{"id":23280269,"url":"https://github.com/moldyn/msmpathfinder","last_synced_at":"2025-08-21T13:31:17.407Z","repository":{"id":50449622,"uuid":"223379616","full_name":"moldyn/MSMPathfinder","owner":"moldyn","description":"Finding pathways from an Markov State Model","archived":false,"fork":false,"pushed_at":"2022-07-29T07:55:21.000Z","size":61,"stargazers_count":7,"open_issues_count":0,"forks_count":1,"subscribers_count":1,"default_branch":"master","last_synced_at":"2023-03-05T09:53:04.969Z","etag":null,"topics":["cpp","markov-chain-monte-carlo","msm","path-sampling","pathfinding"],"latest_commit_sha":null,"homepage":null,"language":"C++","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/moldyn.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":"CITATION.cff","codeowners":null,"security":null,"support":null}},"created_at":"2019-11-22T10:24:57.000Z","updated_at":"2023-02-01T09:01:42.000Z","dependencies_parsed_at":"2022-09-06T11:10:42.716Z","dependency_job_id":null,"html_url":"https://github.com/moldyn/MSMPathfinder","commit_stats":null,"previous_names":[],"tags_count":null,"template":null,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/moldyn%2FMSMPathfinder","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/moldyn%2FMSMPathfinder/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/moldyn%2FMSMPathfinder/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/moldyn%2FMSMPathfinder/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/moldyn","download_url":"https://codeload.github.com/moldyn/MSMPathfinder/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":230515634,"owners_count":18238285,"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":["cpp","markov-chain-monte-carlo","msm","path-sampling","pathfinding"],"created_at":"2024-12-19T23:31:24.227Z","updated_at":"2024-12-19T23:31:24.814Z","avatar_url":"https://github.com/moldyn.png","language":"C++","readme":"# MSMPathfinder\nFinding pathways from an Markov State Model.\n\nThis software package provides tools for finding pathways based on Markov state\nmodels. It is required to represent the matrix as an row-normalized matrix,\nwhere each row sums up to 1 and all entries are strictly greater 1.\nThis package contains a proof-of-concept implementation of an suggested\nalgorithm (see citations). If the matrix contains more than 100 highly\nconnected states or a few hundred sparsly connected states the MCMC is\npreferable.\n\nThe essential functions are:\n  - `MSMPathfinder paths`: see citation for further information\n  - `MSMPathfinder mcmcsingle`: Markov chain Monte Carlo propagation\n\n For further information simply call both submodule with added `-h` flag.\n\n\n# Documentation\nAll options are well documented and may be viewed by `MSMPathfinder -h`.\n\n\n# Citations\nThe underlying methods are based on the following article:\n  - D. Nagel, A. Weber and G. Stock,\n    *MSMPathfinder: Identification of pathways in Markov state models*,\n    J. Chem. Theory Comput., 16, 7874 (2020);\n    DOI: [10.1021/acs.jctc.0c00774](https://doi.org/10.1021/acs.jctc.0c00774)\n\nWe kindly ask you to cite this article if you use this software package for\npublished works.\n\n\n# Licensing\nThis project was created by [moldyn-nagel](https://github.com/moldyn-nagel).\n\nCopyright (c) 2020-2021, Daniel Nagel\nAll rights reserved.\n\nRedistribution and use in source and binary forms, with or without\nmodification, are permitted provided that the following conditions are met:\n\n1. Redistributions of source code must retain the above copyright notice,\n   this list of conditions and the following disclaimer.\n\n2. Redistributions in binary form must reproduce the above copyright notice,\n   this list of conditions and the following disclaimer in the documentation\n   and/or other materials provided with the distribution.\n\nTHIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS \"AS IS\" AND ANY\nEXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES\nOF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT\nSHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,\nSPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT\nOF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)\nHOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR\nTORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,\nEVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.\n\n\n# Installation\n## Requirements\n required:\n  -  **BOOST \u003e= 1.49**\n  -  **cmake \u003e= 2.8**\n  -  a **recent** C++ compiler (e.g. GNU g++ \u003e= 4.9, must\n     support C++11 standard)\n\n\n## Quick-Start\n\nTo quickly get a working binary\n\n```bash\n# clone the repo\ngit clone https://github.com/moldyn/MSMPathfinder.git\n\n# create a build folder inside the code directory\ncd MSMPathfinder\nmkdir build\n\n# change to the build directory and prepare make\n# if installition is not desired you can execute \"cmake ..\" instead\ncd build\ncmake .. -DCMAKE_INSTALL_PREFIX=/my/installation/path\n\n# then compile and install the package to /my/installation/path\n# (or any other path you chose above) by invoking\nmake\nmake install\n```\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmoldyn%2Fmsmpathfinder","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmoldyn%2Fmsmpathfinder","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmoldyn%2Fmsmpathfinder/lists"}