I’m not able to see output files created by arpeggio.py algorithm. Harry Jubb created it for Linux, so I’ve been struggling to find the adaptations for Windows.
This is my code :
docker run --rm -v C:\directory:/filelocation -it arpeggio python arpeggio.py /file.pdb -s RESNAME:xxx -v
INFO//12:21:10.618//Loaded PDB structure (BioPython)
INFO//12:21:10.620//Detected that the input structure contains hydrogens. Hydrogen addition will be skipped.
INFO//12:21:10.871//Loaded PDB structure (OpenBabel)
INFO//12:21:10.884//Mapped OB to BioPython atoms and vice-versa.
INFO//12:21:11.066//Determined atom explicit and implicit valences, bond orders, atomic numbers, formal charge and number of bound hydrogens.
WARNING//12:21:11.116//Chain termini could not be determined for chain E. It may not be a polypeptide chain.
INFO//12:21:11.119//Determined polypeptide residues, chain breaks, termini
INFO//12:21:11.322//Percieved and stored rings.
INFO//12:21:11.345//Perceived and stored amide groups.
INFO//12:21:11.354//Added hydrogens to BioPython atoms.
INFO//12:21:11.359//Added VdW radii.
INFO//12:21:11.365//Added covalent radii.
INFO//12:21:11.378//Assigned rings to residues.
INFO//12:21:11.508//Expanded to binding site.
INFO//12:21:11.509//Flagged selection rings.
INFO//12:21:11.510//Completed new NeighbourSearch.
INFO//12:21:11.606//Calculated pairwise contacts.
INFO//12:21:11.794//Program End. Maximum memory usage was xx MB.
But, is not adding this :
This created a bunch of files in the current directory
The original code created by Harry Jubb is this :
docker run --rm -v "$(pwd)":/run -u `id -u`:`id -g` -it harryjubb/arpeggio python arpeggio.py /run/file.pdb -s RESNAME:xxx -v
However, “$(pwd)”:/run -u
id -g works for Linux and not for Windows. Thus, that’s why I added C:\directory:/filelocation . I couldn’t type user id and group id since docker is working as a virtual image.