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r236
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MsdsdInconsistentResidueNumbersError.java 172 (13 years ago) by duarte: Got rid of some unnecessary warnings
GraphIdNotFoundError.java 172 (13 years ago) by duarte: Got rid of some unnecessary warnings
PdbaseInconsistencyError.java 172 (13 years ago) by duarte: Got rid of some unnecessary warnings
GenericContact.java 185 (13 years ago) by duarte: Implemented hashCode method in Contact and GenericContact. Was necessary to use these classes as keys in Maps Fixed bug in equals method in GenericContact Changed middle character from "\t" to " " in toString
EdgeNbh.java 196 (13 years ago) by duarte: Added toString and getMotifFullGaps missing in EdgeNbh
NbhProbDistribution.java 199 (13 years ago) by duarte: Implemented getRanks()
GraphFileFormatError.java 208 (13 years ago) by duarte: 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
PdbfileFormatError.java 208 (13 years ago) by duarte: 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
PdbChainCodeNotFoundError.java 215 (13 years ago) by stehr: 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
PdbCodeNotFoundError.java 215 (13 years ago) by stehr: 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
Interval.java 222 (13 years ago) by duarte: New secstruct2resinterval TreeMap to store secondary structure elements as a map of ss string ids to intervals New class Interval
MsdsdPdb.java 226 (13 years ago) by duarte: 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
PdbasePdb.java 226 (13 years ago) by duarte: 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
PdbfilePdb.java 226 (13 years ago) by duarte: 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
Box.java 228 (13 years ago) by duarte: Now can do crossed contacts also with geometric hashing Renamed getGraphGeometricHashing to get_graph (so interface remains as it was before we introduced the geometric hashing)
AA.java 229 (13 years ago) by duarte: Now calculate_dist_matrix returns the matrix with residue serials as indices (rather than atom serials) Now AA.isValidSingleCT and AA.isValidMultiCT check also for crossed cases
NodeSet.java 230 (13 years ago) by stehr: added class NodeSet
NodeNbh.java 233 (13 years ago) by duarte: Added method getCopy
DbGraph.java 234 (13 years ago) by duarte: Made ContactList a TreeSet instead of an ArrayList, should improve performance (log(n) rather than linear) REFACTORING: ContactList -> EdgeSet Contact -> Edge
Graph.java 234 (13 years ago) by duarte: Made ContactList a TreeSet instead of an ArrayList, should improve performance (log(n) rather than linear) REFACTORING: ContactList -> EdgeSet Contact -> Edge
FileGraph.java 234 (13 years ago) by duarte: Made ContactList a TreeSet instead of an ArrayList, should improve performance (log(n) rather than linear) REFACTORING: ContactList -> EdgeSet Contact -> Edge
EdgeSet.java 234 (13 years ago) by duarte: Made ContactList a TreeSet instead of an ArrayList, should improve performance (log(n) rather than linear) REFACTORING: ContactList -> EdgeSet Contact -> Edge
Edge.java 234 (13 years ago) by duarte: Made ContactList a TreeSet instead of an ArrayList, should improve performance (log(n) rather than linear) REFACTORING: ContactList -> EdgeSet Contact -> Edge
Pdb.java 236 (13 years ago) by duarte: Fixed bug. Was not doing correctly reflection along smallest principal axis in is_reflection case
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