Revision 609 - (view) (annotate) - [select for diffs]
Modified Wed Apr 30 14:11:50 2008 UTC (16 years, 5 months ago) by duarte
File length: 5981 byte(s)
Diff to previous 492

Extracted constant NULL_CHAIN_CODE that was still hard-coded in MANY places. Now should be safe to replace the value of the constant from "NULL" to something else.
Using TemplateList.readIdsListFile() in averageGraph, dumpseq and genGraph so that is now a standard way of reading list files with pdbcodes/chaincodes.
NOTE: this introduces an incompatibility with legacy list files: we can't read a NULL pdb chain code with the "NULL" string e.g. '1i1b NULL'. This is fine because since PDB-REMEDIATED all NULL chains are now "A".
Fixed a few things and made more standard the scripts dumpseq and genGraph

Revision 492 - (view) (annotate) - [select for diffs]
Modified Wed Jan 2 13:18:57 2008 UTC (16 years, 9 months ago) by duarte
File length: 5968 byte(s)
Copied from: branches/aglappe-jung/calculateGridDensity.java revision 491
Diff to previous 441

Copied the aglappe-jung branch into trunk.

Revision 441 - (view) (annotate) - [select for diffs]
Modified Thu Nov 29 15:19:37 2007 UTC (16 years, 10 months ago) by duarte
Original Path: branches/aglappe-jung/calculateGridDensity.java
File length: 5968 byte(s)
Diff to previous 419

Now Pdb constructors don't load data but rather intialise the pdbCode, loading occurs upon call of load(pdbChainCode,modelSerial)
New methods getChains() and getModels() in all Pdb classes
New Exception PdbLoadError
New tester for getChains and getModels: testGetChains
Changed all calls to Pdb construction accordingly (includes changing excpetions)

Revision 419 - (view) (annotate) - [select for diffs]
Modified Thu Nov 22 14:09:18 2007 UTC (16 years, 11 months ago) by duarte
Original Path: branches/aglappe-jung/calculateGridDensity.java
File length: 6000 byte(s)
Diff to previous 303

Re-branching for JUNG2 development

Revision 303 - (view) (annotate) - [select for diffs]
Modified Mon Aug 27 14:29:18 2007 UTC (17 years, 1 month ago) by stehr
File length: 6000 byte(s)
Diff to previous 250

added writeResultsToFile()

Revision 250 - (view) (annotate) - [select for diffs]
Added Mon Aug 6 14:48:37 2007 UTC (17 years, 2 months ago) by stehr
File length: 3357 byte(s)

added application to count grid density, suppressed warning for secondary structure reassignment