calculate solvent fraction from pdb (cctbx)

solvent_fraction.py

import iotbx.pdb
import mmtbx.utils
from mmtbx.scaling.matthews import p_vm_calculator

def run(pdbin):
  pdb_inp = iotbx.pdb.input(pdbin)
  xray_structure = pdb_inp.xray_structure_simple()
  print "Read from %s" % pdb_in
  xray_structure.show_summary(prefix="  ")
  print
  print "Mask-based calculation"
  print " Solvent Content:", mmtbx.utils.f_000(xray_structure=xray_structure).solvent_fraction
  print

  hierarchy = pdb_inp.construct_hierarchy()
  counts = hierarchy.overall_counts()
  num_aa = counts.resname_classes.get("common_amino_acid", 0)
  num_na = counts.resname_classes.get("common_rna_dna", 0)
  print "Sequence-based calculation"
  print " Number of amino acids: %d" % num_aa
  print " Number of       bases: %d" % num_na

  vm_calc = p_vm_calculator(xray_structure.crystal_symmetry(), n_residues=num_aa, n_bases=num_na)
  print " Solvent Content: ", vm_calc.solc(vm=vm_calc.vm(copies=1))
# run()

if __name__ == "__main__":
  import sys
  pdb_in = sys.argv[1]
  run(pdb_in)