 ../
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AAinfo.java
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520
(16 years ago)
by duarte:
Fixed to be able to run CMView under Abbot (because of abbot getResourceAsStream bug). The ABBOT_FIX flag is turned off.
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AIGEdge.java
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492
(16 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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AIGNode.java
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492
(16 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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AIGraph.java
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503
(16 years ago)
by filippis:
createGraphDb:
-scop_graph table added
-!!!!residue serial fields (num, i_num, j_num) are changed to unsigned
!!!!ProtStructGraph:
-interSSE variable added
-getResidueSerial abstract method added
-restrictContactsBetweenSs method added
!!!!AIGraph:
-getResidueSerial method added
RIGraph:
-!!!!getResidueSerial method added
-scop graphs are written to db correctly
-interSSE variable taken into account for CR db field
DbRIgraph:
-changes made so to be able to read from db using a scop id
-interSSE and minSeqSep are set now in get_db_graph_info()
-!!!!FIXED BUG:fullLength in read_graph_from_db is not set to the size of the serials2nodes TreeMap instead of the maximum serial in serials2nodes. It was giving wrong result for scop graphs.
testDbRIGraph added:
It reads one graph from a source db based either
-on pdbcode, chaincode and graph properties or
-on scop id and graph properties or
-on a graph id
and it writes the graph to a destination db.
Pdb:
-unused scop regions are now removed in restrictToScopDomain
-unused residues are also removed from resser2pdbresser, pdbresser2resser, resser2allrsa, resser2scrsa, resser2consurfhsspscore, resser2consurfhsspcolor, catalSiteSet
-!!!!sequence is reset to scop sequence and fullLength to the length of the scop sequence
CatalSiteSet:
- removeCatalSiteRes(int resser) method added
CatalyticSite:
-remRes(int resser) method added
Scop:
-remove(ScopRegion e) method added
genDbGraph:Comments only added to demonstrate new functionality.
-comment added to show how to use restrictContactsBetweenSs
-comment added to show how to use restrictToScopDomain
-runDssp now is always run and not only when mode != "GRAPH". This has been changed since now the contact range might depend on the ss assignment (restrictContactsBetweenSs) and we want to ensure consistent results
-runNaccess moved to the bottom so it is always run last. In this way if restrictToScopDomain is used, we don't have to run naccess twice.
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Alignment.java
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517
(16 years ago)
by duarte:
Changed Alignment class so that both alignment and sequence indexing are starting at 1 (before alignment indices were starting at 0). Also mapping is now done through arrays not maps.
Changed all other classes using Alignment to accommodate this.
NOTE: graph averaging hasn't been tested after the change
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AlignmentConstructionError.java
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492
(16 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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Box.java
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492
(16 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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CaspRRFileData.java
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492
(16 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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CaspRRFileRIGraph.java
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497
(16 years ago)
by duarte:
Extracted some constants: NO_PDB_CODE, NO_PDB_CHAIN_CODE, NO_CONTACT_TYPE, NO_CUTOFF
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CatalSiteSet.java
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514
(16 years ago)
by filippis:
Latest scop and csa versions updated.
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CatalyticSite.java
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503
(16 years ago)
by filippis:
createGraphDb:
-scop_graph table added
-!!!!residue serial fields (num, i_num, j_num) are changed to unsigned
!!!!ProtStructGraph:
-interSSE variable added
-getResidueSerial abstract method added
-restrictContactsBetweenSs method added
!!!!AIGraph:
-getResidueSerial method added
RIGraph:
-!!!!getResidueSerial method added
-scop graphs are written to db correctly
-interSSE variable taken into account for CR db field
DbRIgraph:
-changes made so to be able to read from db using a scop id
-interSSE and minSeqSep are set now in get_db_graph_info()
-!!!!FIXED BUG:fullLength in read_graph_from_db is not set to the size of the serials2nodes TreeMap instead of the maximum serial in serials2nodes. It was giving wrong result for scop graphs.
testDbRIGraph added:
It reads one graph from a source db based either
-on pdbcode, chaincode and graph properties or
-on scop id and graph properties or
-on a graph id
and it writes the graph to a destination db.
Pdb:
-unused scop regions are now removed in restrictToScopDomain
-unused residues are also removed from resser2pdbresser, pdbresser2resser, resser2allrsa, resser2scrsa, resser2consurfhsspscore, resser2consurfhsspcolor, catalSiteSet
-!!!!sequence is reset to scop sequence and fullLength to the length of the scop sequence
CatalSiteSet:
- removeCatalSiteRes(int resser) method added
CatalyticSite:
-remRes(int resser) method added
Scop:
-remove(ScopRegion e) method added
genDbGraph:Comments only added to demonstrate new functionality.
-comment added to show how to use restrictContactsBetweenSs
-comment added to show how to use restrictToScopDomain
-runDssp now is always run and not only when mode != "GRAPH". This has been changed since now the contact range might depend on the ss assignment (restrictContactsBetweenSs) and we want to ensure consistent results
-runNaccess moved to the bottom so it is always run last. In this way if restrictToScopDomain is used, we don't have to run naccess twice.
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CiffileFormatError.java
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492
(16 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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CiffilePdb.java
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492
(16 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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ConformationsNotSameSizeError.java
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492
(16 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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ContactType.java
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492
(16 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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DbRIGraph.java
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513
(16 years ago)
by filippis:
Fixing the fixed bug!
-if graph read is chain graph, then fullLength is set to the maximum observed residue serial
-else if graph is scop graph, then fullLength is set to the number of observed residues
NOTE:In the case of a wholechain scop graph, there might be inconsistensy between a graph I created with Pdb/RIGraph classes and stored in db and the corresponding graph i read from db. Specifically, the fullLength of graph I equals the length of the chain while the fullLength of graph i equals the number of observed residues.
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EC.java
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502
(16 years ago)
by stehr:
EC, CatalSiteSet: added typing to some iterators to avoid eclipse warning
Interval: added typing to Comparator to avoid eclipse warning
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ECRegion.java
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492
(16 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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FastaFileFormatError.java
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492
(16 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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FileFormatError.java
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492
(16 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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FileRIGraph.java
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497
(16 years ago)
by duarte:
Extracted some constants: NO_PDB_CODE, NO_PDB_CHAIN_CODE, NO_CONTACT_TYPE, NO_CUTOFF
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FileTypeGuesser.java
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492
(16 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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GraphFileFormatError.java
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492
(16 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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GraphIODb.java
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492
(16 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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GraphIOGDLFile.java
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492
(16 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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GraphIdNotFoundError.java
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492
(16 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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IntPairComparator.java
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492
(16 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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IntPairSet.java
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492
(16 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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Interval.java
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515
(16 years ago)
by stehr:
Interval: allow spaces in residue selection strings
RIGNbhood: added method getNeighbors
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IntervalSet.java
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492
(16 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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MaxClusterRunner.java
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492
(16 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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MsdsdInconsistentResidueNumbersError.java
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492
(16 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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MsdsdPdb.java
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492
(16 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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NbhProbDistribution.java
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492
(16 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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NbhoodBackgrnd.java
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492
(16 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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PairwiseAlignmentConverter.java
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517
(16 years ago)
by duarte:
Changed Alignment class so that both alignment and sequence indexing are starting at 1 (before alignment indices were starting at 0). Also mapping is now done through arrays not maps.
Changed all other classes using Alignment to accommodate this.
NOTE: graph averaging hasn't been tested after the change
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PairwiseSequenceAlignment.java
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499
(16 years ago)
by duarte:
Got rid of check for equality of tags
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Pdb.java
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518
(16 years ago)
by filippis:
checkConsurf: if the file is not found and the chain code given is "A", we check now also for results for NULL chain code
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PdbChainCodeNotFoundError.java
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492
(16 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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PdbCodeNotFoundError.java
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492
(16 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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PdbLoadError.java
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492
(16 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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PdbaseInconsistencyError.java
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492
(16 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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PdbasePdb.java
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492
(16 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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PdbfileFormatError.java
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492
(16 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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PdbfilePdb.java
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492
(16 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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PirFileFormatError.java
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492
(16 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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PredEval.java
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492
(16 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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ProtStructGraph.java
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503
(16 years ago)
by filippis:
createGraphDb:
-scop_graph table added
-!!!!residue serial fields (num, i_num, j_num) are changed to unsigned
!!!!ProtStructGraph:
-interSSE variable added
-getResidueSerial abstract method added
-restrictContactsBetweenSs method added
!!!!AIGraph:
-getResidueSerial method added
RIGraph:
-!!!!getResidueSerial method added
-scop graphs are written to db correctly
-interSSE variable taken into account for CR db field
DbRIgraph:
-changes made so to be able to read from db using a scop id
-interSSE and minSeqSep are set now in get_db_graph_info()
-!!!!FIXED BUG:fullLength in read_graph_from_db is not set to the size of the serials2nodes TreeMap instead of the maximum serial in serials2nodes. It was giving wrong result for scop graphs.
testDbRIGraph added:
It reads one graph from a source db based either
-on pdbcode, chaincode and graph properties or
-on scop id and graph properties or
-on a graph id
and it writes the graph to a destination db.
Pdb:
-unused scop regions are now removed in restrictToScopDomain
-unused residues are also removed from resser2pdbresser, pdbresser2resser, resser2allrsa, resser2scrsa, resser2consurfhsspscore, resser2consurfhsspcolor, catalSiteSet
-!!!!sequence is reset to scop sequence and fullLength to the length of the scop sequence
CatalSiteSet:
- removeCatalSiteRes(int resser) method added
CatalyticSite:
-remRes(int resser) method added
Scop:
-remove(ScopRegion e) method added
genDbGraph:Comments only added to demonstrate new functionality.
-comment added to show how to use restrictContactsBetweenSs
-comment added to show how to use restrictToScopDomain
-runDssp now is always run and not only when mode != "GRAPH". This has been changed since now the contact range might depend on the ss assignment (restrictContactsBetweenSs) and we want to ensure consistent results
-runNaccess moved to the bottom so it is always run last. In this way if restrictToScopDomain is used, we don't have to run naccess twice.
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RIGCommonNbhood.java
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512
(16 years ago)
by duarte:
Added getCommanSeparatedResSerials to RIGCommonNbhood
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RIGEdge.java
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492
(16 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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RIGEnsemble.java
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495
(16 years ago)
by stehr:
added main function and loading from Multi-model PDB files
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RIGNbhood.java
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515
(16 years ago)
by stehr:
Interval: allow spaces in residue selection strings
RIGNbhood: added method getNeighbors
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RIGNode.java
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492
(16 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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RIGraph.java
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503
(16 years ago)
by filippis:
createGraphDb:
-scop_graph table added
-!!!!residue serial fields (num, i_num, j_num) are changed to unsigned
!!!!ProtStructGraph:
-interSSE variable added
-getResidueSerial abstract method added
-restrictContactsBetweenSs method added
!!!!AIGraph:
-getResidueSerial method added
RIGraph:
-!!!!getResidueSerial method added
-scop graphs are written to db correctly
-interSSE variable taken into account for CR db field
DbRIgraph:
-changes made so to be able to read from db using a scop id
-interSSE and minSeqSep are set now in get_db_graph_info()
-!!!!FIXED BUG:fullLength in read_graph_from_db is not set to the size of the serials2nodes TreeMap instead of the maximum serial in serials2nodes. It was giving wrong result for scop graphs.
testDbRIGraph added:
It reads one graph from a source db based either
-on pdbcode, chaincode and graph properties or
-on scop id and graph properties or
-on a graph id
and it writes the graph to a destination db.
Pdb:
-unused scop regions are now removed in restrictToScopDomain
-unused residues are also removed from resser2pdbresser, pdbresser2resser, resser2allrsa, resser2scrsa, resser2consurfhsspscore, resser2consurfhsspcolor, catalSiteSet
-!!!!sequence is reset to scop sequence and fullLength to the length of the scop sequence
CatalSiteSet:
- removeCatalSiteRes(int resser) method added
CatalyticSite:
-remRes(int resser) method added
Scop:
-remove(ScopRegion e) method added
genDbGraph:Comments only added to demonstrate new functionality.
-comment added to show how to use restrictContactsBetweenSs
-comment added to show how to use restrictToScopDomain
-runDssp now is always run and not only when mode != "GRAPH". This has been changed since now the contact range might depend on the ss assignment (restrictContactsBetweenSs) and we want to ensure consistent results
-runNaccess moved to the bottom so it is always run last. In this way if restrictToScopDomain is used, we don't have to run naccess twice.
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Scop.java
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514
(16 years ago)
by filippis:
Latest scop and csa versions updated.
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ScopRegion.java
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492
(16 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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SecStrucElement.java
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505
(16 years ago)
by duarte:
Now converting also secondary structure in pairwise alignment graph conversion
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SecondaryStructure.java
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492
(16 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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aapairsBounds.dat
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492
(16 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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contactTypes.dat
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492
(16 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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