Metadata-Version: 2.1
Name: prolif
Version: 0.1.2
Summary: Protein-Ligand Interaction Fingerprints
Home-page: https://github.com/cbouy/ProLIF
Author: Cédric Bouysset
Author-email: bouysset.cedric@gmail.com
License: Apache License, Version 2.0
Project-URL: Source, https://github.com/cbouy/ProLIF/
Project-URL: Bug Reports, https://github.com/cbouy/ProLIF/issues
Project-URL: Say Thanks!, https://saythanks.io/to/cbouy
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        # ProLIF
        Protein-Ligand Interaction Fingerprints
        
        :warning: This project is under active development, and might be subject to drastic changes. Use at your own risks :warning:
        
        ## Description
        
        ProLIF is a tool designed to generate Interaction FingerPrints (IFP) and compute similarity scores for protein-ligand interactions, given a reference ligand and a list of binding-site residues.
        
        ## Installation
        
        ProLIF is written in Python 3, and uses the following non-standard libraries:
        * numpy
        * [rdkit](http://www.rdkit.org/docs/Install.html)
        
        
        Make sure RDKit is installed before proceeding to the next step:
        ```
        conda install -c rdkit rdkit
        ```
        
        Once this is done, you can download the package with Pip:
        ```
        pip install prolif
        ```
        
        ## Usage
        
        ```
        INPUT arguments:
          -r fileName, --reference fileName
                                Path to your reference ligand.
          -l fileName [fileName ...], --ligand fileName [fileName ...]
                                Path to your ligand(s).
          -p fileName, --protein fileName
                                Path to your protein.
          --residues RESIDUES [RESIDUES ...]
                                Residues chosen for the interactions. Default: automatically detect residues within --cutoff of the reference ligand
          --cutoff float        Cutoff for automatic residue detection: distance between centroids. Default: 12.0 Å
          --json fileName       Path to a custom parameters file. Default: /home/cedric/Dropbox/work/prolif/prolif/parameters.json
        
        OUTPUT arguments:
          -o filename, --output filename
                                Path to the output CSV file
          --log level           Set the level of the logger. Default: ERROR
          -v, --version         Show version and exit
        
        Other arguments:
          --interactions bit [bit ...]
                                List of interactions used to build the fingerprint.
                                              │          Class         Ligand        Residue
                                              │―――――――――――――――――――――――――――――――――――――――――――――
                                      HBdonor │  Hydrogen bond          donor       acceptor
                                   HBacceptor │  Hydrogen bond       acceptor          donor
                                      XBdonor │   Halogen bond          donor       acceptor
                                   XBacceptor │   Halogen bond       acceptor          donor
                                       cation │          Ionic         cation          anion
                                        anion │          Ionic          anion         cation
                                  hydrophobic │    Hydrophobic    hydrophobic    hydrophobic
                                   FaceToFace │    Pi-stacking       aromatic       aromatic
                                   FaceToEdge │    Pi-stacking       aromatic       aromatic
                                    pi-cation │      Pi-cation       aromatic         cation
                                    cation-pi │      Pi-cation         cation       aromatic
                                      MBdonor │          Metal          metal         ligand
                                   MBacceptor │          Metal         ligand          metal
                                Default: HBdonor HBacceptor cation anion FaceToFace FaceToEdge hydrophobic
          --score {tanimoto,dice,tversky}
                                Similarity score between molecule A and B :
                                Let 'a' and 'b' be the number of bits activated in molecules A and B, and 'c' the number of activated bits in common.
                                    -) tanimoto : c/(a+b-c). Used by default
                                    -) dice     : 2c/(a+b)
                                    -) tversky  : c/(alpha*(a-c)+beta*(b-c)+c)
          --alpha int           Alpha parameter for Tversky. Default: 0.7
          --beta int            Beta parameter for Tversky. Default: 0.3
        
        Mandatory arguments: --reference --ligand --protein
        MOL2 files only.
        ```
        
        ## License
        
        Unless otherwise noted, all files in this directory and all subdirectories are distributed under the Apache License, Version 2.0:
        ```
           Copyright 2017-2018 Cédric BOUYSSET
        
           Licensed under the Apache License, Version 2.0 (the "License");
           you may not use this file except in compliance with the License.
           You may obtain a copy of the License at
        
               http://www.apache.org/licenses/LICENSE-2.0
        
           Unless required by applicable law or agreed to in writing, software
           distributed under the License is distributed on an "AS IS" BASIS,
           WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
           See the License for the specific language governing permissions and
           limitations under the License.
        ```
        
Keywords: science chemistry biology drug-design chemoinformatics virtual-screening
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Environment :: Console
Classifier: Operating System :: OS Independent
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Chemistry
Requires-Python: >=3
Description-Content-Type: text/markdown
