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.
- Make sure Java is installed on your system and can be run with the command
java
- 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. - Extract it to a place where you store software
Program execution¶
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?
- Ye Y & Godzik A (2003) Flexible structure alignment by chaining aligned fragment pairs allowing twists. Bioinformatics 19 Suppl 2: ii246–55 Available at: https://www.ncbi.nlm.nih.gov/pubmed/14534198
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