removing extra files

5 files changed, 0 insertions, 196 deletions

diff --git a/CHANGES.txt b/CHANGES.txt
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--- a/CHANGES.txt
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-Changelog
----------
-# 2.1.0
-* maintainer changed to PharmAI GmbH
-* full compatibility to Python 3 and OpenBabel 3
-* Docker and Singularity support, Deployment to Docker Hub
-* dropped support for OpenBabel 2, Python 2
-* reorganization of modules
-* migrates to proper logging pattern
-* code quality enhancements
-* adds option to disable non-deterministic protonation of structures (`--nohydro`)
-* protonated structures are now stored to guarantee consistent interaction detection
-* new options to change verbosity levels
-
-# 1.4.5
-* Updates contact info
-
-# 1.4.4
-* Improved parameters for water bridge detection
-* Added unit test for PDB structure 1HPX
-* PEP8 Changes
-* Improved imports
-
-# 1.4.3
-* Adds information on covalent linkages to XML files
-* __Anaconda package__ (provided by `Ikagami`)
-
-# 1.4.2
-* Adds "--name" option to change name of output files
-* Adds "--nopdbcanmap" option to skip calculation of canonical->PDB mapping which can lead to segfaults with OpenBabel
-* Improved handling of ligand names
-
-# 1.4.1
-* Improved import of modules
-* Corrections for README and documentation
-* Several improvements for error handling
-* independence from PyMOL when used without visualization features
-
-# 1.4.0
-* __Full Python 3 Compatibility__
-* __Read PDB files from stdin with "-f -" and write to stdout with "-O" (capital "O")__
-* Improves handling of fixed PDB files
-* Option to turn off writing fixed PDB structures to a file ("--nofixfile")
-
-### 1.3.5
-* Preparation for Python 3: Imports
-* small correction for PDB fixing
-* includes TODO files with user suggestions
-* license adapted to GNU GPLv2
-
-### 1.3.4
-* __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
-
-### 1.3.3
-* __Adds XML Parser module for PLIP XML files__
-* Detection of intramolecular interactions with --intra
-* improved error correction in PDB files
-
-### 1.3.2
-* __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
-
-### 1.3.1
-* __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
-
-### 1.3.0
-* __Batch processing__
-* Improvements to verbose mode and textual output
-
-### 1.2.3
-* __Better support for files from MD and docking software__
-* __Fixes issues with large and complex structures__
-* Speed optimizations
-
-
-### 1.2.2
-* __Option to consider alternate atom locations (e.g. for ligands with several conformations__
-* Automatic fixing of missing ligand names
-* Improved handling of broken PDB files and non-standard filenames
-* Improved error handling
-
-### 1.2.1
-* __Mapping of canonical atom order to PDB atom order for each ligand__
-* __Introduction of debug mode (--debug)__
-* More robust visualization
-* Handling of negative residue numbers for more cases
-* Composite members in alphabetical order
-* Fixes errors in aromatic ring detection
-* Code improvements
-
-### 1.2.0
-* __Support for DNA and RNA as ligands__
-* __Detection of metal complexes with proteins/ligands, including prediction of geometry__
-* __Extended result files with detailed information on binding site residues and unpaired atoms__
-*__Support for zipped and gzipped files__
-* Rich verbose mode in command line with information on detected functional groups and interactions
-* Automatic fixing of common errors in custom PDB files
-* Refined binding site selection
-* Better overall performance
-* Initial test suite for metal coordination
-* Classification of ligands
-* Improves detection of aromatic rings and interactions involving aromatic rings
-* Single nucleotides and ions not excluded anymore as ligands
-* Generation of canonical smiles for complete (composite) ligands
-* Generation of txt files is now optional
-* Basic support for PDBQT files
-* Correct handling of negative chain positions of ligands
-* Improved check for valid PDB IDs
-* Fixes several bugs
-
-
-
-### 1.1.1
-* __Detailed information on binding site residues in XML files__
-* Improved extraction of binding site residues
-* Information whether halogen bonds are made with side- or main chain of protein
-
-#### 1.1.0
-* __Folder structure and setup.py for automatic installation using pip__
-* __H-Bond Donor Prioritization (see documentation for details)__
-* Adds separate changelog
-* Updated documentation and citation information
-* Reduction of blacklist usage
-* Information on excluded ligands in result files
-
-#### 1.0.2
-* __Automatic grouping of composite ligands (e.g. polysaccharides)__
-* __Proper handling of alternative conformations in PDB structures__
-* __Exclusion of modified residues as ligands__
-* __Improved detection of hydrogen bonds__
-* __Prioritization of hydrogen bonds__
-* Adds atom type description in the output files
-* Basic support for usage on Windows (without multithreading)
-* Option to turn multithreading off by setting maxthreads to 0
-* Improved detection of hydrogen bond donors in ligands
-* Adaption of standard parameters
-* Fixes a bug in PyMOL visualization script leading to missing or wrong interactions with pseudoatoms
-* Fixes a bug leading to duplicate or triplicate detection of identical pi-cation interactions with guanidine
-* Adds now unit tests
-* Small changes to existing unit tests for new features
-
-#### 1.0.1
-* __Option to change detection thresholds permanently or for single runs__
-* Option to (de)activate output for images, PyMOL session files and XML files
-* Changed standard behaviour to output of RST report only
-* Information on sidechain/backbone hydrogen bond type
-* Sorted output
-* Detection of more flavors of halogen bonds
-* Fixed bug leading to duplicate interactions with quartamine groups
-
-#### 1.0.0
-* __Initial Release__
diff --git a/pliplogo.png b/pliplogo.png
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--- a/pliplogo.png
+++ /dev/null
diff --git a/requirements.txt b/requirements.txt
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--- a/requirements.txt
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@@ -1,4 +0,0 @@
-lxml~=4.2.1
-numpy~=1.13.3
-pymol~=2.3.0
-openbabel~=3.0.0
\ No newline at end of file
diff --git a/setup.cfg b/setup.cfg
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-[metadata]
-description-file = README.md
\ No newline at end of file
diff --git a/setup.py b/setup.py
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--- a/setup.py
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-from setuptools import setup
-
-setup(name='plip',
-      version='2.1.0-beta',
-      description='PLIP - Fully automated protein-ligand interaction profiler',
-      classifiers=[
-          'Development Status :: 5 - Production/Stable',
-          'Intended Audience :: Science/Research',
-          'Natural Language :: English',
-          'License :: OSI Approved :: GNU General Public License v2 (GPLv2)',
-          'Programming Language :: Python :: 3.6',
-          'Topic :: Scientific/Engineering :: Bio-Informatics'
-      ],
-      url='https://github.com/pharmai/plip',
-      author='PharmAI GmbH',
-      author_email='hello@pharm.ai',
-      license='GPLv2',
-      packages=['plip'],
-      scripts=['plip/plipcmd.py'],
-      install_requires=[
-          'openbabel',
-          'numpy',
-          'lxml',
-          'pymol'
-      ],
-      zip_safe=False)