PDB2PQR 1.4.0 (2009-03)
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New features
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* Updated html/master-index.html, deleted html/index.php.
* Updated pydoc by running genpydoc.sh.
* Added a whitespace option by by putting whitespaces between atom name and residue name, between x and y, and between y and z.
* Added radius for Chlorine in ligff.py.
* Added PEOEPB forcefield, data provided by Paul Czodrowski.
* Updated inputgen.py to write out the electrostatic potential for APBS input file. 
* Updated CHARMM.DAT with two sets of phosphoserine parameters.
* Allowed amino acid chains with only one residue, using --assign-only option.
* Updated server.py.in so that the ligand option is also recorded in usage.txt. 
* Updated HE21, HE22 coordinates in GLN according to the results from AMBER Leap program.
* Updated Makefile.am with Manuel Prinz's patch (removed distclean2 and appended its contents to distclean-local).
* Updated configure.ac, pdb2pqr-opal.py; added AppService_client.py and AppService_types.py with Samir Unni's changes, which fixed earlier problems in invoking Opal services.
* Applied two patches from Manuel Prinz to pdb2pka/pMC_mult.h and pdb2pka/ligand_topology.py. 
* Updated PARSE.DAT with the source of parameters. 
* Created a contrib folder with numpy-1.1.0 package. PDB2PQR will install numpy by default unless any of the following conditions is met:
* Working version of NumPy dectected by autoconf.
* User requests no installation with --disable-pdb2pka option.
* User specifies external NumPy installation.  
* Merged Samir Unni's branch. Now PDB2PQR Opal and APBS Opal services are available (through --with-opal and/or --with-apbs, --with-apbs-opal options at configure stage).
* Added error handling for residue name longer than 4 characters.
* Updated hbond.py with Mike Bradley's definitions for ANGLE_CUTOFF and DIST_CUTOFF by default.
* Removed PyXML-0.8.4, which is not required for ZSI installation.
* Updated propka error message for make adv-test -- propka requires a version of Fortran compiler.
* Updated na.py and PATCHES.xml so that PDB2PQR handles three lettered RNA residue names (ADE, CYT, GUA, THY, and URA) as well.
* Updated NA.xml with HO2' added as an alternative name for H2'', and H5" added as an alternative name for H5''. 
* Updated version numbers in html/ and doc/pydoc/ .
* Updated web server. When selecting user-defined forcefield file from the web server, users should also provide .names file.
* Removed http://enzyme.ucd.ie/Services/pdb2pqr/ from web server list.
* Eliminated the need for protein when processing other types (ligands,  nucleic acids).
* Updated psize.py with Robert Konecny's patch to fix inconsistent assignment of fine grid numbers in some (very) rare cases.
* Made whitespace option available for both command line and web server versions.
* Updated inputgen_pKa.py with the latest version.

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Bug fixes
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* Fixed a legacy bug with the web server (web server doesn't like ligand files generated on Windows or old Mac OS platforms).
* Fixed a bug in configure.ac, so that PDB2PQR no longer checks for Numpy.pth at configure stage.
* Updated pdb2pka/substruct/Makefile.am. 
* Fixed isBackbone bug in definitions.py.
* Fixed a bug for Carboxylic residues in hydrogens.py.
* Fixed a bug in routines.py, which caused hydrogens added in LEU and ILE in eclipsed conformation rather than staggered. 
* Fixed a bug in configure.ac, now it is OK to configure with double slashes in the prefix path, e.g.,  --prefix=/foo/bar//another/path 
* Fixed a bug in nucleic acid naming scheme. 
* Fixed a bug involving MET, GLY as NTERM, CTERM with --ffout option.
* Fixed a bug for PRO as C-terminus with PARSE forcefield. 
* Fixed a bug for ND1 in HIS as hacceptor.
* Fixed the --clean option bug.
* Fixed a bug in CHARMM naming scheme.
* Fixed a bug in test.cpp of the simple test (which is related to recent modifications of 1AFS in Protein Data Bank).
