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

From Proteopedia

Jump to: navigation, search

Contents

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.


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](https://github.com/samirelanduk/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](https://github.com/rasbt/biopandas) for working with molecular structures in pandas DataFrames. Documentation at http://rasbt.github.io/biopandas/.

Proteopedia Page Contributors and Editors (what is this?)

Wayne Decatur

Personal tools