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r659
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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()
tools/ 658 (11 years ago) by stehr: Changed return type of sortMapByValue from Map to LinkedHashMap
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.
sequence/ 651 (11 years ago) by duarte: New class PhiPsiAverager to get consensus of phi/psi angles from a TemplateList and an Alignment. Tested with a few examples and seems to work. The wrapping of angles at 180/-180 is not yet taking into account, i.e. if an interval falls in the region just below 180 and just above -180, no consensus will be found. Pdb: added some checks to methods getPhi/Psi so that it doesn't fail when there's no coordinates. Changed yet again the design of TemplateList/Template. Now loading of PDB data happens upon call of the loadPDBdata method. Changed dependencies accordingly.
sadp/ 501 (11 years ago) by duarte: Changed implementation of Alignment: now based on indices rather than tags. Interface remains mostly the same
proteinstructure/ 659 (11 years ago) by stehr: Also adding caspParents member to graph classes, value will be kept from Pdb if present; adding method to GraphAverager to retrieve the most frequently used parents specified in the templates
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)
graphAveraging/ 659 (11 years ago) by stehr: Also adding caspParents member to graph classes, value will be kept from Pdb if present; adding method to GraphAverager to retrieve the most frequently used parents specified in the templates
actionTools/ 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.
testResidueSelectionString.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.
testPyMol.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.
testMySQLConnection.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
testJUNGframework.java 542 (11 years ago) by duarte: Using Ca/Cg for testing as Ca/Cb is now allowed
testGraph2Pml.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.
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
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.
testClusterConnection.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
scoreTargetMoves.java 567 (11 years ago) by duarte: Now takes targetDb also from command line. Some clean up
rewriteNBHood_parallel.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.
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
minInfoGain.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.
makeNbhTbl.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
make-aglappe.sh 591 (11 years ago) by duarte: Added some missing packages to compilation
listInfoLoss.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.
iterateUpperNbs.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.
iterateNbs.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
iterateNbhood.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.
hashIterNbhood.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
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
genDbGraph.java 514 (11 years ago) by filippis: Latest scop and csa versions updated.
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
dumppdb.java 647 (11 years ago) by filippis:
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
computeEnergies.java 573 (11 years ago) by duarte: Fixed script: was exiting after computing native energy!
compareCMs.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.
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.
cnCoarseNbhood.java 492 (11 years ago) by duarte: Copied the aglappe-jung branch into trunk.
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
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
averageGraph.java 655 (11 years ago) by stehr:
Manifest.txt 553 (11 years ago) by duarte: Changed version in Manifest to 0.9.3
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