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r273
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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
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
EdgeNbh.java 196 (12 years ago) by duarte: Added toString and getMotifFullGaps missing in EdgeNbh
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
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
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
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
NodeSet.java 230 (12 years ago) by stehr: added class NodeSet
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
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
ConformationsNotSameSizeError.java 237 (12 years ago) by duarte: 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
Edge.java 238 (12 years ago) by duarte: Optimised slightly the compareTo method in Edge
NbhProbDistribution.java 242 (12 years ago) by duarte: Got rid of doneRes ArrayList in getRanks, was redundant
Alignment.java 248 (12 years ago) by duarte: Added method hasTag
Box.java 250 (12 years ago) by stehr: added application to count grid density, suppressed warning for secondary structure reassignment
MsdsdPdb.java 259 (12 years ago) by stehr: completed first version of dssp secondary structure assignment, can be switched on/off by status variable in Start, some other little fixes
PdbasePdb.java 259 (12 years ago) by stehr: completed first version of dssp secondary structure assignment, can be switched on/off by status variable in Start, some other little fixes
SecStrucElement.java 259 (12 years ago) by stehr: completed first version of dssp secondary structure assignment, can be switched on/off by status variable in Start, some other little fixes
Pdb.java 260 (12 years ago) by duarte: Implemented write_graph_to_db New member variable model in Graph, thus changed constructor New methods to get degree of a node in Graph New methos in NodeNbh to write other kinds of neighbourhood strings
NodeNbh.java 260 (12 years ago) by duarte: Implemented write_graph_to_db New member variable model in Graph, thus changed constructor New methods to get degree of a node in Graph New methos in NodeNbh to write other kinds of neighbourhood strings
Graph.java 260 (12 years ago) by duarte: Implemented write_graph_to_db New member variable model in Graph, thus changed constructor New methods to get degree of a node in Graph New methos in NodeNbh to write other kinds of neighbourhood strings
PdbfilePdb.java 263 (12 years ago) by duarte: Fixed potential bug in regex for ATOM lines
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