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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