def start_coot_and_wait(pdb_file,
map_file,
data_file,
work_dir=None,
coot_cmd="coot",
needs_rebuild=False,
log=None):
if (log is None): log = sys.stdout
if (work_dir is None): work_dir = os.getcwd()
if (not os.path.isdir(work_dir)):
os.makedirs(work_dir)
import mmtbx.maps.utils
from libtbx.str_utils import make_header
from libtbx import easy_run
from libtbx import group_args
import cootbx
base_script = __file__.replace(".pyc", ".py")
os.chdir(work_dir)
if (os.path.exists("coot_out_tmp.pdb")):
os.remove("coot_out_tmp.pdb")
if (os.path.exists("coot_out.pdb")):
os.remove("coot_out.pdb")
f = open("edit_in_coot.py", "w")
f.write(open(base_script).read())
f.write("\n")
f.write("import coot\n")
cootbx.write_disable_nomenclature_errors(f)
f.write("m = manager(\"%s\", \"%s\", needs_rebuild=%s)\n" %
(pdb_file, map_file, needs_rebuild))
f.close()
make_header("Interactive editing in Coot", log)
easy_run.call("\"%s\" --no-state-script --script edit_in_coot.py &" %
coot_cmd)
print >> log, " Waiting for coot_out_tmp.pdb to appear at %s" % \
str(time.asctime())
base_dir = os.path.dirname(pdb_file)
tmp_file = os.path.join(base_dir, "coot_out_tmp.pdb")
edit_file = os.path.join(base_dir, "coot_tmp_edits.pdb")
maps_file = os.path.join(base_dir, ".NEW_MAPS")
while (True):
if (os.path.isfile(tmp_file)):
print >> log, " Coot editing complete at %s" % str(time.asctime())
break
elif (os.path.isfile(maps_file)):
t1 = time.time()
assert os.path.isfile(edit_file)
mmtbx.maps.utils.create_map_from_pdb_and_mtz(
pdb_file=edit_file,
mtz_file=data_file,
output_file=os.path.join(base_dir, "maps_for_coot.mtz"),
fill=True,
out=log)
t2 = time.time()
print >> log, "Calculated new map coefficients in %.1fs" % (t2 -
t1)
os.remove(maps_file)
else:
time.sleep(t_wait / 1000.)
shutil.move(tmp_file, "coot_out.pdb")
mmtbx.maps.utils.create_map_from_pdb_and_mtz(
pdb_file="coot_out.pdb",
mtz_file=data_file,
output_file="coot_out_maps.mtz",
fill=True,
out=log)
new_model = os.path.join(work_dir, "coot_out.pdb")
new_map = os.path.join(work_dir, "coot_out_maps.mtz")
skip_rebuild = None
if (needs_rebuild):
if (os.path.isfile(os.path.join(base_dir, "NO_BUILD"))):
skip_rebuild = True
else:
skip_rebuild = False
return group_args(pdb_file=new_model,
map_file=new_map,
skip_rebuild=skip_rebuild)
def start_coot_and_wait(pdb_file,
map_file,
ligand_files,
ligand_ccs,
cif_files=(),
work_dir=None,
coot_cmd="coot",
log=None):
from iotbx import file_reader
from libtbx.str_utils import make_header
from libtbx import easy_run
import cootbx
assert (len(ligand_files) > 0) and (len(ligand_files) == len(ligand_ccs))
if (log is None): log = sys.stdout
cwd = os.getcwd()
if (work_dir is None): work_dir = cwd
if (not os.path.isdir(work_dir)):
os.makedirs(work_dir)
os.chdir(work_dir)
base_script = __file__.replace(".pyc", ".py")
ligand_xyzs = []
for pdb_file in ligand_files:
pdb_file = to_str(pdb_file)
pdb_in = file_reader.any_file(pdb_file, force_type="pdb")
pdb_in.assert_file_type("pdb")
coords = pdb_in.file_object.atoms().extract_xyz()
ligand_xyzs.append(coords.mean())
ligand_info = zip(ligand_files, ligand_ccs, ligand_xyzs)
f = open("edit_in_coot.py", "w")
f.write(open(base_script).read())
f.write("\n")
f.write("import coot\n")
cootbx.write_disable_nomenclature_errors(f)
f.write("read_pdb(\"%s\")\n" % to_str(pdb_file))
f.write("auto_read_make_and_draw_maps(\"%s\")\n" % to_str(map_file))
for cif_file in cif_files:
f.write("read_cif_dictionary(\"%s\")\n" % to_str(cif_file))
f.write("m = manager(%s)\n" % str(ligand_info))
f.close()
make_header("Ligand selection in Coot", log)
rc = easy_run.call("\"%s\" --no-state-script --script edit_in_coot.py &" %
coot_cmd)
if (rc != 0):
raise RuntimeError("Launching Coot failed with status %d" % rc)
print >> log, " Waiting for user input at %s" % str(time.asctime())
out_file = ".COOT_LIGANDS"
output_files = output_ccs = None
while (True):
if (os.path.isfile(out_file)):
print >> log, " Coot editing complete at %s" % str(time.asctime())
ligand_indices = [int(i) for i in open(out_file).read().split()]
output_files = []
for i in ligand_indices:
ligand_file = os.path.join(work_dir,
"coot_ligand_out_%d.pdb" % (i + 1))
output_files.append(ligand_file)
output_ccs = [ligand_ccs[i] for i in ligand_indices]
break
else:
time.sleep(t_wait / 1000.)
assert (output_files is not None)
os.chdir(cwd)
return output_files, output_ccs
def start_coot_and_wait (
pdb_file,
map_file,
ligand_files,
ligand_ccs,
cif_files=(),
work_dir=None,
coot_cmd="coot",
log=None) :
from iotbx import file_reader
from libtbx.str_utils import make_header
from libtbx import easy_run
import cootbx
assert (len(ligand_files) > 0) and (len(ligand_files) == len(ligand_ccs))
if (log is None) : log = sys.stdout
cwd = os.getcwd()
if (work_dir is None) : work_dir = cwd
if (not os.path.isdir(work_dir)) :
os.makedirs(work_dir)
os.chdir(work_dir)
base_script = __file__.replace(".pyc", ".py")
ligand_xyzs = []
for pdb_file in ligand_files :
pdb_file = to_str(pdb_file)
pdb_in = file_reader.any_file(pdb_file, force_type="pdb")
pdb_in.assert_file_type("pdb")
coords = pdb_in.file_object.atoms().extract_xyz()
ligand_xyzs.append(coords.mean())
ligand_info = zip(ligand_files, ligand_ccs, ligand_xyzs)
f = open("edit_in_coot.py", "w")
f.write(open(base_script).read())
f.write("\n")
f.write("import coot\n")
cootbx.write_disable_nomenclature_errors(f)
f.write("read_pdb(\"%s\")\n" % to_str(pdb_file))
f.write("auto_read_make_and_draw_maps(\"%s\")\n" % to_str(map_file))
for cif_file in cif_files :
f.write("read_cif_dictionary(\"%s\")\n" % to_str(cif_file))
f.write("m = manager(%s)\n" % str(ligand_info))
f.close()
make_header("Ligand selection in Coot", log)
rc = easy_run.call("\"%s\" --no-state-script --script edit_in_coot.py &" %
coot_cmd)
if (rc != 0) :
raise RuntimeError("Launching Coot failed with status %d" % rc)
print >> log, " Waiting for user input at %s" % str(time.asctime())
out_file = ".COOT_LIGANDS"
output_files = output_ccs = None
while (True) :
if (os.path.isfile(out_file)) :
print >> log, " Coot editing complete at %s" % str(time.asctime())
ligand_indices = [ int(i) for i in open(out_file).read().split() ]
output_files = []
for i in ligand_indices :
ligand_file = os.path.join(work_dir, "coot_ligand_out_%d.pdb" % (i+1))
output_files.append(ligand_file)
output_ccs = [ ligand_ccs[i] for i in ligand_indices ]
break
else :
time.sleep(t_wait / 1000.)
assert (output_files is not None)
os.chdir(cwd)
return output_files, output_ccs
def start_coot_and_wait (
pdb_file,
map_file,
data_file,
work_dir=None,
coot_cmd="coot",
needs_rebuild=False,
log=None) :
if (log is None) : log = sys.stdout
if (work_dir is None) : work_dir = os.getcwd()
if (not os.path.isdir(work_dir)) :
os.makedirs(work_dir)
import mmtbx.maps.utils
from libtbx.str_utils import make_header
from libtbx import easy_run
from libtbx import group_args
import cootbx
base_script = __file__.replace(".pyc", ".py")
os.chdir(work_dir)
if (os.path.exists("coot_out_tmp.pdb")) :
os.remove("coot_out_tmp.pdb")
if (os.path.exists("coot_out.pdb")) :
os.remove("coot_out.pdb")
f = open("edit_in_coot.py", "w")
f.write(open(base_script).read())
f.write("\n")
f.write("import coot\n")
cootbx.write_disable_nomenclature_errors(f)
f.write("m = manager(\"%s\", \"%s\", needs_rebuild=%s)\n" %
(pdb_file, map_file, needs_rebuild))
f.close()
make_header("Interactive editing in Coot", log)
easy_run.call("\"%s\" --no-state-script --script edit_in_coot.py &" %
coot_cmd)
print >> log, " Waiting for coot_out_tmp.pdb to appear at %s" % \
str(time.asctime())
base_dir = os.path.dirname(pdb_file)
tmp_file = os.path.join(base_dir, "coot_out_tmp.pdb")
edit_file = os.path.join(base_dir, "coot_tmp_edits.pdb")
maps_file = os.path.join(base_dir, ".NEW_MAPS")
while (True) :
if (os.path.isfile(tmp_file)) :
print >> log, " Coot editing complete at %s" % str(time.asctime())
break
elif (os.path.isfile(maps_file)) :
t1 = time.time()
assert os.path.isfile(edit_file)
mmtbx.maps.utils.create_map_from_pdb_and_mtz(
pdb_file=edit_file,
mtz_file=data_file,
output_file=os.path.join(base_dir, "maps_for_coot.mtz"),
fill=True,
out=log)
t2 = time.time()
print >> log, "Calculated new map coefficients in %.1fs" % (t2-t1)
os.remove(maps_file)
else :
time.sleep(t_wait/1000.)
shutil.move(tmp_file, "coot_out.pdb")
mmtbx.maps.utils.create_map_from_pdb_and_mtz(
pdb_file="coot_out.pdb",
mtz_file=data_file,
output_file="coot_out_maps.mtz",
fill=True,
out=log)
new_model = os.path.join(work_dir, "coot_out.pdb")
new_map = os.path.join(work_dir, "coot_out_maps.mtz")
skip_rebuild = None
if (needs_rebuild) :
if (os.path.isfile(os.path.join(base_dir, "NO_BUILD"))) :
skip_rebuild = True
else :
skip_rebuild = False
return group_args(
pdb_file=new_model,
map_file=new_map,
skip_rebuild=skip_rebuild)