 ../
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actionTools/
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492
(14 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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sadp/
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501
(14 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
(14 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
(14 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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litNet/
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735
(13 years ago)
by stehr:
New package litNet with classes to process our article database
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graphAveraging/
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760
(13 years ago)
by duarte:
Rewrote the secondary structure handling in Alignment. Also changed first parameter in writeFasta to be a PrintStream not an OutputStream
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tests/
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762
(13 years ago)
by duarte:
Added length sanity check tests
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sequence/
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763
(13 years ago)
by duarte:
New method in BlastHit to transform the BlastHit local alignment into one that contains the full sequences of subject and query.
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tinker/
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781
(13 years ago)
by duarte:
Implemented shutdown hook. Now all jobs killed upon CTRL-c.
Now submitting directly the distgeom binary without needing writing a shell script. That removes the dependency on java6 (needed for set execution permission on the shell script).
Introduced (but not in use yet and not fully implemented) the submission of more jobs for failure tolerance.
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tools/
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782
(13 years ago)
by duarte:
New constructor with no arguments for MySQLConnection, it reads connection parameters from ~/.my.cnf.
Modified accordingly the executable classes reconstruct and averageGraph. Now they will only work if user has a .my.cnf.
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proteinstructure/
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783
(13 years ago)
by duarte:
Got rid of the hardcoded mysql server, user, password. Now read from .my.cnf file
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testPymolServer.java
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492
(14 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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testClusterConnection.java
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492
(14 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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testResidueSelectionString.java
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492
(14 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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testMySQLConnection.java
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492
(14 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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testGetChains.java
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492
(14 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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testPdb.java
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492
(14 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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testGraph2Pml.java
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492
(14 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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testPyMol.java
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492
(14 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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compareCMs.java
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492
(14 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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genDbGraph.java
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514
(14 years ago)
by filippis:
Latest scop and csa versions updated.
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testDeltaDistanceMap.java
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517
(14 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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computeEnergies.java
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573
(14 years ago)
by duarte:
Fixed script: was exiting after computing native energy!
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testDbRIGraph.java
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576
(14 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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doClassifySingleModels.sh
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580
(14 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
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createGraphDb.sh
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580
(14 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
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benchmarkGraphAlgorithm.java
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609
(14 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
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calculateGridDensity.java
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609
(14 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
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testJUNGframework.java
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660
(14 years ago)
by duarte:
Put another test: finding edges is independent of order of indices given for UNDIRECTED.
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dumppdb.java
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687
(13 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.
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dumpseq.java
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687
(13 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.
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genGraph.java
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707
(13 years ago)
by stehr:
minor update of Usage message
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runMD.java
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715
(13 years ago)
by duarte:
New option -s to do split output.
Now converting final gro file to pdb
Fixed bugs:
- now flushing correctly the gromacs.log (by closing log)
- now properly cleaning up temp files (the ones written to /tmp)
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Manifest.txt
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730
(13 years ago)
by duarte:
Updated version to 1.1.0
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addSeq2Mcma.java
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769
(13 years ago)
by stehr:
added methods and executables to calculate 3d superimpositions using PolyposeRunner
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compareAlignments.java
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769
(13 years ago)
by stehr:
added methods and executables to calculate 3d superimpositions using PolyposeRunner
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superimposeMult.java
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771
(13 years ago)
by stehr:
now taking command line parameters
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pairwiseSeqId.java
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774
(13 years ago)
by stehr:
updated output of pairwiseSeqId
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make-aglappe.sh
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777
(13 years ago)
by duarte:
Added drmaa.jar to make file
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reconstruct.java
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782
(13 years ago)
by duarte:
New constructor with no arguments for MySQLConnection, it reads connection parameters from ~/.my.cnf.
Modified accordingly the executable classes reconstruct and averageGraph. Now they will only work if user has a .my.cnf.
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averageGraph.java
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782
(13 years ago)
by duarte:
New constructor with no arguments for MySQLConnection, it reads connection parameters from ~/.my.cnf.
Modified accordingly the executable classes reconstruct and averageGraph. Now they will only work if user has a .my.cnf.
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