 ../
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tools/
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492
(16 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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actionTools/
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492
(16 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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sadp/
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501
(16 years ago)
by duarte:
Changed implementation of Alignment: now based on indices rather than tags. Interface remains mostly the same
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vecmath/
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524
(16 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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ppi/
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539
(16 years ago)
by stehr:
some refactoring in TinkerRunner and related classes (moved forceConstant parameter from constructor to reconstruct method; made force field file type an enum)
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graphAveraging/
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546
(16 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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tinker/
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574
(16 years ago)
by duarte:
Introduced another check in runMinimize: now we check for CHKXYZ warnings, that happened when the xyz file is somehow not well formatted. In some cases that leads to strange output in minimize.
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proteinstructure/
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575
(16 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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iterateNbhood.java
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492
(16 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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iterateUpperNbs.java
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492
(16 years ago)
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testClusterConnection.java
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492
(16 years ago)
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testResidueSelectionString.java
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492
(16 years ago)
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testMySQLConnection.java
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492
(16 years ago)
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testGetChains.java
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492
(16 years ago)
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writeTargetMoves.java
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492
(16 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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genGraph.java
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492
(16 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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benchmarkGraphAlgorithm.java
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492
(16 years ago)
by duarte:
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hashIterNbhood.java
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492
(16 years ago)
by duarte:
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testPdb.java
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492
(16 years ago)
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rewriteNBHood_parallel.java
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492
(16 years ago)
by duarte:
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cnCoarseNbhood.java
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492
(16 years ago)
by duarte:
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testPymolServer.java
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492
(16 years ago)
by duarte:
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listInfoGain.java
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492
(16 years ago)
by duarte:
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cnHashIterNbhood.java
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492
(16 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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cnEvalTargetNbhood.java
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492
(16 years ago)
by duarte:
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testGraph2Pml.java
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492
(16 years ago)
by duarte:
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cnex1.java
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492
(16 years ago)
by duarte:
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iterateUpperNbhood.java
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492
(16 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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listInfoLoss.java
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492
(16 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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rewriteNBHood.java
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492
(16 years ago)
by duarte:
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testPyMol.java
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492
(16 years ago)
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maxInfoGain.java
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492
(16 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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minInfoGain.java
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492
(16 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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makeNbhTbl.java
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492
(16 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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iterEvalNbhood.java
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492
(16 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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calculateGridDensity.java
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492
(16 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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compareCMs.java
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492
(16 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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iterateNbs.java
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492
(16 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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createGraphDb.sh
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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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testDbRIGraph.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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genDbGraph.java
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514
(16 years ago)
by filippis:
Latest scop and csa versions updated.
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testDeltaDistanceMap.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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make-aglappe.sh
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534
(16 years ago)
by duarte:
Now compiling also scripts in default package
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dumpseq.java
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535
(16 years ago)
by duarte:
Added option to output to standard output
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testJUNGframework.java
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542
(16 years ago)
by duarte:
Using Ca/Cg for testing as Ca/Cb is now allowed
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Manifest.txt
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553
(16 years ago)
by duarte:
Changed version in Manifest to 0.9.3
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scoreTargetMoves.java
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567
(16 years ago)
by duarte:
Now takes targetDb also from command line. Some clean up
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averageGraph.java
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569
(16 years ago)
by duarte:
Change command line parameters: eliminated -c and -C. Now pdb codes and chain codes are read together as a xxxxA string that we then split to get pdb/chain codes. The list of templates is now read from file.
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computeEnergies.java
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573
(16 years ago)
by duarte:
Fixed script: was exiting after computing native energy!
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reconstruct.java
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575
(16 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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