dist_rank.py

Usage and arguments

usage: dist_rank.py [-h] [-pdb PDBF] [-s SEED] [-satom SEEDATOM] [-type DTYPEF] [-max COFF] [-noH] [-store] [-recut] [-byres]

Distance based selection scheme with both residue and functional group partitioning

options:
  -h, --help           show this help message and exit
  -pdb PDBF            pdb file to use
  -s SEED, -seed SEED  seed, examples: A:300,A:301,A:302
  -satom SEEDATOM      atoms to use as center, examples: A:300:CA
  -type DTYPEF         "closest" or "mass" or "avg"
  -max COFF            cutoff/max distance from ligand, default 5A
  -noH, -noh           ignore hydrogens
  -store               store distances and pdb/seed/noH info in all_dists.pkl
  -recut               apply new cutoff to atom distances read from all_dists.pkl
  -byres               use residue grouping instead of FG grouping

Inputs

• -pdb: Processed PDB to be trimmed (required)
  • Given as filename
  • Example: -pdb 2cht_h.pdb
• -s: Seed
  • Given as ch:ID pairs
  • Examples: -s A:203 or -seed A:301,A:302
• -satom: Specific atoms to use as distance center instead of whole seed
  • Given as ch:ID:atom trios
  • Examples: -satom A:203:CA or -satom A:301:CA,A:302:CA
• -type: type of distance to calculate
  • Given as “closest” or “mass” or “avg”
  • closest: distance to closest seed atom
  • mass: distance to center of mass of seed/satom
  • mass: distance to Cartesian center of seed (average of seed coordinates)
  • Examples: -type closest
• -max: distance cutoff
  • Given as number (in Å)
  • Example: -max 5
• -noh/-noH: flag to specify that hydrogens should be ignored in distance calculations
  • No corresponding argument (acts as t/f flag)
  • Hydrogens will also be excluded from calculation of the center of mass/Cartesian center
  • Examples: -noh
• -store: save distances of all atoms to seed so that new cutoff can be applied faster
  • No corresponding argument (acts as t/f flag)
  • saves info to all_dists.pkl
  • Example: -store
• -recut: use previously stored all_dists.pkl instead of calculating distances from scratch
  • No corresponding argument (acts as t/f flag)
  • Example: -recut
• -byres: do distance calculations by residue rather than functional group
  • No corresponding argument (acts as t/f flag)
  • Examples: -byres

Outputs

• sorted_FGs_[type]_[max]_A.dat or sorted_res_[type]_[max]_A.dat: ranked FGs or residues up to given cutoff
• all_dists_table.dat: distances of all atoms in PDB to seed
• res_atoms.dat