Revision 200 - (view) (annotate) - [select for diffs]
Modified Mon Jun 18 17:43:43 2007 UTC (17 years, 3 months ago) by duarte
File length: 13613 byte(s)
Diff to previous 198

New isValidCT methods in AA
New method get_resser_from_atomser in Pdb

Revision 198 - (view) (annotate) - [select for diffs]
Modified Mon Jun 18 08:47:26 2007 UTC (17 years, 3 months ago) by duarte
File length: 12408 byte(s)
Diff to previous 195

AA class is now db independent:
Hard coded getaas2atoms, not getting it anymore from db.

Revision 195 - (view) (annotate) - [select for diffs]
Modified Wed Jun 13 14:24:43 2007 UTC (17 years, 3 months ago) by duarte
File length: 6856 byte(s)
Diff to previous 194

Made contactTypes a String[]

Revision 194 - (view) (annotate) - [select for diffs]
Modified Wed Jun 13 10:57:00 2007 UTC (17 years, 3 months ago) by duarte
File length: 6981 byte(s)
Diff to previous 135

Added contactTypes method and made private methods private

Revision 135 - (view) (annotate) - [select for diffs]
Modified Mon May 14 09:49:04 2007 UTC (17 years, 4 months ago) by duarte
File length: 7097 byte(s)
Diff to previous 126

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 126 - (view) (annotate) - [select for diffs]
Modified Wed May 9 12:04:35 2007 UTC (17 years, 4 months ago) by duarte
File length: 6058 byte(s)
Diff to previous 123

MYSQLUSER now taken from unix name with new getUserName method

Revision 123 - (view) (annotate) - [select for diffs]
Added Wed May 9 10:45:53 2007 UTC (17 years, 4 months ago) by duarte
File length: 5763 byte(s)

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