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r258
File Last Change (rev)
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PdbfilePdb.java 258 (12 years ago) by duarte: Now reading sequence from SEQRES lines. This fixes bug in cmview window was not showing whole contact map because of size of contact map was set to number of observed residues size
Pdb.java 257 (12 years ago) by stehr: fixed bugs in ATOM line export (atom names were wrongly aligned & added three more columns after coordinates), added method to run DSSP (still incomplete)
Graph.java 252 (12 years ago) by duarte: Made constructor public
MsdsdPdb.java 250 (12 years ago) by stehr: added application to count grid density, suppressed warning for secondary structure reassignment
Box.java 250 (12 years ago) by stehr: added application to count grid density, suppressed warning for secondary structure reassignment
PdbasePdb.java 250 (12 years ago) by stehr: added application to count grid density, suppressed warning for secondary structure reassignment
Alignment.java 248 (12 years ago) by duarte: Added method hasTag
NbhProbDistribution.java 242 (12 years ago) by duarte: Got rid of doneRes ArrayList in getRanks, was redundant
Edge.java 238 (12 years ago) by duarte: Optimised slightly the compareTo method in 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
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
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
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
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
(Current path doesn't exist after revision 950)
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