ViewVC Help
View Directory | Revision Log | Download Tarball | View Changeset | Root Listing
root/owl/trunk/src/owl/core/connections/pisa
Sticky Revision:
Sort logs by:
Revision 1312 - Directory Listing
Modified Mon Feb 7 15:00:47 2011 UTC (10 years, 7 months ago) by jmduarteg
Put back the parsing of score p values (was commented out)
Revision 1296 - Directory Listing
Modified Fri Jan 7 11:16:43 2011 UTC (10 years, 8 months ago) by jmduarteg
Bringing back the PISA classes for interface, molecule and residues. We store things first into them and only then convert to our own ChainInterface if needed. This is a much better approach less prone to errors. Tests pass.
Revision 1265 - Directory Listing
Modified Wed Oct 20 08:01:41 2010 UTC (10 years, 11 months ago) by jmduarteg
Now keeping track of ASA calc method
Revision 1258 - Directory Listing
Modified Fri Oct 8 13:15:13 2010 UTC (10 years, 11 months ago) by jmduarteg
Fixed bug: now we properly parse from pisa both the orthonormal and the crystal coords operators.
Added a test for SpaceGroup to test for proper parsing of algebraic strings
Revision 1228 - Directory Listing
Modified Tue Sep 7 15:41:50 2010 UTC (11 years ago) by jmduarteg
Now PISA interfaces using same classes as our own calculated interfaces. Removed all Pisa specific classes (except for connector and parser). Introduce new class ChainInterfaceList which also simplifies some things.
PdbAsymUnitTest passes.
Revision 1217 - Directory Listing
Modified Tue Aug 31 17:11:30 2010 UTC (11 years ago) by jmduarteg
First fully working version (this time hopefully for real...) of interface enumeration. Works for many examples, still there are problems in many others due to area discrepancies with pisa, but those are minor things. The elimination of duplicates is based on chain codes and number of contacting atoms, it is of course possible that 2 different interfaces happen to have the same chain codes and same number of contacting atoms (but unlikely). Would need a more fine grained comparison.
New test class to compare automatically to PISA output.
Revision 1215 - Directory Listing
Modified Fri Aug 27 17:03:45 2010 UTC (11 years ago) by jmduarteg
Fixed bug: using the negative side of the 26 translations was causing an incorrect number of interfaces reported for 1pmm and 1pmo. Not sure why but for the moment reverting to doing the positive side.
Changed cutoff to 5.9, then both 1pmm and 1pmo match pisa.
Better reporting of symops (now based on matrices converted to algebraic notation), before was not totally correct.
Still problems with the code as it does not match pisa for some examples (probably many), e.g. for 7odc reports 4 instead of 6 interfaces.
Revision 1108 - Directory Listing
Modified Thu Jun 10 16:27:48 2010 UTC (11 years, 3 months ago) by jmduarteg
Now parsing the symmetry operators.
Revision 1101 - Directory Listing
Modified Wed Jun 9 09:26:27 2010 UTC (11 years, 3 months ago) by jmduarteg
Now serializable (to be able to write them to file)
Revision 1096 - Directory Listing
Modified Fri Jun 4 14:48:12 2010 UTC (11 years, 3 months ago) by jmduarteg
Minor doc fix
Revision 1087 - Directory Listing
Modified Mon May 31 15:41:25 2010 UTC (11 years, 3 months ago) by jmduarteg
Improved the getRimAndCore method
Revision 1085 - Directory Listing
Modified Mon May 31 13:45:03 2010 UTC (11 years, 3 months ago) by jmduarteg
Some new methods
Revision 1083 - Directory Listing
Modified Mon May 31 13:31:23 2010 UTC (11 years, 3 months ago) by hstehr
fixed bug in printf statement because pdbResSer has changed from int to String
Revision 1082 - Directory Listing
Modified Fri May 28 15:00:31 2010 UTC (11 years, 3 months ago) by jmduarteg
Fixed bug in getRimAndCore, now we do end the loop correctly at the hard cutoff value.
Revision 1079 - Directory Listing
Modified Fri May 28 12:52:31 2010 UTC (11 years, 3 months ago) by jmduarteg
Improved the rim and core calculation. The pdb res serial is now a String in PisaResidue (because of insertion codes)
Revision 1078 - Directory Listing
Modified Thu May 27 10:33:41 2010 UTC (11 years, 3 months ago) by jmduarteg
Now parsing the seq_num residue number.
Revision 1077 - Directory Listing
Modified Thu May 27 09:51:50 2010 UTC (11 years, 3 months ago) by jmduarteg
Fixed a bug in PISA xml parser: pdb code was upper case, need to convert to lower case.
Some new functionality in PISA classes
Revision 1075 - Directory Listing
Added Fri May 21 17:33:34 2010 UTC (11 years, 4 months ago) by jmduarteg
PISA connection and xml interfaces description parser