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r279
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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
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
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
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
Edge.java 238 (12 years ago) by duarte: Optimised slightly the compareTo method in Edge
EdgeNbh.java 196 (12 years ago) by duarte: Added toString and getMotifFullGaps missing in EdgeNbh
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
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
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 279 (12 years ago) by duarte: Fixed bug in Graph constructor: was not getting correct fullLength (related to last bug fix)
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 278 (12 years ago) by duarte: 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
NbhProbDistribution.java 242 (12 years ago) by duarte: Got rid of doneRes ArrayList in getRanks, was redundant
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
NodeSet.java 230 (12 years ago) by stehr: added class NodeSet
Pdb.java 278 (12 years ago) by duarte: 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
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 278 (12 years ago) by duarte: 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
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 278 (12 years ago) by duarte: 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
SecStrucElement.java 274 (12 years ago) by stehr: Added new SecondaryStructure object to Pdb and Graph
SecondaryStructure.java 276 (12 years ago) by duarte: Added secondary structure to write_graph_to_db New method getNumSecStructureElements in SecondaryStructure
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