{"id":19476852,"url":"https://github.com/openchemistry/fragments","last_synced_at":"2025-04-25T14:32:31.093Z","repository":{"id":55526721,"uuid":"523116420","full_name":"OpenChemistry/fragments","owner":"OpenChemistry","description":"Molecular fragments and inorganic ligands for rapidly building structures","archived":false,"fork":false,"pushed_at":"2025-01-21T17:21:04.000Z","size":4678,"stargazers_count":11,"open_issues_count":5,"forks_count":4,"subscribers_count":5,"default_branch":"main","last_synced_at":"2025-04-03T23:03:29.654Z","etag":null,"topics":["chemistry","common-molecule-fragments","molecules","openchemistry"],"latest_commit_sha":null,"homepage":"https://two.avogadro.cc/","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"bsd-3-clause","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/OpenChemistry.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":"2022-08-09T21:40:26.000Z","updated_at":"2025-03-06T15:03:44.000Z","dependencies_parsed_at":"2023-11-12T02:28:48.996Z","dependency_job_id":"96f36011-594f-45eb-9b75-88c4d2f8e329","html_url":"https://github.com/OpenChemistry/fragments","commit_stats":null,"previous_names":[],"tags_count":2,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/OpenChemistry%2Ffragments","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/OpenChemistry%2Ffragments/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/OpenChemistry%2Ffragments/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/OpenChemistry%2Ffragments/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/OpenChemistry","download_url":"https://codeload.github.com/OpenChemistry/fragments/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":250834199,"owners_count":21494927,"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":["chemistry","common-molecule-fragments","molecules","openchemistry"],"created_at":"2024-11-10T19:42:14.116Z","updated_at":"2025-04-25T14:32:26.490Z","avatar_url":"https://github.com/OpenChemistry.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Fragments\n\n![Contributions Welcome](https://img.shields.io/badge/contributions-welcome-blue)\n\nMolecular fragments and inorganic ligands for rapidly building structures\n\n- a variety of ligands for inorganic complexes, including haptic structures\n- many kinds of functional group pieces for \"click to add\" (e.g., phenyl groups)\n- amino acids for a peptide builder\n- monomers for a polymer builder\n\n## Programmatic addition of fragments\n\nComplement a virtual environment of Python with the `requirements.txt`.  This as\nwell as the required scripts are compiled in sub folder `scripts`.\n\nFor functional groups, SMILES are recorded in the `groups.smi` files, assuming\nthe attachment point is on the left-hand side, e.g.\n\n```\nSC#N thiocyanate\n```\n\n![](thiocyanate.png)\n\nThe functional group files can then be generated:\n\n```shell\npython scripts/rdkit-fragments.py new-groups.smi\n```\n\nIn general, it is safer to create a new SMILES file for new functional groups -\nand then append to the groups.smi after generation. This way, only new files are\ncreated and the existing files are not overwritten.\n\nThe `rdkit-fragments.py` script will generate SVG using `rdkit` depiction and\nPNG (using `cairosvg`) preview images for each functional group. Only the PNG\nimages should be added to the repository, since Avogadro does not support SVG\nicons currently.\n\nIt will also generate a SDF / Molfile using `rdkit` ETKDGv3 conformer generation\nand MMFF94 geometry optimization.\n\nThe SDF should be converted to CJSON by Open Babel or Avogadro before adding to\nthe repository.\n\nIf RDKit depictions need revision, edit the SVG file (or create a new one from\na program like ChemDraw or ChemDoodle). The `svg2png.py` script uses `cairosvg`\nto generate a new PNG image with the appropriate resolution.\n\n## Manual Creation of Ligands\n\nIn some cases, the geometry produced by the scripts is poor and a ligand or\nfunctional group needs to be created manually. To manually build new ligands, \nfollow the instructions on\n\u003chttps://two.avogadro.cc/docs/tools/template-tool.html#creating-new-ligands\u003e.\n\nThe structure preview by `depict-ligands.py` of .smi by\nAvogadro highlights the site of complexation temporarily occupied by the dummy\natom `*` by a dot colored in rgb(255,127,127), or #ff7f7f.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fopenchemistry%2Ffragments","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fopenchemistry%2Ffragments","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fopenchemistry%2Ffragments/lists"}