├── .github └── workflows │ ├── publish_to_pypi.yml │ └── run_tests.yml ├── .gitignore ├── LICENSE ├── MANIFEST.in ├── README.md ├── padelpy ├── PaDEL-Descriptor │ ├── Descriptors.xls │ ├── PaDEL-Descriptor.jar │ ├── descriptors.xml │ ├── lib │ │ ├── ambit2-base-2.4.7-SNAPSHOT.jar │ │ ├── ambit2-core-2.4.7-SNAPSHOT.jar │ │ ├── ambit2-smarts-2.4.7-SNAPSHOT.jar │ │ ├── appframework-1.0.3.jar │ │ ├── cdk-1.4.15.jar │ │ ├── commons-cli-1.2.jar │ │ ├── guava-17.0.jar │ │ ├── jama.jar │ │ ├── jgrapht-0.6.0.jar │ │ ├── l2fprod-common-all.jar │ │ ├── libPaDEL-Descriptor.jar │ │ ├── libPaDEL-Jobs.jar │ │ ├── libPaDEL.jar │ │ ├── swing-worker-1.1.jar │ │ ├── vecmath1.2-1.14.jar │ │ └── xom-1.1.jar │ └── license │ │ ├── LICENSE.txt │ │ ├── README - CDK │ │ ├── lgpl-2.1.txt │ │ └── lgpl.license ├── __init__.py ├── functions.py ├── py.typed ├── version.py └── wrapper.py ├── pyproject.toml └── tests ├── aspirin_3d.sdf └── test_all.py /.github/workflows/publish_to_pypi.yml: -------------------------------------------------------------------------------- 1 | name: Upload new PaDELPy version to PyPI 2 | 3 | on: 4 | release: 5 | types: [published] 6 | 7 | permissions: 8 | contents: read 9 | 10 | jobs: 11 | deploy: 12 | runs-on: ubuntu-latest 13 | steps: 14 | - name: Checkout 15 | uses: actions/checkout@v3 16 | - name: Set up Python 3.11 17 | uses: actions/setup-python@v3 18 | with: 19 | python-version: '3.11' 20 | - name: Install dependencies 21 | run: | 22 | python -m pip install --upgrade pip 23 | pip install build 24 | - name: Build package 25 | run: python -m build 26 | - name: Publish package to PyPI 27 | uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29 28 | with: 29 | user: __token__ 30 | password: ${{ secrets.PYPI_API_TOKEN }} -------------------------------------------------------------------------------- /.github/workflows/run_tests.yml: -------------------------------------------------------------------------------- 1 | name: Run PaDELPy tests 2 | 3 | on: [push] 4 | 5 | jobs: 6 | build: 7 | runs-on: ubuntu-latest 8 | steps: 9 | - name: Checkout 10 | uses: actions/checkout@v3 11 | - name: Set up Python 3.11 12 | uses: actions/setup-python@v3 13 | with: 14 | python-version: '3.11' 15 | - name: Install dependencies 16 | run: | 17 | python -m pip install --upgrade pip 18 | pip install build 19 | pip install pytest pytest-md 20 | - name: Install package 21 | run: python -m pip install . 22 | - name: Run tests 23 | uses: pavelzw/pytest-action@v2 24 | with: 25 | emoji: false 26 | report-title: 'PaDELPy test report' -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | # Prerequisites 2 | *.d 3 | 4 | # Compiled object files 5 | *.slo 6 | *.lo 7 | *.o 8 | *.obj 9 | 10 | # Precompiled headers 11 | *.gch 12 | *.pch 13 | 14 | # Compiled dynamic libraries 15 | *.so 16 | *.so.[0-9]* 17 | *.dylib 18 | *.dll 19 | 20 | # Fortran module files 21 | *.mod 22 | *.smod 23 | 24 | # Compiled static libraries 25 | *.lai 26 | *.la 27 | *.a 28 | *.lib 29 | 30 | # Executables 31 | *.exe 32 | *.out 33 | *.app 34 | 35 | # Byte-compiled / optimized / DLL files 36 | __pycache__/ 37 | *.py[cod] 38 | *$py.class 39 | 40 | # Distribution / packaging 41 | .Python 42 | build/ 43 | develop-eggs/ 44 | dist/ 45 | downloads/ 46 | eggs/ 47 | .eggs/ 48 | lib/ 49 | lib64/ 50 | parts/ 51 | sdist/ 52 | var/ 53 | wheels/ 54 | .installed.cfg 55 | MANIFEST 56 | *.egg-info/ 57 | *.egg 58 | *.manifest 59 | *.spec 60 | pip-log.txt 61 | pip-delete-this-directory.txt 62 | # Unit test / coverage reports 63 | htmlcov/ 64 | .tox/ 65 | .coverage 66 | .coverage.* 67 | .cache 68 | nosetests.xml 69 | coverage.xml 70 | *,cover 71 | .pytest_cache/ 72 | 73 | # Documentation 74 | doc/html/ 75 | doc/latex/ 76 | doc/man/ 77 | doc/xml/ 78 | doc/_build/ 79 | doc/source 80 | doc/modules 81 | 82 | # Environments 83 | .env 84 | .venv 85 | env/ 86 | venv/ 87 | ENV/ 88 | 89 | # Editor junk 90 | tags 91 | [._]*.s[a-v][a-z] 92 | [._]*.sw[a-p] 93 | [._]s[a-v][a-z] 94 | [._]sw[a-p] 95 | *~ 96 | \#*\# 97 | .\#* 98 | .ropeproject 99 | .idea/ 100 | .spyderproject 101 | .spyproject 102 | .vscode/ 103 | # Mac .DS_Store 104 | .DS_Store 105 | 106 | # jupyter notebook checkpoints 107 | .ipynb_checkpoints 108 | 109 | # version file generated by rob 110 | padelpy/_version.py 111 | 112 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | MIT License 2 | 3 | Copyright (c) 2019 UMass Lowell Energy and Combustion Research Laboratory 4 | 5 | Permission is hereby granted, free of charge, to any person obtaining a copy 6 | of this software and associated documentation files (the "Software"), to deal 7 | in the Software without restriction, including without limitation the rights 8 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 9 | copies of the Software, and to permit persons to whom the Software is 10 | furnished to do so, subject to the following conditions: 11 | 12 | The above copyright notice and this permission notice shall be included in all 13 | copies or substantial portions of the Software. 14 | 15 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 16 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 17 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 18 | AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 19 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 20 | OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE 21 | SOFTWARE. 22 | -------------------------------------------------------------------------------- /MANIFEST.in: -------------------------------------------------------------------------------- 1 | include README.md 2 | include LICENSE 3 | include *.py 4 | 5 | graft padelpy/PaDEL-Descriptor/ 6 | recursive-exclude * __pycache__ 7 | recursive-exclude * *.py[co] -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | [![UML Energy & Combustion Research Laboratory](https://sites.uml.edu/hunter-mack/files/2021/11/ECRL_final.png)](http://faculty.uml.edu/Hunter_Mack/) 2 | 3 | # PaDELPy: A Python wrapper for PaDEL-Descriptor software 4 | 5 | [![GitHub version](https://badge.fury.io/gh/ecrl%2Fpadelpy.svg)](https://badge.fury.io/gh/ecrl%2Fpadelpy) 6 | [![PyPI version](https://badge.fury.io/py/padelpy.svg)](https://badge.fury.io/py/padelpy) 7 | [![GitHub license](https://img.shields.io/badge/license-MIT-blue.svg)](https://raw.githubusercontent.com/ecrl/padelpy/master/LICENSE.txt) 8 | 9 | PaDELPy provides a Python wrapper for the [PaDEL-Descriptor](https://pubmed.ncbi.nlm.nih.gov/21425294/) molecular descriptor calculation software. It was created to allow direct access to the PaDEL-Descriptor command-line interface via Python. 10 | 11 | ## Installation 12 | 13 | Installation via pip: 14 | 15 | ``` 16 | $ pip install padelpy 17 | ``` 18 | 19 | Installation via cloned repository: 20 | 21 | ``` 22 | $ git clone https://github.com/ecrl/padelpy 23 | $ cd padelpy 24 | $ pip install . 25 | ``` 26 | 27 | PaDEL-Descriptor is bundled into PaDELPy, therefore an external installation/download of PaDEL-Descriptor is not necessary. There are currently no additional Python dependencies for PaDELPy, however it requires an installation of the [Java JRE](https://www.oracle.com/technetwork/java/javase/downloads/jre8-downloads-2133155.html) version 6+. 28 | 29 | ## Basic Usage 30 | 31 | In addition to providing a complete interface between Python and PaDEL-Descriptor's command line tool, PaDELPy offers two functions to acquire descriptors/fingerprints within Python - obtaining descriptors/fingerprints from a SMILES string, and obtaining descriptors/fingerprints from an MDL MolFile. 32 | 33 | ### SMILES to Descriptors/Fingerprints 34 | 35 | The "from_smiles" function accepts a SMILES string or list of SMILES strings as an argument, and returns a Python dictionary with descriptor/fingerprint names/values as keys/values respectively - if multiple SMILES strings are supplied, "from_smiles" returns a list of dictionaries. 36 | 37 | ```python 38 | from padelpy import from_smiles 39 | 40 | # calculate molecular descriptors for propane 41 | descriptors = from_smiles('CCC') 42 | 43 | # calculate molecular descriptors for propane and butane 44 | descriptors = from_smiles(['CCC', 'CCCC']) 45 | 46 | # in addition to descriptors, calculate PubChem fingerprints 47 | desc_fp = from_smiles('CCC', fingerprints=True) 48 | 49 | # only calculate fingerprints 50 | fingerprints = from_smiles('CCC', fingerprints=True, descriptors=False) 51 | 52 | # setting the number of threads, this uses one cpu thread to compute descriptors 53 | descriptors = from_smiles(['CCC', 'CCCC'], threads = 1) 54 | 55 | # save descriptors to a CSV file 56 | _ = from_smiles('CCC', output_csv='descriptors.csv') 57 | ``` 58 | 59 | ### MDL MolFile to Descriptors/Fingerprints 60 | 61 | The "from_mdl" function accepts a filepath (to an MDL MolFile) as an argument, and returns a list. Each list element is a dictionary with descriptors/fingerprints corresponding to each supplied molecule (indexed as they appear in the MolFile). 62 | 63 | ```python 64 | from padelpy import from_mdl 65 | 66 | # calculate molecular descriptors for molecules in `mols.mdl` 67 | descriptors = from_mdl('mols.mdl') 68 | 69 | # in addition to descriptors, calculate PubChem fingerprints 70 | desc_fp = from_mdl('mols.mdl', fingerprints=True) 71 | 72 | # only calculate fingerprints 73 | fingerprints = from_mdl('mols.mdl', fingerprints=True, descriptors=False) 74 | 75 | # setting the number of threads, this uses one cpu thread to compute descriptors 76 | desc_fp = from_mdl('mols.mdl', threads=1) 77 | 78 | # save descriptors to a CSV file 79 | _ = from_mdl('mols.mdl', output_csv='descriptors.csv') 80 | ``` 81 | 82 | ### SDF to Descriptors/Fingerprints 83 | 84 | The "from_sdf" function accepts a filepath as an argument, and returns a list. 85 | Each list element is a dictionary with descriptors/fingerprints corresponding to each supplied 86 | molecule (indexed as they appear in the SDF file). 87 | 88 | ```python 89 | from padelpy import from_sdf 90 | 91 | # calculate molecular descriptors for molecules in `mols.sdf` 92 | descriptors = from_sdf('mols.sdf') 93 | 94 | # in addition to descriptors, calculate PubChem fingerprints 95 | desc_fp = from_sdf('mols.sdf', fingerprints=True) 96 | 97 | # only calculate fingerprints 98 | fingerprints = from_sdf('mols.sdf', fingerprints=True, descriptors=False) 99 | 100 | # setting the number of threads, this uses one cpu thread to compute descriptors 101 | desc_fp = from_mdl('mols.sdf', threads=1) 102 | 103 | # save descriptors to a CSV file 104 | _ = from_sdf('mols.sdf', output_csv='descriptors.csv') 105 | ``` 106 | 107 | ### Command Line Wrapper 108 | 109 | Alternatively, you can have more control over PaDEL-Descriptor with the command-line wrapper function. Any combination of arguments supported by PaDEL-Descriptor can be accepted by the "padeldescriptor" function. 110 | 111 | ```python 112 | from padelpy import padeldescriptor 113 | 114 | # to supply a configuration file 115 | padeldescriptor(config='\\path\\to\\config') 116 | 117 | # to supply an input (MDL) and output file 118 | padeldescriptor(mol_dir='molecules.mdl', d_file='descriptors.csv') 119 | 120 | # to supply an input (SDF) and output file 121 | padeldescriptor(mol_dir='molecules.sdf', d_file='descriptors.csv') 122 | 123 | # a SMILES file can be supplied 124 | padeldescriptor(mol_dir='molecules.smi', d_file='descriptors.csv') 125 | 126 | # a path to a directory containing structural files can be supplied 127 | padeldescriptor(mol_dir='\\path\\to\\mols\\', d_file='descriptors.csv') 128 | 129 | # to calculate 2-D and 3-D descriptors 130 | padeldescriptor(d_2d=True, d_3d=True) 131 | 132 | # to calculate PubChem fingerprints 133 | padeldescriptor(fingerprints=True) 134 | 135 | # to convert molecule into a 3-D structure 136 | padeldescriptor(convert3d=True) 137 | 138 | # to supply a descriptortypes file 139 | padeldescriptor(descriptortype='\\path\\to\\descriptortypes') 140 | 141 | # to detect aromaticity 142 | padeldescriptor(detectaromaticity=True) 143 | 144 | # to calculate fingerprints 145 | padeldescriptor(fingerprints=True) 146 | 147 | # to save process status to a log file 148 | padeldescriptor(log=True) 149 | 150 | # to remove salts from the molecule(s) 151 | padeldescriptor(removesalt=True) 152 | 153 | # to retain 3-D coordinates when standardizing 154 | padeldescriptor(retain3d=True) 155 | 156 | # to retain order (output same order as input) 157 | padeldescriptor(retainorder=True) 158 | 159 | # to standardize nitro groups to N(:O):O 160 | padeldescriptor(standardizenitro=True) 161 | 162 | # to standardize tautomers 163 | padeldescriptor(standardizetautomers=True) 164 | 165 | # to specify a SMIRKS tautomers file 166 | padeldescriptor(tautomerlist='\\path\\to\\tautomers\\') 167 | 168 | # to use filenames as molecule names 169 | padeldescriptor(usefilenameasmolname=True) 170 | 171 | # to set the maximum number of compounds in a resulting descriptors file 172 | padeldescriptor(maxcpdperfile=32) 173 | 174 | # to set the maximum runtime (in mS) per molecule 175 | padeldescriptor(maxruntime=10000) 176 | 177 | # to set the maximum number of waiting jobs in the queue 178 | padeldescriptor(waitingjobs=10) 179 | 180 | # to set the maximum number of threads used 181 | padeldescriptor(threads=2) 182 | 183 | # to prevent padel-splash image from loading. 184 | padeldescriptor(headless=True) 185 | 186 | ``` 187 | 188 | ## Contributing, Reporting Issues and Other Support 189 | 190 | To contribute to PaDELPy, make a pull request. Contributions should include tests for new features added, as well as extensive documentation. 191 | 192 | To report problems with the software or feature requests, file an issue. When reporting problems, include information such as error messages, your OS/environment and Python version. 193 | 194 | For additional support/questions, contact Travis Kessler (Travis_Kessler@student.uml.edu). 195 | -------------------------------------------------------------------------------- /padelpy/PaDEL-Descriptor/Descriptors.xls: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ecrl/padelpy/19427b58427a6de705257fd8ee74768a3122d515/padelpy/PaDEL-Descriptor/Descriptors.xls -------------------------------------------------------------------------------- /padelpy/PaDEL-Descriptor/PaDEL-Descriptor.jar: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ecrl/padelpy/19427b58427a6de705257fd8ee74768a3122d515/padelpy/PaDEL-Descriptor/PaDEL-Descriptor.jar -------------------------------------------------------------------------------- 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Interpretation of Sections 15 and 16. 611 | 612 | If the disclaimer of warranty and limitation of liability provided 613 | above cannot be given local legal effect according to their terms, 614 | reviewing courts shall apply local law that most closely approximates 615 | an absolute waiver of all civil liability in connection with the 616 | Program, unless a warranty or assumption of liability accompanies a 617 | copy of the Program in return for a fee. 618 | 619 | END OF TERMS AND CONDITIONS -------------------------------------------------------------------------------- /padelpy/PaDEL-Descriptor/license/README - CDK: -------------------------------------------------------------------------------- 1 | CDK The Chemical Development Kit 2 | 3 | Copyright 1997-2007 The CDK Development Team 4 | License: LGPL, see doc/lgpl.license 5 | 6 | 1. Introduction 7 | 8 | You are currently reading the README file for the Chemistry Development Project (CDK). 9 | This project is hosted under http://cdk.sourceforge.net 10 | Please refer to these pages for updated information and the latest version of the CDK. 11 | 12 | The CDK is an open-source library of algorithms for structural chemo- and bioinformatics, implemented in 13 | the programming language Java(tm). The library is published under terms of the the 14 | GNU Lesser General Public License. This has implications on what you can do with sources and 15 | binaries of the CDK library. For details, please refer to the file LICENSE, which should have been 16 | provided with this distribution. 17 | 18 | PLEASE NOTE: This is a library of useful data structures and algorithms to manipulated them 19 | from the area of structural chemo- and bioinformatics. As such, it is intended for the use by 20 | programmers, who wish to save some effort by reusing code. It is not intended for the enduser. 21 | If you consider yourself to be more like user, you might not find what you wanted. 22 | Please refer to other projects like the JChemPaint project (http://jchempaint.sourceforge.net) 23 | or the Jmol project (http://jmol.sourceforge.net) for programs that actually take advantage of the 24 | CDK library. 25 | 26 | 2. Compiling 27 | 28 | Compiling and jar-ing the software is done with Jakarta's 29 | Ant (http://jakarta.apache.org/ant/) and requires Java 1.5.0 or better: 30 | 31 | cdk/$ ls build.xml 32 | build.xml 33 | cdk/$ ant 34 | 35 | "ant -p" gives a list of possible compilation targets. The default target is 'dist-all', which 36 | creates a number of .jar files in the 'dist' directory corresponding to subsets of the CDK 37 | functionality. For convenience, one large .jar file containing everything can be created using the 38 | target 'dist-large' (using the command "ant dist-large"). This is also created in dist/jar and is 39 | typically named something like 'cdk-cvs-20060303.jar'. 40 | 41 | 2.1 Creating the JavaDoc documentation for the API 42 | 43 | The JavaDoc documentation for the API describes all of the CDK classes in detail. It functions as 44 | the user manual for the CDK, although you should also look at the list of examples and tutorials 45 | below. This documentation is created by 'ant' from the Java source code for the CDK as follows: 46 | 47 | cdk/$ ls javadoc.xml 48 | javadoc.xml 49 | cdk/$ ant -buildfile javadoc.xml 50 | 51 | The documenation is created as a series of .html pages in doc/api. If you use firefox, you can read 52 | the documentation using the following command: 53 | 54 | cdk/$ firefox doc/api/index.html 55 | 56 | 3. Running tests 57 | 58 | After you compiled the code, you can do "ant test-all" to run the test suite of non-interactive, automated 59 | tests. You might need to copy an appropriate junit.jar into your $ANT_HOME/lib 60 | directory or somewhere else in your classpath. 61 | Upon "ant dist-all test-dist-all test-all", you should see something like: 62 | 63 | test: 64 | Running org.openscience.cdk.test.CDKTests 65 | Tests run: 1065, Failures: 7, Errors: 1, Time elapsed: 27,55 sec 66 | 67 | As you can see, the vast majority of tests ran successfully, but that there 68 | are failures and errors. The $CDK_HOME/reports/results.txt file contains 69 | information about the outcome of the tests. Some tests might fail intentionally 70 | to mark know issues in CDK. 71 | 72 | There are also run interactive tests, like the Controller2DTest. In order to try them, you can edit the "run" 73 | target in the build.xml file to look like this: 74 | 75 | 76 | 77 | 78 | 79 | 80 | 81 | 82 | 83 | 84 | 85 | 86 | 87 | 88 | 89 | Then, a "ant run" should give you a window where you can add bonds to a given structure. 90 | Currently, there are more than 2500 test, of which a large part tests the data, datadebug and 91 | nonotify classes. 92 | 93 | 4. Using CDK 94 | 95 | CDK is a class library intended to be used by other programs. It will not run 96 | as a stand-alone program, although it contains some GUI- and command 97 | line applications. In order to use the CDK in your program, you need to build 98 | the distribution jars by running "ant dist-all". They will end up in 99 | $CDK_HOME/dist/jar. Copy all cdk-*.jars as well as all jars from $CDK_HOME/jar 100 | to the lib directory of the project for which you intend to have CDK support and 101 | use them as you would use any other third party jar. 102 | 103 | Alternatively, run "ant dist-large" to create a jar cdk-svn-YYYYMMDD.jar in 104 | $CDK_HOME/dist/jar. This large jar contains all the CDK code and all third 105 | party libraries that code depends on. 106 | 107 | 5. Examples and tutorials 108 | 109 | To get started using the CDK, you may be interested in the following websites which contain 110 | examples and tutorials: 111 | * http://www.chemistry-development-kit.org 112 | * http://blue.chem.psu.edu/~rajarshi/code/java 113 | * http://www.redbrick.dcu.ie/~noel/CDKJython.html 114 | 115 | Further examples can also be found in issues of the CDK News: 116 | * http://cdknews.org/ 117 | 118 | -------------------------------------------------------------------------------- /padelpy/PaDEL-Descriptor/license/lgpl-2.1.txt: -------------------------------------------------------------------------------- 1 | GNU LESSER GENERAL PUBLIC LICENSE 2 | Version 2.1, February 1999 3 | 4 | Copyright (C) 1991, 1999 Free Software Foundation, Inc. 5 | 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA 6 | Everyone is permitted to copy and distribute verbatim copies 7 | of this license document, but changing it is not allowed. 8 | 9 | [This is the first released version of the Lesser GPL. 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Here is a sample; alter the names: 495 | 496 | Yoyodyne, Inc., hereby disclaims all copyright interest in the 497 | library `Frob' (a library for tweaking knobs) written by James Random Hacker. 498 | 499 | [signature of Ty Coon], 1 April 1990 500 | Ty Coon, President of Vice 501 | 502 | That's all there is to it! 503 | 504 | 505 | -------------------------------------------------------------------------------- /padelpy/__init__.py: -------------------------------------------------------------------------------- 1 | from .wrapper import padeldescriptor 2 | from .functions import from_mdl, from_smiles, from_sdf 3 | -------------------------------------------------------------------------------- /padelpy/functions.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | # -*- coding: utf-8 -*- 3 | # 4 | # padelpy/functions.py 5 | # v.0.1.10 6 | # Developed in 2021 by Travis Kessler 7 | # 8 | # Contains various functions commonly used with PaDEL-Descriptor 9 | # 10 | 11 | import warnings 12 | import random 13 | # stdlib. imports 14 | from collections import OrderedDict 15 | from csv import DictReader 16 | from datetime import datetime 17 | from os import remove 18 | from re import IGNORECASE, compile 19 | from time import sleep 20 | 21 | # PaDELPy imports 22 | from padelpy import padeldescriptor 23 | 24 | __all__ = [ 25 | "from_mdl", 26 | "from_smiles", 27 | "from_sdf", 28 | ] 29 | 30 | 31 | def from_smiles(smiles, 32 | output_csv: str = None, 33 | descriptors: bool = True, 34 | fingerprints: bool = False, 35 | timeout: int = 60, 36 | maxruntime: int = -1, 37 | threads: int = -1 38 | ) -> OrderedDict: 39 | """ from_smiles: converts SMILES string to QSPR descriptors/fingerprints. 40 | 41 | Args: 42 | smiles (str, list): SMILES string for a given molecule, or a list of 43 | SMILES strings 44 | output_csv (str): if supplied, saves descriptors to this CSV file 45 | descriptors (bool): if `True`, calculates descriptors 46 | fingerprints (bool): if `True`, calculates fingerprints 47 | timeout (int): maximum time, in seconds, for conversion 48 | maxruntime (int): maximum running time per molecule in seconds. default=-1. 49 | threads (int): number of threads to use; defaults to -1 for max available 50 | 51 | Returns: 52 | list or OrderedDict: if multiple SMILES strings provided, returns a 53 | list of OrderedDicts, else single OrderedDict; each OrderedDict 54 | contains labels and values for each descriptor generated for each 55 | supplied molecule 56 | """ 57 | # unit conversion for maximum running time per molecule 58 | # seconds -> milliseconds 59 | if maxruntime != -1: 60 | maxruntime = maxruntime * 1000 61 | 62 | timestamp = datetime.now().strftime("%Y%m%d%H%M%S%f")#[:-3] 63 | filename = timestamp + str(random.randint(int(1e8),int(1e9))) 64 | 65 | with open("{}.smi".format(filename), "w") as smi_file: 66 | if type(smiles) == str: 67 | smi_file.write(smiles) 68 | elif type(smiles) == list: 69 | smi_file.write("\n".join(smiles)) 70 | else: 71 | raise RuntimeError("Unknown input format for `smiles`: {}".format( 72 | type(smiles) 73 | )) 74 | smi_file.close() 75 | 76 | save_csv = True 77 | if output_csv is None: 78 | save_csv = False 79 | output_csv = "{}.csv".format(timestamp) 80 | 81 | for attempt in range(3): 82 | try: 83 | padeldescriptor( 84 | mol_dir="{}.smi".format(filename), 85 | d_file=output_csv, 86 | convert3d=True, 87 | retain3d=True, 88 | d_2d=descriptors, 89 | d_3d=descriptors, 90 | fingerprints=fingerprints, 91 | sp_timeout=timeout, 92 | retainorder=True, 93 | maxruntime=maxruntime, 94 | threads=threads 95 | ) 96 | break 97 | except RuntimeError as exception: 98 | if attempt == 2: 99 | remove("{}.smi".format(filename)) 100 | if not save_csv: 101 | sleep(0.5) 102 | try: 103 | remove(output_csv) 104 | except FileNotFoundError as e: 105 | warnings.warn(e, RuntimeWarning) 106 | raise RuntimeError(exception) 107 | else: 108 | continue 109 | except KeyboardInterrupt as kb_exception: 110 | remove("{}.smi".format(filename)) 111 | if not save_csv: 112 | try: 113 | remove(output_csv) 114 | except FileNotFoundError as e: 115 | warnings.warn(e, RuntimeWarning) 116 | raise kb_exception 117 | 118 | with open(output_csv, "r", encoding="utf-8") as desc_file: 119 | reader = DictReader(desc_file) 120 | rows = [row for row in reader] 121 | desc_file.close() 122 | 123 | remove("{}.smi".format(filename)) 124 | if not save_csv: 125 | remove(output_csv) 126 | 127 | if type(smiles) == list and len(rows) != len(smiles): 128 | raise RuntimeError("PaDEL-Descriptor failed on one or more mols." + 129 | " Ensure the input structures are correct.") 130 | elif type(smiles) == str and len(rows) == 0: 131 | raise RuntimeError( 132 | "PaDEL-Descriptor failed on {}.".format(smiles) + 133 | " Ensure input structure is correct." 134 | ) 135 | 136 | for idx, r in enumerate(rows): 137 | if len(r) == 0: 138 | raise RuntimeError( 139 | "PaDEL-Descriptor failed on {}.".format(smiles[idx]) + 140 | " Ensure input structure is correct." 141 | ) 142 | 143 | for idx in range(len(rows)): 144 | del rows[idx]["Name"] 145 | 146 | if type(smiles) == str: 147 | return rows[0] 148 | return rows 149 | 150 | 151 | def from_mdl(mdl_file: str, 152 | output_csv: str = None, 153 | descriptors: bool = True, 154 | fingerprints: bool = False, 155 | timeout: int = 60, 156 | maxruntime: int = -1, 157 | threads: int = -1 158 | ) -> list: 159 | """ from_mdl: converts MDL file into QSPR descriptors/fingerprints; 160 | multiple molecules may be represented in the MDL file 161 | 162 | Args: 163 | mdl_file (str): path to MDL file 164 | output_csv (str): if supplied, saves descriptors/fingerprints here 165 | descriptors (bool): if `True`, calculates descriptors 166 | fingerprints (bool): if `True`, calculates fingerprints 167 | timeout (int): maximum time, in seconds, for conversion 168 | maxruntime (int): maximum running time per molecule in seconds. default=-1. 169 | 170 | Returns: 171 | list: list of dicts, where each dict corresponds sequentially to a 172 | compound in the supplied MDL file 173 | """ 174 | 175 | is_mdl = compile(r".*\.mdl$", IGNORECASE) 176 | if is_mdl.match(mdl_file) is None: 177 | raise ValueError("MDL file must have a `.mdl` extension: {}".format( 178 | mdl_file 179 | )) 180 | 181 | rows = _from_mdl_lower(mol_file=mdl_file, 182 | output_csv=output_csv, 183 | descriptors=descriptors, 184 | fingerprints=fingerprints, 185 | timeout=timeout, 186 | maxruntime=maxruntime, 187 | threads=threads 188 | ) 189 | return rows 190 | 191 | 192 | def from_sdf(sdf_file: str, 193 | output_csv: str = None, 194 | descriptors: bool = True, 195 | fingerprints: bool = False, 196 | timeout: int = 60, 197 | maxruntime: int = -1, 198 | threads: int = -1 199 | ) -> list: 200 | """ Converts sdf file into QSPR descriptors/fingerprints. 201 | Multiple molecules may be represented in the sdf file 202 | 203 | Args: 204 | sdf_file (str): path to sdf file 205 | output_csv (str): if supplied, saves descriptors/fingerprints here 206 | descriptors (bool): if `True`, calculates descriptors 207 | fingerprints (bool): if `True`, calculates fingerprints 208 | timeout (int): maximum time, in seconds, for conversion 209 | maxruntime (int): maximum running time per molecule in seconds. default=-1. 210 | 211 | 212 | Returns: 213 | list: list of dicts, where each dict corresponds sequentially to a compound in the 214 | supplied sdf file 215 | """ 216 | 217 | is_sdf = compile(r".*\.sdf$", IGNORECASE) 218 | if is_sdf.match(sdf_file) is None: 219 | raise ValueError("sdf file must have a `.sdf` extension: {}".format( 220 | sdf_file 221 | )) 222 | 223 | rows = _from_mdl_lower(mol_file=sdf_file, 224 | output_csv=output_csv, 225 | descriptors=descriptors, 226 | fingerprints=fingerprints, 227 | timeout=timeout, 228 | maxruntime=maxruntime, 229 | threads=threads 230 | ) 231 | return rows 232 | 233 | 234 | def _from_mdl_lower(mol_file: str, 235 | output_csv: str = None, 236 | descriptors: bool = True, 237 | fingerprints: bool = False, 238 | timeout: int = 60, 239 | maxruntime: int = -1, 240 | threads: int = -1 241 | ) -> list: 242 | # unit conversion for maximum running time per molecule 243 | # seconds -> milliseconds 244 | if maxruntime != -1: 245 | maxruntime = maxruntime * 1000 246 | 247 | save_csv = True 248 | if output_csv is None: 249 | save_csv = False 250 | output_csv = "{}.csv".format( 251 | datetime.now().strftime("%Y%m%d%H%M%S%f")[:-3] 252 | ) 253 | 254 | for attempt in range(3): 255 | try: 256 | padeldescriptor( 257 | maxruntime=maxruntime, 258 | mol_dir=mol_file, 259 | d_file=output_csv, 260 | convert3d=True, 261 | retain3d=True, 262 | retainorder=True, 263 | d_2d=descriptors, 264 | d_3d=descriptors, 265 | fingerprints=fingerprints, 266 | sp_timeout=timeout, 267 | threads=threads 268 | ) 269 | break 270 | except RuntimeError as exception: 271 | if attempt == 2: 272 | if not save_csv: 273 | sleep(0.5) 274 | try: 275 | remove(output_csv) 276 | except FileNotFoundError as e: 277 | warnings.warn(e, RuntimeWarning) 278 | raise RuntimeError(exception) 279 | else: 280 | continue 281 | 282 | with open(output_csv, "r", encoding="utf-8") as desc_file: 283 | reader = DictReader(desc_file) 284 | rows = [row for row in reader] 285 | desc_file.close() 286 | if not save_csv: 287 | remove(output_csv) 288 | if len(rows) == 0: 289 | raise RuntimeError("PaDEL-Descriptor returned no calculated values." + 290 | " Ensure the input structure is correct.") 291 | for row in rows: 292 | del row["Name"] 293 | 294 | return rows 295 | -------------------------------------------------------------------------------- /padelpy/py.typed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ecrl/padelpy/19427b58427a6de705257fd8ee74768a3122d515/padelpy/py.typed -------------------------------------------------------------------------------- /padelpy/version.py: -------------------------------------------------------------------------------- 1 | import pkg_resources 2 | 3 | __version__ = pkg_resources.get_distribution("padelpy").version 4 | -------------------------------------------------------------------------------- /padelpy/wrapper.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | # -*- coding: utf-8 -*- 3 | # 4 | # padelpy/wrapper.py 5 | # v.0.1.10 6 | # Developed in 2021 by Travis Kessler 7 | # 8 | # Contains the `padeldescriptor` function, a wrapper for PaDEL-Descriptor 9 | # 10 | 11 | # stdlib. imports 12 | from os.path import abspath, dirname, join 13 | from shutil import which 14 | from subprocess import PIPE, Popen 15 | from time import sleep 16 | 17 | # PaDEL-Descriptor is packaged with PaDELPy 18 | _PADEL_PATH = join( 19 | dirname(abspath(__file__)), 20 | 'PaDEL-Descriptor', 21 | 'PaDEL-Descriptor.jar' 22 | ) 23 | 24 | __all__ = [ 25 | "padeldescriptor", 26 | ] 27 | 28 | 29 | def _popen_timeout(command: str, timeout: int) -> tuple: 30 | """Calls PaDEL-Descriptor, with optional subprocess timeout 31 | 32 | Args: 33 | command (str): command to execute via subprocess.Popen 34 | timeout (int): if not None, times out after this many seconds 35 | 36 | Returns: 37 | tuple: (stdout of process, stderr of process) 38 | """ 39 | 40 | p = Popen(command.split(), stdout=PIPE, stderr=PIPE) 41 | if timeout is not None: 42 | for t in range(timeout): 43 | sleep(1) 44 | if p.poll() is not None: 45 | return p.communicate() 46 | p.kill() 47 | return (-1, b'PaDEL-Descriptor timed out during subprocess call') 48 | else: 49 | return p.communicate() 50 | 51 | 52 | def padeldescriptor(maxruntime: int = -1, 53 | waitingjobs: int = -1, 54 | threads: int = -1, 55 | d_2d: bool = False, 56 | d_3d: bool = False, 57 | config: str = None, 58 | convert3d: bool = False, 59 | descriptortypes: str = None, 60 | detectaromaticity: bool = False, 61 | mol_dir: str = None, 62 | d_file: str = None, 63 | fingerprints: bool = False, 64 | log: bool = False, 65 | maxcpdperfile: int = 0, 66 | removesalt: bool = False, 67 | retain3d: bool = False, 68 | retainorder: bool = True, 69 | standardizenitro: bool = False, 70 | standardizetautomers: bool = False, 71 | tautomerlist: str = None, 72 | usefilenameasmolname: bool = False, 73 | sp_timeout: int = None, 74 | headless: bool = True 75 | ) -> None: 76 | """padeldescriptor: complete wrapper for PaDEL-Descriptor descriptor/ 77 | fingerprint generation software 78 | 79 | Args: 80 | maxruntime (int): maximum running time per molecule (in mS); defaults 81 | to -1 (unlimited) 82 | waitingjobs (int): maximum number of jobs to store in queue for worker 83 | threads to process; defaults to -1 (50 * max threads) 84 | threads (int): maximum number of threads to use; defaults to -1 (equal 85 | to number of CPU cores) 86 | d_2d (bool): if `True`, calculates 2-D descriptors 87 | d_3d (bool): if `True`, calculates 3-D descriptors 88 | config (str): path to configuration file (optional) 89 | convert3d (bool): if `True`, converts molecule to 3-D 90 | descriptortypes (str): path to descriptor types file (optional) 91 | detectaromaticity (bool): if `True`, removes existing aromaticity 92 | information and automatically detect aromaticity in the molecule 93 | before calculation of descriptors 94 | mol_dir (str): path to directory (or file) containing structural files 95 | d_file (str): path to file to save calculated descriptors to 96 | fingerprints (bool): if `True`, calculates fingerprints 97 | log (bool): if `True`, creates a log file (same as descriptors file, 98 | with .log extension) 99 | maxcpdperfile (int): maximum number of compounds to be stored in each 100 | descriptor file; defaults to 0 (unlimited) 101 | removesalt (bool): if `True`, removes salt from the molecule 102 | retain3d (bool): if `True`, retains 3-D coordinates when standardizing 103 | structure 104 | retainorder (bool): if `True`, retains order of molecules in 105 | structural files for descriptor file 106 | standardizenitro (bool): if `True`, standardizes nitro groups to 107 | N(:O):O 108 | standardizetautomers (bool): if `True`, standardizes tautomers 109 | tautomerlist (str): path to SMIRKS tautomers file (optional) 110 | usefilenameasmolname (bool): if `True`, uses filename (minus the 111 | extension) as the molecule name 112 | headless (bool): if `True`, prevents Padel-splash image from loading. 113 | 114 | Returns: 115 | None 116 | """ 117 | 118 | if which('java') is None: 119 | raise ReferenceError( 120 | 'Java JRE 6+ not found (required for PaDEL-Descriptor)' 121 | ) 122 | if headless: 123 | command = 'java -Djava.awt.headless=true -jar {}'.format(_PADEL_PATH) 124 | else: 125 | command = 'java -jar {}'.format(_PADEL_PATH) 126 | command += ' -maxruntime {}'.format(maxruntime) 127 | command += ' -waitingjobs {}'.format(waitingjobs) 128 | command += ' -threads {}'.format(threads) 129 | command += ' -maxcpdperfile {}'.format(maxcpdperfile) 130 | if d_2d is True: 131 | command += ' -2d' 132 | if d_3d is True: 133 | command += ' -3d' 134 | if config is not None: 135 | command += ' -config {}'.format(config) 136 | if convert3d is True: 137 | command += ' -convert3d' 138 | if descriptortypes is not None: 139 | command += ' -descriptortypes {}'.format(descriptortypes) 140 | if detectaromaticity is True: 141 | command += ' -detectaromaticity' 142 | if mol_dir is not None: 143 | command += ' -dir {}'.format(mol_dir) 144 | if d_file is not None: 145 | command += ' -file {}'.format(d_file) 146 | if fingerprints is True: 147 | command += ' -fingerprints' 148 | if log is True: 149 | command += ' -log' 150 | if removesalt is True: 151 | command += ' -removesalt' 152 | if retain3d is True: 153 | command += ' -retain3d' 154 | if retainorder is True: 155 | command += ' -retainorder' 156 | if standardizenitro is True: 157 | command += ' -standardizenitro' 158 | if standardizetautomers is True: 159 | command += ' -standardizetautomers' 160 | if tautomerlist is not None: 161 | command += ' -tautomerlist {}'.format(tautomerlist) 162 | if usefilenameasmolname is True: 163 | command += ' -usefilenameasmolname' 164 | 165 | _, err = _popen_timeout(command, sp_timeout) 166 | if err != b'': 167 | raise RuntimeError('PaDEL-Descriptor encountered an error: {}'.format( 168 | err.decode('utf-8') 169 | )) 170 | return 171 | -------------------------------------------------------------------------------- /pyproject.toml: -------------------------------------------------------------------------------- 1 | [build-system] 2 | requires = ["setuptools>=61.0"] 3 | build-backend = "setuptools.build_meta" 4 | 5 | [tool.setuptools] 6 | include-package-data = true 7 | 8 | [project] 9 | name = "padelpy" 10 | version = "0.1.16" 11 | authors = [ 12 | { name="Travis Kessler", email="travis.j.kessler@gmail.com" }, 13 | ] 14 | description = "A Python wrapper for PaDEL-Descriptor software" 15 | readme = "README.md" 16 | requires-python = ">=3.11" 17 | classifiers = [ 18 | "Programming Language :: Python :: 3.11", 19 | "License :: OSI Approved :: MIT License", 20 | "Operating System :: OS Independent", 21 | ] 22 | 23 | [project.urls] 24 | "Homepage" = "https://github.com/ecrl/padelpy" 25 | "Bug Tracker" = "https://github.com/ecrl/padelpy/issues" 26 | 27 | [tool.pytest.ini_options] 28 | filterwarnings = [ 29 | "ignore::DeprecationWarning", 30 | ] -------------------------------------------------------------------------------- /tests/aspirin_3d.sdf: -------------------------------------------------------------------------------- 1 | 2244 2 | -OEChem-12012120113D 3 | 4 | 21 21 0 0 0 0 0 0 0999 V2000 5 | 1.2333 0.5540 0.7792 O 0 0 0 0 0 0 0 0 0 0 0 0 6 | -0.6952 -2.7148 -0.7502 O 0 0 0 0 0 0 0 0 0 0 0 0 7 | 0.7958 -2.1843 0.8685 O 0 0 0 0 0 0 0 0 0 0 0 0 8 | 1.7813 0.8105 -1.4821 O 0 0 0 0 0 0 0 0 0 0 0 0 9 | -0.0857 0.6088 0.4403 C 0 0 0 0 0 0 0 0 0 0 0 0 10 | -0.7927 -0.5515 0.1244 C 0 0 0 0 0 0 0 0 0 0 0 0 11 | -0.7288 1.8464 0.4133 C 0 0 0 0 0 0 0 0 0 0 0 0 12 | -2.1426 -0.4741 -0.2184 C 0 0 0 0 0 0 0 0 0 0 0 0 13 | -2.0787 1.9238 0.0706 C 0 0 0 0 0 0 0 0 0 0 0 0 14 | -2.7855 0.7636 -0.2453 C 0 0 0 0 0 0 0 0 0 0 0 0 15 | -0.1409 -1.8536 0.1477 C 0 0 0 0 0 0 0 0 0 0 0 0 16 | 2.1094 0.6715 -0.3113 C 0 0 0 0 0 0 0 0 0 0 0 0 17 | 3.5305 0.5996 0.1635 C 0 0 0 0 0 0 0 0 0 0 0 0 18 | -0.1851 2.7545 0.6593 H 0 0 0 0 0 0 0 0 0 0 0 0 19 | -2.7247 -1.3605 -0.4564 H 0 0 0 0 0 0 0 0 0 0 0 0 20 | -2.5797 2.8872 0.0506 H 0 0 0 0 0 0 0 0 0 0 0 0 21 | -3.8374 0.8238 -0.5090 H 0 0 0 0 0 0 0 0 0 0 0 0 22 | 3.7290 1.4184 0.8593 H 0 0 0 0 0 0 0 0 0 0 0 0 23 | 4.2045 0.6969 -0.6924 H 0 0 0 0 0 0 0 0 0 0 0 0 24 | 3.7105 -0.3659 0.6426 H 0 0 0 0 0 0 0 0 0 0 0 0 25 | -0.2555 -3.5916 -0.7337 H 0 0 0 0 0 0 0 0 0 0 0 0 26 | 1 5 1 0 0 0 0 27 | 1 12 1 0 0 0 0 28 | 2 11 1 0 0 0 0 29 | 2 21 1 0 0 0 0 30 | 3 11 2 0 0 0 0 31 | 4 12 2 0 0 0 0 32 | 5 6 1 0 0 0 0 33 | 5 7 2 0 0 0 0 34 | 6 8 2 0 0 0 0 35 | 6 11 1 0 0 0 0 36 | 7 9 1 0 0 0 0 37 | 7 14 1 0 0 0 0 38 | 8 10 1 0 0 0 0 39 | 8 15 1 0 0 0 0 40 | 9 10 2 0 0 0 0 41 | 9 16 1 0 0 0 0 42 | 10 17 1 0 0 0 0 43 | 12 13 1 0 0 0 0 44 | 13 18 1 0 0 0 0 45 | 13 19 1 0 0 0 0 46 | 13 20 1 0 0 0 0 47 | M END 48 | > 49 | 2244 50 | 51 | $$$$ 52 | -------------------------------------------------------------------------------- /tests/test_all.py: -------------------------------------------------------------------------------- 1 | import pytest 2 | 3 | from padelpy import from_sdf, from_smiles 4 | 5 | 6 | def test_from_smiles(): 7 | descriptors = from_smiles('CCC') 8 | assert len(descriptors) == 1875 9 | assert float(descriptors['MW']) == pytest.approx(44.0626, 1e-4) 10 | assert int(descriptors['nC']) == 3 11 | 12 | 13 | def test_multiple_smiles(): 14 | smiles = ['CCC', 'CCCC'] 15 | descriptors = from_smiles(smiles) 16 | assert len(descriptors) == 2 17 | assert len(descriptors[0]) == 1875 18 | 19 | 20 | def test_errors(): 21 | bad_smiles = 'SJLDFGSJ' 22 | with pytest.raises(RuntimeError): 23 | _ = from_smiles(bad_smiles) 24 | bad_smiles = ['SJLDFGSJ', 'CCC'] 25 | with pytest.raises(RuntimeError): 26 | _ = from_smiles(bad_smiles) 27 | 28 | 29 | def test_from_sdf(): 30 | descriptors = from_sdf('tests/aspirin_3d.sdf')[0] 31 | assert len(descriptors) == 1875 32 | assert float(descriptors['MW']) == pytest.approx(180.04225, 1e-4) 33 | assert float(descriptors['SsCH3']) == pytest.approx(1.2209, 1e-4) 34 | assert int(descriptors['nC']) == 9 35 | --------------------------------------------------------------------------------