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r382
File (rev) Last Change
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contactTypes.dat 326 (12 years ago) by duarte: Removed class AA and replace it by AAinfo, which reads contact types from separate file contactTypes.dat New class ContactType which contains atoms for each contact type and residue. A static object for each contact type is loaded into AAinfo upon reading the contactTypes.dat file Changed all references accordingly
aapairsBounds.dat 335 (12 years ago) by duarte: Now ConstraintsMaker works also for multi atom contact types (BB and SC) and crosses (either BB/SC or any cross to a single atom contact type) New file aapairsBounds.dat with values for aminoacid side chains distance lower and upper bounds taken from statistics of a set of pdb representatives New in AAinfo: aapairs2bounds and changed getUpperBoundDistance, getUpperBoundDistance to accomodate aapairs2bounds PRMInfo: now for amber "OXT" gets transformed into "O"
SimilarityGraph.java 352 (12 years ago) by stehr: Major redesign of NodeSet, now contains objects of new class Node. Nodes are essentially integer which can have additional properties. Added equals methods to NodeSet, EdgeSet, NodesAndEdges. Moved some methods from SimilarityGraph to NodesAndEdges.
SecondaryStructure.java 276 (12 years ago) by duarte: Added secondary structure to write_graph_to_db New method getNumSecStructureElements in SecondaryStructure
SecStrucElement.java 382 (11 years ago) by filippis: Methods added for: -parsing CSA -parsing EC -parsing CONSURF-HSSP -running & parsing Naccess -parsing SCOP -writing residues' info in a db table Modifications have been also made in DSSP parsing: -sheet serial is taken into account -flexibility in reduced state preferred
ScopRegion.java 382 (11 years ago) by filippis: Methods added for: -parsing CSA -parsing EC -parsing CONSURF-HSSP -running & parsing Naccess -parsing SCOP -writing residues' info in a db table Modifications have been also made in DSSP parsing: -sheet serial is taken into account -flexibility in reduced state preferred
Scop.java 382 (11 years ago) by filippis: Methods added for: -parsing CSA -parsing EC -parsing CONSURF-HSSP -running & parsing Naccess -parsing SCOP -writing residues' info in a db table Modifications have been also made in DSSP parsing: -sheet serial is taken into account -flexibility in reduced state preferred
PredEval.java 362 (12 years ago) by stehr: renamed precision to accuracy (in accordance with Casp)
PdbfilePdb.java 360 (12 years ago) by stehr: Graph,PredEval: added fields coverage and title to predEval (and evalPrediction) GraphAverager: added method to return average graph (with weighted edges) PdbfilePdb: fixed bug when reading from Casp prediction files
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 336 (12 years ago) by stehr: extracted constant NULL_CHAIN_CODE from ...Pdb classes, added copy() methods to NodeSet and EdgeSet, added some functionality to NodesAndEdges, new class SimilarityGraph
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 382 (11 years ago) by filippis: Methods added for: -parsing CSA -parsing EC -parsing CONSURF-HSSP -running & parsing Naccess -parsing SCOP -writing residues' info in a db table Modifications have been also made in DSSP parsing: -sheet serial is taken into account -flexibility in reduced state preferred
PairwiseAlignmentGraphConverter.java 372 (11 years ago) by lpetzo:
PairwiseAlignmentConverter.java 372 (11 years ago) by lpetzo:
NodesAndEdges.java 352 (12 years ago) by stehr: Major redesign of NodeSet, now contains objects of new class Node. Nodes are essentially integer which can have additional properties. Added equals methods to NodeSet, EdgeSet, NodesAndEdges. Moved some methods from SimilarityGraph to NodesAndEdges.
NodeSet.java 352 (12 years ago) by stehr: Major redesign of NodeSet, now contains objects of new class Node. Nodes are essentially integer which can have additional properties. Added equals methods to NodeSet, EdgeSet, NodesAndEdges. Moved some methods from SimilarityGraph to NodesAndEdges.
NodeNbh.java 326 (12 years ago) by duarte: Removed class AA and replace it by AAinfo, which reads contact types from separate file contactTypes.dat New class ContactType which contains atoms for each contact type and residue. A static object for each contact type is loaded into AAinfo upon reading the contactTypes.dat file Changed all references accordingly
Node.java 352 (12 years ago) by stehr: Major redesign of NodeSet, now contains objects of new class Node. Nodes are essentially integer which can have additional properties. Added equals methods to NodeSet, EdgeSet, NodesAndEdges. Moved some methods from SimilarityGraph to NodesAndEdges.
NbhProbDistribution.java 242 (12 years ago) by duarte: Got rid of doneRes ArrayList in getRanks, was redundant
MsdsdPdb.java 336 (12 years ago) by stehr: extracted constant NULL_CHAIN_CODE from ...Pdb classes, added copy() methods to NodeSet and EdgeSet, added some functionality to NodesAndEdges, new class SimilarityGraph
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
GraphAverager.java 379 (11 years ago) by stehr: redesign of TinkerRunner: added 2 reconstruct methods, one which generates normal tinker output for a given number of models, and one fully automatic one which simply returns one pdb object; updated reconstruct.java to make use of the new TinkerRunner method; updated GraphAverager: now assigning edgetype and cutoff to consensus graph
Graph.java 378 (11 years ago) by stehr: finally implemented the setCutoff method ;)
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 361 (12 years ago) by duarte: Now weights are kept in the Edge objects rather than separately in a member variable in Graph
EdgeSet.java 372 (11 years ago) by lpetzo:
EdgeNbh.java 326 (12 years ago) by duarte: Removed class AA and replace it by AAinfo, which reads contact types from separate file contactTypes.dat New class ContactType which contains atoms for each contact type and residue. A static object for each contact type is loaded into AAinfo upon reading the contactTypes.dat file Changed all references accordingly
Edge.java 352 (12 years ago) by stehr: Major redesign of NodeSet, now contains objects of new class Node. Nodes are essentially integer which can have additional properties. Added equals methods to NodeSet, EdgeSet, NodesAndEdges. Moved some methods from SimilarityGraph to NodesAndEdges.
ECRegion.java 382 (11 years ago) by filippis: Methods added for: -parsing CSA -parsing EC -parsing CONSURF-HSSP -running & parsing Naccess -parsing SCOP -writing residues' info in a db table Modifications have been also made in DSSP parsing: -sheet serial is taken into account -flexibility in reduced state preferred
EC.java 382 (11 years ago) by filippis: Methods added for: -parsing CSA -parsing EC -parsing CONSURF-HSSP -running & parsing Naccess -parsing SCOP -writing residues' info in a db table Modifications have been also made in DSSP parsing: -sheet serial is taken into account -flexibility in reduced state preferred
DbGraph.java 361 (12 years ago) by duarte: Now weights are kept in the Edge objects rather than separately in a member variable in Graph
ContactType.java 326 (12 years ago) by duarte: Removed class AA and replace it by AAinfo, which reads contact types from separate file contactTypes.dat New class ContactType which contains atoms for each contact type and residue. A static object for each contact type is loaded into AAinfo upon reading the contactTypes.dat file Changed all references accordingly
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
CiffilePdb.java 357 (12 years ago) by duarte: Fixed bug: now does correctly quoting for any of the 3 cases: "", '' or ;;. Does also correctly multiline parsing of ;; quoted fields. Passed testing on cullpdb 90 (more than 9000 pdb entries)
CiffileFormatError.java 314 (12 years ago) by duarte: Checking number of fields per line in loop elements and throwing exception if count is not correect Doing tokenisation of lines through new function that takes care of possible quoted string with spaces New exception CiffileFormatError Checking 1st line of cif file has correct format: data_1xxx, if not throwing exception
CatalyticSite.java 382 (11 years ago) by filippis: Methods added for: -parsing CSA -parsing EC -parsing CONSURF-HSSP -running & parsing Naccess -parsing SCOP -writing residues' info in a db table Modifications have been also made in DSSP parsing: -sheet serial is taken into account -flexibility in reduced state preferred
CatalSiteSet.java 382 (11 years ago) by filippis: Methods added for: -parsing CSA -parsing EC -parsing CONSURF-HSSP -running & parsing Naccess -parsing SCOP -writing residues' info in a db table Modifications have been also made in DSSP parsing: -sheet serial is taken into account -flexibility in reduced state preferred
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 372 (11 years ago) by lpetzo:
AAinfo.java 372 (11 years ago) by lpetzo:
(Current path doesn't exist after revision 950)
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