ViewVC Help
View Directory | Revision Log | Download Tarball | View Changeset | Root Listing
root/owl/trunk/proteinstructure
r410
File (rev) Last Change
 ../
contactTypes.dat 407 (11 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
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 407 (11 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
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)
PirFileFormatError.java 385 (11 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 (11 years ago) by duarte: Not forcing upper casing of chainPdbCode. pdb chain codes are case sensitive!!!
PdbfileFormatError.java 385 (11 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
PdbasePdb.java 401 (11 years ago) by duarte: Not forcing upper casing of chainPdbCode. pdb chain codes are case sensitive!!!
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 410 (11 years ago) by filippis: minor change
PairwiseSequenceAlignment.java 399 (11 years ago) by stehr: added class PairwiseSequenceAlignment
PairwiseAlignmentGraphConverter.java 385 (11 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
PairwiseAlignmentConverter.java 406 (11 years ago) by duarte: Reverting to last revision, changes made in 405 were wrong
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 394 (11 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)
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 401 (11 years ago) by duarte: Not forcing upper casing of chainPdbCode. pdb chain codes are case sensitive!!!
MsdsdInconsistentResidueNumbersError.java 172 (12 years ago) by duarte: Got rid of some unnecessary warnings
MaxClusterRunner.java 391 (11 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)
IntervalSet.java 405 (11 years ago) by duarte: Alignment and PairwiseAlignmentConverter now using Interval, IntervalSet and TreeSet<Integer> to replace Edge, EdgeSet and NodeSet New class IntervalSet
Interval.java 405 (11 years ago) by duarte: Alignment and PairwiseAlignmentConverter now using Interval, IntervalSet and TreeSet<Integer> to replace Edge, EdgeSet and NodeSet New class IntervalSet
GraphIdNotFoundError.java 172 (12 years ago) by duarte: Got rid of some unnecessary warnings
GraphFileFormatError.java 385 (11 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
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 407 (11 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
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
FileFormatError.java 385 (11 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
FastaFileFormatError.java 385 (11 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
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 407 (11 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
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 402 (11 years ago) by duarte: Forgot CiffilePdb!: not forcing upper casing of chainPdbCode. pdb chain codes are case sensitive!!!
CiffileFormatError.java 385 (11 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
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
AlignmentConstructionError.java 385 (11 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
Alignment.java 405 (11 years ago) by duarte: Alignment and PairwiseAlignmentConverter now using Interval, IntervalSet and TreeSet<Integer> to replace Edge, EdgeSet and NodeSet New class IntervalSet
AAinfo.java 372 (11 years ago) by lpetzo:
(Current path doesn't exist after revision 950)
         53 files shown