Plip

* Preparation for Python 3: Imports
* small correction for PDB fixing
* includes TODO files with user suggestions
* license adapted to GNU GPLv2

* __DNA/RNA can be selected as receptor with --dnareceptor__
* __Composite ligands and intra-protein mode: Annotation which part of the ligand interacts with the receptor__
* Improved handling of NMR structures
* Filter for extremely large ligands
* Speed-up for file reading and parallel visualization
* More debugging messages

* __Adds XML Parser module for PLIP XML files__
* Detection of intramolecular interactions with --intra
* improved error correction in PDB files

* __Processing of protein-peptide interactions via --peptides__
* option to keep modified residues as ligands (--keepmod)
* Improved code for reports
* Smart ordering of ligand in composite compounds
* Fixes handling and visualization of DNA/RNA

* __Support for amino acids as ligands__
* __Plugin-ready for PyMOL and Chimera__
* Refactores code and optimized input
* Improved verbose and debug log system
* Bugfixes for problems affecting some structures with aromatic rings

* __Batch processing__
* Improvements to verbose mode and textual output