{"id":21292053,"url":"https://github.com/ecrl/alvadescpy","last_synced_at":"2025-07-11T16:31:15.689Z","repository":{"id":98594920,"uuid":"190467679","full_name":"ecrl/alvadescpy","owner":"ecrl","description":"A Python wrapper for alvaDesc software","archived":false,"fork":false,"pushed_at":"2024-10-15T21:31:34.000Z","size":24,"stargazers_count":9,"open_issues_count":0,"forks_count":3,"subscribers_count":2,"default_branch":"master","last_synced_at":"2024-10-17T09:32:17.728Z","etag":null,"topics":["command-line-wrapper","computational-chemistry","molecular-descriptors","molecular-fingerprints"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/ecrl.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2019-06-05T20:59:06.000Z","updated_at":"2024-10-15T21:31:13.000Z","dependencies_parsed_at":null,"dependency_job_id":"855d8bd1-e9f5-451e-ab8f-cfd39798aa31","html_url":"https://github.com/ecrl/alvadescpy","commit_stats":{"total_commits":16,"total_committers":2,"mean_commits":8.0,"dds":0.0625,"last_synced_commit":"5b6e0f0901362fe71eeb30d9cc1a03be948f1872"},"previous_names":[],"tags_count":5,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ecrl%2Falvadescpy","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ecrl%2Falvadescpy/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ecrl%2Falvadescpy/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ecrl%2Falvadescpy/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/ecrl","download_url":"https://codeload.github.com/ecrl/alvadescpy/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":225741248,"owners_count":17516895,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["command-line-wrapper","computational-chemistry","molecular-descriptors","molecular-fingerprints"],"created_at":"2024-11-21T13:47:25.009Z","updated_at":"2024-11-21T13:47:25.703Z","avatar_url":"https://github.com/ecrl.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![UML Energy \u0026 Combustion Research Laboratory](https://sites.uml.edu/hunter-mack/files/2021/11/ECRL_final.png)](http://faculty.uml.edu/Hunter_Mack/)\n\n# alvaDescPy: A Python wrapper for alvaDesc software\n\n[![GitHub version](https://badge.fury.io/gh/ecrl%2Falvadescpy.svg)](https://badge.fury.io/gh/ecrl%2Falvadescpy)\n[![PyPI version](https://badge.fury.io/py/alvadescpy.svg)](https://badge.fury.io/py/alvadescpy)\n[![GitHub license](https://img.shields.io/badge/license-MIT-blue.svg)](https://raw.githubusercontent.com/ecrl/alvadescpy/master/LICENSE.txt)\n\nalvaDescPy provides a Python wrapper for the [alvaDesc](https://www.alvascience.com/alvadesc/) molecular descriptor calculation software. It was created to allow direct access to the alvaDesc command-line interface via Python.\n\nImportant Notice:\n\nPlease note that alvaDescPy is an independent project and was not developed by Alvascience. You can find the official alvaDesc Python interface on Alvascience website: https://www.alvascience.com/python-alvadesc/.\n\n## Installation\n\nInstallation via pip:\n\n```\n$ pip install alvadescpy\n```\n\nInstallation via cloned repository:\n\n```\n$ git clone https://github.com/ecrl/alvadescpy\n$ cd alvadescpy\n$ pip install .\n```\n\nThere are currently no additional dependencies for alvaDescPy, however it requires a valid, licensed installation of [alvaDesc](https://www.alvascience.com/alvadesc/).\n\n## Basic Usage\n\nalvaDescPy assumes the location of alvaDesc's command-line interface is located at your OS's default location. If alvaDesc is located in a different location, you can change the path:\n\n```python\nfrom alvadescpy import CONFIG\n\nCONFIG['alvadesc_path'] = '\\\\path\\\\to\\\\alvaDescCLI'\n```\n\nalvaDescPy provides direct access to all alvaDesc command line arguments via the \"alvadesc\" function:\n\n```python\nfrom alvadescpy import alvadesc\n\n# providing an XML script file\nalvadesc(script='my_script.xml')\n\n# supplying a SMILES string returns a list of descriptors\ndescriptors = alvadesc(ismiles='CCC', descriptors='ALL')\n\n# a Python dictionary is returned if labels are desired\ndescriptors = alvadesc(ismiles='CCC', descriptors='ALL', labels=True)\n\n# specific descriptors can be calculated\ndescriptors = alvadesc(ismiles='CCC', descriptors=['MW', 'AMW'], labels=True)\n\n# input/output files (and input type) can be specified\nalvadesc(\n    input_file='mols.mdl',\n    inputtype='MDL',\n    descriptors='ALL',\n    output='descriptors.txt'\n)\n\n# various fingerprints can be calculated\necfp = alvadesc(ismiles='CCC', ecfp=True)\npfp = alvadesc(ismiles='CCC', pfp=True)\nmaccsfp = alvadesc(ismiles='CCC', pfp=True)\n\n# fingerprint hash size, min/max fragment length, bits/pattern and other\n#   options can be specified\necfp = alvadesc(\n    ismiles='CCC',\n    ecfp=True,\n    fpsize=2048,\n    fpmin=1,\n    fpmax=4,\n    bits=4,\n    fpoptions='- Additional Options -'\n)\n\n# alvaDesc uses a number of threads equal to the maximum number of CPUs, but\n#   can be changed\ndescriptors=alvadesc(ismiles='CCC', descriptors='ALL', threads=4)\n```\n\nalvaDescPy also provides the \"smiles_to_descriptors\" function:\n\n```python\nfrom alvadescpy import smiles_to_descriptors\n\n# returns a list of descriptor values\ndescriptors = smiles_to_descriptors('CCC', descriptors='ALL')\n\n# returns a dictionary of descriptor labels, values\ndescriptors = smiles_to_descriptors('CCC', descriptors='ALL', labels=True)\n\n# returns a dictionary containing MW, AMW labels, values\ndescriptors = smiles_to_descriptors(\n    'CCC',\n    descriptors=['MW', 'AMW'],\n    labels=True\n)\n```\n\n## Contributing, Reporting Issues and Other Support\n\nTo contribute to alvaDescPy, make a pull request. Contributions should include tests for new features added, as well as extensive documentation.\n\nTo 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.\n\nFor additional support/questions, contact Travis Kessler (Travis_Kessler@student.uml.edu).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fecrl%2Falvadescpy","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fecrl%2Falvadescpy","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fecrl%2Falvadescpy/lists"}