{"id":21194432,"url":"https://github.com/patonlab/molcomplex","last_synced_at":"2026-01-02T06:20:15.338Z","repository":{"id":232856540,"uuid":"289984268","full_name":"patonlab/molcomplex","owner":"patonlab","description":"Command line and webapp for retrosynthetic disconnections, molecular complexity and synthetic accessibility metrics","archived":false,"fork":false,"pushed_at":"2024-08-14T01:58:58.000Z","size":73126,"stargazers_count":14,"open_issues_count":0,"forks_count":2,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-02-21T21:51:18.364Z","etag":null,"topics":["complexity-score","disconnections","molecular-complexity","molecular-descriptors","retrosynthetic-analysis","synthesizability"],"latest_commit_sha":null,"homepage":"https://ccas.nd.edu","language":"Roff","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/patonlab.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":"SUPPORT.md","governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2020-08-24T16:43:55.000Z","updated_at":"2025-01-08T05:33:48.000Z","dependencies_parsed_at":null,"dependency_job_id":"b2b921fc-33d4-425f-a626-71094f92c548","html_url":"https://github.com/patonlab/molcomplex","commit_stats":null,"previous_names":["patonlab/molcomplex"],"tags_count":3,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/patonlab%2Fmolcomplex","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/patonlab%2Fmolcomplex/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/patonlab%2Fmolcomplex/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/patonlab%2Fmolcomplex/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/patonlab","download_url":"https://codeload.github.com/patonlab/molcomplex/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":243648407,"owners_count":20324870,"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":["complexity-score","disconnections","molecular-complexity","molecular-descriptors","retrosynthetic-analysis","synthesizability"],"created_at":"2024-11-20T19:22:10.361Z","updated_at":"2026-01-02T06:20:15.301Z","avatar_url":"https://github.com/patonlab.png","language":"Roff","funding_links":[],"categories":[],"sub_categories":[],"readme":"![MolComplex](https://github.com/patonlab/molcomplex/blob/master/molcomplex_logo.png)\n                                                                                                                                                                                                                                                                                  \nImplementing a variety of complementary metrics for molecular complexity and synthetic accessibility.\n\nA collaboration with the Sarpong group to understand complexity of molecules\n\n# Requirements\n- numpy, pandas\n- rdkit\n- openbabel\n- mordred \n- SYBA (conda install -c lich syba)\n\n## Set up conda environment directly using the yml file:\nTo install the required packages through Conda, use the env.yml file as follows and the activate the environment: \n1. `conda env create -f env.yml`\n2. `conda activate mc`\nThis will set up the environment with molcomplex installed.\n\n## For installation by cloning the GitHub folder, perform the follwoing steps:\n1. Download the zipped folder or clone using: `git clone https://github.com/patonlab/molcomplex.git`  \n2. Navigate to the installed folder and run: `python setup.py install`. This will install `molcomplex` in the environment you are present in. \n3. Install necessary dependencies using the following: `conda install -c lich syba`, `conda install -c conda-forge rdkit`, and `conda install -c conda-forge openbabel`\n\n## Recommended installation and update guide\nIn a nutshell, `molcomplex` and its dependencies are installed/updated as follows:  \n\n`pip install molcomplex`\n\n`conda install -c conda-forge openbabel rdkit Mordred`\n\n`conda install lich::syba`\n\n`conda install numpy pandas`\n\n## Usage\nTo display the options type:\n\n``python -m molcomplex -h``\n\nThe `molcomplex` package can be utilised as follows to obtain a csv with complexity scores.\n\n``python -m molcomplex -f examples/test.txt``\n\nTo write to CSV add in the following:\n\n``python -m molcomplex -f examples/test.txt --csv``\n\nTo perform a retro analysis by breaking down bonds to get complexity scores for precursors of the input SMILES add the following option:\n\n``python -m molcomplex -f examples/test.txt --csv --retro``\n\n## Usage APP\nTo run the web app perform the following steps:\n1. Navigate to the webapp folder: `cd mcwebapp`\n2. Run the app as follows: `python molcomplexapp.py`\n3. copy paste the `http://127.0.0.1:8050/` or similar into web browser to utilise as an app.\n\n\n# Metrics implemented\n- Bertz Complexity (CT) Score (JACS 1981, 103, 3241-3243)\n- Balaban J Score (Chem. Phys. Lett. 1982, 89, 399-404)\n- Coley SCScore (J. Chem. Inf. Model. 2018, 58, 2, 252)\n- IPC: Bonchev \u0026 Trinajstic's information content of the coefficients of the characteristic polynomial of the adjacency matrix of a hydrogen-suppressed graph of a molecule (J. Chem. Phys. 1977, 67, 4517-4533)\n- Ertl SA_Score (J. Cheminform. 2009, 1, 8)\n- Boettcher Score (J. Chem. Inf. Model. 2016, 56, 3, 462–470)\n- Rücker's total walk count (twc) index: Rücker, G.; Rücker, C. Counts of All Walks as Atomic and Molecular Descriptors. (J. Chem. Inf. Comput. Sci. 1993, 33, 683-695)\n- Proudfoot's Cm index based on atom environments: Proudfoot, J. R. A path based approach to assessing molecular complexity. Bioorganic Med. Chem. Lett. 27, 2014–2017 (2017)\n- Kappa Shape Indices 1, 2 \u0026 3 (Quant. Struct. Act. Relat. 1986, 5, 1-7)\n- McGowan Volume (Chromatographia, 1987, 23, 243-246)\n- Labute Approximate Surface Area (Methods Mol Biol 2004, 275, 261-78)\n- Van der Waals Volume Atomic and Bond Contributions (J. Org. Chem. 2003, 68, 7368-7373).\n- Zagreb Index \n- MOE Type Desciptors (Labute ASA, PEOE VSA, SMR VSA, SLogP VSA)\n- SYBA Score (J. Cheminformatics 2020, 12, 35)\n- Multiple additional 2D metrics.\n\n\n# Metrics to implement:\n\n- Bertz’s Ns and Nt index: Bertz, S. H. \u0026 Sommer, T. J. Rigorous mathematical approaches to strategic bonds and synthetic analysis based on conceptually simple new complexity indices. Chem. Commun. 16, 2409–2410 (1997).\n\n- Randić's zeta index: Randić, M. \u0026 Plavšić, D. Characterization of molecular complexity. Int. J. Quantum Chem. 91, 20–31 (2002).\n\n- https://www.nature.com/articles/s41598-018-37253-8\n\nTwo noteworthy substructure-based methods are:\n- Barone, R. \u0026 Chanon, M. A new and simple approach to chemical complexity. Application to the synthesis of natural products. J. Chem. Inf. Comput. Sci. 41, 269–272 (2001).\n\n- Whitlock, H. W. On the structure of total synthesis of complex natural products. J. Org. Chem. 63, 7982–7989 (1998).\n\n\n# Citation:\n\nMolecular Complexity-Inspired Synthetic Strategies Toward the Calyciphylline A-type Daphniphyllum Alkaloids Himalensine A and Daphenylline. Wright, B. A.; Okada, T.; Regni, A.; Luchini, G.; Sowndarya, S. V. S.; Chaisan, N.; Kölbl, S.; Kim, S. F.; Paton, R. S.; Sarpong, R. S. _submmitted_ **2024**\n\n# Acknowledgment:\n\nThis material is based upon work supported by the U.S. National Science Foundation under the NSF Center for Computer Assisted Synthesis (C-CAS), grant number CHE–2202693.\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpatonlab%2Fmolcomplex","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fpatonlab%2Fmolcomplex","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpatonlab%2Fmolcomplex/lists"}