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r412
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AAinfo.java 372 (12 years ago) by lpetzo:
Alignment.java 405 (12 years ago) by duarte: Alignment and PairwiseAlignmentConverter now using Interval, IntervalSet and TreeSet<Integer> to replace Edge, EdgeSet and NodeSet New class IntervalSet
AlignmentConstructionError.java 385 (12 years ago) by lpetzo: NEW TYPES --------- - FileFormatError - FastaFileFormatError - PirFileFormatError - AlignmentConstructionError MODIFICATIONS ------------- class Alignment: - introduced new exceptions to be throw whenever file format error have been detected or any other construction errors occur - changed accession rules of function getGapCharacter from "public" to "public static" - new functions: * writeFasta class CiffileFormatError: - changed super class from Exception to the new FileFormatError class class GraphFileFormatError: - s. class CiffileFormatError class PairwiseAlignmentConverter: - added exception handling features due to class Alignment class PairwiseAlignmentGraphConverter: - s. class PairwiseAlignmentConverter class PdbFileFormatError: - s. class CifffileFormatError
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
CatalSiteSet.java 382 (12 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
CatalyticSite.java 382 (12 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
CiffileFormatError.java 385 (12 years ago) by lpetzo: NEW TYPES --------- - FileFormatError - FastaFileFormatError - PirFileFormatError - AlignmentConstructionError MODIFICATIONS ------------- class Alignment: - introduced new exceptions to be throw whenever file format error have been detected or any other construction errors occur - changed accession rules of function getGapCharacter from "public" to "public static" - new functions: * writeFasta class CiffileFormatError: - changed super class from Exception to the new FileFormatError class class GraphFileFormatError: - s. class CiffileFormatError class PairwiseAlignmentConverter: - added exception handling features due to class Alignment class PairwiseAlignmentGraphConverter: - s. class PairwiseAlignmentConverter class PdbFileFormatError: - s. class CifffileFormatError
CiffilePdb.java 402 (12 years ago) by duarte: Forgot CiffilePdb!: not forcing upper casing of chainPdbCode. pdb chain codes are case sensitive!!!
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
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
DbGraph.java 407 (12 years ago) by filippis: contactTypes.dat -SC_CAGLY contact type added SecStrucElement.java -getSheetSerial method is now public Pdb.java -writeToDbFast added Graph.java -write_graph_to_db_fast -expBB,CW,CT,CR,w,d are now taken into account in a correct way -node_id, sssid, sheetSerial and turn are now also filled in DbGraph.java -expBB,CW,CT,CR,w,d are now taken into account in a correct way -directionality is also taken into account now when reading edges genDbGraph.java -sequence separation added as option createGraphDb.java added
EC.java 382 (12 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
ECRegion.java 382 (12 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
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.
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
EdgeSet.java 372 (12 years ago) by lpetzo:
FastaFileFormatError.java 385 (12 years ago) by lpetzo: NEW TYPES --------- - FileFormatError - FastaFileFormatError - PirFileFormatError - AlignmentConstructionError MODIFICATIONS ------------- class Alignment: - introduced new exceptions to be throw whenever file format error have been detected or any other construction errors occur - changed accession rules of function getGapCharacter from "public" to "public static" - new functions: * writeFasta class CiffileFormatError: - changed super class from Exception to the new FileFormatError class class GraphFileFormatError: - s. class CiffileFormatError class PairwiseAlignmentConverter: - added exception handling features due to class Alignment class PairwiseAlignmentGraphConverter: - s. class PairwiseAlignmentConverter class PdbFileFormatError: - s. class CifffileFormatError
FileFormatError.java 385 (12 years ago) by lpetzo: NEW TYPES --------- - FileFormatError - FastaFileFormatError - PirFileFormatError - AlignmentConstructionError MODIFICATIONS ------------- class Alignment: - introduced new exceptions to be throw whenever file format error have been detected or any other construction errors occur - changed accession rules of function getGapCharacter from "public" to "public static" - new functions: * writeFasta class CiffileFormatError: - changed super class from Exception to the new FileFormatError class class GraphFileFormatError: - s. class CiffileFormatError class PairwiseAlignmentConverter: - added exception handling features due to class Alignment class PairwiseAlignmentGraphConverter: - s. class PairwiseAlignmentConverter class PdbFileFormatError: - s. class CifffileFormatError
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
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 407 (12 years ago) by filippis: contactTypes.dat -SC_CAGLY contact type added SecStrucElement.java -getSheetSerial method is now public Pdb.java -writeToDbFast added Graph.java -write_graph_to_db_fast -expBB,CW,CT,CR,w,d are now taken into account in a correct way -node_id, sssid, sheetSerial and turn are now also filled in DbGraph.java -expBB,CW,CT,CR,w,d are now taken into account in a correct way -directionality is also taken into account now when reading edges genDbGraph.java -sequence separation added as option createGraphDb.java added
GraphAverager.java 379 (12 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
GraphFileFormatError.java 385 (12 years ago) by lpetzo: NEW TYPES --------- - FileFormatError - FastaFileFormatError - PirFileFormatError - AlignmentConstructionError MODIFICATIONS ------------- class Alignment: - introduced new exceptions to be throw whenever file format error have been detected or any other construction errors occur - changed accession rules of function getGapCharacter from "public" to "public static" - new functions: * writeFasta class CiffileFormatError: - changed super class from Exception to the new FileFormatError class class GraphFileFormatError: - s. class CiffileFormatError class PairwiseAlignmentConverter: - added exception handling features due to class Alignment class PairwiseAlignmentGraphConverter: - s. class PairwiseAlignmentConverter class PdbFileFormatError: - s. class CifffileFormatError
GraphIdNotFoundError.java 172 (12 years ago) by duarte: Got rid of some unnecessary warnings
Interval.java 405 (12 years ago) by duarte: Alignment and PairwiseAlignmentConverter now using Interval, IntervalSet and TreeSet<Integer> to replace Edge, EdgeSet and NodeSet New class IntervalSet
IntervalSet.java 405 (12 years ago) by duarte: Alignment and PairwiseAlignmentConverter now using Interval, IntervalSet and TreeSet<Integer> to replace Edge, EdgeSet and NodeSet New class IntervalSet
MaxClusterRunner.java 391 (12 years ago) by stehr: started implementing a wrapper for the Maxcluster application (some related code is now in SimilarityGraph but should be moved to MaxClusterRunner in the future)
MsdsdInconsistentResidueNumbersError.java 172 (12 years ago) by duarte: Got rid of some unnecessary warnings
MsdsdPdb.java 401 (12 years ago) by duarte: Not forcing upper casing of chainPdbCode. pdb chain codes are case sensitive!!!
NbhProbDistribution.java 242 (12 years ago) by duarte: Got rid of doneRes ArrayList in getRanks, was redundant
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.
NodeNbh.java 394 (12 years ago) by duarte: New method getMotifReducedAlphabet to get neighbourhood strings in Michael's reduced style (must pass a Graph with weights which indicate BB or SC domination)
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.
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.
PairwiseAlignmentConverter.java 406 (12 years ago) by duarte: Reverting to last revision, changes made in 405 were wrong
PairwiseAlignmentGraphConverter.java 385 (12 years ago) by lpetzo: NEW TYPES --------- - FileFormatError - FastaFileFormatError - PirFileFormatError - AlignmentConstructionError MODIFICATIONS ------------- class Alignment: - introduced new exceptions to be throw whenever file format error have been detected or any other construction errors occur - changed accession rules of function getGapCharacter from "public" to "public static" - new functions: * writeFasta class CiffileFormatError: - changed super class from Exception to the new FileFormatError class class GraphFileFormatError: - s. class CiffileFormatError class PairwiseAlignmentConverter: - added exception handling features due to class Alignment class PairwiseAlignmentGraphConverter: - s. class PairwiseAlignmentConverter class PdbFileFormatError: - s. class CifffileFormatError
PairwiseSequenceAlignment.java 399 (12 years ago) by stehr: added class PairwiseSequenceAlignment
Pdb.java 412 (12 years ago) by filippis: Changes in Pdb -checkConsurfHssp: in the mistakes calculated I add now at the end the difference between the number of residues and the number of consurf scores -writeAtomLines has now a boolean argument called pdbCompatible: if pdbCompatible is true, then only the first character of chainCode and not the 'whole' chainCode is exported to the file. -another WriteAtomLines has also been added without this extra argument for backwards compatibility: default value for pdbCompatible is false -dump2pdbfile has also been changed in similar way -runDssp and runNaccess now call the above methods with true pdbCompatible Changes in genDbGraph -1 summary output line has been added to provide info about csa, naccess, scop, ec, dssp, ... -DSSP is run with 3state
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 401 (12 years ago) by duarte: Not forcing upper casing of chainPdbCode. pdb chain codes are case sensitive!!!
PdbfileFormatError.java 385 (12 years ago) by lpetzo: NEW TYPES --------- - FileFormatError - FastaFileFormatError - PirFileFormatError - AlignmentConstructionError MODIFICATIONS ------------- class Alignment: - introduced new exceptions to be throw whenever file format error have been detected or any other construction errors occur - changed accession rules of function getGapCharacter from "public" to "public static" - new functions: * writeFasta class CiffileFormatError: - changed super class from Exception to the new FileFormatError class class GraphFileFormatError: - s. class CiffileFormatError class PairwiseAlignmentConverter: - added exception handling features due to class Alignment class PairwiseAlignmentGraphConverter: - s. class PairwiseAlignmentConverter class PdbFileFormatError: - s. class CifffileFormatError
PdbfilePdb.java 401 (12 years ago) by duarte: Not forcing upper casing of chainPdbCode. pdb chain codes are case sensitive!!!
PirFileFormatError.java 385 (12 years ago) by lpetzo: NEW TYPES --------- - FileFormatError - FastaFileFormatError - PirFileFormatError - AlignmentConstructionError MODIFICATIONS ------------- class Alignment: - introduced new exceptions to be throw whenever file format error have been detected or any other construction errors occur - changed accession rules of function getGapCharacter from "public" to "public static" - new functions: * writeFasta class CiffileFormatError: - changed super class from Exception to the new FileFormatError class class GraphFileFormatError: - s. class CiffileFormatError class PairwiseAlignmentConverter: - added exception handling features due to class Alignment class PairwiseAlignmentGraphConverter: - s. class PairwiseAlignmentConverter class PdbFileFormatError: - s. class CifffileFormatError
PredEval.java 362 (12 years ago) by stehr: renamed precision to accuracy (in accordance with Casp)
Scop.java 382 (12 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 (12 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
SecStrucElement.java 407 (12 years ago) by filippis: contactTypes.dat -SC_CAGLY contact type added SecStrucElement.java -getSheetSerial method is now public Pdb.java -writeToDbFast added Graph.java -write_graph_to_db_fast -expBB,CW,CT,CR,w,d are now taken into account in a correct way -node_id, sssid, sheetSerial and turn are now also filled in DbGraph.java -expBB,CW,CT,CR,w,d are now taken into account in a correct way -directionality is also taken into account now when reading edges genDbGraph.java -sequence separation added as option createGraphDb.java added
SecondaryStructure.java 276 (12 years ago) by duarte: Added secondary structure to write_graph_to_db New method getNumSecStructureElements in SecondaryStructure
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.
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"
contactTypes.dat 407 (12 years ago) by filippis: contactTypes.dat -SC_CAGLY contact type added SecStrucElement.java -getSheetSerial method is now public Pdb.java -writeToDbFast added Graph.java -write_graph_to_db_fast -expBB,CW,CT,CR,w,d are now taken into account in a correct way -node_id, sssid, sheetSerial and turn are now also filled in DbGraph.java -expBB,CW,CT,CR,w,d are now taken into account in a correct way -directionality is also taken into account now when reading edges genDbGraph.java -sequence separation added as option createGraphDb.java added
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