MMCIF bugfix

Minor Bugfix on MMCIF format support & alternate locations that weren't read correctly.
CI back to functional as well.

Bugfix release on MMCIF support with new version molfile plugin

This release contains the latest version of the molfile plugin from vmd with especially updated pdbxplugin and adapted for fpocket use. The plugin is built-in as shared library for osx (intel chips) and linux 64 bit architectures. If others are needed, you'd need to compile it yourself here: https//github.com/Discngine/molfile_plugin

MMCIF & peptide support

Major release enabling the user to use mmCIF as input and output format with fpocket
Several command line flags were added enabling more advanced epitope characterization, descriptor extraction, parameter optimization and scoring function refinement especially with applications on biologics (protein protein complexes, protein DNA, protein RNA complexes):

-c char : (Default is none): Use this flag to choose which chains you want to delete before running fpocket. The selected chains can be specified with ',' or ':' delimiters, for example you can use it '-c B,D' or '-c B:D'. You can delete up to 20 different chains.

-k char : (Default is none): Use this flag to choose which chains you want to keep before running fpocket. The selected chains can be specified with ',' or ':' delimiters, for example you can use it '-k A,B,E' or '-k A:B:E'. You can keep up to 20 different chains.

-a char : (Default is none): With this flag you can select a chain you want to be considered as a ligand. Works the same way as the "-r" flag but with a whole chain. Only a single chain can be chosen, for example '-a D'.

-w char : (Default is 'd') : With this flag you are able to choose what kind of writing file output you want, 'd' -> default (same format outpout as input)| 'b' or "both"-> both pdb and mmcif | 'p' or "pdb"-> pdb | 'm' or "cif" or "mmcif" -> mmcif, for example "-w cif" or "-w p"

Docker Support, CI and testing framework

Added dockerfile & official fpocket image on dockerhub: https://hub.docker.com/repository/docker/fpocket/fpocket

Added pytest based regression testing framework for development

Added first shot of azure pipelines to automatically build & test on Linux and MacOS

Documentation update

Major documentation update porting the old pdf / odt documentation to markdown and updating to the most recent fpocket version with new command line flags for fpocket and mdpocket.

pdb list flag Bugfix for mdpocket

Bugfix release for the Issue #24
Support python3 for python scripts

Compilation bugfix release - support for OSX clang

This is a minor bugfix release after a lot of issues compiling fpocket and mdpocket due to the introduction of the molfile plugin into fpocket.
Compilation has been split up in fpocket vs mdpocket. So if you only want to compile fpocket, you can do so by typing:
make fpocket
No need to have all the netcdf stuff for that!

to compile mdpocket:
make mdpocket

I also added clang and compilation support on 64 bit OSX machines. SO now, 64 bit linux and osx are supported which is pretty cool.

A few improvements on the README.md, but there's still a lot of things to be done

Bugfix on -d flag output of fpocket

with previous release the output returned using the -d flag in fpocket was broken due to some misbehaviour on output directory creation. THis should be fixed now here.

Qhull update to 2015.2

This release integrates the new version of qhull.
We observed major issues of qvoronoi to work on systems with sets of coordinates not centered around 0. This has been fixed in the latest version of qhull...thus the integration. Results should be also more precise and less sensible to noise (in theory).

Here the full qhull source code is included and qvoronoi and qconvex have been adapted for fpocket.

Desmond Support added to mdpocket

• Desmond (dtr) support has now been added to mdpocket.
• Minor bugfixes during compilation and a bit of clean up of the code (unused variables etc).
• Also, Copyright has also been updated. MIT license everywhere now.