/
run_harvest.py
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/
run_harvest.py
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from __future__ import division
import iotbx.pdb
import mmtbx.model
import math
from libtbx import group_args
import os
from libtbx.utils import null_out
from scitbx.array_family import flex
from libtbx import easy_run
from mmtbx.command_line import emringer
def get_latest(files):
indices = []
for f in files:
try:
indices.append(int(f.replace("cycle_","").replace("_refined.pdb","")))
except KeyboardInterrupt: raise
except: return None
last = max(indices)
return "cycle_%d_refined.pdb"%last
def show_geo(fn, prefix):
pdb_inp = iotbx.pdb.input(file_name=fn)
model = mmtbx.model.manager(model_input = pdb_inp, build_grm = True,
log = null_out())
mes = "%s %s"%(prefix,
model.geometry_statistics(use_hydrogens=False).show_short())
return model, mes
def get_z(fn):
cmd = " ".join(["phenix.development.rama_z_score", fn])
r = easy_run.fully_buffered(cmd).raise_if_errors()
return round(float(r.stdout_lines[-5].split()[2].replace(",","")), 2)
def get_emringer(pdb_file, map_file):
result = emringer.run(
args=[pdb_file, map_file], out=null_out(), verbose=False)[1].score
return result
def run():
# Must run in cryo-EM folder!
root = os.getcwd()
folders = ["6i5a","3j63","5fn5_6iyc_A/c","3a5x","5ly6"]
for folder in folders:
folder_1 = "/".join([root, folder])
print folder_1, "-"*(79-len(folder_1))
if(not os.path.isdir(folder_1)):
print " ...does not exist, skip."
continue
#
map_file = None
for fi in os.listdir(folder_1):
if(fi.endswith(".map") or fi.endswith(".ccp4")):
map_file = "/".join([folder_1, fi])
assert os.path.isfile(map_file)
#
start = "/".join([folder_1, "initial.pdb"])
assert os.path.isfile(start)
z1 = get_z(start)
emr1 = get_emringer(start, map_file)
model_1, mes1 = show_geo(start, prefix=" start:")
print mes1, "z_score:", z1, "EMRinger: %4.2f"%emr1
#
for sub_ in os.listdir(folder_1):
sub = "/".join([folder_1, sub_])
if(not os.path.isdir(sub)): continue
if "opt" in sub: continue
refined = "/".join([sub,"real_space_refined.pdb"])
msg=""
if(not os.path.isfile(refined)):
msg="<<< WARNING: no final refined model."
print " ", sub_, msg
sub1 = "/".join([sub, "pdb"])
if(not os.path.isdir(sub1)):
print " not there:", sub1
continue
files = []
for fn in os.listdir(sub1):
if(not fn.endswith(".pdb")): continue
files.append(fn)
refined = get_latest(files = files)
if(refined is None):
print " No refined model."
continue
refined = "/".join([sub1, refined])
assert os.path.isfile(refined)
#
model_2, mes2 = show_geo(refined, prefix=" final:")
z2 = get_z(refined)
emr2 = get_emringer(refined, map_file)
s1 = model_1.get_sites_cart()
s2 = model_2.get_sites_cart()
dist = flex.sqrt((s1 - s2).dot())
print mes2, "min/max/mean(start, final): %5.3f %5.3f %5.3f"%\
dist.min_max_mean().as_tuple(), "z_score:", z2, "EMRinger: %4.2f"%emr2
if(__name__ == "__main__"):
run()