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r688
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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/ 680 (11 years ago) by duarte: New feature: now we can enforce omega trans conformation for the torsion angle of the peptide bond. New method in Pdb: getOmega
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/ 688 (11 years ago) by duarte: Fixed bugs in averageGraph: - output of benchmark statistics and pairwise comparison was overlapping - benchmark mode was broken after introduction of align mode (when no sequence file given we were always creating dummy sequence in both align or benchmark modes) Improved: - better handling of modes through mode variable that takes 1 of 3 states - better input check - in align mode now calling another GraphAverager constructor instead of creating dummy seq/tag within averageGraph - changed constructor in GraphAverager: now sequence not a parameter, instead taken from alignment. Check for input moved down to averageGraph - now allowing alignments that contain other sequences than the target and the templates - new exception GraphAveragerError thrown in GraphAverager constructor when sequences of alignment and templates don't match
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/ 688 (11 years ago) by duarte: Fixed bugs in averageGraph: - output of benchmark statistics and pairwise comparison was overlapping - benchmark mode was broken after introduction of align mode (when no sequence file given we were always creating dummy sequence in both align or benchmark modes) Improved: - better handling of modes through mode variable that takes 1 of 3 states - better input check - in align mode now calling another GraphAverager constructor instead of creating dummy seq/tag within averageGraph - changed constructor in GraphAverager: now sequence not a parameter, instead taken from alignment. Check for input moved down to averageGraph - now allowing alignments that contain other sequences than the target and the templates - new exception GraphAveragerError thrown in GraphAverager constructor when sequences of alignment and templates don't match
actionTools/ 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 660 (11 years ago) by duarte: Put another test: finding edges is independent of order of indices given for UNDIRECTED.
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.
reconstruct.java 680 (11 years ago) by duarte: New feature: now we can enforce omega trans conformation for the torsion angle of the peptide bond. New method in Pdb: getOmega
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
genDbGraph.java 514 (11 years ago) by filippis: Latest scop and csa versions updated.
dumpseq.java 687 (11 years ago) by duarte: Improved dump scripts: - new feature: dumps first chain if one not specified - current dir now default - better help text Fixed bug in dumppdb: was trying to close Output stream after exception.
dumppdb.java 687 (11 years ago) by duarte: Improved dump scripts: - new feature: dumps first chain if one not specified - current dir now default - better help text Fixed bug in dumppdb: was trying to close Output stream after exception.
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.
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 688 (11 years ago) by duarte: Fixed bugs in averageGraph: - output of benchmark statistics and pairwise comparison was overlapping - benchmark mode was broken after introduction of align mode (when no sequence file given we were always creating dummy sequence in both align or benchmark modes) Improved: - better handling of modes through mode variable that takes 1 of 3 states - better input check - in align mode now calling another GraphAverager constructor instead of creating dummy seq/tag within averageGraph - changed constructor in GraphAverager: now sequence not a parameter, instead taken from alignment. Check for input moved down to averageGraph - now allowing alignments that contain other sequences than the target and the templates - new exception GraphAveragerError thrown in GraphAverager constructor when sequences of alignment and templates don't match
Manifest.txt 553 (11 years ago) by duarte: Changed version in Manifest to 0.9.3
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