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| -rw-r--r-- | CHANGES.txt | 164 | ||||
| -rw-r--r-- | pliplogo.png | bin | 31773 -> 0 bytes | |||
| -rw-r--r-- | requirements.txt | 4 | ||||
| -rw-r--r-- | setup.cfg | 2 | ||||
| -rw-r--r-- | setup.py | 26 |
5 files changed, 0 insertions, 196 deletions
diff --git a/CHANGES.txt b/CHANGES.txt deleted file mode 100644 index 529636e..0000000 --- a/CHANGES.txt +++ /dev/null @@ -1,164 +0,0 @@ -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 Binary files differdeleted file mode 100644 index 212e7a2..0000000 --- a/pliplogo.png +++ /dev/null diff --git a/requirements.txt b/requirements.txt deleted file mode 100644 index 6d4d07c..0000000 --- a/requirements.txt +++ /dev/null @@ -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 deleted file mode 100644 index 224a779..0000000 --- a/setup.cfg +++ /dev/null @@ -1,2 +0,0 @@ -[metadata] -description-file = README.md
\ No newline at end of file diff --git a/setup.py b/setup.py deleted file mode 100644 index 823e7e5..0000000 --- a/setup.py +++ /dev/null @@ -1,26 +0,0 @@ -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) |
