Creating my branch.

git-svn-id: https://svn.code.sf.net/p/pdb2pqr/code/branches/monson-dev@978 a31b80ef-cfbe-4eed-bdb8-f46006999a5b
Adding propka30 to my dev branch.

git-svn-id: https://svn.code.sf.net/p/pdb2pqr/code/branches/monson-dev@980 a31b80ef-cfbe-4eed-bdb8-f46006999a5b
First pass at using Propka 3.0. It works, but it is still in the "duct tape and chewing gum" phase. Still more clean up to do.

git-svn-id: https://svn.code.sf.net/p/pdb2pqr/code/branches/monson-dev@983 a31b80ef-cfbe-4eed-bdb8-f46006999a5b
More cleanup of code. 

Fixed Atom.__str__ method to actually reflect the original file contents.

git-svn-id: https://svn.code.sf.net/p/pdb2pqr/code/branches/monson-dev@984 a31b80ef-cfbe-4eed-bdb8-f46006999a5b
Update configure to not try to compile propka anymore. 

Removed propka 1.

git-svn-id: https://svn.code.sf.net/p/pdb2pqr/code/branches/monson-dev@985 a31b80ef-cfbe-4eed-bdb8-f46006999a5b
Added attribution to propka code.

git-svn-id: https://svn.code.sf.net/p/pdb2pqr/code/branches/monson-dev@987 a31b80ef-cfbe-4eed-bdb8-f46006999a5b
Removed propka stuff from configure.


git-svn-id: https://svn.code.sf.net/p/pdb2pqr/code/branches/monson-dev@988 a31b80ef-cfbe-4eed-bdb8-f46006999a5b
Fixed broken PQR output.

Still need to check if PDB representation of Atom is correct.

git-svn-id: https://svn.code.sf.net/p/pdb2pqr/code/branches/monson-dev@989 a31b80ef-cfbe-4eed-bdb8-f46006999a5b
Restored Algorithms import in NEWligand_topology.py. (If I can't import it then pdb2pka was not compiled.)

Added attribution to extensions/__init__.py

Fixed capitalization of force field in PQR header.

git-svn-id: https://svn.code.sf.net/p/pdb2pqr/code/branches/monson-dev@992 a31b80ef-cfbe-4eed-bdb8-f46006999a5b
Updated attribution for propka 3.0.

git-svn-id: https://svn.code.sf.net/p/pdb2pqr/code/branches/monson-dev@993 a31b80ef-cfbe-4eed-bdb8-f46006999a5b
Updated template for extensions in documentation.

Cleaned up change logs. Only 1.7.1a branch needs new changes.

Updated reported version number in trunk.

Updated INSTALL file to reflect the need for 2.6.

git-svn-id: https://svn.code.sf.net/p/pdb2pqr/code/branches/monson-dev@997 a31b80ef-cfbe-4eed-bdb8-f46006999a5b
Learned how to spell extension... again.

git-svn-id: https://svn.code.sf.net/p/pdb2pqr/code/branches/monson-dev@1003 a31b80ef-cfbe-4eed-bdb8-f46006999a5b
Fixed white space and various warnings in propka30 code and hydrogens.py

Fixed crash caused by rounding error.

git-svn-id: https://svn.code.sf.net/p/pdb2pqr/code/branches/monson-dev@1005 a31b80ef-cfbe-4eed-bdb8-f46006999a5b
And the ChangeLog.

git-svn-id: https://svn.code.sf.net/p/pdb2pqr/code/branches/monson-dev@1006 a31b80ef-cfbe-4eed-bdb8-f46006999a5b
Cleaned up and improved extensions.

git-svn-id: https://svn.code.sf.net/p/pdb2pqr/code/branches/monson-dev@1008 a31b80ef-cfbe-4eed-bdb8-f46006999a5b
Added first version of resinter. 

Cleaned up some code.

git-svn-id: https://svn.code.sf.net/p/pdb2pqr/code/branches/monson-dev@1010 a31b80ef-cfbe-4eed-bdb8-f46006999a5b
Added some doc strings.

Finished up resinter plugin.

Fixed printAtoms function mucking with data structures.

git-svn-id: https://svn.code.sf.net/p/pdb2pqr/code/branches/monson-dev@1011 a31b80ef-cfbe-4eed-bdb8-f46006999a5b
Change log.

git-svn-id: https://svn.code.sf.net/p/pdb2pqr/code/branches/monson-dev@1012 a31b80ef-cfbe-4eed-bdb8-f46006999a5b
Reduced number of combinations checked by resinter.

git-svn-id: https://svn.code.sf.net/p/pdb2pqr/code/branches/monson-dev@1013 a31b80ef-cfbe-4eed-bdb8-f46006999a5b
Updated resinter. Now has two methods for generating combinations of residue titration states. The slow method figure all combinations and the fast method only the minimum number of whole protein titration combinations needed to test each possible pairing of residue titration states.

Added options to allow the user to pick.

git-svn-id: https://svn.code.sf.net/p/pdb2pqr/code/branches/monson-dev@1014 a31b80ef-cfbe-4eed-bdb8-f46006999a5b