User:Wayne Decatur/Code for Molecular Structure and Visualization Work: Difference between revisions
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m add Dockerfiles I have made for molecular structure work |
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*** A script written in Python 2.x to merge multiple PDB files as individual models in a single PDB file. The individual models are placed in a single folder.. | *** A script written in Python 2.x to merge multiple PDB files as individual models in a single PDB file. The individual models are placed in a single folder.. | ||
*** It has advanced options that let you control the order of the individual models or control the starting numbering for the first model. | *** It has advanced options that let you control the order of the individual models or control the starting numbering for the first model. | ||
** And more available [https://github.com/fomightez/structurework/tree/master/python_scripts here], with several of them demonstrated actively in Jupyter notebooks by launching 'binder' sessions from .[https://github.com/fomightez/cl_demo-binder here]. | |||
* In addition to my [https://github.com/fomightez/structurework/tree/master/python_scripts Python Scripts for Molecular Structure Analysis], my [https://github.com/fomightez/pymol-binder pymol-binder] adds some of my own code in for handling structures via PyMOL. | |||
==Webserver for Python code== | ==Webserver for Python code== | ||
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* [https://github.com/fomightez/cnssolve1pt21_docker Dockerfile] to build images that will compile CNSsolve 1.21. A modified version of CNS to run the scripts for XL-MS Protein assembly, that software is referred to as XL-MOD in the publication [https://www.ncbi.nlm.nih.gov/pubmed/27111507 here]. | * [https://github.com/fomightez/cnssolve1pt21_docker Dockerfile] to build images that will compile CNSsolve 1.21. A modified version of CNS to run the scripts for XL-MS Protein assembly, that software is referred to as XL-MOD in the publication [https://www.ncbi.nlm.nih.gov/pubmed/27111507 here]. | ||
* [https://github.com/fomightez/xlmod_docker Dockerfile] for a modified version of CNS to run the scripts for XL-MS Protein assembly, that software is referred to as XL-MOD in the publication [https://www.ncbi.nlm.nih.gov/pubmed/27111507 here]. | * [https://github.com/fomightez/xlmod_docker Dockerfile] for a modified version of CNS to run the scripts for XL-MS Protein assembly, that software is referred to as XL-MOD in the publication [https://www.ncbi.nlm.nih.gov/pubmed/27111507 here]. | ||
==Related Python resources by others== | |||
*[https://github.com/samirelanduk/atomium atomium] is a Python library for opening and saving .pdb, .cif and .xyz files, and presenting and manipulating the information contained within. Documentation is at https://atomium.samireland.com/ . | |||
*[https://github.com/rasbt/biopandas Biopandas] for working with molecular structures in pandas DataFrames. Documentation at http://rasbt.github.io/biopandas/. | |||
