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Revision 636 - Directory Listing
Modified Thu May 15 12:03:58 2008 UTC (11 years, 5 months ago) by stehr
added 'title' member to Pdb and Template objects, currently only set when loading from Pdbase
Revision 635 - Directory Listing
Modified Thu May 15 08:44:59 2008 UTC (11 years, 5 months ago) by duarte
Changed default gravity value and default IDENTITY_SCORE for similarity graph
Revision 634 - Directory Listing
Modified Wed May 14 14:46:38 2008 UTC (11 years, 5 months ago) by duarte
Fixed bug in BlastUtils.writeClusterGraph: was not working at all. Wrong curly brackets, was still using a GDT cutoff instead of rmsd and was never getting Pdb correctly out of the Template.
Two new members in Template: GTGHit and BlastHit, so we can reference back to the hit if needed (like if we want to get the evalue/score). Got rid on MySQLConnection as a member, not very nice design, now a parameter for the specific methods that need to query for PDB data.
Revision 632 - Directory Listing
Modified Wed May 14 09:32:41 2008 UTC (11 years, 5 months ago) by duarte
Got rid of the refined/unrefined field when writing CASP TS files. Now we should be complying correctly with the CASP 8 format.
Revision 631 - Directory Listing
Modified Tue May 13 15:30:39 2008 UTC (11 years, 5 months ago) by duarte
Now writing the PDB ids for the PARENT fields of CASP TS files correctly (with underscore between pdb code and chain code)
Revision 629 - Directory Listing
Modified Tue May 13 10:55:21 2008 UTC (11 years, 5 months ago) by duarte
Now also copying caspMethodStr and caspAuthorStr in AIGraph.
Updated java docs
Revision 624 - Directory Listing
Modified Fri May 9 14:16:54 2008 UTC (11 years, 5 months ago) by duarte
Fixed bug: now try/catch of getPdbInfo moved down to getPdb and getScopSccsString (getScopSccsString was throwing NullPointer when pdb load failed)
Revision 622 - Directory Listing
Modified Fri May 9 12:56:27 2008 UTC (11 years, 5 months ago) by duarte
Added code to be able to filter out template ids (pdb codes) by maximum release date.
Some improvements in Hit classes.
Revision 621 - Directory Listing
Modified Thu May 8 17:17:07 2008 UTC (11 years, 5 months 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.
Revision 620 - Directory Listing
Modified Thu May 8 13:17:36 2008 UTC (11 years, 5 months ago) by duarte
Added a few more methods to the Template classes: Template now behaves differently in that it doesn't load the PDB data on construction but on demand (when calling getPdb() or getScop())

Revision 619 - Directory Listing
Modified Thu May 8 10:13:10 2008 UTC (11 years, 5 months ago) by duarte
Added methods to be able to print "graphical" output for GTGHits, all equivalent to the methods in BlastHit
Added compare() and writeIdsToFile() in TemplateList.
Revision 618 - Directory Listing
Modified Wed May 7 12:06:56 2008 UTC (11 years, 5 months ago) by duarte
Initial commit of GTG parsing classes.
Added method in PdbasePdb to map observed residue sequence serials to internal (cif) residue serials
Revision 617 - Directory Listing
Modified Tue May 6 16:16:49 2008 UTC (11 years, 5 months ago) by duarte
New method getObservedSequence
Revision 616 - Directory Listing
Modified Tue May 6 13:12:33 2008 UTC (11 years, 5 months ago) by duarte
Fixed error output of PdbCodeNotFoundException
Revision 614 - Directory Listing
Modified Mon May 5 14:07:16 2008 UTC (11 years, 5 months ago) by stehr
PdbfilePdb: catching previously unhandled NumberFormatException, added method setSequence() to override sequence read from file (needed for Casp prediction where 'real' sequence is known but residues may be missing in prediction)
RIGEnsemble: many changes
Revision 609 - Directory Listing
Modified Wed Apr 30 14:11:50 2008 UTC (11 years, 5 months 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
Revision 608 - Directory Listing
Modified Wed Apr 30 10:37:53 2008 UTC (11 years, 5 months ago) by duarte
Introduced a new load method, so that is possible to specify cif chain codes (asym_ids) as input. Default is as before: input is pdbChainCode. NOT TESTED.
Revision 607 - Directory Listing
Modified Wed Apr 30 09:02:55 2008 UTC (11 years, 5 months ago) by duarte
Moved readTemplatesFile method to TemplateList class (as a static)
Revision 606 - Directory Listing
Modified Tue Apr 29 16:02:17 2008 UTC (11 years, 5 months ago) by duarte
Improved javadocs and comments
Revision 605 - Directory Listing
Modified Tue Apr 29 11:52:46 2008 UTC (11 years, 5 months ago) by stehr
changed regexp for Casp header to allow target tag with lower case 't'
Revision 603 - Directory Listing
Modified Tue Apr 29 10:29:34 2008 UTC (11 years, 5 months ago) by duarte
Added method writeToCaspTSFile. Outsourced writing the headers for PDB files and CASP TS files to other methods.
Refactored dumpseq to writeSeqToFile.
Improved a lot the java docs.
Revision 596 - Directory Listing
Modified Thu Apr 24 10:50:35 2008 UTC (11 years, 5 months ago) by filippis
RIGraph:
-getCommonEdgesCount added
Revision 594 - Directory Listing
Modified Tue Apr 22 09:06:57 2008 UTC (11 years, 5 months ago) by stehr
removed import which caused a warning
Revision 592 - Directory Listing
Modified Tue Apr 22 09:04:14 2008 UTC (11 years, 5 months ago) by stehr
fixed one null pointer bug and some spelling mistakes
Revision 590 - Directory Listing
Modified Fri Apr 11 14:43:53 2008 UTC (11 years, 6 months ago) by duarte
Added code to run psipred.
Fixed a few minor bugs.
Revision 589 - Directory Listing
Modified Wed Apr 9 16:16:08 2008 UTC (11 years, 6 months ago) by duarte
New classes Template, TemplateList to be used in homology modelling pipeline.
Modified BlastUtils to use TemplateList class
Revision 588 - Directory Listing
Modified Wed Apr 9 09:40:22 2008 UTC (11 years, 6 months ago) by filippis
write_graph_to_motiffile:
-node serials are assigned now only to non-orphan nodes
Revision 587 - Directory Listing
Modified Tue Apr 8 15:56:18 2008 UTC (11 years, 6 months ago) by stehr
fixed bug in writing to gdl file (gravity 1 -> 1.0)
Revision 586 - Directory Listing
Modified Tue Apr 8 15:41:02 2008 UTC (11 years, 6 months ago) by stehr
changed some parameters for writing GDL files
Revision 585 - Directory Listing
Modified Tue Apr 8 15:40:36 2008 UTC (11 years, 6 months ago) by stehr
added method calculateSequenceIndependentMatrix()
Revision 582 - Directory Listing
Modified Tue Apr 8 12:36:49 2008 UTC (11 years, 6 months ago) by filippis
RIGraph:
-bugs in write_graph_to_db methods concerning the node_id field have been fixed.
Revision 580 - Directory Listing
Modified Tue Apr 8 10:01:57 2008 UTC (11 years, 6 months 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
Revision 576 - Directory Listing
Modified Tue Apr 1 15:56:06 2008 UTC (11 years, 6 months 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.

Revision 575 - Directory Listing
Modified Tue Apr 1 09:37:23 2008 UTC (11 years, 6 months 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
Revision 570 - Directory Listing
Modified Thu Mar 20 10:02:08 2008 UTC (11 years, 6 months ago) by duarte
Added comments and better javadoc for the get_graph methods
Revision 568 - Directory Listing
Modified Sun Mar 9 16:15:19 2008 UTC (11 years, 7 months ago) by duarte
Correction in javadoc
Revision 563 - Directory Listing
Modified Thu Mar 6 16:05:57 2008 UTC (11 years, 7 months ago) by duarte
Added new convenience method printSummary
Revision 562 - Directory Listing
Modified Thu Mar 6 13:19:21 2008 UTC (11 years, 7 months ago) by duarte
RIGEnsemble doesn't extend ArrayList anymore, now the ensemble ArrayList is a member, so we now must use the RIGEnsemble interface exclusively
Revision 559 - Directory Listing
Modified Thu Mar 6 11:35:22 2008 UTC (11 years, 7 months ago) by duarte
Fixed bug: was printing the value of accuracy for the coverage field.
Revision 558 - Directory Listing
Modified Thu Mar 6 10:52:11 2008 UTC (11 years, 7 months ago) by duarte
Changed dumpseq: now complies with FASTA format (80 characters per line) and tag is now pdbCode+pdbChainCode (with no underscore)
Revision 557 - Directory Listing
Modified Tue Mar 4 16:26:30 2008 UTC (11 years, 7 months ago) by duarte
New method writeToPaulFile
Revision 556 - Directory Listing
Modified Tue Mar 4 15:31:49 2008 UTC (11 years, 7 months ago) by filippis
Added mirror() method in Pdb class
Added getComplement() method in RIGraph class
Revision 552 - Directory Listing
Modified Fri Feb 22 15:26:34 2008 UTC (11 years, 7 months ago) by duarte
Now throwing exception in checkLengths().
Now fast checking of FASTA/PIR format (we check if first non-empty line starts with ">")
Revision 551 - Directory Listing
Modified Thu Feb 21 18:51:53 2008 UTC (11 years, 7 months ago) by duarte
Fixed bug: now reading/writing #MODEL field in contact map files
In Pdb writeAtomLines now prints a nicer header with source info depending on source: file or db
Revision 550 - Directory Listing
Modified Thu Feb 21 14:26:13 2008 UTC (11 years, 7 months ago) by stehr
changed header of contact map file from #AGLAPPE... to #CMVIEW...; when reading, both are accepted to ensure backwards compatibility
Revision 548 - Directory Listing
Modified Thu Feb 21 08:42:22 2008 UTC (11 years, 7 months ago) by duarte
Fixed bug: write_graph_to_file now writes blank instead of "null" when pdbCode, pdbChainCode or chainCode are null.
Revision 547 - Directory Listing
Modified Wed Feb 20 16:20:26 2008 UTC (11 years, 7 months ago) by stehr
Added constant NO_SEQ_SEP_VAL
Revision 546 - Directory Listing
Modified Wed Feb 20 15:53:51 2008 UTC (11 years, 7 months 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

Revision 543 - Directory Listing
Modified Mon Feb 18 18:04:27 2008 UTC (11 years, 7 months ago) by duarte
Now forcing i<j in CASP RR files (as specified by the CASP RR format)
Revision 533 - Directory Listing
Modified Tue Feb 12 11:50:05 2008 UTC (11 years, 8 months ago) by duarte
New constructor to read from simple graph files, i.e. list of contacts without any headers
Revision 532 - Directory Listing
Modified Fri Feb 8 12:07:10 2008 UTC (11 years, 8 months ago) by spriya
Fixed bug: addEdgeIJ was not checking for presence of contacts
Revision 531 - Directory Listing
Modified Tue Feb 5 15:48:25 2008 UTC (11 years, 8 months ago) by spriya
Added convenience methods: containsVertexI, addEdgeIJ
Revision 530 - Directory Listing
Modified Tue Feb 5 15:08:00 2008 UTC (11 years, 8 months ago) by spriya
New methods getFisrt/Last residue serial
Revision 529 - Directory Listing
Modified Tue Feb 5 14:53:57 2008 UTC (11 years, 8 months ago) by spriya
Drop sequence comparison in compare. Now we compare only length
New method getSize in RIGNbhood to be used instead of size that returns neighborhood size + 1
Revision 528 - Directory Listing
Modified Tue Feb 5 14:31:46 2008 UTC (11 years, 8 months ago) by duarte
Fixed bug in compare(), was not checking correctly for sequence matching
Revision 524 - Directory Listing
Modified Tue Jan 29 12:03:32 2008 UTC (11 years, 8 months 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()
Revision 522 - Directory Listing
Modified Fri Jan 18 16:51:31 2008 UTC (11 years, 8 months ago) by stehr
Minor change of some error message
Revision 521 - Directory Listing
Modified Wed Jan 16 17:58:38 2008 UTC (11 years, 8 months ago) by duarte
Fixed bug! actually it was not an abbot bug but our own, now calling AAinfo.class correctly (instead of System.getRunTime()....). With this abbot runs fine without any dirty fixes
Revision 520 - Directory Listing
Modified Wed Jan 16 15:35:36 2008 UTC (11 years, 8 months ago) by duarte
Fixed to be able to run CMView under Abbot (because of abbot getResourceAsStream bug). The ABBOT_FIX flag is turned off.
Revision 518 - Directory Listing
Modified Tue Jan 15 16:18:33 2008 UTC (11 years, 9 months ago) by filippis
checkConsurf: if the file is not found and the chain code given is "A", we check now also for results for NULL chain code 
Revision 517 - Directory Listing
Modified Tue Jan 15 13:19:36 2008 UTC (11 years, 9 months 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
Revision 516 - Directory Listing
Modified Mon Jan 14 14:25:14 2008 UTC (11 years, 9 months ago) by duarte
Removed PairwiseAlignmentGraphConverter, not needed anymore by CMView + was very buggy
Improved some comments/java docs
Revision 515 - Directory Listing
Modified Mon Jan 14 10:02:28 2008 UTC (11 years, 9 months ago) by stehr
Interval: allow spaces in residue selection strings
RIGNbhood: added method getNeighbors
Revision 514 - Directory Listing
Modified Fri Jan 11 14:59:43 2008 UTC (11 years, 9 months ago) by filippis
Latest scop and csa versions updated.
Revision 513 - Directory Listing
Modified Fri Jan 11 13:33:56 2008 UTC (11 years, 9 months ago) by filippis
Fixing the fixed bug!
-if graph read is chain graph, then fullLength is set to the maximum observed residue serial
-else if graph is scop graph, then fullLength is set to the number of observed residues
NOTE:In the case of a wholechain scop graph, there might be inconsistensy between a graph I created with Pdb/RIGraph classes and stored in db and the corresponding graph i read from db. Specifically, the fullLength of graph I equals the length of the chain while the fullLength of graph i equals the number of observed residues.
Revision 512 - Directory Listing
Modified Fri Jan 11 10:57:40 2008 UTC (11 years, 9 months ago) by duarte
Added getCommanSeparatedResSerials to RIGCommonNbhood
Revision 509 - Directory Listing
Modified Thu Jan 10 16:22:03 2008 UTC (11 years, 9 months ago) by stehr
added some comments
Revision 508 - Directory Listing
Modified Thu Jan 10 15:39:00 2008 UTC (11 years, 9 months ago) by stehr
Fixed bug in DSSP secondary structure assignment, first element was starting at index 0
Revision 506 - Directory Listing
Modified Thu Jan 10 14:46:11 2008 UTC (11 years, 9 months ago) by duarte
New method to convert secondary structure
Revision 505 - Directory Listing
Modified Thu Jan 10 13:37:09 2008 UTC (11 years, 9 months ago) by duarte
Now converting also secondary structure in pairwise alignment graph conversion
Revision 504 - Directory Listing
Modified Thu Jan 10 10:30:46 2008 UTC (11 years, 9 months ago) by stehr
Fixed three compiler warnings for unused imports (DbRIGraph, Pdb) and an untyped iterator (CatalSiteSet)
Revision 503 - Directory Listing
Modified Tue Jan 8 19:51:39 2008 UTC (11 years, 9 months 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.


Revision 502 - Directory Listing
Modified Tue Jan 8 11:00:15 2008 UTC (11 years, 9 months ago) by stehr
EC, CatalSiteSet: added typing to some iterators to avoid eclipse warning
Interval: added typing to Comparator to avoid eclipse warning
Revision 501 - Directory Listing
Modified Tue Jan 8 10:04:46 2008 UTC (11 years, 9 months ago) by duarte
Changed implementation of Alignment: now based on indices rather than tags. Interface remains mostly the same
Revision 500 - Directory Listing
Modified Mon Jan 7 13:41:26 2008 UTC (11 years, 9 months ago) by duarte
New functionality: now we can get sequences and reset tags based on the order the sequences appear on the file.
Revision 499 - Directory Listing
Modified Fri Jan 4 15:00:11 2008 UTC (11 years, 9 months ago) by duarte
Got rid of check for equality of tags
Revision 498 - Directory Listing
Modified Thu Jan 3 17:16:03 2008 UTC (11 years, 9 months ago) by duarte
Now also copying the CASP RR identifier fields in RIGraph.copy() and in PairwiseAlignmentGraphConverter.converGraph().
Revision 497 - Directory Listing
Modified Thu Jan 3 14:20:03 2008 UTC (11 years, 9 months ago) by duarte
Extracted some constants: NO_PDB_CODE, NO_PDB_CHAIN_CODE, NO_CONTACT_TYPE, NO_CUTOFF
Revision 495 - Directory Listing
Modified Wed Jan 2 14:07:57 2008 UTC (11 years, 9 months ago) by stehr
added main function and loading from Multi-model PDB files
Revision 492 - Directory Listing
Modified Wed Jan 2 13:18:57 2008 UTC (11 years, 9 months ago) by duarte
Copied from: branches/aglappe-jung/proteinstructure revision 491
Copied the aglappe-jung branch into trunk.

Revision 487 - Directory Listing
Modified Thu Dec 20 11:19:54 2007 UTC (11 years, 9 months ago) by stehr
Original Path: branches/aglappe-jung/proteinstructure
added new classes RIGEnsemble and FileTypeGuesser (used by Casp Consensus Contact prediction)
Revision 482 - Directory Listing
Modified Wed Dec 19 14:23:32 2007 UTC (11 years, 9 months ago) by stehr
Original Path: branches/aglappe-jung/proteinstructure
added missing class for RR file i/o
Revision 481 - Directory Listing
Modified Wed Dec 19 14:22:36 2007 UTC (11 years, 9 months ago) by stehr
Original Path: branches/aglappe-jung/proteinstructure
added reading from and writing to casp contact prediction (RR) files
Revision 480 - Directory Listing
Modified Wed Dec 19 12:54:56 2007 UTC (11 years, 9 months ago) by duarte
Original Path: branches/aglappe-jung/proteinstructure
New method calculateRadGyration
Revision 478 - Directory Listing
Modified Mon Dec 17 17:03:24 2007 UTC (11 years, 9 months ago) by lpetzo
Original Path: branches/aglappe-jung/proteinstructure
if the pdb file contains SEQRES records we do not allow the sequence length to be shorter than the full-length of the graph. otherwise a PdbfileFormatError is thrown in function read_data_from_file()
Revision 477 - Directory Listing
Modified Mon Dec 17 14:31:38 2007 UTC (11 years, 9 months ago) by duarte
Original Path: branches/aglappe-jung/proteinstructure
Adapted IO methods in NodesAndEdges to JUNG framework:
added 2 classes: 
- GraphIODb: does reading and writing a Graph<V,E> from/to database
- GraphIOGDLFile: does writing of a Graph<V,E> to GDL file for aiSee exporting

Revision 475 - Directory Listing
Modified Thu Dec 13 15:37:40 2007 UTC (11 years, 10 months ago) by duarte
Original Path: branches/aglappe-jung/proteinstructure
Now maxcluster ranking works in all cases. 
Fixed some bugs and tested for both rmsd and gdt
Revision 474 - Directory Listing
Modified Thu Dec 13 13:45:01 2007 UTC (11 years, 10 months ago) by duarte
Original Path: branches/aglappe-jung/proteinstructure
Moved max cluster methods from SimilarityGraph to MaxClusterRunner. Removed SimilarityGraph
Now MaxClusterRunner can do all modes of maxcluster: ranking, matrix, and pairwise
Changed default for DEFAULT_FORCE_CONSTANT in TinkerRunner to 10.0
Revision 472 - Directory Listing
Modified Thu Dec 13 10:18:10 2007 UTC (11 years, 10 months ago) by lpetzo
Original Path: branches/aglappe-jung/proteinstructure
new function: createSelectionString(TreeSet<Integer>)
Revision 470 - Directory Listing
Modified Wed Dec 12 12:03:49 2007 UTC (11 years, 10 months ago) by stehr
Original Path: branches/aglappe-jung/proteinstructure
Pdb objects now return strictly PdbLoadErrors (before, GetterErrors were thrown)
Revision 469 - Directory Listing
Modified Tue Dec 11 14:23:07 2007 UTC (11 years, 10 months ago) by duarte
Original Path: branches/aglappe-jung/proteinstructure
Fixed potentially dangerous bug: was constructing edges wrongly!: with i residue number as the weight!
Revision 468 - Directory Listing
Modified Tue Dec 11 10:11:39 2007 UTC (11 years, 10 months ago) by duarte
Original Path: branches/aglappe-jung/proteinstructure
Fixed bug: now assigning frequency 0 to case where countTotal=0 (no observations)
Revision 465 - Directory Listing
Modified Fri Dec 7 16:53:10 2007 UTC (11 years, 10 months ago) by duarte
Original Path: branches/aglappe-jung/proteinstructure
New feature: now Pdb objects can be restricted to SCOP domains
New member field sid in Pdb and ProtStructGraph if Pdb/ProtStructGraph is restricted to SCOP domain
Revision 464 - Directory Listing
Modified Fri Dec 7 12:01:27 2007 UTC (11 years, 10 months ago) by lpetzo
Original Path: branches/aglappe-jung/proteinstructure
added getter function for the cif-filename
Revision 463 - Directory Listing
Modified Thu Dec 6 19:26:59 2007 UTC (11 years, 10 months ago) by duarte
Original Path: branches/aglappe-jung/proteinstructure
Minor change: comments
Revision 462 - Directory Listing
Modified Thu Dec 6 19:18:19 2007 UTC (11 years, 10 months ago) by duarte
Original Path: branches/aglappe-jung/proteinstructure
Minor change: javadoc
Revision 461 - Directory Listing
Modified Thu Dec 6 19:15:50 2007 UTC (11 years, 10 months ago) by duarte
Original Path: branches/aglappe-jung/proteinstructure
Fixed bug: in removeVertex we were calling getResidueSerial instead of getAtomSerial
Revision 460 - Directory Listing
Modified Thu Dec 6 18:14:59 2007 UTC (11 years, 10 months ago) by duarte
Original Path: branches/aglappe-jung/proteinstructure
Now overriding removeEdge(E) to fix a bug in SparseGraph JUNG2 alpha2
Not implementing anymore SimpleGraph (was useless and it will be removed in coming JUNG2 releases)

Revision 459 - Directory Listing
Modified Thu Dec 6 15:05:43 2007 UTC (11 years, 10 months ago) by stehr
Original Path: branches/aglappe-jung/proteinstructure
moved GraphAverager to subpackage, added removeVertex function to RIGraph and AIGraph, added getEdgeFromSerials and containsEdgeIJ functions to ProtStructGraph
Revision 456 - Directory Listing
Modified Tue Dec 4 19:03:54 2007 UTC (11 years, 10 months ago) by duarte
Original Path: branches/aglappe-jung/proteinstructure
Now also reads secondary structure
Revision 455 - Directory Listing
Modified Tue Dec 4 19:01:47 2007 UTC (11 years, 10 months ago) by duarte
Original Path: branches/aglappe-jung/proteinstructure
Minor change : fixed comments
Revision 454 - Directory Listing
Modified Tue Dec 4 18:58:14 2007 UTC (11 years, 10 months ago) by duarte
Original Path: branches/aglappe-jung/proteinstructure
Fixed bug: getCommaSeparatedResSerials was failing when there was 0 neighbors
Revision 452 - Directory Listing
Modified Tue Dec 4 15:40:17 2007 UTC (11 years, 10 months ago) by duarte
Original Path: branches/aglappe-jung/proteinstructure
New class NbhoodBackgrnd representing a set of neighbourhoods loaded from a set of graphs of a non redundant pdb structures set.
Rewrote RIGNbhood so that the TreeMap now contains also the central residue. Added methods equals() and match().
Adapted RIGraph.getNbhood to the new constructor in RIGNbhood
Revision 448 - Directory Listing
Modified Tue Dec 4 15:19:15 2007 UTC (11 years, 10 months ago) by lpetzo
Original Path: branches/aglappe-jung/proteinstructure
class *Pdb:
- implemented new exception handling scheme for function Getter.get() -> getChains() and getModels() throw all possible exceptions encapsulated in GetterError exceptions
Revision 444 - Directory Listing
Modified Tue Dec 4 10:18:21 2007 UTC (11 years, 10 months ago) by filippis
Original Path: branches/aglappe-jung/proteinstructure
Pdb.java:
-calc_atom_dist_matrix method added
-calc_dist_matrix works also for multi atom contact types by choosing the min distance
Revision 443 - Directory Listing
Modified Fri Nov 30 13:38:35 2007 UTC (11 years, 10 months ago) by duarte
Original Path: branches/aglappe-jung/proteinstructure
Now not using ORDER BY in nodes and edges queries, was useless and slowing down queries
Now reading correctly empty graphs, just keeping it empty without throwing exception
Revision 441 - Directory Listing
Modified Thu Nov 29 15:19:37 2007 UTC (11 years, 10 months ago) by duarte
Original Path: branches/aglappe-jung/proteinstructure
Now Pdb constructors don't load data but rather intialise the pdbCode, loading occurs upon call of load(pdbChainCode,modelSerial)
New methods getChains() and getModels() in all Pdb classes
New Exception PdbLoadError
New tester for getChains and getModels: testGetChains
Changed all calls to Pdb construction accordingly (includes changing excpetions)
Revision 438 - Directory Listing
Modified Wed Nov 28 15:44:57 2007 UTC (11 years, 10 months ago) by filippis
Original Path: branches/aglappe-jung/proteinstructure
AAInfo
-isValidContactType, isValidSingleAtomContactType, isValidMultipleAtomContactType takes into account the directionality, the overlapping atoms and the "+"
-isOverlapping method has been added

AIGEdge
-copy method added

AIGNode
-equals and copy methods has been added

AIGraph
-getRIGraph now takes argument directed and directionality doesn't depend anymore on isCrossed
-distances are now set for RIGNodes in getRIGraph
-for undirected, crossed graphs we take care not to add parallel RIGedges in getRIGraph
-we set now the secondaryStructure object of RIGraph in getRIGraph
-addGraph has been added

Box
-we throw away wrong check in getDistancesWithinBox - read the comment

DbRIGraph
-constructors now take argument directed and directionality doesn't depend anymore on isCrossed
-distances are read also from db and set for RIGEdges

Pdb
-get_graph now takes as argument directed and directionality doesn't depend anymore on isCrossed
-there is check for forbidden cts in get_graph
-cts with + are taken into account in get_graph

RIGEdge
-setAtomWeight and setDistance methods have been added

RIGNode
-equals method has been added

RIGraph
-getObsLength has been deleted
-we take care now of the new cts (+,undirected crossed), of null secondary structure case and of distances in write_graph_to_db and write_graph_to_db_fast

genDbGraph
-argument for directionality is now added


Revision 435 - Directory Listing
Modified Wed Nov 28 12:11:11 2007 UTC (11 years, 10 months ago) by duarte
Original Path: branches/aglappe-jung/proteinstructure
Reverted to unobserved RIGNodes not present in the RIGraph
Revision 434 - Directory Listing
Modified Wed Nov 28 09:34:44 2007 UTC (11 years, 10 months ago) by duarte
Original Path: branches/aglappe-jung/proteinstructure
Changed behaviour of observed/unobserved nodes in RIGraph: now unobserved RIGnodes are also in the RIGraph, tagged with observed=false.
Thus getObsLength() in ProtStructGraph (which by the way was not working for AIGraphs) is now only in RIGraph and adapted to the new way of tagging unobserved nodes.
New method hasSequence() in ProtStrucGraph and Pdb: it is important to know that from now only if hasSequence()==true we put the unobserved nodes in RIGraph, otherwise we don't put them (as before)
Revision 433 - Directory Listing
Modified Tue Nov 27 17:58:26 2007 UTC (11 years, 10 months ago) by duarte
Original Path: branches/aglappe-jung/proteinstructure
Added more comments

Revision 428 - Directory Listing
Modified Mon Nov 26 16:01:11 2007 UTC (11 years, 10 months ago) by duarte
Original Path: branches/aglappe-jung/proteinstructure
Fixed bug: was missing last sequence element when adding gap nodes
Revision 427 - Directory Listing
Modified Mon Nov 26 15:57:37 2007 UTC (11 years, 10 months ago) by duarte
Original Path: branches/aglappe-jung/proteinstructure
Fixed bug in PairwiseAlignmentGraphConverter: was not adding the nodes for gaps, also some other minor bugs fixed in copying of objects
Fixed bug in getAllCommonNbhSizes, 1) now returning a HashMap on 
Pair<Integer>, not Pair<RIGNode> 2) was filling cells when size=0
Added method getIncidentNodes to IntPairSet as a temporary fix

Revision 426 - Directory Listing
Modified Fri Nov 23 18:04:15 2007 UTC (11 years, 10 months ago) by duarte
Original Path: branches/aglappe-jung/proteinstructure
Now PairWiseAlignmentConverter and PairwiseAlignmentGraphConverter work in the new JUNG framework.
New class IntPairComparator
Now sorting output in RIGraph.write_graph_to_file
Revision 424 - Directory Listing
Modified Fri Nov 23 14:21:33 2007 UTC (11 years, 10 months ago) by duarte
Original Path: branches/aglappe-jung/proteinstructure
Added last i/o method from old Graph (write to file in Ioannis network format)
Using now the more correct degree, indegree, outdegree methods instead of count neighbor methods
Fixed the write_graph_to_file method name in executables in default package

Revision 423 - Directory Listing
Modified Fri Nov 23 13:37:17 2007 UTC (11 years, 10 months ago) by duarte
Original Path: branches/aglappe-jung/proteinstructure
New methods in RIGraph copy() and compare(other)
Basic testing of copy introduced on testJUNGframework
Revision 422 - Directory Listing
Modified Fri Nov 23 10:08:40 2007 UTC (11 years, 10 months ago) by duarte
Original Path: branches/aglappe-jung/proteinstructure
Now selection string stuff working: transfered methods from old NodeSet to Interval as static methods.
Revision 421 - Directory Listing
Modified Thu Nov 22 19:42:11 2007 UTC (11 years, 10 months ago) by duarte
Original Path: branches/aglappe-jung/proteinstructure
Now graph generation in Pdb also works when we pass a crossed contact type with overlapping atom sets, e.g. ALL/BB (changes were: added a couple of new conditions in Box and in Pdb's AIGraph getGraph(ct,cutoff))
Loads of better comments
Revision 420 - Directory Listing
Modified Thu Nov 22 17:27:44 2007 UTC (11 years, 10 months ago) by duarte
Original Path: branches/aglappe-jung/proteinstructure
First implementation of the new graph framework using JUNG2. Still a few classes to fix, but all basic functionality is there.
NOTE: at the moment ProtStructGraph is a SparseGraph which doesn't guarantee that the graph has no parallel or loop edges (I thought that would be solved by using the SimpleGraph interface but it doesn't, that's only a marker interface)
Revision 419 - Directory Listing
Modified Thu Nov 22 14:09:18 2007 UTC (11 years, 10 months ago) by duarte
Original Path: branches/aglappe-jung/proteinstructure
Re-branching for JUNG2 development
Revision 414 - Directory Listing
Modified Thu Nov 22 10:09:50 2007 UTC (11 years, 10 months ago) by duarte
Minor changes. Got rid of some warnings
Revision 412 - Directory Listing
Modified Wed Nov 21 16:12:26 2007 UTC (11 years, 10 months ago) by filippis
Changes in Pdb
-checkConsurfHssp: in the mistakes calculated I add now at the end the difference between the number of residues and the number of consurf scores

-writeAtomLines has now a boolean argument called pdbCompatible: if pdbCompatible is true, then only the first character of chainCode and not the 'whole' chainCode is exported to the file.
-another WriteAtomLines has also been added without this extra argument for backwards compatibility: default value for pdbCompatible is false
-dump2pdbfile has also been changed in similar way
-runDssp and runNaccess now call the above methods with true pdbCompatible

Changes in genDbGraph
-1 summary output line has been added to provide info about csa, naccess, scop, ec, dssp, ...
-DSSP is run with 3state
Revision 410 - Directory Listing
Modified Tue Nov 20 19:40:36 2007 UTC (11 years, 10 months ago) by filippis
minor change
Revision 408 - Directory Listing
Modified Tue Nov 20 18:44:03 2007 UTC (11 years, 10 months ago) by filippis
minor change
Revision 407 - Directory Listing
Modified Tue Nov 20 18:41:56 2007 UTC (11 years, 10 months ago) by filippis
contactTypes.dat 
-SC_CAGLY contact type added

SecStrucElement.java
-getSheetSerial method is now public

Pdb.java
-writeToDbFast added

Graph.java
-write_graph_to_db_fast
-expBB,CW,CT,CR,w,d are now taken into account in a correct way
-node_id, sssid, sheetSerial and turn are now also filled in

DbGraph.java
-expBB,CW,CT,CR,w,d are now taken into account in a correct way
-directionality is also taken into account now when reading edges

genDbGraph.java
-sequence separation added as option

createGraphDb.java added

Revision 406 - Directory Listing
Modified Tue Nov 20 16:50:32 2007 UTC (11 years, 10 months ago) by duarte
Reverting to last revision, changes made in 405 were wrong
Revision 405 - Directory Listing
Modified Tue Nov 20 16:37:54 2007 UTC (11 years, 10 months ago) by duarte
Alignment and PairwiseAlignmentConverter now using Interval, IntervalSet and TreeSet<Integer> to replace Edge, EdgeSet and NodeSet
New class IntervalSet
Revision 404 - Directory Listing
Modified Fri Nov 16 17:22:33 2007 UTC (11 years, 11 months ago) by duarte
Not asserting anymore pdbChainCode to be uppercase. pdb chain codes are case sensitive!
Revision 403 - Directory Listing
Modified Fri Nov 16 16:52:03 2007 UTC (11 years, 11 months ago) by filippis
OXT is taken into account now also for BB contact type
Revision 402 - Directory Listing
Modified Thu Nov 15 16:15:32 2007 UTC (11 years, 11 months ago) by duarte
Forgot CiffilePdb!: not forcing upper casing of chainPdbCode. pdb chain codes are case sensitive!!!
Revision 401 - Directory Listing
Modified Thu Nov 15 15:58:30 2007 UTC (11 years, 11 months ago) by duarte
Not forcing upper casing of chainPdbCode. pdb chain codes are case sensitive!!!
Revision 400 - Directory Listing
Modified Tue Nov 13 15:55:30 2007 UTC (11 years, 11 months ago) by filippis
-pdb_seq_num is used instead of auth_seq_num in get_ressers_mappings. Now resser2pdbresser contains all residues even the unobserved ones. This has been changed in PdbasePdb and CiffilePdb classes.

-pdb_strand_id not needed in the query in read_seq in PdbasePdb class. Asym_id and pdb_strand_id have 1-1 mapping in case sensitive mode.

-comments have been added about the entity_id-asym_id-pdb_strand_id 1-1-1 mapping and some filters in queries that are no longer necessary.
Revision 399 - Directory Listing
Modified Mon Nov 12 15:56:00 2007 UTC (11 years, 11 months ago) by stehr
added class PairwiseSequenceAlignment
Revision 397 - Directory Listing
Modified Thu Nov 8 16:04:21 2007 UTC (11 years, 11 months ago) by filippis
Pdb code forced to lowercase in CiffilePdb
Revision 394 - Directory Listing
Modified Thu Nov 8 12:40:01 2007 UTC (11 years, 11 months ago) by duarte
New method getMotifReducedAlphabet to get neighbourhood strings in Michael's reduced style (must pass a Graph with weights which indicate BB or SC domination)
Revision 391 - Directory Listing
Modified Thu Nov 8 11:22:40 2007 UTC (11 years, 11 months ago) by stehr
started implementing a wrapper for the Maxcluster application (some related code is now in SimilarityGraph but should be moved to MaxClusterRunner in the future)
Revision 388 - Directory Listing
Modified Thu Nov 8 11:14:01 2007 UTC (11 years, 11 months ago) by duarte
New method setSequence
Revision 387 - Directory Listing
Modified Wed Nov 7 21:37:20 2007 UTC (11 years, 11 months ago) by filippis
deleted the print part in the checkCSA method in pdb class
Revision 385 - Directory Listing
Modified Wed Nov 7 17:32:43 2007 UTC (11 years, 11 months ago) by lpetzo
NEW TYPES
---------
- FileFormatError
- FastaFileFormatError
- PirFileFormatError
- AlignmentConstructionError

MODIFICATIONS
-------------
class Alignment:
- introduced new exceptions to be throw whenever file format error have been detected or any other construction errors occur
- changed accession rules of function getGapCharacter from "public" to "public static"
- new functions:
 * writeFasta
 
class CiffileFormatError:
- changed super class from Exception to the new FileFormatError class

class GraphFileFormatError:
- s. class CiffileFormatError

class PairwiseAlignmentConverter:
- added exception handling features due to class Alignment

class PairwiseAlignmentGraphConverter:
- s. class PairwiseAlignmentConverter

class PdbFileFormatError:
- s. class CifffileFormatError
Revision 384 - Directory Listing
Modified Tue Nov 6 18:53:11 2007 UTC (11 years, 11 months ago) by filippis
hasCSA and getCSA methods added in Pdb.java
Revision 383 - Directory Listing
Modified Tue Nov 6 18:35:17 2007 UTC (11 years, 11 months ago) by filippis
inSameSheet, isOther and getSheetSerial methods added in SecStrucElement
Revision 382 - Directory Listing
Modified Tue Nov 6 15:42:05 2007 UTC (11 years, 11 months ago) by filippis
Methods added for:
-parsing CSA
-parsing EC
-parsing CONSURF-HSSP
-running & parsing Naccess
-parsing SCOP
-writing residues' info in a db table

Modifications have been also made in DSSP parsing:
-sheet serial is taken into account
-flexibility in reduced state preferred
Revision 380 - Directory Listing
Modified Fri Nov 2 17:26:43 2007 UTC (11 years, 11 months ago) by lpetzo
added a new version of getDiffDistMap(...) that take a sequence alignment as an input to allow for residue mappings between two pdb-models of different size
Revision 379 - Directory Listing
Modified Fri Nov 2 14:22:54 2007 UTC (11 years, 11 months ago) by stehr
redesign of TinkerRunner: added 2 reconstruct methods, one which generates normal tinker output for a given number of models, and one fully automatic one which simply returns one pdb object;
updated reconstruct.java to make use of the new TinkerRunner method;
updated GraphAverager: now assigning edgetype and cutoff to consensus graph

Revision 378 - Directory Listing
Modified Thu Nov 1 15:46:58 2007 UTC (11 years, 11 months ago) by stehr
finally implemented the setCutoff method ;)
Revision 377 - Directory Listing
Modified Thu Nov 1 15:02:56 2007 UTC (11 years, 11 months ago) by stehr
fixed nasty bug in constructor Graph(sequence) (residue indexing was wrong)
Revision 376 - Directory Listing
Modified Thu Nov 1 14:14:24 2007 UTC (11 years, 11 months ago) by stehr
added method setCutoff() and some javadocs
Revision 374 - Directory Listing
Modified Wed Oct 31 16:40:29 2007 UTC (11 years, 11 months ago) by duarte
Fixed bug: getContacts was not copying weights
Got rid of useless copyKeepingNodes(), made main Graph constructor public. Some new setters and getters
Revision 372 - Directory Listing
Modified Wed Oct 31 10:20:22 2007 UTC (11 years, 11 months ago) by lpetzo

Revision 365 - Directory Listing
Modified Tue Oct 23 08:36:58 2007 UTC (11 years, 11 months ago) by duarte
New method getEdge in EdgeSet, necessary since we introduced weights in the Edge class. To retrieve them we first need to retrieve the actual Edge object
Revision 363 - Directory Listing
Modified Fri Oct 19 15:45:49 2007 UTC (11 years, 11 months ago) by filippis
Method writeUndirUnweightGraphToNetworkFiles added in Graph class
Revision 362 - Directory Listing
Modified Thu Oct 18 15:08:09 2007 UTC (11 years, 11 months ago) by stehr
renamed precision to accuracy (in accordance with Casp)
Revision 361 - Directory Listing
Modified Wed Oct 17 17:40:18 2007 UTC (11 years, 11 months ago) by duarte
Now weights are kept in the Edge objects rather than separately in a member variable in Graph
Revision 360 - Directory Listing
Modified Wed Oct 17 16:10:28 2007 UTC (11 years, 11 months ago) by stehr
Graph,PredEval: added fields coverage and title to predEval (and evalPrediction)
GraphAverager: added method to return average graph (with weighted edges)
PdbfilePdb: fixed bug when reading from Casp prediction files
Revision 357 - Directory Listing
Modified Wed Oct 17 08:01:13 2007 UTC (12 years ago) by duarte
Fixed bug: now does correctly quoting for any of the 3 cases: "", '' or ;;. Does also correctly multiline parsing of ;; quoted fields. Passed testing on cullpdb 90 (more than 9000 pdb entries)
Revision 356 - Directory Listing
Modified Sat Oct 13 15:55:41 2007 UTC (12 years ago) by duarte
Fixed bug: wasn't tokenising well when first field in line was quoted
Revision 355 - Directory Listing
Modified Fri Oct 12 18:42:37 2007 UTC (12 years ago) by duarte
FIXED BUG: now doesn't fail with records that are delimited with \n; ;\n
Method tokeniseFields is now completely rewritten: is what does all the magic of parsing all the oddities of the mmcif format
Using RandomAccessFile to open the file only once and then seek to the positions we need to scan at each point. Might be slower due to the RandomAccessFile that does no buffering. Also maybe because the new tokenisation is not very optimal
Now parseCifFile does the whole parsing calling also the submethods instead of calling them in the constructor
Revision 353 - Directory Listing
Modified Thu Oct 11 13:00:12 2007 UTC (12 years ago) by duarte
Changed constructor with all parameters to protected, now shouldn't be used at all outside of package
Revision 352 - Directory Listing
Modified Thu Oct 11 12:49:08 2007 UTC (12 years ago) by stehr
Major redesign of NodeSet, now contains objects of new class Node. Nodes are essentially integer which can have additional properties. Added equals methods to NodeSet, EdgeSet, NodesAndEdges. Moved some methods from SimilarityGraph to NodesAndEdges.
Revision 345 - Directory Listing
Modified Wed Oct 10 16:27:12 2007 UTC (12 years ago) by duarte
Fixed documentation
Revision 337 - Directory Listing
Modified Thu Oct 4 10:12:49 2007 UTC (12 years ago) by stehr
Added two new constructors for Graph (sequence only and no parameters), changed interface of GraphAverager (pass target sequence instead of target graph), extracted constant DEFAULT_WEIGHT in Edge.
Revision 336 - Directory Listing
Modified Tue Oct 2 16:14:20 2007 UTC (12 years ago) by stehr
extracted constant NULL_CHAIN_CODE from ...Pdb classes, added copy() methods to NodeSet and EdgeSet, added some functionality to NodesAndEdges, new class SimilarityGraph
Revision 335 - Directory Listing
Modified Tue Oct 2 14:59:28 2007 UTC (12 years ago) by duarte
Now ConstraintsMaker works also for multi atom contact types (BB and SC) and crosses (either BB/SC or any cross to a single atom contact type)
New file aapairsBounds.dat with values for aminoacid side chains distance lower and upper bounds taken from statistics of a set of pdb representatives
New in AAinfo: aapairs2bounds and changed getUpperBoundDistance, getUpperBoundDistance to accomodate aapairs2bounds
PRMInfo: now for amber "OXT" gets transformed into "O"
Revision 334 - Directory Listing
Modified Tue Oct 2 07:35:26 2007 UTC (12 years ago) by stehr
New class NodesAndEdges (simple graph class), some added javadocs
Revision 332 - Directory Listing
Modified Mon Oct 1 16:20:06 2007 UTC (12 years ago) by stehr
added constructor for trivial alignment, renamed getSequence to getAlignedSequence
Revision 331 - Directory Listing
Modified Mon Oct 1 16:12:48 2007 UTC (12 years ago) by duarte
Better handling of graph averaging for different thresholds
Refactored predict to doAveraging, not returning anymore a Grap but rather modifying the reference
Revision 330 - Directory Listing
Modified Mon Oct 1 15:57:22 2007 UTC (12 years ago) by stehr
added a weight field to Edge class (set using alternative constructor, maintaining backwards compatibility)
Revision 329 - Directory Listing
Modified Mon Oct 1 15:41:28 2007 UTC (12 years ago) by duarte
Added GraphAverager class and PredEval class. GraphAverager copied from HomologyPredictor (in CMPredict): doing the averaging correctly now
Added method evaluatePrediction to Graph
Some refactoring in Alignment and better javadocs
Revision 328 - Directory Listing
Modified Mon Oct 1 10:57:08 2007 UTC (12 years ago) by duarte
First commit of ConstraintsMaker (and PRMInfo needed for it)
Does correct atom serial mapping when using amber prm files, except for some atoms of ASP, ARG, GLU, PHE, TYR (where there are some nomenclature differences between amber and pdb)
Does not work yet with multi atom contact types, should work fine for all single atom contact types and for crossed single atom contact types
The pdb/xyz atom mapping using coordinates (as in python) is commented out because it doesn't work due to rounding differences between java and fortran
Thus the PRMInfo class was needed, at the moment can read only amber prm files
Some new methods and better javadoc in Pdb.
Some new methods in AAinfo
Revision 326 - Directory Listing
Modified Thu Sep 20 14:49:55 2007 UTC (12 years ago) by duarte
Removed class AA and replace it by AAinfo, which reads contact types from separate file contactTypes.dat
New class ContactType which contains atoms for each contact type and residue. A static object for each contact type is loaded into AAinfo upon reading the contactTypes.dat file
Changed all references accordingly
Revision 325 - Directory Listing
Modified Thu Sep 20 10:48:55 2007 UTC (12 years ago) by stehr
added parsing of residue selection strings
Revision 324 - Directory Listing
Modified Tue Sep 18 16:28:58 2007 UTC (12 years ago) by duarte
2 new methods: getAllAtomSerials, getAtomCoord
Revision 323 - Directory Listing
Modified Tue Sep 18 14:13:14 2007 UTC (12 years ago) by duarte
Moved tinker stuff to its own package
Revision 322 - Directory Listing
Modified Tue Sep 18 13:59:33 2007 UTC (12 years ago) by duarte
Initial commit of TinkerRunner and exception class to go with it TinkerError
Revision 320 - Directory Listing
Modified Tue Sep 18 08:38:33 2007 UTC (12 years ago) by stehr
added calculation of difference distance map
Revision 319 - Directory Listing
Modified Mon Sep 17 16:10:32 2007 UTC (12 years ago) by stehr
added constructors for loading from online pdb
Revision 318 - Directory Listing
Modified Mon Sep 17 10:37:31 2007 UTC (12 years ago) by stehr
added some javadoc comments
Revision 317 - Directory Listing
Modified Thu Sep 13 16:09:10 2007 UTC (12 years, 1 month ago) by duarte
Fixed some comments
Revision 315 - Directory Listing
Modified Thu Sep 13 08:13:40 2007 UTC (12 years, 1 month ago) by duarte
Now parsing each element in different methods (re-opening the file). Parsing first pdbx_poly_seq_scheme so we get the chainCode that we can use for reading the rest
Now taking care of cases where struct_sheet_range is not a loop element
In tokeniseFields now also unquoting double-quoted strings
Tested on a set of 12000 entries
Revision 314 - Directory Listing
Modified Wed Sep 12 14:50:48 2007 UTC (12 years, 1 month ago) by duarte
Checking number of fields per line in loop elements and throwing exception if count is not correect
Doing tokenisation of lines through new function that takes care of possible quoted string with spaces
New exception CiffileFormatError
Checking 1st line of cif file has correct format: data_1xxx, if not throwing exception

Revision 311 - Directory Listing
Modified Thu Aug 30 17:31:38 2007 UTC (12 years, 1 month ago) by duarte
Fixed buf: sometimes struct_conf can be non-loop elements, now also taking care of that particular case
Revision 310 - Directory Listing
Modified Thu Aug 30 16:00:08 2007 UTC (12 years, 1 month ago) by duarte
Bug with '?' in auth_seq_num was not really fixed. Now should be fine: behaviour is the same as PdbasePdb
Revision 309 - Directory Listing
Modified Thu Aug 30 15:55:53 2007 UTC (12 years, 1 month ago) by duarte
Fixed bug: needed to read alt locs in advance in another scan of the file because the order of the elements in the cif file is not guaranteed. As read of atom_site needs of alt locs, we need to do first the parsing of atom_sites_alt
Revision 308 - Directory Listing
Modified Thu Aug 30 14:54:38 2007 UTC (12 years, 1 month ago) by duarte
Fixed bugs:
- was reading HETATM lines as well as ATOM in atom_site
- auth_seq_num with '?' not taken now when populating the pdbresser2resser map (same behaviour as in PdbasePdb)
- now using chainCodeStr and auth_asym_id to identify chains in pdbx_poly_seq_scheme, struct_conf and struct_sheet_range. atom_site is not guaranteed to appear in file before all the others so we can't rely on having read a chainCode (asym_id) when parsing the other elements
Revision 307 - Directory Listing
Modified Thu Aug 30 10:41:55 2007 UTC (12 years, 1 month ago) by duarte
Now taking indices for fields from parsed field names. Still only minimal testing
Revision 306 - Directory Listing
Modified Thu Aug 30 09:09:24 2007 UTC (12 years, 1 month ago) by duarte
First implementation of mmCIF file parser. Tested minimally.
Revision 305 - Directory Listing
Modified Wed Aug 29 09:46:32 2007 UTC (12 years, 1 month ago) by duarte
Got rid of useless (and potential bug) chainCode=getChainCode (self reference!)
Revision 302 - Directory Listing
Modified Mon Aug 27 14:28:23 2007 UTC (12 years, 1 month ago) by stehr
changes to calcGridDensity, now also counts number of neighbouring non-empty grid cells
Revision 301 - Directory Listing
Modified Mon Aug 27 14:26:48 2007 UTC (12 years, 1 month ago) by stehr
changed constant for unknown pdb code from "Unknown" to XXXX
Revision 288 - Directory Listing
Modified Fri Aug 17 15:03:22 2007 UTC (12 years, 1 month ago) by spriya
Better checks for sequence equality in compare
Revision 287 - Directory Listing
Modified Fri Aug 17 14:32:14 2007 UTC (12 years, 1 month ago) by duarte
Now also filling chain_pdb_code in write_graph_to_db
Revision 286 - Directory Listing
Modified Fri Aug 17 12:40:00 2007 UTC (12 years, 1 month ago) by spriya
Fixed bug in  compare, wasn't assigning new weights
Revision 284 - Directory Listing
Modified Thu Aug 16 14:57:31 2007 UTC (12 years, 2 months ago) by duarte
Introduced weights in Graph objects: we can read them from file or db and write them into file or db. On calling pdb.get_graph the weighs are taken as number of atom-edges per residue-edge (similar to Ioannis weights in chain_graph tables)
Revision 283 - Directory Listing
Modified Wed Aug 15 10:22:36 2007 UTC (12 years, 2 months ago) by duarte
Wasn't deep copying secondary structure when passing it to Graph
Revision 282 - Directory Listing
Modified Tue Aug 14 16:15:59 2007 UTC (12 years, 2 months ago) by duarte
Made get_graph a bit less memory hungry, by using a float[][] instead of double[][]
Not printing warnings about missing atoms anymore
Revision 281 - Directory Listing
Modified Tue Aug 14 13:49:52 2007 UTC (12 years, 2 months ago) by stehr
fixed little bug in NodeNbh
Revision 280 - Directory Listing
Modified Tue Aug 14 12:38:51 2007 UTC (12 years, 2 months ago) by stehr
changed internal implementation of runDssp method (not using getFullLength anymore)
Revision 279 - Directory Listing
Modified Tue Aug 14 12:26:28 2007 UTC (12 years, 2 months ago) by duarte
Fixed bug in Graph constructor: was not getting correct fullLength (related to last bug fix)
Revision 278 - Directory Listing
Modified Tue Aug 14 12:14:04 2007 UTC (12 years, 2 months ago) by duarte
Fixed bug with getFullLength when reading from pdb file
Now if SEQRES was missing then fullLength is maximum observed residue number instead of total number of observed residue numbers
New member variables obsLength and fullLength
Revision 276 - Directory Listing
Modified Tue Aug 14 10:53:27 2007 UTC (12 years, 2 months ago) by duarte
Added secondary structure to write_graph_to_db
New method getNumSecStructureElements in SecondaryStructure
Revision 275 - Directory Listing
Modified Tue Aug 14 10:28:01 2007 UTC (12 years, 2 months ago) by duarte
Fixed bug: wasn't taken into account OXT atoms in calculating the ALL graph
Revision 274 - Directory Listing
Modified Tue Aug 14 10:26:32 2007 UTC (12 years, 2 months ago) by stehr
Added new SecondaryStructure object to Pdb and Graph
Revision 263 - Directory Listing
Modified Mon Aug 13 11:48:23 2007 UTC (12 years, 2 months ago) by duarte
Fixed potential bug in regex for ATOM lines
Revision 262 - Directory Listing
Modified Mon Aug 13 08:55:05 2007 UTC (12 years, 2 months ago) by duarte
Was still not fixed!, forgot to insert X for non standard aa
Revision 261 - Directory Listing
Modified Mon Aug 13 08:53:11 2007 UTC (12 years, 2 months ago) by duarte
Fixed reading of SEQRES, was putting nulls for non-standard aas
Revision 260 - Directory Listing
Modified Fri Aug 10 18:30:47 2007 UTC (12 years, 2 months ago) by duarte
Implemented write_graph_to_db
New member variable model in Graph, thus changed constructor
New methods to get degree of a node in Graph
New methos in NodeNbh to write other kinds of neighbourhood strings
Revision 259 - Directory Listing
Modified Fri Aug 10 16:40:44 2007 UTC (12 years, 2 months ago) by stehr
completed first version of dssp secondary structure assignment, can be switched on/off by status variable in Start, some other little fixes
Revision 258 - Directory Listing
Modified Fri Aug 10 16:06:53 2007 UTC (12 years, 2 months ago) by duarte
Now reading sequence from SEQRES lines. This fixes bug in cmview window was not showing whole contact map because of size of contact map was set to number of observed residues size
Revision 257 - Directory Listing
Modified Thu Aug 9 16:43:32 2007 UTC (12 years, 2 months ago) by stehr
fixed bugs in ATOM line export (atom names were wrongly aligned & added three more columns after coordinates), added method to run DSSP (still incomplete)
Revision 256 - Directory Listing
Modified Thu Aug 9 14:21:39 2007 UTC (12 years, 2 months ago) by duarte
Added getNumAtoms
Revision 255 - Directory Listing
Modified Thu Aug 9 13:45:10 2007 UTC (12 years, 2 months ago) by stehr
PdbfilePdb now also accepts Casp prediction files ('PFRMAT TS' instead of 'HEADER')
Revision 252 - Directory Listing
Modified Thu Aug 9 10:37:14 2007 UTC (12 years, 2 months ago) by duarte
Made constructor public
Revision 250 - Directory Listing
Modified Mon Aug 6 14:48:37 2007 UTC (12 years, 2 months ago) by stehr
added application to count grid density, suppressed warning for secondary structure reassignment
Revision 249 - Directory Listing
Modified Sat Aug 4 17:53:11 2007 UTC (12 years, 2 months ago) by duarte
New methods containsContact and resetContacts
Revision 248 - Directory Listing
Modified Sat Aug 4 17:50:00 2007 UTC (12 years, 2 months ago) by duarte
Added method hasTag
Revision 247 - Directory Listing
Modified Sat Aug 4 17:07:23 2007 UTC (12 years, 2 months ago) by duarte
Made regex a constant and added | and \\-
Revision 246 - Directory Listing
Modified Sat Aug 4 17:00:58 2007 UTC (12 years, 2 months ago) by duarte
Doing now everythin with maps (using seqTags) rather than arrays. Cleaned up, refactored, using more consistent naming
Revision 245 - Directory Listing
Modified Sat Aug 4 15:40:20 2007 UTC (12 years, 2 months ago) by duarte
Added reverse map (from sequences serials to alignment serials) and did a bit of refactoring
Revision 244 - Directory Listing
Modified Wed Aug 1 14:34:36 2007 UTC (12 years, 2 months ago) by duarte
Initial commit of Alignmnent, a class representing a multiple sequence alignment
Revision 242 - Directory Listing
Modified Wed Aug 1 07:47:18 2007 UTC (12 years, 2 months ago) by duarte
Got rid of doneRes ArrayList in getRanks, was redundant
Revision 241 - Directory Listing
Modified Tue Jul 31 16:38:13 2007 UTC (12 years, 2 months ago) by duarte
Now dealing correctly with ties.
Implemented getResiduesSortedByRank
Changed dist to be a TreeMap
Revision 240 - Directory Listing
Modified Tue Jul 31 13:51:59 2007 UTC (12 years, 2 months ago) by duarte
Fixed bug in delEdge. Wasn't taking care of if contact was given as i>j in undirected case. Also recount of contacts and set of modified to true was wrong
Revision 239 - Directory Listing
Modified Mon Jul 30 10:57:28 2007 UTC (12 years, 2 months ago) by duarte
Fixed bug in addEdge method. In case of undirected we need to check that the contact is inserted in the right order j>i
Revision 238 - Directory Listing
Modified Fri Jul 20 10:02:03 2007 UTC (12 years, 2 months ago) by duarte
Optimised slightly the compareTo method in Edge
Revision 237 - Directory Listing
Modified Thu Jul 19 14:23:35 2007 UTC (12 years, 2 months ago) by duarte
Now rmsd calculation works for 2 Pdb objects where there are missing residues (unobserved) or missing atoms
New Exception ConformationNotSameSizeError
Still not printing out individual distances between 2 conformations (altghough it is possible)
Can't specify yet a restricted range of residues to calculate rmsd only with them
Revision 236 - Directory Listing
Modified Thu Jul 19 12:57:29 2007 UTC (12 years, 2 months ago) by duarte
Fixed bug. Was not doing correctly reflection along smallest principal axis in is_reflection case
Revision 235 - Directory Listing
Modified Thu Jul 19 12:43:12 2007 UTC (12 years, 2 months ago) by duarte
Implemented rmsd calculation (based on Jama matrix package)
rmsd method still not taking care of unobserved or missing atoms. Also not returning individual distances between optimally superimposed structures (although it can calculate them in commented out code)

Revision 234 - Directory Listing
Modified Tue Jul 10 14:14:58 2007 UTC (12 years, 3 months ago) by duarte
Made ContactList a TreeSet instead of an ArrayList, should improve performance (log(n) rather than linear)
REFACTORING: 
ContactList -> EdgeSet
Contact -> Edge
Revision 233 - Directory Listing
Modified Tue Jul 10 13:01:50 2007 UTC (12 years, 3 months ago) by duarte
Added method getCopy
Revision 232 - Directory Listing
Modified Tue Jul 10 13:00:23 2007 UTC (12 years, 3 months ago) by duarte
Now checking in addEdge that we don't duplicate edges
New methods: get2ndshell, copyKeepingNodes
Revision 230 - Directory Listing
Modified Mon Jul 9 15:35:01 2007 UTC (12 years, 3 months ago) by stehr
added class NodeSet
Revision 229 - Directory Listing
Modified Mon Jul 9 15:02:24 2007 UTC (12 years, 3 months ago) by duarte
Now calculate_dist_matrix returns the matrix with residue serials as indices (rather than atom serials)
Now AA.isValidSingleCT and AA.isValidMultiCT check also for crossed cases
Revision 228 - Directory Listing
Modified Mon Jul 9 14:32:47 2007 UTC (12 years, 3 months ago) by duarte
Now can do crossed contacts also with geometric hashing
Renamed getGraphGeometricHashing to get_graph (so interface remains as it was before we introduced the geometric hashing)
Revision 226 - Directory Listing
Modified Fri Jul 6 13:43:30 2007 UTC (12 years, 3 months ago) by duarte
First geometric hashing implementation for calculating graph (with new class Box). Only does non-crossed cts
Geometrich hashing graph calculation kept in a separate method than normal get_graph. Still either of the methods can be used.
Using javax.vectormath objects for the vectors (distance method also from that)
Using TreeMap for get_coords_for_ct
Revision 224 - Directory Listing
Modified Thu Jul 5 13:42:37 2007 UTC (12 years, 3 months ago) by duarte
Now calculate distance matrix uses HashMap instead of TreeMap
Needed to change the hashCode function in Contact to make it faster
Revision 223 - Directory Listing
Modified Thu Jul 5 10:17:30 2007 UTC (12 years, 3 months ago) by duarte
Added cross contacts to isValidCT
Revision 222 - Directory Listing
Modified Wed Jul 4 15:39:01 2007 UTC (12 years, 3 months ago) by duarte
New secstruct2resinterval TreeMap to store secondary structure elements as a map of ss string ids to intervals
New class Interval
Revision 219 - Directory Listing
Modified Tue Jul 3 15:38:21 2007 UTC (12 years, 3 months ago) by duarte
Now reading also secondary structure (in a map of residue serials to secondary structure identifiers)
Revision 217 - Directory Listing
Modified Fri Jun 29 09:04:00 2007 UTC (12 years, 3 months ago) by stehr
now casting pdb codes to lower and pdb chain codes to upper in all constructors
Revision 216 - Directory Listing
Modified Fri Jun 29 08:30:55 2007 UTC (12 years, 3 months ago) by duarte
Fixed bug: ATOM lines printing was locale dependant, thus was printing ',' for decimal separators in some locales
Revision 215 - Directory Listing
Modified Thu Jun 28 15:43:04 2007 UTC (12 years, 3 months ago) by stehr
some clean up of exceptions in Pdb and Graph classes:
merged PdbAcCodeNotFoundError and MsdAcCodeNotFoundError into PdbCodeNotFoundError,
created new PdbChainCodeNotFound, got rid of stderr output, throwing exceptions with informative messages instead
Revision 212 - Directory Listing
Modified Thu Jun 28 09:26:34 2007 UTC (12 years, 3 months ago) by duarte
Fixed bug in regex introduced in last revision
Revision 211 - Directory Listing
Modified Thu Jun 28 09:22:26 2007 UTC (12 years, 3 months ago) by duarte
Fixed graph file format checking, was not working properly
Revision 210 - Directory Listing
Modified Wed Jun 27 15:57:39 2007 UTC (12 years, 3 months ago) by duarte
Now throwing also SQLExceptions for individual queries, not just for connections
Revision 209 - Directory Listing
Modified Wed Jun 27 15:14:31 2007 UTC (12 years, 3 months ago) by duarte
Throwing exception also in case graph file not in right format at all (no #AGLAPPE in 1st line)
Fixed bug: was not reading correctly #PDB CHAIN CODE
Revision 208 - Directory Listing
Modified Wed Jun 27 14:42:12 2007 UTC (12 years, 3 months ago) by duarte
FIXED BUGS:
- directed was not set when reading from cm file
- pdbChainCode not set when reading from db given pdbCode
- filling pdbresser2resser and resser2pdbresser hashmaps also in reading from pdb file
- using "A" as chainCode when reading from pdb file
- some error handling for file formats: new exception classes GraphFileFormatError and PdbfileFormatError
Revision 207 - Directory Listing
Modified Wed Jun 27 11:06:34 2007 UTC (12 years, 3 months ago) by duarte
Restructured construction of Pdb and Graph objects: now subclasses for each case
Cleaned up and made consistent database connections
Now can also pass a MySQLConnection in all cases (as well as having default values for a default connection)
PdbaseInfo and MsdsdInfo classes removed: now merged into PdbasePdb and MsdsdPdb respectively
Updated following this changes testPdb and compareCMs

Revision 206 - Directory Listing
Modified Tue Jun 26 17:01:48 2007 UTC (12 years, 3 months ago) by duarte
Major refactoring:
 accode -> pdbCode
 chaincode -> pdbChainCode
 chain -> chainCode
Major change of signatures (publics to privates)
Implemented getters for needed member variables
Major clean up
Revision 203 - Directory Listing
Modified Tue Jun 26 14:25:58 2007 UTC (12 years, 3 months ago) by duarte
Using apache xmlrpc version 3.0 in PyMolServerOutputStream
Revision 202 - Directory Listing
Modified Thu Jun 21 17:18:11 2007 UTC (12 years, 3 months ago) by duarte
MySQLConnection now throwing SQLException on connect
Many files changed following this: all calling classes now re-throwing or catching the SQLException
Revision 200 - Directory Listing
Modified Mon Jun 18 17:43:43 2007 UTC (12 years, 3 months ago) by duarte
New isValidCT methods in AA
New method get_resser_from_atomser in Pdb
Revision 199 - Directory Listing
Modified Mon Jun 18 09:03:39 2007 UTC (12 years, 3 months ago) by duarte
Implemented getRanks()
Revision 198 - Directory Listing
Modified Mon Jun 18 08:47:26 2007 UTC (12 years, 3 months ago) by duarte
AA class is now db independent:
Hard coded getaas2atoms, not getting it anymore from db.
Revision 196 - Directory Listing
Modified Wed Jun 13 15:05:31 2007 UTC (12 years, 4 months ago) by duarte
Added toString and getMotifFullGaps missing in EdgeNbh
Revision 195 - Directory Listing
Modified Wed Jun 13 14:24:43 2007 UTC (12 years, 4 months ago) by duarte
Made contactTypes a String[]
Revision 194 - Directory Listing
Modified Wed Jun 13 10:57:00 2007 UTC (12 years, 4 months ago) by duarte
Added contactTypes method and made private methods private
Revision 193 - Directory Listing
Modified Wed Jun 13 07:57:31 2007 UTC (12 years, 4 months ago) by duarte
Moved motif static methods to Background class. They didn't belong here
Revision 192 - Directory Listing
Modified Tue Jun 12 18:27:20 2007 UTC (12 years, 4 months ago) by duarte
Made contacts public
Revision 191 - Directory Listing
Modified Tue Jun 12 17:15:17 2007 UTC (12 years, 4 months ago) by duarte
New method getAllEdgeNbhSizes
Revision 190 - Directory Listing
Modified Tue Jun 12 13:38:46 2007 UTC (12 years, 4 months ago) by duarte
NEW FEATURE: mapping of pdb residue serials and internal serials in the Pdb object

Revision 189 - Directory Listing
Modified Tue Jun 12 10:38:29 2007 UTC (12 years, 4 months ago) by duarte
Added basic compare method to the Graph class and test class compareCMs
Revision 186 - Directory Listing
Modified Thu Jun 7 10:42:13 2007 UTC (12 years, 4 months ago) by duarte
FIXED BUG: The returned regex in motif2regex was wrong, needed a ".*" at the beginning
Revision 185 - Directory Listing
Modified Thu Jun 7 09:14:46 2007 UTC (12 years, 4 months ago) by duarte
Implemented hashCode method in Contact and GenericContact. Was necessary to use these classes as keys in Maps
Fixed bug in equals method in GenericContact
Changed middle character from "\t" to " " in toString
Revision 184 - Directory Listing
Modified Wed Jun 6 10:02:24 2007 UTC (12 years, 4 months ago) by duarte
New class GenericContact. To store a generic contact, i.e. a pair of residue types
Revision 183 - Directory Listing
Modified Tue Jun 5 14:32:04 2007 UTC (12 years, 4 months ago) by duarte
Fixed bug: calculateEntropy was wrong when a pi was 0
Revision 182 - Directory Listing
Modified Tue Jun 5 13:41:05 2007 UTC (12 years, 4 months ago) by duarte
FIXED BUG: the switch statement was missing the breaks
This was causing strange behaviour in counts NodeBackground getSize methods and also was making them being too slow
Revision 181 - Directory Listing
Modified Tue Jun 5 12:27:49 2007 UTC (12 years, 4 months ago) by duarte
New class NbhProbDistribution
In NodeNbh implemented a few static classes to convert between different motifs and to match motifs using differing criteria

Revision 179 - Directory Listing
Modified Thu May 31 09:41:41 2007 UTC (12 years, 4 months ago) by duarte
FIXED BUG: fixed restrictContactsToMax/MinRange. Couldn't delete contacts at the same time as looping in them
NEW CLASSES NodeNbh and EdgeNbh, now used in getNodeNbh and getEdgeNbh
New method getResidueType
Revision 178 - Directory Listing
Modified Tue May 29 08:01:46 2007 UTC (12 years, 4 months ago) by duarte
Fixed bug in getMaxRange method, was not assigning to the max variable
Added toString method to Contact
Revision 175 - Directory Listing
Modified Fri May 25 17:31:58 2007 UTC (12 years, 4 months ago) by duarte
FIXED BUG in initialisation of fullLength when reading from file. In case of no sequence and nodes provided, was not getting correctly the maximum value for contacts. Now using the method getMaxContact from new class ContactList
NEW FUNCTIONALITY in Graph:
-New member variable modified
-New methods addEdge, delEdge, restrictContactsToMaxRange, restrictContactsToMinRange, getContacts, getNodes, copy
-Improved slightly the implementation of getEdgeNbh 
FIXED BUG in initialisation of fullLenght when reading from file. In case of no sequence and nodes provided, was not getting correctly the maximum value for contacts. Now using the method getMaxContact from ContactList
New class ContactList
NEW FUNCTIONALITY in Graph:
-New member variable modified
-New methods addEdge, delEdge, restrictContactsToMaxRange, restrictContactsToMinRange, getContacts, getNodes, copy
-Improved slightly the implementation of getEdgeNbh 
New method getRange in Contact
Revision 172 - Directory Listing
Modified Fri May 25 13:41:19 2007 UTC (12 years, 4 months ago) by duarte
Got rid of some unnecessary warnings
Revision 165 - Directory Listing
Modified Thu May 24 15:43:13 2007 UTC (12 years, 4 months ago) by duarte
New functionality: added methods to get node/edge neighbours
Revision 161 - Directory Listing
Modified Thu May 24 10:12:41 2007 UTC (12 years, 4 months ago) by stehr
made Graph.directed public
Revision 159 - Directory Listing
Modified Thu May 24 09:37:25 2007 UTC (12 years, 4 months ago) by duarte
Moved ContactMap and EdgeState out of this repository. 
Extra functionality of ContactMap now in Graph:
- new member variables fullLength, obsLength, numContacts. New method getIntMatrix
- removed getCM method
Revision 158 - Directory Listing
Modified Tue May 22 15:37:15 2007 UTC (12 years, 4 months ago) by duarte
FIXED BUG in get_db_graph_info, was not dealing well with the case of chaincode being NULL in the database
Revision 157 - Directory Listing
Modified Tue May 22 12:04:43 2007 UTC (12 years, 4 months ago) by duarte
FIXED BUG: in getCM when directed was passing a reference to the contacts object and not deep copying it!
Revision 156 - Directory Listing
Modified Tue May 22 10:40:04 2007 UTC (12 years, 4 months ago) by duarte
Now passing also chaincode from Pdb object to Graph object in get_graph
Revision 155 - Directory Listing
Modified Tue May 22 10:13:03 2007 UTC (12 years, 4 months ago) by duarte
Fixed bug: wasn't initialising accode, chain and chaincode when reading to file. Now all set to "" when not present in file
Revision 154 - Directory Listing
Modified Fri May 18 09:32:28 2007 UTC (12 years, 4 months ago) by duarte
Recoded chain reading in read_pdb_data_from_file to make it clearer, no change in functionality
Revision 153 - Directory Listing
Modified Wed May 16 17:22:08 2007 UTC (12 years, 5 months ago) by duarte
NEW FUNCTIONALITY: Reading from pdb file given chain code or model serial fully implemented
Changed the chain that is dumped in dump2pdbfile directly to the Pdb.chain field i.e. internal chain identifier
Loads of new comments, including java doc for all constructors
Revision 152 - Directory Listing
Modified Wed May 16 14:12:50 2007 UTC (12 years, 5 months ago) by duarte
FIXED 2 BUGS. NEW FEATURE reading graph from db given graph_id
Bugs:
- nodes TreeMap in read_graph_from_file contained one letter res codes, now three letter codes
- in getCM was passing residues as a TreeMap of nums to three letter residue types, now passing one letter residue types
New constructor for getting graph from db given graph_id, new method to go with that get_db_graph_info

Revision 146 - Directory Listing
Modified Tue May 15 13:51:17 2007 UTC (12 years, 5 months ago) by duarte
Made cutoff and ct public
Revision 145 - Directory Listing
Modified Tue May 15 13:28:24 2007 UTC (12 years, 5 months ago) by duarte
Made some fields public: sequence, accode, chaincode, model
Revision 144 - Directory Listing
Modified Tue May 15 12:13:31 2007 UTC (12 years, 5 months ago) by duarte
NEW FEATURE: Read and write graphs from file fully implemented.

Refactored read_contacts_from_file to read_graph_from_file. Now can read other fields as well as contacts. Also gets nodes if sequence present
New method write_graph_to_file

Revision 143 - Directory Listing
Modified Tue May 15 10:06:47 2007 UTC (12 years, 5 months ago) by duarte
FIXED BUG: last commit didn't fix bug correctly:
Changed the ContactMap constructor to put into residueNums and residueTypes nums from 1 to maximum of residues.keySet()

Made public accode and chain fields in Graph
Revision 142 - Directory Listing
Modified Tue May 15 08:33:44 2007 UTC (12 years, 5 months ago) by duarte
FIXED BUG: getCM wasn't working well when reading from db and there were unobserved residues

Now setting the sequence to blank when reading from db. Also when reading from file (still nodes reading is not implemented)
In ContactMap constructor different handling when sequence is blank
Revision 141 - Directory Listing
Modified Mon May 14 15:51:54 2007 UTC (12 years, 5 months ago) by duarte
Changed input in constructor for reading from db: chain->chaincode
Now getgraphid initialises too the internal chain code (pchain_code from graph db)
Revision 140 - Directory Listing
Modified Mon May 14 15:34:21 2007 UTC (12 years, 5 months ago) by stehr
Made Pdb.acccode public
Revision 139 - Directory Listing
Modified Mon May 14 15:29:08 2007 UTC (12 years, 5 months ago) by duarte
Changed default accode and chaincode to "Unknown" when reading from pdb file
Revision 138 - Directory Listing
Modified Mon May 14 14:58:29 2007 UTC (12 years, 5 months ago) by duarte
FIXED BUG: wasn't setting the chain field when reading from msdsd
Revision 137 - Directory Listing
Modified Mon May 14 14:53:09 2007 UTC (12 years, 5 months ago) by stehr
Made chain field in PDB class public
Revision 136 - Directory Listing
Modified Mon May 14 14:50:44 2007 UTC (12 years, 5 months ago) by duarte
FIXED BUG: pdb data load from msdsd wasn't working for NULL chaincodes
Revision 135 - Directory Listing
Modified Mon May 14 09:49:04 2007 UTC (12 years, 5 months ago) by duarte
NEW FUNCTIONALITY: reading of graph from db is fully implemented for all cases

New chain member variable in the Info classes, read in get_asym_id (Pdbase) and in get_chain_id (Msdsd)
Reading chain also in Pdb in read_pdb_data_from_file
Not reading chain anymore in read_atomData of PdbaseInfo
Added oneletter2threeletter and getoneletter2threeletter to AA class
Changes in Graph:
- added db static vars and getUserName method
- new member variables graphid and sm_id
- new method read_graph_from_db to read contacts, nodes (and sequence from nodes) from db
- new method getgraphid
New Exception class GraphIdNotFoundError
Revision 134 - Directory Listing
Modified Mon May 14 07:52:10 2007 UTC (12 years, 5 months ago) by duarte
Implemented basic reading contacts from file
Revision 133 - Directory Listing
Modified Fri May 11 09:37:38 2007 UTC (12 years, 5 months ago) by duarte
New functionality: now can create a Pdb object passing a model serial for NMR structures. Not implemented when reading from pdb files!
Revision 131 - Directory Listing
Modified Thu May 10 15:53:14 2007 UTC (12 years, 5 months ago) by duarte
2 new convenience methods: getBoolMatrix and getIntMatrix
Got rid of method to print constraint equations, was useless
Revision 130 - Directory Listing
Modified Thu May 10 15:52:24 2007 UTC (12 years, 5 months ago) by duarte
NEW FEATURE: reading pdb data from msdsd
New classes MsdsdInfo and its exception classes
FIXED BUG in dump2pdbfile in Pdb: was not sorting the atom lines
Revision 129 - Directory Listing
Modified Thu May 10 13:12:32 2007 UTC (12 years, 5 months ago) by duarte
NEW FUNCTIONALITY: can retrieve now a ContactMap object from a Graph object
New method getCM in Graph. New member variables: sequence, accode, chain, nodes, directed
Passing more data from Pdb to Graph in get_graph
New constructor in ContactMap
Revision 128 - Directory Listing
Modified Wed May 9 16:29:39 2007 UTC (12 years, 5 months ago) by duarte
ContactMap and EdgeState classes moved here from CMPredict repository
Revision 127 - Directory Listing
Modified Wed May 9 14:54:02 2007 UTC (12 years, 5 months ago) by duarte
Implemented read of pdb data from pdb file.
FIXED BUG in dumping of pdb file. Was missing end of line in atom lines
Added more tests in testPdb

Revision 126 - Directory Listing
Modified Wed May 9 12:04:35 2007 UTC (12 years, 5 months ago) by duarte
MYSQLUSER now taken from unix name with new getUserName method
Revision 124 - Directory Listing
Modified Wed May 9 11:57:24 2007 UTC (12 years, 5 months ago) by duarte
Added error handling for PdbaseInfo: 2 new exception classes
Revision 123 - Directory Listing
Added Wed May 9 10:45:53 2007 UTC (12 years, 5 months ago) by duarte
Initial commit of the proteinstructure package. Contains classes to use pdb protein structures