def run(args, params=None, out=sys.stdout, log=sys.stderr):
# params keyword is for running program from GUI dialog
if (((len(args) == 0) and (params is None)) or
((len(args) > 0) and ((args[0] == "-h") or (args[0] == "--help")))):
show_usage()
return
# parse command-line arguments
if (params is None):
pcl = iotbx.phil.process_command_line_with_files(
args=args,
master_phil_string=master_phil_str,
pdb_file_def="file_name")
work_params = pcl.work.extract()
# or use parameters defined by GUI
else:
work_params = params
pdb_files = work_params.file_name
work_params.secondary_structure.enabled = True
assert work_params.format in [
"phenix", "phenix_refine", "phenix_bonds", "pymol", "refmac",
"kinemage", "pdb"
]
if work_params.quiet:
out = cStringIO.StringIO()
pdb_combined = iotbx.pdb.combine_unique_pdb_files(file_names=pdb_files)
pdb_structure = iotbx.pdb.input(source_info=None,
lines=flex.std_string(
pdb_combined.raw_records))
cs = pdb_structure.crystal_symmetry()
corrupted_cs = False
if cs is not None:
if [cs.unit_cell(), cs.space_group()].count(None) > 0:
corrupted_cs = True
cs = None
elif cs.unit_cell().volume() < 10:
corrupted_cs = True
cs = None
if cs is None:
if corrupted_cs:
print >> out, "Symmetry information is corrupted, "
else:
print >> out, "Symmetry information was not found, "
print >> out, "putting molecule in P1 box."
from cctbx import uctbx
atoms = pdb_structure.atoms()
box = uctbx.non_crystallographic_unit_cell_with_the_sites_in_its_center(
sites_cart=atoms.extract_xyz(), buffer_layer=3)
atoms.set_xyz(new_xyz=box.sites_cart)
cs = box.crystal_symmetry()
defpars = mmtbx.model.manager.get_default_pdb_interpretation_params()
defpars.pdb_interpretation.automatic_linking.link_carbohydrates = False
defpars.pdb_interpretation.c_beta_restraints = False
defpars.pdb_interpretation.clash_guard.nonbonded_distance_threshold = None
model = mmtbx.model.manager(model_input=pdb_structure,
crystal_symmetry=cs,
pdb_interpretation_params=defpars,
stop_for_unknowns=False)
pdb_hierarchy = model.get_hierarchy()
geometry = model.get_restraints_manager().geometry
if len(pdb_hierarchy.models()) != 1:
raise Sorry("Multiple models not supported.")
ss_from_file = None
if (hasattr(pdb_structure, "extract_secondary_structure")
and not work_params.ignore_annotation_in_file):
ss_from_file = pdb_structure.extract_secondary_structure()
m = manager(pdb_hierarchy=pdb_hierarchy,
geometry_restraints_manager=geometry,
sec_str_from_pdb_file=ss_from_file,
params=work_params.secondary_structure,
verbose=work_params.verbose)
# bp_p = nucleic_acids.get_basepair_plane_proxies(
# pdb_hierarchy,
# m.params.secondary_structure.nucleic_acid.base_pair,
# geometry)
# st_p = nucleic_acids.get_stacking_proxies(
# pdb_hierarchy,
# m.params.secondary_structure.nucleic_acid.stacking_pair,
# geometry)
# hb_b, hb_a = nucleic_acids.get_basepair_hbond_proxies(pdb_hierarchy,
# m.params.secondary_structure.nucleic_acid.base_pair)
result_out = cStringIO.StringIO()
# prefix_scope="refinement.pdb_interpretation"
# prefix_scope=""
prefix_scope = ""
if work_params.format == "phenix_refine":
prefix_scope = "refinement.pdb_interpretation"
elif work_params.format == "phenix":
prefix_scope = "pdb_interpretation"
ss_phil = None
working_phil = m.as_phil_str(master_phil=sec_str_master_phil)
phil_diff = sec_str_master_phil.fetch_diff(source=working_phil)
if work_params.format in ["phenix", "phenix_refine"]:
comment = "\n".join([
"# These parameters are suitable for use in e.g. phenix.real_space_refine",
"# or geometry_minimization. To use them in phenix.refine add ",
"# 'refinement.' if front of pdb_interpretation."
])
if work_params.format == "phenix_refine":
comment = "\n".join([
"# These parameters are suitable for use in phenix.refine only.",
"# To use them in other Phenix tools remove ",
"# 'refinement.' if front of pdb_interpretation."
])
print >> result_out, comment
if (prefix_scope != ""):
print >> result_out, "%s {" % prefix_scope
if work_params.show_all_params:
working_phil.show(prefix=" ", out=result_out)
else:
phil_diff.show(prefix=" ", out=result_out)
if (prefix_scope != ""):
print >> result_out, "}"
elif work_params.format == "pdb":
print >> result_out, m.actual_sec_str.as_pdb_str()
elif work_params.format == "phenix_bonds":
raise Sorry("Not yet implemented.")
elif work_params.format in ["pymol", "refmac", "kinemage"]:
m.show_summary(log=out)
(hb_proxies, hb_angle_proxies, planarity_proxies,
parallelity_proxies) = m.create_all_new_restraints(
pdb_hierarchy=pdb_hierarchy, grm=geometry, log=out)
if hb_proxies.size() > 0:
if work_params.format == "pymol":
file_load_add = "load %s" % work_params.file_name[0]
# surprisingly, pymol handles filenames with whitespaces without quotes...
print >> result_out, file_load_add
bonds_in_format = hb_proxies.as_pymol_dashes(
pdb_hierarchy=pdb_hierarchy)
elif work_params.format == "kinemage":
bonds_in_format = hb_proxies.as_kinemage(
pdb_hierarchy=pdb_hierarchy)
else:
bonds_in_format = hb_proxies.as_refmac_restraints(
pdb_hierarchy=pdb_hierarchy)
print >> result_out, bonds_in_format
if hb_angle_proxies.size() > 0:
if work_params.format == "pymol":
angles_in_format = hb_angle_proxies.as_pymol_dashes(
pdb_hierarchy=pdb_hierarchy)
print >> result_out, angles_in_format
result = result_out.getvalue()
out_prefix = os.path.basename(work_params.file_name[0])
if work_params.output_prefix is not None:
out_prefix = work_params.output_prefix
filename = "%s_ss.eff" % out_prefix
if work_params.format == "pymol":
filename = "%s_ss.pml" % out_prefix
outf = open(filename, "w")
outf.write(result)
outf.close()
print >> out, result
return os.path.abspath(filename)
def run (args, params=None, out=sys.stdout, log=sys.stderr) :
# params keyword is for running program from GUI dialog
if ( ((len(args) == 0) and (params is None)) or
((len(args) > 0) and ((args[0] == "-h") or (args[0] == "--help"))) ):
show_usage()
return
# parse command-line arguments
if (params is None):
pcl = iotbx.phil.process_command_line_with_files(
args=args,
master_phil_string=master_phil_str,
pdb_file_def="file_name")
work_params = pcl.work.extract()
# or use parameters defined by GUI
else:
work_params = params
pdb_files = work_params.file_name
work_params.secondary_structure.enabled=True
assert work_params.format in ["phenix", "phenix_refine", "phenix_bonds",
"pymol", "refmac", "kinemage", "pdb"]
if work_params.quiet :
out = cStringIO.StringIO()
pdb_combined = iotbx.pdb.combine_unique_pdb_files(file_names=pdb_files)
pdb_structure = iotbx.pdb.input(source_info=None,
lines=flex.std_string(pdb_combined.raw_records))
cs = pdb_structure.crystal_symmetry()
corrupted_cs = False
if cs is not None:
if [cs.unit_cell(), cs.space_group()].count(None) > 0:
corrupted_cs = True
cs = None
elif cs.unit_cell().volume() < 10:
corrupted_cs = True
cs = None
if cs is None:
if corrupted_cs:
print >> out, "Symmetry information is corrupted, "
else:
print >> out, "Symmetry information was not found, "
print >> out, "putting molecule in P1 box."
from cctbx import uctbx
atoms = pdb_structure.atoms()
box = uctbx.non_crystallographic_unit_cell_with_the_sites_in_its_center(
sites_cart=atoms.extract_xyz(),
buffer_layer=3)
atoms.set_xyz(new_xyz=box.sites_cart)
cs = box.crystal_symmetry()
from mmtbx.monomer_library import pdb_interpretation, server
import mmtbx
import mmtbx.command_line.geometry_minimization
mon_lib_srv = server.server()
ener_lib = server.ener_lib()
defpars = mmtbx.command_line.geometry_minimization.master_params().extract()
defpars.pdb_interpretation.automatic_linking.link_carbohydrates=False
defpars.pdb_interpretation.c_beta_restraints=False
defpars.pdb_interpretation.clash_guard.nonbonded_distance_threshold=None
processed_pdb_file = pdb_interpretation.process(
mon_lib_srv = mon_lib_srv,
ener_lib = ener_lib,
pdb_inp = pdb_structure,
crystal_symmetry = cs,
params = defpars.pdb_interpretation,
force_symmetry = True)
pdb_hierarchy = processed_pdb_file.all_chain_proxies.pdb_hierarchy
geometry = processed_pdb_file.geometry_restraints_manager()
geometry.pair_proxies(processed_pdb_file.xray_structure().sites_cart())
pdb_hierarchy.atoms().reset_i_seq()
if len(pdb_hierarchy.models()) != 1 :
raise Sorry("Multiple models not supported.")
ss_from_file = None
if hasattr(pdb_structure, "extract_secondary_structure"):
ss_from_file = pdb_structure.extract_secondary_structure()
m = manager(pdb_hierarchy=pdb_hierarchy,
geometry_restraints_manager=geometry,
sec_str_from_pdb_file=ss_from_file,
params=work_params.secondary_structure,
verbose=work_params.verbose)
# bp_p = nucleic_acids.get_basepair_plane_proxies(
# pdb_hierarchy,
# m.params.secondary_structure.nucleic_acid.base_pair,
# geometry)
# st_p = nucleic_acids.get_stacking_proxies(
# pdb_hierarchy,
# m.params.secondary_structure.nucleic_acid.stacking_pair,
# geometry)
# hb_b, hb_a = nucleic_acids.get_basepair_hbond_proxies(pdb_hierarchy,
# m.params.secondary_structure.nucleic_acid.base_pair)
result_out = cStringIO.StringIO()
# prefix_scope="refinement.pdb_interpretation"
# prefix_scope=""
prefix_scope=""
if work_params.format == "phenix_refine":
prefix_scope = "refinement.pdb_interpretation"
elif work_params.format == "phenix":
prefix_scope = "pdb_interpretation"
ss_phil = None
working_phil = m.as_phil_str(master_phil=sec_str_master_phil)
phil_diff = sec_str_master_phil.fetch_diff(source=working_phil)
if work_params.format in ["phenix", "phenix_refine"]:
comment = "\n".join([
"# These parameters are suitable for use in e.g. phenix.real_space_refine",
"# or geometry_minimization. To use them in phenix.refine add ",
"# 'refinement.' if front of pdb_interpretation."])
if work_params.format == "phenix_refine":
comment = "\n".join([
"# These parameters are suitable for use in phenix.refine only.",
"# To use them in other Phenix tools remove ",
"# 'refinement.' if front of pdb_interpretation."])
print >> result_out, comment
if (prefix_scope != "") :
print >> result_out, "%s {" % prefix_scope
if work_params.show_all_params :
working_phil.show(prefix=" ", out=result_out)
else :
phil_diff.show(prefix=" ", out=result_out)
if (prefix_scope != "") :
print >> result_out, "}"
elif work_params.format == "pdb":
print >> result_out, m.actual_sec_str.as_pdb_str()
elif work_params.format == "phenix_bonds" :
raise Sorry("Not yet implemented.")
elif work_params.format in ["pymol", "refmac", "kinemage"] :
m.show_summary(log=out)
(hb_proxies, hb_angle_proxies, planarity_proxies,
parallelity_proxies) = m.create_all_new_restraints(
pdb_hierarchy=pdb_hierarchy,
grm=geometry,
log=out)
if hb_proxies.size() > 0:
if work_params.format == "pymol" :
bonds_in_format = hb_proxies.as_pymol_dashes(
pdb_hierarchy=pdb_hierarchy)
elif work_params.format == "kinemage" :
bonds_in_format = hb_proxies.as_kinemage(
pdb_hierarchy=pdb_hierarchy)
else :
bonds_in_format = hb_proxies.as_refmac_restraints(
pdb_hierarchy=pdb_hierarchy)
print >> result_out, bonds_in_format
result = result_out.getvalue()
filename = "%s_ss.eff" %os.path.basename(work_params.file_name[0])
outf = open(filename, "w")
outf.write(result)
outf.close()
print >> out, result
return os.path.abspath(filename)