Revision 326 - (view) (annotate) - [select for diffs]
Modified Thu Sep 20 14:49:55 2007 UTC (17 years ago) by duarte
File length: 4876 byte(s)
Diff to previous 284

Removed class AA and replace it by AAinfo, which reads contact types from separate file contactTypes.dat
New class ContactType which contains atoms for each contact type and residue. A static object for each contact type is loaded into AAinfo upon reading the contactTypes.dat file
Changed all references accordingly

Revision 284 - (view) (annotate) - [select for diffs]
Modified Thu Aug 16 14:57:31 2007 UTC (17 years, 1 month ago) by duarte
File length: 4872 byte(s)
Diff to previous 234

Introduced weights in Graph objects: we can read them from file or db and write them into file or db. On calling pdb.get_graph the weighs are taken as number of atom-edges per residue-edge (similar to Ioannis weights in chain_graph tables)

Revision 234 - (view) (annotate) - [select for diffs]
Modified Tue Jul 10 14:14:58 2007 UTC (17 years, 2 months ago) by duarte
File length: 4592 byte(s)
Diff to previous 212

Made ContactList a TreeSet instead of an ArrayList, should improve performance (log(n) rather than linear)
REFACTORING: 
ContactList -> EdgeSet
Contact -> Edge

Revision 212 - (view) (annotate) - [select for diffs]
Modified Thu Jun 28 09:26:34 2007 UTC (17 years, 3 months ago) by duarte
File length: 4599 byte(s)
Diff to previous 211

Fixed bug in regex introduced in last revision

Revision 211 - (view) (annotate) - [select for diffs]
Modified Thu Jun 28 09:22:26 2007 UTC (17 years, 3 months ago) by duarte
File length: 4599 byte(s)
Diff to previous 209

Fixed graph file format checking, was not working properly

Revision 209 - (view) (annotate) - [select for diffs]
Modified Wed Jun 27 15:14:31 2007 UTC (17 years, 3 months ago) by duarte
File length: 4511 byte(s)
Diff to previous 208

Throwing exception also in case graph file not in right format at all (no #AGLAPPE in 1st line)
Fixed bug: was not reading correctly #PDB CHAIN CODE

Revision 208 - (view) (annotate) - [select for diffs]
Modified Wed Jun 27 14:42:12 2007 UTC (17 years, 3 months ago) by duarte
File length: 4300 byte(s)
Diff to previous 207

FIXED BUGS:
- directed was not set when reading from cm file
- pdbChainCode not set when reading from db given pdbCode
- filling pdbresser2resser and resser2pdbresser hashmaps also in reading from pdb file
- using "A" as chainCode when reading from pdb file
- some error handling for file formats: new exception classes GraphFileFormatError and PdbfileFormatError

Revision 207 - (view) (annotate) - [select for diffs]
Added Wed Jun 27 11:06:34 2007 UTC (17 years, 3 months ago) by duarte
File length: 4216 byte(s)

Restructured construction of Pdb and Graph objects: now subclasses for each case
Cleaned up and made consistent database connections
Now can also pass a MySQLConnection in all cases (as well as having default values for a default connection)
PdbaseInfo and MsdsdInfo classes removed: now merged into PdbasePdb and MsdsdPdb respectively
Updated following this changes testPdb and compareCMs