User:Wayne Decatur/Code for Molecular Structure and Visualization Work: Difference between revisions

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* [https://github.com/fomightez/structurework/tree/master/spartan_fixer SPARTAN_FIXER]
* [https://github.com/fomightez/structurework/tree/master/spartan_fixer SPARTAN_FIXER]
** a python program that fixes Spartan'08 output files in so-called PDB format, converting them to be true PDB format. The fixed files can then easily be used in Jmol.
** a Python (2.x) program that fixes Spartan'08 output files in so-called PDB format, converting them to be true PDB format. The fixed files can then easily be used in Jmol.
** A webserver version of this is is running [http://fomightez.pythonanywhere.com/spartan_fixer/ here]. You can enter your data and have it analyzed without needing to download anything.
** A webserver version of this is is running [http://fomightez.pythonanywhere.com/spartan_fixer/ here]. You can enter your data and have it analyzed without needing to download anything.
** Written in Python 2.x.
* [https://github.com/fomightez/structurework/blob/master/python_scripts/multiple_model_PDB_file_splitter.py multiple_model_PDB_file_splitter.py]
** It takes a multiple model PDB file and splits up the models to produce as output each of the models as a separate PDB file.
**You specify the structure file when you call the program.
** Written in Python 2.x.
* [https://github.com/fomightez/structurework/blob/master/python_scripts/super_basic_multiple_model_PDB_file_splitter.py super_basic_multiple_model_PDB_file_splitter.py]
** A very basic multiple model PDB file splitting script written in Python 2.x.
** It takes a multiple model PDB file and splits up the models to produce as output each of the models as a separate PDB file.
** This basic version requires you to paste the complete PDB file text into the script before you run it.  I put this out here in case it helps anyone understand what is going on; it was inspired by code at [http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Split_NMR-style_multiple_model_pdb_files_into_individual_models here]
* [https://github.com/fomightez/structurework/tree/master/python_scripts Wayne Decatur's Python Scripts for Molecular Structure Analysis]
* [https://github.com/fomightez/structurework/tree/master/python_scripts Wayne Decatur's Python Scripts for Molecular Structure Analysis]
** [https://github.com/fomightez/structurework/blob/master/python_scripts/multiple_model_PDB_file_splitter.py multiple_model_PDB_file_splitter.py]
*** It takes a multiple model PDB file and splits up the models to produce as output each of the models as a separate PDB file.
***You specify the structure file when you call the program.
*** Written in Python 2.x.
** [https://github.com/fomightez/structurework/blob/master/python_scripts/super_basic_multiple_model_PDB_file_splitter.py super_basic_multiple_model_PDB_file_splitter.py]
*** A very basic multiple model PDB file splitting script written in Python 2.x.
*** It takes a multiple model PDB file and splits up the models to produce as output each of the models as a separate PDB file.
*** This basic version requires you to paste the complete PDB file text into the script before you run it.  I put this out here in case it helps anyone understand what is going on; it was inspired by code at [http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Split_NMR-style_multiple_model_pdb_files_into_individual_models here]
** [https://github.com/fomightez/structurework/blob/master/python_scripts/super_basic_multiple_model_PDB_file_splitter.py merge_multi_PDBs_into_single_file.py]
*** 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.
** 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==
==Webserver for Python code==
* Much of the more involved code featured here is running in a webserver form [http://fomightez.pythonanywhere.com/spartan_fixer/ here]. You can enter your data and have it analyzed without needing to download anything.
* Much of the more involved code featured for Spartan_Fixer is running in a webserver form [http://fomightez.pythonanywhere.com/spartan_fixer/ here]. You can enter your data and have it analyzed without needing to download anything.


==Code==
==Obtaining the Python Code==
See [http://fomightez.github.io/ here] for getting my code in a form you can use on your machine or that you can modify.
See [http://fomightez.github.io/ here] for getting my code in a form you can use on your machine or that you can modify.
==Dockerfiles==
* [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].
==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/.
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