This program is meant to enable comprehensive querying of the PDB utilizing a fragmentation of every structure (and each chain) looking for matches based on backbone geometry - initially independent of all other properties. Under the hood the Java Apache Spark API is used in conjunction with the mmtf-spark project.
Conceptually, this allows for a strictly spatial search of fragments that utilize similar geometry to accomplish important chemistry.
Window (fragment) size can be varied, and the only required input is a PDB file of the query fragment. The query fragment should be identical in length to the window size chosen.
Example Output
Planned improvements:
- Improve scoring metric and add statistics that guide a threshold or cutoff
- Output results in more parsable format (CSV)
- Make executable build
- Add sequence motif filter (regex for fragments)
- Add filter to only let a PDB ID occur once (currently implemented in python PML generating script)
Potential future improvements:
- GUI
- Automated checking of pre-fragmented HADOOP sequence files
- Automated updating of HADOOP sequence files with additions/changes to PDB
- Inline creation of PML script to open results in PyMOL (currently implemented with a separate python script)
Many thanks to @lafita for all his work on this project and the UCSD actively developing mmtf-spark. This software is in development and as such is provided as is, with no guarantees.