User:Wayne Decatur/Code for Molecular Structure and Visualization Work: Difference between revisions
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** 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 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. | ||
* [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 | * 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/. | |||
Latest revision as of 19:12, 19 September 2019
My Python Code for Various Molecular Structure Visualization and Analysis Tasks
- SPARTAN_FIXER
- 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 here. You can enter your data and have it analyzed without needing to download anything.
- Wayne Decatur's Python Scripts for Molecular Structure Analysis
- 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.
- 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 here
- 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 here, with several of them demonstrated actively in Jupyter notebooks by launching 'binder' sessions from .here.
- multiple_model_PDB_file_splitter.py
- In addition to my Python Scripts for Molecular Structure Analysis, my pymol-binder adds some of my own code in for handling structures via PyMOL.
Webserver for Python code
- Much of the more involved code featured for Spartan_Fixer is running in a webserver form here. You can enter your data and have it analyzed without needing to download anything.
Obtaining the Python Code
See here for getting my code in a form you can use on your machine or that you can modify.
Dockerfiles
- 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 here.
- 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 here.
Related Python resources by others
- 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/ .
- Biopandas for working with molecular structures in pandas DataFrames. Documentation at https://rasbt.github.io/biopandas/.
