{"id":47829345,"url":"https://github.com/basf/precomplex_generator","last_synced_at":"2026-04-03T20:07:18.182Z","repository":{"id":45573460,"uuid":"505414220","full_name":"basf/precomplex_generator","owner":"basf","description":"The precomplex generator is a tool for obtaining suitable input structures for automated transition-state (TS) searches (precomplexes) based on single-ended reaction path optimization algorithms.","archived":false,"fork":false,"pushed_at":"2024-02-21T18:04:34.000Z","size":797,"stargazers_count":5,"open_issues_count":2,"forks_count":4,"subscribers_count":6,"default_branch":"main","last_synced_at":"2024-05-14T00:06:03.145Z","etag":null,"topics":["quantum-chemistry","reaction-mechanism","reaction-network","transition-state"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/basf.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGES.md","contributing":null,"funding":null,"license":"LICENSE.txt","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2022-06-20T11:33:42.000Z","updated_at":"2024-02-22T03:17:38.000Z","dependencies_parsed_at":"2022-08-26T02:43:13.953Z","dependency_job_id":null,"html_url":"https://github.com/basf/precomplex_generator","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/basf/precomplex_generator","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/basf%2Fprecomplex_generator","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/basf%2Fprecomplex_generator/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/basf%2Fprecomplex_generator/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/basf%2Fprecomplex_generator/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/basf","download_url":"https://codeload.github.com/basf/precomplex_generator/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/basf%2Fprecomplex_generator/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":31374101,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-04-03T17:53:18.093Z","status":"ssl_error","status_checked_at":"2026-04-03T17:53:17.617Z","response_time":107,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.6:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"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":["quantum-chemistry","reaction-mechanism","reaction-network","transition-state"],"created_at":"2026-04-03T20:07:17.574Z","updated_at":"2026-04-03T20:07:18.174Z","avatar_url":"https://github.com/basf.png","language":"Python","readme":"# Overview\n\nThe precomplex generator is a tool for obtaining suitable input structures for automated transition-state (TS) searches (precomplexes) based on single-ended reaction path optimization algorithms. Our strategy is applicable to uni- and bimolecular reactions as well as pseudo-termolecular reaction for a broad range of molecular structures. The precomplex generator rotates around selected bonds to obtain a structure in which the reaction centers are well aligned.\n\n\n# Requirements:\n\n```\n  - python=3.10.8\n  - OpenBabel=3.1.1\n  - numpy=1.23.4\n  - Cython=3.0.11\n  - wheel=0.44.0\n  - Networkx=3.3\n  - Pymatgen=2024.9.17.1\n```\n# How to directly use the precomplex generator:\nWe provide precompiled Fortran code and Python files, which can be directly used if local library compatibility is given (RHEL7 or similar OS).\n\n```\n1. Clone the Github repository to your current directory ($PWD):\n   git clone https://github.com/basf/precomplex_generator.git\n\n2. Add the PYTHONPATH to your PYTHONPATH's:\n   export PYTHONPATH=$PWD/precomplex_generator:$PYTHONPATH\n   export PYTHONPATH=$PWD/precompiled_fortran_code:$PYTHONPATH\n\n3. Add alias for convenience:\n   export top_dir=$PWD \n   alias prec_gen='python3 $top_dir/precomplex_generator/precomplex_generator/main.py'\n\n```\n# How to install the precomplex generator (.egg):\n```\n1. Clone the Github repository to your current directory ($PWD):\n   git clone https://github.com/basf/precomplex_generator.git\n   \n2. For installation, we provide an install.sh script. \n   Caution: This script will only work, if python and openbabel are already available!\n   cd precomplex_generator\n   source install.sh\n```\n\n# How to run the precomplex_generator:\n```\nYou find examples in the EXAMPLES folder.\n\nOnly the reactant XYZ file(s) as well as the rule.txt file are required.\nThe rule.txt file contains the \"reaction rule\" in terms of atom-specific bond formations/breakages.\nThe COMMAND file contains the respective command you need.\n\nFor example:\nprec_gen mol_name_1 mol_name_2 -r rule.txt\n```\n\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbasf%2Fprecomplex_generator","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbasf%2Fprecomplex_generator","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbasf%2Fprecomplex_generator/lists"}