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Revision 284 - Directory Listing
Modified Thu Aug 16 14:57:31 2007 UTC (12 years, 3 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, 3 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, 3 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, 3 months ago) by stehr
fixed little bug in NodeNbh
Revision 280 - Directory Listing
Modified Tue Aug 14 12:38:51 2007 UTC (12 years, 3 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, 3 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, 3 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, 3 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, 3 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, 3 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, 3 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, 4 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, 4 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, 4 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, 4 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, 4 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, 4 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, 4 months ago) by duarte
Added getNumAtoms
Revision 255 - Directory Listing
Modified Thu Aug 9 13:45:10 2007 UTC (12 years, 4 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, 4 months ago) by duarte
Made constructor public
Revision 250 - Directory Listing
Modified Mon Aug 6 14:48:37 2007 UTC (12 years, 4 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, 4 months ago) by duarte
New methods containsContact and resetContacts
Revision 248 - Directory Listing
Modified Sat Aug 4 17:50:00 2007 UTC (12 years, 4 months ago) by duarte
Added method hasTag
Revision 247 - Directory Listing
Modified Sat Aug 4 17:07:23 2007 UTC (12 years, 4 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, 4 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, 4 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, 4 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, 4 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, 4 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, 4 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, 4 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, 4 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, 4 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, 4 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, 4 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, 5 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, 5 months ago) by duarte
Added method getCopy
Revision 232 - Directory Listing
Modified Tue Jul 10 13:00:23 2007 UTC (12 years, 5 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, 5 months ago) by stehr
added class NodeSet
Revision 229 - Directory Listing
Modified Mon Jul 9 15:02:24 2007 UTC (12 years, 5 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, 5 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, 5 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, 5 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, 5 months ago) by duarte
Added cross contacts to isValidCT
Revision 222 - Directory Listing
Modified Wed Jul 4 15:39:01 2007 UTC (12 years, 5 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, 5 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, 5 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, 5 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, 5 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, 5 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, 5 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, 5 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, 5 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, 5 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, 5 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, 5 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, 5 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, 5 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, 5 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, 5 months ago) by duarte
Implemented getRanks()
Revision 198 - Directory Listing
Modified Mon Jun 18 08:47:26 2007 UTC (12 years, 5 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, 5 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, 5 months ago) by duarte
Made contactTypes a String[]
Revision 194 - Directory Listing
Modified Wed Jun 13 10:57:00 2007 UTC (12 years, 6 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, 6 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, 6 months ago) by duarte
Made contacts public
Revision 191 - Directory Listing
Modified Tue Jun 12 17:15:17 2007 UTC (12 years, 6 months ago) by duarte
New method getAllEdgeNbhSizes
Revision 190 - Directory Listing
Modified Tue Jun 12 13:38:46 2007 UTC (12 years, 6 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, 6 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, 6 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, 6 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, 6 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, 6 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, 6 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, 6 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, 6 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, 6 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, 6 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, 6 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, 6 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, 6 months ago) by stehr
made Graph.directed public
Revision 159 - Directory Listing
Modified Thu May 24 09:37:25 2007 UTC (12 years, 6 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, 6 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, 6 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, 6 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, 6 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, 6 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, 6 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, 6 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, 6 months ago) by duarte
Made cutoff and ct public
Revision 145 - Directory Listing
Modified Tue May 15 13:28:24 2007 UTC (12 years, 6 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, 6 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, 6 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, 6 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, 6 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, 6 months ago) by stehr
Made Pdb.acccode public
Revision 139 - Directory Listing
Modified Mon May 14 15:29:08 2007 UTC (12 years, 6 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, 6 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, 6 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, 6 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, 6 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, 6 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, 7 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, 7 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, 7 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, 7 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, 7 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, 7 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, 7 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, 7 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, 7 months ago) by duarte
Initial commit of the proteinstructure package. Contains classes to use pdb protein structures