Converts mpdb files to a set of frames in xyzr format given a reference PQR file.
- Provide an mpdb trajectory file (recomended), or a functioning catdcd executable in the wotking directory together with a reference PDB file and a TRR file.
catdcd binary here
Example of mpdb creation with catdcd: ./catdcd -s <structureName>.pdb -o <structureName>.mpdb -otype pdb -trr <structureName>.trr
- pip install numpy and regex
IMPORTANT Provide also a reference PQR file (tipically, from the reference PDB file using softwares like pdb2pqr).
In the working directory given <structureName>.pqr and <structureName>.mpdb, run python3 mpdb2xyzr.py <structureName>
python3 mpdb2xyzr.py --mpdb <structureName>
Automatically generates the mpdb file by calling catdcd. catdcd must be present in the working directory together with <structureName>.trr and <structureName>.pdb
Type python3 mpdb2xyzr.py -h or --help for more informations.
The script automatically creates a results folder containing a sub-folder named as the structure name (same as the mpdb and pqr filename). Within this folder a folder containing all xyzr frames. Frames are numbered from 1 to max_frame with leading zeros padding.
A. Raffo, L. Gagliardi, U. Fugacci, L. Sagresti, S. Grandinetti, G. Brancato S. Biasotti, W. Rocchia. "Chanalyzer: a computational geometry approach for the analysis of protein channel shape and dynamics", under review at Frontiers in Molecular Biosciences, 2022.