Revision 250 - (view) (annotate) - [select for diffs]
Modified Mon Aug 6 14:48:37 2007 UTC (17 years, 6 months ago) by stehr
File length: 14984 byte(s)
Diff to previous 237

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

Revision 237 - (view) (annotate) - [select for diffs]
Modified Thu Jul 19 14:23:35 2007 UTC (17 years, 7 months ago) by duarte
File length: 14972 byte(s)
Diff to previous 226

Now rmsd calculation works for 2 Pdb objects where there are missing residues (unobserved) or missing atoms
New Exception ConformationNotSameSizeError
Still not printing out individual distances between 2 conformations (altghough it is possible)
Can't specify yet a restricted range of residues to calculate rmsd only with them

Revision 226 - (view) (annotate) - [select for diffs]
Modified Fri Jul 6 13:43:30 2007 UTC (17 years, 7 months ago) by duarte
File length: 14654 byte(s)
Diff to previous 222

First geometric hashing implementation for calculating graph (with new class Box). Only does non-crossed cts
Geometrich hashing graph calculation kept in a separate method than normal get_graph. Still either of the methods can be used.
Using javax.vectormath objects for the vectors (distance method also from that)
Using TreeMap for get_coords_for_ct

Revision 222 - (view) (annotate) - [select for diffs]
Modified Wed Jul 4 15:39:01 2007 UTC (17 years, 7 months ago) by duarte
File length: 14614 byte(s)
Diff to previous 219

New secstruct2resinterval TreeMap to store secondary structure elements as a map of ss string ids to intervals
New class Interval

Revision 219 - (view) (annotate) - [select for diffs]
Modified Tue Jul 3 15:38:21 2007 UTC (17 years, 7 months ago) by duarte
File length: 14145 byte(s)
Diff to previous 217

Now reading also secondary structure (in a map of residue serials to secondary structure identifiers)

Revision 217 - (view) (annotate) - [select for diffs]
Modified Fri Jun 29 09:04:00 2007 UTC (17 years, 8 months ago) by stehr
File length: 9946 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, 8 months ago) by stehr
File length: 9825 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, 8 months ago) by duarte
File length: 9865 byte(s)
Diff to previous 207

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

Revision 207 - (view) (annotate) - [select for diffs]
Added Wed Jun 27 11:06:34 2007 UTC (17 years, 8 months ago) by duarte
File length: 10120 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