Revision
555 -
Directory Listing
Modified
Thu Feb 28 14:29:15 2008 UTC
(16 years, 7 months ago)
by
duarte
Tagging 0.9.3 for CMView release 0.9.3
Revision
552 -
Directory Listing
Modified
Fri Feb 22 15:26:34 2008 UTC
(16 years, 8 months ago)
by
duarte
Original Path:
trunk/proteinstructure
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
(16 years, 8 months ago)
by
duarte
Original Path:
trunk/proteinstructure
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
(16 years, 8 months ago)
by
stehr
Original Path:
trunk/proteinstructure
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
(16 years, 8 months ago)
by
duarte
Original Path:
trunk/proteinstructure
Fixed bug: write_graph_to_file now writes blank instead of "null" when pdbCode, pdbChainCode or chainCode are null.
Revision
546 -
Directory Listing
Modified
Wed Feb 20 15:53:51 2008 UTC
(16 years, 8 months ago)
by
duarte
Original Path:
trunk/proteinstructure
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
(16 years, 8 months ago)
by
duarte
Original Path:
trunk/proteinstructure
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
(16 years, 8 months ago)
by
duarte
Original Path:
trunk/proteinstructure
New constructor to read from simple graph files, i.e. list of contacts without any headers
Revision
529 -
Directory Listing
Modified
Tue Feb 5 14:53:57 2008 UTC
(16 years, 8 months ago)
by
spriya
Original Path:
trunk/proteinstructure
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
(16 years, 8 months ago)
by
duarte
Original Path:
trunk/proteinstructure
Fixed bug in compare(), was not checking correctly for sequence matching
Revision
524 -
Directory Listing
Modified
Tue Jan 29 12:03:32 2008 UTC
(16 years, 8 months ago)
by
duarte
Original Path:
trunk/proteinstructure
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
521 -
Directory Listing
Modified
Wed Jan 16 17:58:38 2008 UTC
(16 years, 9 months ago)
by
duarte
Original Path:
trunk/proteinstructure
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
(16 years, 9 months ago)
by
duarte
Original Path:
trunk/proteinstructure
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
(16 years, 9 months ago)
by
filippis
Original Path:
trunk/proteinstructure
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
(16 years, 9 months ago)
by
duarte
Original Path:
trunk/proteinstructure
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
(16 years, 9 months ago)
by
duarte
Original Path:
trunk/proteinstructure
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
(16 years, 9 months ago)
by
stehr
Original Path:
trunk/proteinstructure
Interval: allow spaces in residue selection strings
RIGNbhood: added method getNeighbors
Revision
513 -
Directory Listing
Modified
Fri Jan 11 13:33:56 2008 UTC
(16 years, 9 months ago)
by
filippis
Original Path:
trunk/proteinstructure
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
508 -
Directory Listing
Modified
Thu Jan 10 15:39:00 2008 UTC
(16 years, 9 months ago)
by
stehr
Original Path:
trunk/proteinstructure
Fixed bug in DSSP secondary structure assignment, first element was starting at index 0
Revision
505 -
Directory Listing
Modified
Thu Jan 10 13:37:09 2008 UTC
(16 years, 9 months ago)
by
duarte
Original Path:
trunk/proteinstructure
Now converting also secondary structure in pairwise alignment graph conversion
Revision
504 -
Directory Listing
Modified
Thu Jan 10 10:30:46 2008 UTC
(16 years, 9 months ago)
by
stehr
Original Path:
trunk/proteinstructure
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
(16 years, 9 months ago)
by
filippis
Original Path:
trunk/proteinstructure
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
(16 years, 9 months ago)
by
stehr
Original Path:
trunk/proteinstructure
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
(16 years, 9 months ago)
by
duarte
Original Path:
trunk/proteinstructure
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
(16 years, 9 months ago)
by
duarte
Original Path:
trunk/proteinstructure
New functionality: now we can get sequences and reset tags based on the order the sequences appear on the file.
Revision
498 -
Directory Listing
Modified
Thu Jan 3 17:16:03 2008 UTC
(16 years, 9 months ago)
by
duarte
Original Path:
trunk/proteinstructure
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
(16 years, 9 months ago)
by
duarte
Original Path:
trunk/proteinstructure
Extracted some constants: NO_PDB_CODE, NO_PDB_CHAIN_CODE, NO_CONTACT_TYPE, NO_CUTOFF
Revision
478 -
Directory Listing
Modified
Mon Dec 17 17:03:24 2007 UTC
(16 years, 10 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
(16 years, 10 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
474 -
Directory Listing
Modified
Thu Dec 13 13:45:01 2007 UTC
(16 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
465 -
Directory Listing
Modified
Fri Dec 7 16:53:10 2007 UTC
(16 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
460 -
Directory Listing
Modified
Thu Dec 6 18:14:59 2007 UTC
(16 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
(16 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
452 -
Directory Listing
Modified
Tue Dec 4 15:40:17 2007 UTC
(16 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
(16 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
(16 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
(16 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
(16 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
(16 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
434 -
Directory Listing
Modified
Wed Nov 28 09:34:44 2007 UTC
(16 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
427 -
Directory Listing
Modified
Mon Nov 26 15:57:37 2007 UTC
(16 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
(16 years, 11 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
(16 years, 11 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
421 -
Directory Listing
Modified
Thu Nov 22 19:42:11 2007 UTC
(16 years, 11 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
(16 years, 11 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
412 -
Directory Listing
Modified
Wed Nov 21 16:12:26 2007 UTC
(16 years, 11 months ago)
by
filippis
Original Path:
trunk/proteinstructure
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
407 -
Directory Listing
Modified
Tue Nov 20 18:41:56 2007 UTC
(16 years, 11 months ago)
by
filippis
Original Path:
trunk/proteinstructure
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
405 -
Directory Listing
Modified
Tue Nov 20 16:37:54 2007 UTC
(16 years, 11 months ago)
by
duarte
Original Path:
trunk/proteinstructure
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
(16 years, 11 months ago)
by
duarte
Original Path:
trunk/proteinstructure
Not asserting anymore pdbChainCode to be uppercase. pdb chain codes are case sensitive!
Revision
402 -
Directory Listing
Modified
Thu Nov 15 16:15:32 2007 UTC
(16 years, 11 months ago)
by
duarte
Original Path:
trunk/proteinstructure
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
(16 years, 11 months ago)
by
duarte
Original Path:
trunk/proteinstructure
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
(16 years, 11 months ago)
by
filippis
Original Path:
trunk/proteinstructure
-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
394 -
Directory Listing
Modified
Thu Nov 8 12:40:01 2007 UTC
(16 years, 11 months ago)
by
duarte
Original Path:
trunk/proteinstructure
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
(16 years, 11 months ago)
by
stehr
Original Path:
trunk/proteinstructure
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
385 -
Directory Listing
Modified
Wed Nov 7 17:32:43 2007 UTC
(16 years, 11 months ago)
by
lpetzo
Original Path:
trunk/proteinstructure
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
383 -
Directory Listing
Modified
Tue Nov 6 18:35:17 2007 UTC
(16 years, 11 months ago)
by
filippis
Original Path:
trunk/proteinstructure
inSameSheet, isOther and getSheetSerial methods added in SecStrucElement
Revision
382 -
Directory Listing
Modified
Tue Nov 6 15:42:05 2007 UTC
(16 years, 11 months ago)
by
filippis
Original Path:
trunk/proteinstructure
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
(16 years, 11 months ago)
by
lpetzo
Original Path:
trunk/proteinstructure
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
(16 years, 11 months ago)
by
stehr
Original Path:
trunk/proteinstructure
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
377 -
Directory Listing
Modified
Thu Nov 1 15:02:56 2007 UTC
(16 years, 11 months ago)
by
stehr
Original Path:
trunk/proteinstructure
fixed nasty bug in constructor Graph(sequence) (residue indexing was wrong)
Revision
374 -
Directory Listing
Modified
Wed Oct 31 16:40:29 2007 UTC
(16 years, 11 months ago)
by
duarte
Original Path:
trunk/proteinstructure
Fixed bug: getContacts was not copying weights
Got rid of useless copyKeepingNodes(), made main Graph constructor public. Some new setters and getters
Revision
365 -
Directory Listing
Modified
Tue Oct 23 08:36:58 2007 UTC
(17 years ago)
by
duarte
Original Path:
trunk/proteinstructure
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
361 -
Directory Listing
Modified
Wed Oct 17 17:40:18 2007 UTC
(17 years ago)
by
duarte
Original Path:
trunk/proteinstructure
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
(17 years ago)
by
stehr
Original Path:
trunk/proteinstructure
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
(17 years ago)
by
duarte
Original Path:
trunk/proteinstructure
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
355 -
Directory Listing
Modified
Fri Oct 12 18:42:37 2007 UTC
(17 years ago)
by
duarte
Original Path:
trunk/proteinstructure
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
(17 years ago)
by
duarte
Original Path:
trunk/proteinstructure
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
(17 years ago)
by
stehr
Original Path:
trunk/proteinstructure
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
337 -
Directory Listing
Modified
Thu Oct 4 10:12:49 2007 UTC
(17 years ago)
by
stehr
Original Path:
trunk/proteinstructure
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
(17 years ago)
by
stehr
Original Path:
trunk/proteinstructure
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
(17 years ago)
by
duarte
Original Path:
trunk/proteinstructure
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
332 -
Directory Listing
Modified
Mon Oct 1 16:20:06 2007 UTC
(17 years ago)
by
stehr
Original Path:
trunk/proteinstructure
added constructor for trivial alignment, renamed getSequence to getAlignedSequence
Revision
331 -
Directory Listing
Modified
Mon Oct 1 16:12:48 2007 UTC
(17 years ago)
by
duarte
Original Path:
trunk/proteinstructure
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
(17 years ago)
by
stehr
Original Path:
trunk/proteinstructure
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
(17 years ago)
by
duarte
Original Path:
trunk/proteinstructure
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
(17 years ago)
by
duarte
Original Path:
trunk/proteinstructure
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
(17 years, 1 month ago)
by
duarte
Original Path:
trunk/proteinstructure
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
322 -
Directory Listing
Modified
Tue Sep 18 13:59:33 2007 UTC
(17 years, 1 month ago)
by
duarte
Original Path:
trunk/proteinstructure
Initial commit of TinkerRunner and exception class to go with it TinkerError
Revision
315 -
Directory Listing
Modified
Thu Sep 13 08:13:40 2007 UTC
(17 years, 1 month ago)
by
duarte
Original Path:
trunk/proteinstructure
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
(17 years, 1 month ago)
by
duarte
Original Path:
trunk/proteinstructure
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
(17 years, 1 month ago)
by
duarte
Original Path:
trunk/proteinstructure
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
(17 years, 1 month ago)
by
duarte
Original Path:
trunk/proteinstructure
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
(17 years, 1 month ago)
by
duarte
Original Path:
trunk/proteinstructure
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
(17 years, 1 month ago)
by
duarte
Original Path:
trunk/proteinstructure
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
(17 years, 1 month ago)
by
duarte
Original Path:
trunk/proteinstructure
Now taking indices for fields from parsed field names. Still only minimal testing
Revision
305 -
Directory Listing
Modified
Wed Aug 29 09:46:32 2007 UTC
(17 years, 1 month ago)
by
duarte
Original Path:
trunk/proteinstructure
Got rid of useless (and potential bug) chainCode=getChainCode (self reference!)
Revision
302 -
Directory Listing
Modified
Mon Aug 27 14:28:23 2007 UTC
(17 years, 1 month ago)
by
stehr
Original Path:
trunk/proteinstructure
changes to calcGridDensity, now also counts number of neighbouring non-empty grid cells
Revision
284 -
Directory Listing
Modified
Thu Aug 16 14:57:31 2007 UTC
(17 years, 2 months ago)
by
duarte
Original Path:
trunk/proteinstructure
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
282 -
Directory Listing
Modified
Tue Aug 14 16:15:59 2007 UTC
(17 years, 2 months ago)
by
duarte
Original Path:
trunk/proteinstructure
Made get_graph a bit less memory hungry, by using a float[][] instead of double[][]
Not printing warnings about missing atoms anymore
Revision
280 -
Directory Listing
Modified
Tue Aug 14 12:38:51 2007 UTC
(17 years, 2 months ago)
by
stehr
Original Path:
trunk/proteinstructure
changed internal implementation of runDssp method (not using getFullLength anymore)
Revision
279 -
Directory Listing
Modified
Tue Aug 14 12:26:28 2007 UTC
(17 years, 2 months ago)
by
duarte
Original Path:
trunk/proteinstructure
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
(17 years, 2 months ago)
by
duarte
Original Path:
trunk/proteinstructure
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
(17 years, 2 months ago)
by
duarte
Original Path:
trunk/proteinstructure
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
(17 years, 2 months ago)
by
duarte
Original Path:
trunk/proteinstructure
Fixed bug: wasn't taken into account OXT atoms in calculating the ALL graph
Revision
260 -
Directory Listing
Modified
Fri Aug 10 18:30:47 2007 UTC
(17 years, 2 months ago)
by
duarte
Original Path:
trunk/proteinstructure
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
(17 years, 2 months ago)
by
stehr
Original Path:
trunk/proteinstructure
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
(17 years, 2 months ago)
by
duarte
Original Path:
trunk/proteinstructure
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
(17 years, 2 months ago)
by
stehr
Original Path:
trunk/proteinstructure
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
255 -
Directory Listing
Modified
Thu Aug 9 13:45:10 2007 UTC
(17 years, 2 months ago)
by
stehr
Original Path:
trunk/proteinstructure
PdbfilePdb now also accepts Casp prediction files ('PFRMAT TS' instead of 'HEADER')
Revision
250 -
Directory Listing
Modified
Mon Aug 6 14:48:37 2007 UTC
(17 years, 2 months ago)
by
stehr
Original Path:
trunk/proteinstructure
added application to count grid density, suppressed warning for secondary structure reassignment
Revision
246 -
Directory Listing
Modified
Sat Aug 4 17:00:58 2007 UTC
(17 years, 2 months ago)
by
duarte
Original Path:
trunk/proteinstructure
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
(17 years, 2 months ago)
by
duarte
Original Path:
trunk/proteinstructure
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
(17 years, 2 months ago)
by
duarte
Original Path:
trunk/proteinstructure
Initial commit of Alignmnent, a class representing a multiple sequence alignment
Revision
241 -
Directory Listing
Modified
Tue Jul 31 16:38:13 2007 UTC
(17 years, 2 months ago)
by
duarte
Original Path:
trunk/proteinstructure
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
(17 years, 2 months ago)
by
duarte
Original Path:
trunk/proteinstructure
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
(17 years, 2 months ago)
by
duarte
Original Path:
trunk/proteinstructure
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
237 -
Directory Listing
Modified
Thu Jul 19 14:23:35 2007 UTC
(17 years, 3 months ago)
by
duarte
Original Path:
trunk/proteinstructure
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
(17 years, 3 months ago)
by
duarte
Original Path:
trunk/proteinstructure
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
(17 years, 3 months ago)
by
duarte
Original Path:
trunk/proteinstructure
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
(17 years, 3 months ago)
by
duarte
Original Path:
trunk/proteinstructure
Made ContactList a TreeSet instead of an ArrayList, should improve performance (log(n) rather than linear)
REFACTORING:
ContactList -> EdgeSet
Contact -> Edge
Revision
232 -
Directory Listing
Modified
Tue Jul 10 13:00:23 2007 UTC
(17 years, 3 months ago)
by
duarte
Original Path:
trunk/proteinstructure
Now checking in addEdge that we don't duplicate edges
New methods: get2ndshell, copyKeepingNodes
Revision
229 -
Directory Listing
Modified
Mon Jul 9 15:02:24 2007 UTC
(17 years, 3 months ago)
by
duarte
Original Path:
trunk/proteinstructure
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
(17 years, 3 months ago)
by
duarte
Original Path:
trunk/proteinstructure
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
(17 years, 3 months ago)
by
duarte
Original Path:
trunk/proteinstructure
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
(17 years, 3 months ago)
by
duarte
Original Path:
trunk/proteinstructure
Now calculate distance matrix uses HashMap instead of TreeMap
Needed to change the hashCode function in Contact to make it faster
Revision
222 -
Directory Listing
Modified
Wed Jul 4 15:39:01 2007 UTC
(17 years, 3 months ago)
by
duarte
Original Path:
trunk/proteinstructure
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
(17 years, 3 months ago)
by
duarte
Original Path:
trunk/proteinstructure
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
(17 years, 3 months ago)
by
stehr
Original Path:
trunk/proteinstructure
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
(17 years, 3 months ago)
by
duarte
Original Path:
trunk/proteinstructure
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
(17 years, 3 months ago)
by
stehr
Original Path:
trunk/proteinstructure
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
210 -
Directory Listing
Modified
Wed Jun 27 15:57:39 2007 UTC
(17 years, 3 months ago)
by
duarte
Original Path:
trunk/proteinstructure
Now throwing also SQLExceptions for individual queries, not just for connections
Revision
209 -
Directory Listing
Modified
Wed Jun 27 15:14:31 2007 UTC
(17 years, 3 months ago)
by
duarte
Original Path:
trunk/proteinstructure
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
(17 years, 3 months ago)
by
duarte
Original Path:
trunk/proteinstructure
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
(17 years, 3 months ago)
by
duarte
Original Path:
trunk/proteinstructure
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
(17 years, 3 months ago)
by
duarte
Original Path:
trunk/proteinstructure
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
202 -
Directory Listing
Modified
Thu Jun 21 17:18:11 2007 UTC
(17 years, 4 months ago)
by
duarte
Original Path:
trunk/proteinstructure
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
(17 years, 4 months ago)
by
duarte
Original Path:
trunk/proteinstructure
New isValidCT methods in AA
New method get_resser_from_atomser in Pdb
Revision
198 -
Directory Listing
Modified
Mon Jun 18 08:47:26 2007 UTC
(17 years, 4 months ago)
by
duarte
Original Path:
trunk/proteinstructure
AA class is now db independent:
Hard coded getaas2atoms, not getting it anymore from db.
Revision
193 -
Directory Listing
Modified
Wed Jun 13 07:57:31 2007 UTC
(17 years, 4 months ago)
by
duarte
Original Path:
trunk/proteinstructure
Moved motif static methods to Background class. They didn't belong here
Revision
190 -
Directory Listing
Modified
Tue Jun 12 13:38:46 2007 UTC
(17 years, 4 months ago)
by
duarte
Original Path:
trunk/proteinstructure
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
(17 years, 4 months ago)
by
duarte
Original Path:
trunk/proteinstructure
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
(17 years, 4 months ago)
by
duarte
Original Path:
trunk/proteinstructure
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
(17 years, 4 months ago)
by
duarte
Original Path:
trunk/proteinstructure
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
(17 years, 4 months ago)
by
duarte
Original Path:
trunk/proteinstructure
New class GenericContact. To store a generic contact, i.e. a pair of residue types
Revision
182 -
Directory Listing
Modified
Tue Jun 5 13:41:05 2007 UTC
(17 years, 4 months ago)
by
duarte
Original Path:
trunk/proteinstructure
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
(17 years, 4 months ago)
by
duarte
Original Path:
trunk/proteinstructure
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
(17 years, 4 months ago)
by
duarte
Original Path:
trunk/proteinstructure
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
(17 years, 4 months ago)
by
duarte
Original Path:
trunk/proteinstructure
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
(17 years, 5 months ago)
by
duarte
Original Path:
trunk/proteinstructure
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
159 -
Directory Listing
Modified
Thu May 24 09:37:25 2007 UTC
(17 years, 5 months ago)
by
duarte
Original Path:
trunk/proteinstructure
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
(17 years, 5 months ago)
by
duarte
Original Path:
trunk/proteinstructure
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
(17 years, 5 months ago)
by
duarte
Original Path:
trunk/proteinstructure
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
(17 years, 5 months ago)
by
duarte
Original Path:
trunk/proteinstructure
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
(17 years, 5 months ago)
by
duarte
Original Path:
trunk/proteinstructure
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
(17 years, 5 months ago)
by
duarte
Original Path:
trunk/proteinstructure
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
(17 years, 5 months ago)
by
duarte
Original Path:
trunk/proteinstructure
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
(17 years, 5 months ago)
by
duarte
Original Path:
trunk/proteinstructure
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
144 -
Directory Listing
Modified
Tue May 15 12:13:31 2007 UTC
(17 years, 5 months ago)
by
duarte
Original Path:
trunk/proteinstructure
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
(17 years, 5 months ago)
by
duarte
Original Path:
trunk/proteinstructure
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
(17 years, 5 months ago)
by
duarte
Original Path:
trunk/proteinstructure
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
(17 years, 5 months ago)
by
duarte
Original Path:
trunk/proteinstructure
Changed input in constructor for reading from db: chain->chaincode
Now getgraphid initialises too the internal chain code (pchain_code from graph db)
Revision
139 -
Directory Listing
Modified
Mon May 14 15:29:08 2007 UTC
(17 years, 5 months ago)
by
duarte
Original Path:
trunk/proteinstructure
Changed default accode and chaincode to "Unknown" when reading from pdb file
Revision
136 -
Directory Listing
Modified
Mon May 14 14:50:44 2007 UTC
(17 years, 5 months ago)
by
duarte
Original Path:
trunk/proteinstructure
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
(17 years, 5 months ago)
by
duarte
Original Path:
trunk/proteinstructure
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
133 -
Directory Listing
Modified
Fri May 11 09:37:38 2007 UTC
(17 years, 5 months ago)
by
duarte
Original Path:
trunk/proteinstructure
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
(17 years, 5 months ago)
by
duarte
Original Path:
trunk/proteinstructure
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
(17 years, 5 months ago)
by
duarte
Original Path:
trunk/proteinstructure
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
(17 years, 5 months ago)
by
duarte
Original Path:
trunk/proteinstructure
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
(17 years, 5 months ago)
by
duarte
Original Path:
trunk/proteinstructure
ContactMap and EdgeState classes moved here from CMPredict repository
Revision
127 -
Directory Listing
Modified
Wed May 9 14:54:02 2007 UTC
(17 years, 5 months ago)
by
duarte
Original Path:
trunk/proteinstructure
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
123 -
Directory Listing
Added
Wed May 9 10:45:53 2007 UTC
(17 years, 5 months ago)
by
duarte
Original Path:
trunk/proteinstructure
Initial commit of the proteinstructure package. Contains classes to use pdb protein structures