thu May 10 13:12:32 2007 UTC (17 years, 5 months ago) by duarte

NEW FUNCTIONALITY: can retrieve now a ContactMap object from a Graph object
New method getCM in Graph. New member variables: sequence, accode, chain, nodes, directed
Passing more data from Pdb to Graph in get_graph
New constructor in ContactMap

Revision 128 - Directory Listing
Modified Wed May 9 16:29:39 2007 UTC (17 years, 5 months ago) by duarte

ContactMap and EdgeState classes moved here from CMPredict repository

Revision 127 - Directory Listing
Modified Wed May 9 14:54:02 2007 UTC (17 years, 5 months ago) by duarte

Implemented read of pdb data from pdb file.
FIXED BUG in dumping of pdb file. Was missing end of line in atom lines
Added more tests in testPdb

Revision 126 - Directory Listing
Modified Wed May 9 12:04:35 2007 UTC (17 years, 5 months ago) by duarte

MYSQLUSER now taken from unix name with new getUserName method

Revision 124 - Directory Listing
Modified Wed May 9 11:57:24 2007 UTC (17 years, 5 months ago) by duarte

Added error handling for PdbaseInfo: 2 new exception classes

Revision 123 - Directory Listing
Added Wed May 9 10:45:53 2007 UTC (17 years, 5 months ago) by duarte

Initial commit of the proteinstructure package. Contains classes to use pdb protein structures