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r284
File (rev) Last Change
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SecondaryStructure.java 276 (12 years ago) by duarte: Added secondary structure to write_graph_to_db New method getNumSecStructureElements in SecondaryStructure
SecStrucElement.java 274 (12 years ago) by stehr: Added new SecondaryStructure object to Pdb and Graph
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
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
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
PdbaseInconsistencyError.java 172 (12 years ago) by duarte: Got rid of some unnecessary warnings
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
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
Pdb.java 284 (12 years ago) by duarte: Introduced weights in Graph objects: we can read them from file or db and write them into file or db. On calling pdb.get_graph the weighs are taken as number of atom-edges per residue-edge (similar to Ioannis weights in chain_graph tables)
NodeSet.java 230 (12 years ago) by stehr: added class NodeSet
NodeNbh.java 281 (12 years ago) by stehr: fixed little bug in NodeNbh
NbhProbDistribution.java 242 (12 years ago) by duarte: Got rid of doneRes ArrayList in getRanks, was redundant
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
MsdsdInconsistentResidueNumbersError.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
GraphIdNotFoundError.java 172 (12 years ago) by duarte: Got rid of some unnecessary warnings
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
Graph.java 284 (12 years ago) by duarte: Introduced weights in Graph objects: we can read them from file or db and write them into file or db. On calling pdb.get_graph the weighs are taken as number of atom-edges per residue-edge (similar to Ioannis weights in chain_graph tables)
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
FileGraph.java 284 (12 years ago) by duarte: Introduced weights in Graph objects: we can read them from file or db and write them into file or db. On calling pdb.get_graph the weighs are taken as number of atom-edges per residue-edge (similar to Ioannis weights in chain_graph tables)
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
EdgeNbh.java 196 (12 years ago) by duarte: Added toString and getMotifFullGaps missing in EdgeNbh
Edge.java 238 (12 years ago) by duarte: Optimised slightly the compareTo method in Edge
DbGraph.java 284 (12 years ago) by duarte: Introduced weights in Graph objects: we can read them from file or db and write them into file or db. On calling pdb.get_graph the weighs are taken as number of atom-edges per residue-edge (similar to Ioannis weights in chain_graph tables)
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
Box.java 282 (12 years ago) by duarte: Made get_graph a bit less memory hungry, by using a float[][] instead of double[][] Not printing warnings about missing atoms anymore
Alignment.java 248 (12 years ago) by duarte: Added method hasTag
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
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