Revision 157 - (view) (annotate) - [select for diffs]
Modified Tue May 22 12:04:43 2007 UTC (17 years, 4 months ago) by duarte
File length: 14077 byte(s)
Diff to previous 156

FIXED BUG: in getCM when directed was passing a reference to the contacts object and not deep copying it!

Revision 156 - (view) (annotate) - [select for diffs]
Modified Tue May 22 10:40:04 2007 UTC (17 years, 4 months ago) by duarte
File length: 13955 byte(s)
Diff to previous 155

Now passing also chaincode from Pdb object to Graph object in get_graph

Revision 155 - (view) (annotate) - [select for diffs]
Modified Tue May 22 10:13:03 2007 UTC (17 years, 4 months ago) by duarte
File length: 13909 byte(s)
Diff to previous 152

Fixed bug: wasn't initialising accode, chain and chaincode when reading to file. Now all set to "" when not present in file

Revision 152 - (view) (annotate) - [select for diffs]
Modified Wed May 16 14:12:50 2007 UTC (17 years, 4 months ago) by duarte
File length: 13751 byte(s)
Diff to previous 146

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 - (view) (annotate) - [select for diffs]
Modified Tue May 15 13:51:17 2007 UTC (17 years, 4 months ago) by duarte
File length: 11310 byte(s)
Diff to previous 145

Made cutoff and ct public

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Modified Tue May 15 13:28:24 2007 UTC (17 years, 4 months ago) by duarte
File length: 11296 byte(s)
Diff to previous 144

Made some fields public: sequence, accode, chaincode, model

Revision 144 - (view) (annotate) - [select for diffs]
Modified Tue May 15 12:13:31 2007 UTC (17 years, 4 months ago) by duarte
File length: 11289 byte(s)
Diff to previous 143

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 - (view) (annotate) - [select for diffs]
Modified Tue May 15 10:06:47 2007 UTC (17 years, 4 months ago) by duarte
File length: 9215 byte(s)
Diff to previous 142

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 - (view) (annotate) - [select for diffs]
Modified Tue May 15 08:33:44 2007 UTC (17 years, 4 months ago) by duarte
File length: 9201 byte(s)
Diff to previous 141

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 - (view) (annotate) - [select for diffs]
Modified Mon May 14 15:51:54 2007 UTC (17 years, 4 months ago) by duarte
File length: 8536 byte(s)
Diff to previous 135

Changed input in constructor for reading from db: chain->chaincode
Now getgraphid initialises too the internal chain code (pchain_code from graph db)

Revision 135 - (view) (annotate) - [select for diffs]
Modified Mon May 14 09:49:04 2007 UTC (17 years, 4 months ago) by duarte
File length: 8357 byte(s)
Diff to previous 134

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 - (view) (annotate) - [select for diffs]
Modified Mon May 14 07:52:10 2007 UTC (17 years, 4 months ago) by duarte
File length: 3795 byte(s)
Diff to previous 129

Implemented basic reading contacts from file

Revision 129 - (view) (annotate) - [select for diffs]
Modified Thu May 10 13:12:32 2007 UTC (17 years, 4 months ago) by duarte
File length: 2243 byte(s)
Diff to previous 123

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 123 - (view) (annotate) - [select for diffs]
Added Wed May 9 10:45:53 2007 UTC (17 years, 4 months ago) by duarte
File length: 651 byte(s)

Initial commit of the proteinstructure package. Contains classes to use pdb protein structures