Revision 407 - (view) (annotate) - [select for diffs]
Modified Tue Nov 20 18:41:56 2007 UTC (16 years, 10 months ago) by filippis
File length: 11604 byte(s)
Diff to previous 361

contactTypes.dat 
-SC_CAGLY contact type added

SecStrucElement.java
-getSheetSerial method is now public

Pdb.java
-writeToDbFast added

Graph.java
-write_graph_to_db_fast
-expBB,CW,CT,CR,w,d are now taken into account in a correct way
-node_id, sssid, sheetSerial and turn are now also filled in

DbGraph.java
-expBB,CW,CT,CR,w,d are now taken into account in a correct way
-directionality is also taken into account now when reading edges

genDbGraph.java
-sequence separation added as option

createGraphDb.java added

Revision 361 - (view) (annotate) - [select for diffs]
Modified Wed Oct 17 17:40:18 2007 UTC (16 years, 11 months ago) by duarte
File length: 10215 byte(s)
Diff to previous 326

Now weights are kept in the Edge objects rather than separately in a member variable in Graph

Revision 326 - (view) (annotate) - [select for diffs]
Modified Thu Sep 20 14:49:55 2007 UTC (17 years ago) by duarte
File length: 10278 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: 10274 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: 10140 byte(s)
Diff to previous 217

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

Revision 217 - (view) (annotate) - [select for diffs]
Modified Fri Jun 29 09:04:00 2007 UTC (17 years, 3 months ago) by stehr
File length: 10147 byte(s)
Diff to previous 215

now casting pdb codes to lower and pdb chain codes to upper in all constructors

Revision 215 - (view) (annotate) - [select for diffs]
Modified Thu Jun 28 15:43:04 2007 UTC (17 years, 3 months ago) by stehr
File length: 10026 byte(s)
Diff to previous 210

some clean up of exceptions in Pdb and Graph classes:
merged PdbAcCodeNotFoundError and MsdAcCodeNotFoundError into PdbCodeNotFoundError,
created new PdbChainCodeNotFound, got rid of stderr output, throwing exceptions with informative messages instead

Revision 210 - (view) (annotate) - [select for diffs]
Modified Wed Jun 27 15:57:39 2007 UTC (17 years, 3 months ago) by duarte
File length: 10022 byte(s)
Diff to previous 208

Now throwing also SQLExceptions for individual queries, not just for connections

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: 10096 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: 9820 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