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Fixed reading of SEQRES, was putting nulls for non-standard aas
completed first version of dssp secondary structure assignment, can be switched on/off by status variable in Start, some other little fixes
Now reading sequence from SEQRES lines. This fixes bug in cmview window was not showing whole contact map because of size of contact map was set to number of observed residues size
PdbfilePdb now also accepts Casp prediction files ('PFRMAT TS' instead of 'HEADER')
added application to count grid density, suppressed warning for secondary structure reassignment
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
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
New secstruct2resinterval TreeMap to store secondary structure elements as a map of ss string ids to intervals New class Interval
Now reading also secondary structure (in a map of residue serials to secondary structure identifiers)
now casting pdb codes to lower and pdb chain codes to upper in all constructors
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
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
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
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