 ../
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AAinfo.java
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524
(12 years ago)
by duarte:
Fixed reading od PDB files. We hope now to be catching all possible errors present in original PDB files, plus we read correctly CASP TS files:
- now reading (and requiring) TARGET record for CASP TS files
- now we always have (and require) a sequence (possibly with ? or X) for all cases: PdbfilePdb, CaspRRFileRIGraph, FileRIGraph.
- in PDB files we throw format exceptions for: insertion codes, residue numbers <=0, non-ascending order of residue numbers in atom lines, when residues of SEQRES seq and ATOM seq don't match. In addition we warn when starting residue in ATOM lines is >100
- we allow PDB files without a HEADER, i.e. only ATOM lines
New fields in Pdb for CAPS identifiers: passed all the way down to RIGraphs in getGraph()
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AIGEdge.java
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492
(12 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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AIGNode.java
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492
(12 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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AIGraph.java
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524
(12 years ago)
by duarte:
Fixed reading od PDB files. We hope now to be catching all possible errors present in original PDB files, plus we read correctly CASP TS files:
- now reading (and requiring) TARGET record for CASP TS files
- now we always have (and require) a sequence (possibly with ? or X) for all cases: PdbfilePdb, CaspRRFileRIGraph, FileRIGraph.
- in PDB files we throw format exceptions for: insertion codes, residue numbers <=0, non-ascending order of residue numbers in atom lines, when residues of SEQRES seq and ATOM seq don't match. In addition we warn when starting residue in ATOM lines is >100
- we allow PDB files without a HEADER, i.e. only ATOM lines
New fields in Pdb for CAPS identifiers: passed all the way down to RIGraphs in getGraph()
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Alignment.java
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552
(12 years ago)
by duarte:
Now throwing exception in checkLengths().
Now fast checking of FASTA/PIR format (we check if first non-empty line starts with ">")
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AlignmentConstructionError.java
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492
(12 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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Box.java
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492
(12 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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CaspRRFileData.java
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492
(12 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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CaspRRFileRIGraph.java
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543
(12 years ago)
by duarte:
Now forcing i<j in CASP RR files (as specified by the CASP RR format)
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CatalSiteSet.java
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514
(12 years ago)
by filippis:
Latest scop and csa versions updated.
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CatalyticSite.java
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503
(12 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
(12 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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CiffilePdb.java
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524
(12 years ago)
by duarte:
Fixed reading od PDB files. We hope now to be catching all possible errors present in original PDB files, plus we read correctly CASP TS files:
- now reading (and requiring) TARGET record for CASP TS files
- now we always have (and require) a sequence (possibly with ? or X) for all cases: PdbfilePdb, CaspRRFileRIGraph, FileRIGraph.
- in PDB files we throw format exceptions for: insertion codes, residue numbers <=0, non-ascending order of residue numbers in atom lines, when residues of SEQRES seq and ATOM seq don't match. In addition we warn when starting residue in ATOM lines is >100
- we allow PDB files without a HEADER, i.e. only ATOM lines
New fields in Pdb for CAPS identifiers: passed all the way down to RIGraphs in getGraph()
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ConformationsNotSameSizeError.java
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492
(12 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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ContactType.java
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492
(12 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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DbRIGraph.java
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576
(12 years ago)
by filippis:
RIGraph:Now you can store unweighted graphs in db and also select the db that contains the ids for the single models.
-paramater weighted added to write_graph_to_db and write_graph_to_db_fast methods. If true, it works as before (atomWeight is written to db field weight) else the db field weight gets always value 1. Methods without this parameter still exist and work as before.
-protected field singleModelsDb and corresponding methods getSingleModelsDb and setSingleModelsDb have been added. All constructors set the singleModelsDb field to DEFAULT_SINGLEMODELS_DB which equals to "ioannis". Changes have been also made to write_graph_to_db and write_graph_to_db_fast methods to deal with the singleModelsDb field.
DbRIGraph, testDbRIGraph:Changes have been also made to address the reading of (un)weighted graphs from db.
doClassifySingleModels.sh has been added. You can create your own table with ids for the single models wherever you want.
createGraphDs.sh: mode to drop tables has been added.
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EC.java
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502
(12 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
(12 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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FastaFileFormatError.java
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492
(12 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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FileFormatError.java
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492
(12 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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FileRIGraph.java
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551
(12 years ago)
by duarte:
Fixed bug: now reading/writing #MODEL field in contact map files
In Pdb writeAtomLines now prints a nicer header with source info depending on source: file or db
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FileTypeGuesser.java
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550
(12 years ago)
by stehr:
changed header of contact map file from #AGLAPPE... to #CMVIEW...; when reading, both are accepted to ensure backwards compatibility
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GraphFileFormatError.java
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492
(12 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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GraphIODb.java
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492
(12 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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GraphIOGDLFile.java
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587
(12 years ago)
by stehr:
fixed bug in writing to gdl file (gravity 1 -> 1.0)
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GraphIdNotFoundError.java
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492
(12 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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IntPairComparator.java
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492
(12 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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IntPairSet.java
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492
(12 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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Interval.java
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515
(12 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
(12 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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MaxClusterRunner.java
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585
(12 years ago)
by stehr:
added method calculateSequenceIndependentMatrix()
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MsdsdInconsistentResidueNumbersError.java
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492
(12 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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MsdsdPdb.java
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492
(12 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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NbhProbDistribution.java
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492
(12 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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NbhoodBackgrnd.java
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492
(12 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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PairwiseAlignmentConverter.java
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517
(12 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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575
(12 years ago)
by filippis:
reconstruct:
-rmsd to mirrored pdb has been added in the report file
Pdb:
-comment for outputing missing atoms added
PairwiseSequenceAlignment:
-constructor with parameters openScore and extendScore for the gaps has been added
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Pdb.java
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589
(12 years ago)
by duarte:
New classes Template, TemplateList to be used in homology modelling pipeline.
Modified BlastUtils to use TemplateList class
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PdbChainCodeNotFoundError.java
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492
(12 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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PdbCodeNotFoundError.java
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492
(12 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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PdbLoadError.java
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492
(12 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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PdbaseInconsistencyError.java
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492
(12 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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PdbasePdb.java
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524
(12 years ago)
by duarte:
Fixed reading od PDB files. We hope now to be catching all possible errors present in original PDB files, plus we read correctly CASP TS files:
- now reading (and requiring) TARGET record for CASP TS files
- now we always have (and require) a sequence (possibly with ? or X) for all cases: PdbfilePdb, CaspRRFileRIGraph, FileRIGraph.
- in PDB files we throw format exceptions for: insertion codes, residue numbers <=0, non-ascending order of residue numbers in atom lines, when residues of SEQRES seq and ATOM seq don't match. In addition we warn when starting residue in ATOM lines is >100
- we allow PDB files without a HEADER, i.e. only ATOM lines
New fields in Pdb for CAPS identifiers: passed all the way down to RIGraphs in getGraph()
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PdbfileFormatError.java
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492
(12 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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PdbfilePdb.java
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551
(12 years ago)
by duarte:
Fixed bug: now reading/writing #MODEL field in contact map files
In Pdb writeAtomLines now prints a nicer header with source info depending on source: file or db
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PirFileFormatError.java
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492
(12 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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PredEval.java
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563
(12 years ago)
by duarte:
Added new convenience method printSummary
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ProtStructGraph.java
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547
(12 years ago)
by stehr:
Added constant NO_SEQ_SEP_VAL
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RIGCommonNbhood.java
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512
(12 years ago)
by duarte:
Added getCommanSeparatedResSerials to RIGCommonNbhood
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RIGEdge.java
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546
(12 years ago)
by duarte:
New feature in GraphAverager: method to write the voters together with the edges; new constructor taking a RIGEnsemble
Fixed bug in RIGEnsemble: was not working for cif files.
Added a graph averaging output to main() in RIGEnsemble
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RIGEnsemble.java
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562
(12 years ago)
by duarte:
RIGEnsemble doesn't extend ArrayList anymore, now the ensemble ArrayList is a member, so we now must use the RIGEnsemble interface exclusively
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RIGNbhood.java
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529
(12 years ago)
by spriya:
Drop sequence comparison in compare. Now we compare only length
New method getSize in RIGNbhood to be used instead of size that returns neighborhood size + 1
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RIGNode.java
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492
(12 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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RIGraph.java
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588
(12 years ago)
by filippis:
write_graph_to_motiffile:
-node serials are assigned now only to non-orphan nodes
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Scop.java
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589
(12 years ago)
by duarte:
New classes Template, TemplateList to be used in homology modelling pipeline.
Modified BlastUtils to use TemplateList class
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ScopRegion.java
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589
(12 years ago)
by duarte:
New classes Template, TemplateList to be used in homology modelling pipeline.
Modified BlastUtils to use TemplateList class
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SecStrucElement.java
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505
(12 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
(12 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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Template.java
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590
(12 years ago)
by duarte:
Added code to run psipred.
Fixed a few minor bugs.
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TemplateList.java
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590
(12 years ago)
by duarte:
Added code to run psipred.
Fixed a few minor bugs.
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aapairsBounds.dat
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492
(12 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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contactTypes.dat
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492
(12 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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