def get_pdb_hierarchy_from_restraints(code):
from mmtbx.monomer_library import server
from iotbx import pdb
mon_lib_server = server.server()
path = mon_lib_server.get_comp_comp_id_direct(code, return_filename=True)
cif_obj = server.read_cif(path)
ligand_inp = pdb.pdb_input(source_info="Model from %s" % path,
lines=flex.split_lines(""))
ligand_hierarchy = ligand_inp.construct_hierarchy()
model = pdb.hierarchy.model()
chain = pdb.hierarchy.chain()
chain.id = 'Z'
rg = pdb.hierarchy.residue_group()
ag = pdb.hierarchy.atom_group()
for block, loops in cif_obj.blocks.items():
if block == 'comp_list': continue
for loop in loops.iterloops():
for row in loop.iterrows():
if '_chem_comp_atom.comp_id' not in row: break
ag.resname = row['_chem_comp_atom.comp_id']
atom = pdb.hierarchy.atom()
atom.name = row['_chem_comp_atom.atom_id']
atom.element = '%2s' % row['_chem_comp_atom.type_symbol']
atom.xyz = (
float(row['_chem_comp_atom.x']),
float(row['_chem_comp_atom.y']),
float(row['_chem_comp_atom.z']),
)
ag.append_atom(atom)
rg.append_atom_group(ag)
chain.append_residue_group(rg)
model.append_chain(chain)
ligand_hierarchy.append_model(model)
ligand_hierarchy.atoms().reset_i_seq()
return ligand_hierarchy
def morph_models (params, out=None, debug=False) :
assert len(params.morph.pdb_file) > 1
assert (len(params.morph.frames) == (len(params.morph.pdb_file) - 1))
if (out is None) : out = sys.stdout
from mmtbx.monomer_library import pdb_interpretation, server
from iotbx import file_reader
pdb_hierarchies = []
for pdb_file in params.morph.pdb_file :
pdb_in = file_reader.any_file(pdb_file, force_type="pdb")
pdb_in.check_file_type("pdb")
hierarchy = pdb_in.file_object.hierarchy
pdb_hierarchies.append(hierarchy)
new_pdb = homogenize_structures(
pdb_hierarchies=pdb_hierarchies,
delete_waters=params.morph.delete_waters,
debug=debug)
mon_lib_srv = server.server()
ener_lib = server.ener_lib()
for cif_file in params.morph.cif_file :
print "Loading CIF file %s" % cif_file
cif_object = server.read_cif(file_name=cif_file)
mon_lib_serv.process_cif_object(cif_object=cif_object, file_name=cif_file)
ener_lib.process_cif_object(cif_object=cif_object, file_name=cif_file)
if (params.morph.minimization.interpolate_dihedrals) :
params.pdb_interpretation.peptide_link.discard_psi_phi = False
processed_pdb_file = pdb_interpretation.process(
mon_lib_srv=mon_lib_srv,
ener_lib=ener_lib,
params=params.pdb_interpretation,
pdb_inp=new_pdb[0],
substitute_non_crystallographic_unit_cell_if_necessary=True)
all_chain_proxies = processed_pdb_file.all_chain_proxies
static_coords = [ all_chain_proxies.pdb_hierarchy.atoms().extract_xyz() ]
for pdb_inp in new_pdb[1:] :
sites = pdb_inp.atoms().extract_xyz()
static_coords.append(sites)
if (params.morph.fitting.align_atoms is not None) :
print >> out, "Superposing on initial structure..."
selection_cache = all_chain_proxies.pdb_hierarchy.atom_selection_cache()
selection = selection_cache.selection(params.morph.fitting.align_atoms)
if (selection.count(True) == 0) :
raise Sorry("No atoms in alignment selection!")
i_ref = params.morph.fitting.reference_structure
sites_fixed = static_coords[i_ref]
j = 0
while (j < len(static_coords)) :
if (j != i_ref) :
sites_moving = static_coords[j]
assert (len(sites_moving) == len(sites_fixed) > 0)
if (params.morph.fitting.sieve_fit) :
from scitbx.math import superpose
lsq_fit = superpose.sieve_fit(
sites_fixed=sites_fixed,
sites_moving=sites_moving,
selection=selection)
sites_moving_new = lsq_fit.r.elems * sites_moving + lsq_fit.t.elems
else :
sites_moving_new = fit_sites(
sites_fixed=sites_fixed,
sites_moving=sites_moving,
selection=selection)
assert (sites_moving_new.size() == sites_moving.size())
static_coords[j] = sites_moving_new
j += 1
print >> out, "Ready to morph"
morphs = []
restraints_manager = processed_pdb_file.geometry_restraints_manager()
for i in range(len(params.morph.pdb_file) - 1) :
morph = adiabatic_mapping(
pdb_hierarchy=all_chain_proxies.pdb_hierarchy,
restraints_manager=restraints_manager,
start_coords = static_coords[i],
end_coords = static_coords[i+1],
params = params.morph.minimization,
nsteps = params.morph.frames[i],
out=out)
morphs.append(morph)
serial = 1
if (params.morph.output_directory is not None) :
output_base = os.path.join(params.morph.output_directory,
params.morph.output_prefix)
else :
output_base = params.morph.output_prefix
for i, morph in enumerate(morphs) :
serial = morph.write_pdb_files(
output_base=output_base,
serial=serial,
serial_format=params.morph.serial_format,
pause=params.morph.pause,
pause_at_end=(i == (len(morphs) - 1)),
log=out)
f = open("%s.pml" % output_base, "w")
for i in range(1, serial) :
format_base = "%s_%s" % (output_base, params.morph.serial_format)
print >> f, "load %s.pdb, morph" % (format_base % i)
f.close()
print >> out, "PyMOL script is %s.pml" % output_base