FATCAT

Description

FATCAT is a structural alignment tool that allows you to determine the similarity of a pair of protein structures.

Warning

Parsing FATCAT results is currently incomplete and will only return TM-scores as of now - but TM-scores only show up in development versions of jFATCAT

Installation instructions

Note

These instructions were created on an Ubuntu 17.04 system.

  1. Make sure Java is installed on your system and can be run with the command java
  2. Download the Java port of FATCAT from the jFATCAT download page, under the section “Older file downloads” with the filename protein-comparison-tool\_<DATE>.tar.gz, with the most recent date.
  3. Extract it to a place where you store software

Program execution

In the shell

To run the program on its own in the shell…

/path/to/software/fatcat/runFATCAT.sh

With ssbio

To run the program using the ssbio Python wrapper, see: ssbio.protein.structure.properties.fatcat.run_fatcat(). Run it on two structures, pointing to the path of the runFATCAT.sh script.

FAQs

  • How do I cite FATCAT?

  • I’m having issues running FATCAT…

    • See the ssbio wiki for (hopefully) some solutions - or add yours in when you find the answer!

API

ssbio.protein.structure.properties.fatcat.parse_fatcat(fatcat_xml)[source]

Parse a FATCAT XML result file.

Parameters:fatcat_xml (str) – Path to FATCAT XML result file
Returns:Parsed information from the output
Return type:dict

Todo

  • Only returning TM-score at the moment
ssbio.protein.structure.properties.fatcat.run_fatcat(structure_path_1, structure_path_2, fatcat_sh, outdir='', silent=False, print_cmd=False, force_rerun=False)[source]

Run FATCAT on two PDB files, and return the path of the XML result file.

Parameters:
  • structure_path_1 (str) – Path to PDB file
  • structure_path_2 (str) – Path to PDB file
  • fatcat_sh (str) – Path to “runFATCAT.sh” executable script
  • outdir (str) – Path to where FATCAT XML output files will be saved
  • silent (bool) – If stdout should be silenced from showing up in Python console output
  • print_cmd (bool) – If command to run FATCAT should be printed to stdout
  • force_rerun (bool) – If FATCAT should be run even if XML output files already exist
Returns:

Path to XML output file

Return type:

str

ssbio.protein.structure.properties.fatcat.run_fatcat_all_by_all(list_of_structure_paths, fatcat_sh, outdir='', silent=True, force_rerun=False)[source]

Run FATCAT on all pairs of structures given a list of structures.

Parameters:
  • list_of_structure_paths (list) – List of PDB file paths
  • fatcat_sh (str) – Path to “runFATCAT.sh” executable script
  • outdir (str) – Path to where FATCAT XML output files will be saved
  • silent (bool) – If command to run FATCAT should be printed to stdout
  • force_rerun (bool) – If FATCAT should be run even if XML output files already exist
Returns:

TM-scores (similarity) between all structures

Return type:

Pandas DataFrame