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Not forcing upper casing of chainPdbCode. pdb chain codes are case sensitive!!!
extracted constant NULL_CHAIN_CODE from ...Pdb classes, added copy() methods to NodeSet and EdgeSet, added some functionality to NodesAndEdges, new class SimilarityGraph
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
Fixed bug with getFullLength when reading from pdb file Now if SEQRES was missing then fullLength is maximum observed residue number instead of total number of observed residue numbers New member variables obsLength and fullLength
Fixed bug: wasn't taken into account OXT atoms in calculating the ALL graph
Added new SecondaryStructure object to Pdb and Graph
completed first version of dssp secondary structure assignment, can be switched on/off by status variable in Start, some other little fixes
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
Now throwing also SQLExceptions for individual queries, not just for connections
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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