{"id":15347377,"url":"https://github.com/vtlim/misc","last_synced_at":"2025-10-10T23:35:31.809Z","repository":{"id":182914673,"uuid":"84164471","full_name":"vtlim/misc","owner":"vtlim","description":"Miscellaneous scripts for research and data analysis using Python, OpenEye Python Toolkit, VMD/Tcl, or Grace.","archived":false,"fork":false,"pushed_at":"2020-05-01T08:09:05.000Z","size":1227,"stargazers_count":0,"open_issues_count":1,"forks_count":0,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-02-08T15:15:38.793Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/vtlim.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2017-03-07T06:43:04.000Z","updated_at":"2020-10-16T22:21:13.000Z","dependencies_parsed_at":"2023-07-22T04:10:02.064Z","dependency_job_id":null,"html_url":"https://github.com/vtlim/misc","commit_stats":null,"previous_names":["vtlim/misc"],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/vtlim%2Fmisc","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/vtlim%2Fmisc/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/vtlim%2Fmisc/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/vtlim%2Fmisc/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/vtlim","download_url":"https://codeload.github.com/vtlim/misc/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":243239704,"owners_count":20259271,"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":[],"created_at":"2024-10-01T11:33:02.937Z","updated_at":"2025-10-10T23:35:26.779Z","avatar_url":"https://github.com/vtlim.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"\n# Contents\n\nThis file last updated: Nov 9 2018  \n\n* Directories\n  * `examples/` \n  * `oechem/` \n  * `pca-viewer/` \n  * `vmd/`\n  * `xmgrace/`\n\n* Scripts\n  * `awksed.py` - Example application to process GROMACS `.top` files to add lines for dihedral restraint.  \n    * Example:  \n      `python awksed.py -i $i.top -s '[ moleculetype ]' -c 1 -a $'[ dihedral_restraints ]\\n; atom1 a2 a3 a4 type=1 phi(ref) dphi kfactor\\n4 3 2 8 1 $i 0 300\\n' -r '$i' -p -1 -o $i.top`\n  * `column_avg.py` \n  * `column_sum.py` \n  * `plotBar.py` - Customizable bar plots.\n  * `plotScatter.py`\n  * `plotXY.py` - Generates XY line plots from input ASCII data file of one `x` column and one or more `y` columns. This script can:\n    * Subsample based on correlation time\n    * Subsample based on running averages\n    * Take in file of uncertainties to plot error bars\n    * Separate a long xy data series into many line plots\n\n* High-level view of contents\n```\n.\n├── awksed.py\n├── column_avg.py\n├── column_sum.py\n├── examples\n│   ├── column_avg\n│   ├── column_sum\n│   ├── plotBar\n│   ├── plotScatter\n│   └── plotXY\n├── oechem\n│   ├── am1wib.py\n│   ├── charge_mols.py\n│   ├── combineSDF.py\n│   ├── examples\n│   ├── plotMultSDF.py\n│   ├── plotSDF.py\n│   └── README.md\n├── openTabs.sh\n├── pca-viewer\n├── plotBar.py\n├── plotScatter.py\n├── plotXY.py\n├── README.md\n├── vmd\n│   ├── drawBox.tcl\n│   ├── move_atoms.tcl\n│   ├── pbchelp.tcl\n│   ├── README.md\n│   └── wrapXY.tcl\n└── xmgrace\n    ├── add2.com\n    ├── hist.com\n    ├── README.md\n    ├── runavg2.com\n    ├── view2.par\n    └── view2runavg.par\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fvtlim%2Fmisc","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fvtlim%2Fmisc","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fvtlim%2Fmisc/lists"}