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r229
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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)
Contact.java 224 (12 years ago) by duarte: Now calculate distance matrix uses HashMap instead of TreeMap Needed to change the hashCode function in Contact to make it faster
ContactList.java 178 (12 years ago) by duarte: Fixed bug in getMaxRange method, was not assigning to the max variable Added toString method to Contact
DbGraph.java 217 (12 years ago) by stehr: now casting pdb codes to lower and pdb chain codes to upper in all constructors
EdgeNbh.java 196 (12 years ago) by duarte: Added toString and getMotifFullGaps missing in EdgeNbh
FileGraph.java 212 (12 years ago) by duarte: Fixed bug in regex introduced in last revision
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
Graph.java 217 (12 years ago) by stehr: now casting pdb codes to lower and pdb chain codes to upper in all constructors
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
GraphIdNotFoundError.java 172 (12 years ago) by duarte: Got rid of some unnecessary warnings
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
MsdsdInconsistentResidueNumbersError.java 172 (12 years ago) by duarte: Got rid of some unnecessary warnings
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
NbhProbDistribution.java 199 (12 years ago) by duarte: Implemented getRanks()
NodeNbh.java 196 (12 years ago) by duarte: Added toString and getMotifFullGaps missing in EdgeNbh
Pdb.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
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
PdbaseInconsistencyError.java 172 (12 years ago) by duarte: Got rid of some unnecessary warnings
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
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
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
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