The PROPKA31 tests fail on Windows 10 Ubuntu 18.04 Windows Subsystem
Linux without any changes. The relative error is less than 1e-3. This
commit chnages the behavior to a test of absolute agreement to a test of
relative error less than 1e-3.
- set VERSION to 3.1.0 (introduce a patch level 0 so that it becomes
easier to publish packages with small fixes, eg for installation)
- got rid of ancient ez_install: just use pip
- updated README and INSTALL
- updated classifiers in setup.py (license: LGPL v2.1 and other meta data);
updated URL to point to http://propka.org because unlike http://propka.ki.ku.dk
it is not completely dead and has a link to the pdb2pqr propka server as well
as the GitHub page
- Fix an issue where non-existing interactions were analyzed.
Bug fix in setIonDeterminants(): skip interactions if either
titratable_group_interaction_atoms or the backbone_interaction_atoms
is empty.
- Set center of COO_group to self.atom if no oxygens present in residue.
COO_group: If self.atom.get_bonded_elements('O') returns an emtpy list
(the residue has missing side-chain), simply set the center of the
group to the <self.atom> atom, instead of the center of the
(non-existing) oxygens.
- Raise more friendly exception in Group.set_center() if an empty atom
set is passed in.
- Cterm_group: Fix crash if residue is missing a carbon.
The previous code would crash if the C-termini residue group was
missing the carbon atom.
- Fix a failure when a HIS residue has missing side-chain atoms.
- Added an entry for Iodine (I) to the valence electrons table.
- Major optimization of the put_atom_in_box() function.
- Major optimization of the protein_precheck() function.
- Minor optimization in radial_volume_desolvation()
- Optimization in top_up() to scale for large structures.
- add the ability to run tests from the top level directory via
'python setup.py test'
- translate runtest.py into a test that runs under this framework
- add a __main__ section to Tests/runtest.py and change its indent to 4
spaces; make no other changes to this script
* 'python setup.py install' will install
- a package 'propka' (which contains everything that 'Source' contained
in the original distribution)
- an executable script 'propka31' (which is identical to the original
'propka.py' script but it is automatically generated via the setuptools
mechanism; it uses propka.run.main().
* 'pip install' will also work
* the README.md file was changed to reflect the alterations
* metadata in the setup.py file was added
NOTE: The licence is still unclear!
