run_opt.py

from __future__ import division
import math, os, sys
import time
import iotbx.pdb
from scitbx.array_family import flex
import mmtbx.model
from libtbx.utils import null_out
from libtbx import easy_run

base=[
    "qr.refine",
    "%s",
    "mode=opt",
    "stpmax=0.2",
    "gradient_only=true", # no problem with running up to upper bound.
    "clustering=false",
    "use_convergence_test=true",
    "rmsd_tolerance=0.001",
    "number_of_micro_cycles=25"
    ]

cmd_cctbx    = " ".join(base+["restraints=cctbx","> %s.log"])
cmd_xtb      = " ".join(base+["restraints=qm","engine_name=xtb","quantum.nproc=8","> %s.log"])
cmd_terachem = " ".join(base+["restraints=qm","engine_name=terachem",
                              "basis=6-31g","> %s.log"])
cmd_mopac    = " ".join(base+["restraints=qm","engine_name=mopac","> %s.log"])

def run(args):
  assert len(args)==1
  mode = args[0]
  assert mode in ["cctbx", "xtb", "terachem", "mopac"]
  #
  if(  mode=="cctbx"):    cmd = cmd_cctbx
  elif(mode=="xtb"):      cmd = cmd_xtb
  elif(mode=="terachem"): cmd = cmd_terachem
  elif(mode=="mopac"):    cmd = cmd_mopac
  else:                   assert 0
  #
  results_prefix = "./%s_opt"%mode
  perturbed_prefix = "./perturbed/"
  rmsd_dirs = ["0.3/","0.6/","0.9/","1.2/","1.5/"]
  base_names = ["0","1","2","3","4","5","6","7","8","9"]
  easy_run.call("rm -rf %s_opt"%mode)
  os.makedirs(results_prefix)
  os.chdir(results_prefix)
  for rmsd_dir in rmsd_dirs:
    print rmsd_dir
    os.makedirs(rmsd_dir)
    for bn in base_names:
      file_name = "../"+perturbed_prefix+rmsd_dir+bn+".pdb"
      if(not os.path.exists(file_name)): assert 0
      cmd_full = cmd%(file_name,bn)
      print "running command:\n%s"%(cmd_full)
      easy_run.call(cmd_full)
      easy_run.call("cp pdb/%s_refined.pdb %s/%s.pdb"%(bn,rmsd_dir,bn))
      easy_run.call("mv %s.log %s"%(bn,rmsd_dir))
      easy_run.call("mv pdb %s/%s_pdb"%(rmsd_dir,bn))


if __name__ == "__main__":
  t0 = time.time()
  run(args=sys.argv[1:])
  print "Time: %6.4f s" % (time.time() - t0)