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r642
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actionTools/ 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
sadp/ 501 (11 years ago) by duarte: Changed implementation of Alignment: now based on indices rather than tags. Interface remains mostly the same
vecmath/ 524 (11 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()
ppi/ 539 (11 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)
tools/ 615 (11 years ago) by stehr: new class tools.Statistics with currently only one method pearson(x,y) to compute the pearson correlation coefficient of two double[] vectors
tinker/ 621 (11 years ago) by stehr: Added members and method to ProtStructGraph and Pdb to write AUTHOR and METHOD fields to Casp files. Added missing reconstructFast methods to TinkerRunner.
proteinstructure/ 641 (11 years ago) by stehr: added option to GraphAverager and averageGraph to create dummy sequence with length of alignment to view the overlaid graphs without mapping to a target sequence
graphAveraging/ 641 (11 years ago) by stehr: added option to GraphAverager and averageGraph to create dummy sequence with length of alignment to view the overlaid graphs without mapping to a target sequence
sequence/ 642 (11 years ago) by duarte: Fixed bug: writeClusterGraph shouldn't try to do anything if there's only one template.
iterateNbhood.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
iterateUpperNbs.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
testClusterConnection.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
testResidueSelectionString.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
testMySQLConnection.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
testGetChains.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
writeTargetMoves.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
hashIterNbhood.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
testPdb.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
rewriteNBHood_parallel.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
cnCoarseNbhood.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
testPymolServer.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
listInfoGain.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
cnHashIterNbhood.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
cnEvalTargetNbhood.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
testGraph2Pml.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
cnex1.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
iterateUpperNbhood.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
listInfoLoss.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
rewriteNBHood.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
testPyMol.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
maxInfoGain.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
minInfoGain.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
makeNbhTbl.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
iterEvalNbhood.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
compareCMs.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
iterateNbs.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
genDbGraph.java 514 (11 years ago) by filippis: Latest scop and csa versions updated.
testDeltaDistanceMap.java 517 (11 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
testJUNGframework.java 542 (11 years ago) by duarte: Using Ca/Cg for testing as Ca/Cb is now allowed
Manifest.txt 553 (11 years ago) by duarte: Changed version in Manifest to 0.9.3
scoreTargetMoves.java 567 (11 years ago) by duarte: Now takes targetDb also from command line. Some clean up
computeEnergies.java 573 (11 years ago) by duarte: Fixed script: was exiting after computing native energy!
reconstruct.java 575 (11 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
testDbRIGraph.java 576 (11 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.
doClassifySingleModels.sh 580 (11 years ago) by filippis: createGraphDb: -the node_id in the single_model_node table changed to AUTO_INCREMENT doClassifySingleModels: -the interSS for CR added RIGraph: -write_graph_to_db methods treat the node_id field in the single_model_node table as AUTO_INCREMENT -write_graph_to_motiffile method added
createGraphDb.sh 580 (11 years ago) by filippis: createGraphDb: -the node_id in the single_model_node table changed to AUTO_INCREMENT doClassifySingleModels: -the interSS for CR added RIGraph: -write_graph_to_db methods treat the node_id field in the single_model_node table as AUTO_INCREMENT -write_graph_to_motiffile method added
make-aglappe.sh 591 (11 years ago) by duarte: Added some missing packages to compilation
genGraph.java 609 (11 years ago) by duarte: Extracted constant NULL_CHAIN_CODE that was still hard-coded in MANY places. Now should be safe to replace the value of the constant from "NULL" to something else. Using TemplateList.readIdsListFile() in averageGraph, dumpseq and genGraph so that is now a standard way of reading list files with pdbcodes/chaincodes. NOTE: this introduces an incompatibility with legacy list files: we can't read a NULL pdb chain code with the "NULL" string e.g. '1i1b NULL'. This is fine because since PDB-REMEDIATED all NULL chains are now "A". Fixed a few things and made more standard the scripts dumpseq and genGraph
benchmarkGraphAlgorithm.java 609 (11 years ago) by duarte: Extracted constant NULL_CHAIN_CODE that was still hard-coded in MANY places. Now should be safe to replace the value of the constant from "NULL" to something else. Using TemplateList.readIdsListFile() in averageGraph, dumpseq and genGraph so that is now a standard way of reading list files with pdbcodes/chaincodes. NOTE: this introduces an incompatibility with legacy list files: we can't read a NULL pdb chain code with the "NULL" string e.g. '1i1b NULL'. This is fine because since PDB-REMEDIATED all NULL chains are now "A". Fixed a few things and made more standard the scripts dumpseq and genGraph
calculateGridDensity.java 609 (11 years ago) by duarte: Extracted constant NULL_CHAIN_CODE that was still hard-coded in MANY places. Now should be safe to replace the value of the constant from "NULL" to something else. Using TemplateList.readIdsListFile() in averageGraph, dumpseq and genGraph so that is now a standard way of reading list files with pdbcodes/chaincodes. NOTE: this introduces an incompatibility with legacy list files: we can't read a NULL pdb chain code with the "NULL" string e.g. '1i1b NULL'. This is fine because since PDB-REMEDIATED all NULL chains are now "A". Fixed a few things and made more standard the scripts dumpseq and genGraph
dumpseq.java 609 (11 years ago) by duarte: Extracted constant NULL_CHAIN_CODE that was still hard-coded in MANY places. Now should be safe to replace the value of the constant from "NULL" to something else. Using TemplateList.readIdsListFile() in averageGraph, dumpseq and genGraph so that is now a standard way of reading list files with pdbcodes/chaincodes. NOTE: this introduces an incompatibility with legacy list files: we can't read a NULL pdb chain code with the "NULL" string e.g. '1i1b NULL'. This is fine because since PDB-REMEDIATED all NULL chains are now "A". Fixed a few things and made more standard the scripts dumpseq and genGraph
averageGraph.java 641 (11 years ago) by stehr: added option to GraphAverager and averageGraph to create dummy sequence with length of alignment to view the overlaid graphs without mapping to a target sequence
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