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# simply read the file and make a molecule
#
def generate_molecule_from_mmcif(comp_id, mmcif_file_name):
coot.read_cif_dictionary(mmcif_file_name)
return coot.get_monomer(comp_id)
# return a molecule number. Return -1 on fail.
#
def generate_molecule_from_mmcif_by_dict_gen(comp_id, mmcif_file_name):
"""return a molecule number. Return -1 on fail."""
global use_mogul
import os
# return a new molecule number, generator is "pyrogen" or "acedrg"
#
def dict_gen(generator, args, working_dir):
stub = comp_id + "-" + generator
log_file_name = os.path.join(working_dir, stub + ".log")
status = coot_utils.popen_command(generator, args, [], log_file_name, True)
if (status != 0):
return -1 # bad molecule
else:
pdb_name = os.path.join(working_dir, stub + ".pdb")
cif_name = os.path.join(working_dir, stub + ".cif")
imol = coot.read_pdb(pdb_name)
coot.read_cif_dictionary(cif_name)
return imol
if not os.path.isfile(mmcif_file_name):
return -1 # fail
if coot.enhanced_ligand_coot_p():
# Use pyrogen if we have mogul
#
if use_mogul:
# pyrogen
#
working_dir = coot_utils.get_directory("coot-pyrogen")
args = ["-r", comp_id, "-d", working_dir, "-c", mmcif_file_name]
dict_gen("pyrogen", args, working_dir)
else:
# acedrg
#
working_dir = coot_utils.get_directory("coot-acedrg")
stub = os.path.join(working_dir, comp_id + "-acedrg")
args = ["-r", comp_id, "-c", mmcif_file_name, "-o", stub]
dict_gen("acedrg", args, working_dir)
else:
# acedrg
#
working_dir = coot_utils.get_directory("coot-acedrg")
args = ["-M", "-r", comp_id, "-c", mmcif_file_name]
# BL says:: different args to above?! Wonder why!? Need to check.
dict_gen("acedrg", args, working_dir)
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