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r235
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Pdb.java 235 (12 years ago) by duarte: Implemented rmsd calculation (based on Jama matrix package) rmsd method still not taking care of unobserved or missing atoms. Also not returning individual distances between optimally superimposed structures (although it can calculate them in commented out code)
DbGraph.java 234 (12 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 (12 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 (12 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 (12 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 (12 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
NodeNbh.java 233 (12 years ago) by duarte: Added method getCopy
NodeSet.java 230 (12 years ago) by stehr: added class NodeSet
AA.java 229 (12 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
Box.java 228 (12 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)
MsdsdPdb.java 226 (12 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 (12 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 (12 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
Interval.java 222 (12 years ago) by duarte: New secstruct2resinterval TreeMap to store secondary structure elements as a map of ss string ids to intervals New class Interval
PdbChainCodeNotFoundError.java 215 (12 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 (12 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
GraphFileFormatError.java 208 (12 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 (12 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
NbhProbDistribution.java 199 (12 years ago) by duarte: Implemented getRanks()
EdgeNbh.java 196 (12 years ago) by duarte: Added toString and getMotifFullGaps missing in EdgeNbh
GenericContact.java 185 (12 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
MsdsdInconsistentResidueNumbersError.java 172 (12 years ago) by duarte: Got rid of some unnecessary warnings
GraphIdNotFoundError.java 172 (12 years ago) by duarte: Got rid of some unnecessary warnings
PdbaseInconsistencyError.java 172 (12 years ago) by duarte: Got rid of some unnecessary warnings
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