def exercise_model_utils () :
pdb_in = get_1yjp_pdb()
residue = pdb_in.hierarchy.only_model().chains()[0].residue_groups()[0].only_atom_group()
sele = pdb_in.hierarchy.atom_selection_cache().selection("resname TYR")
water_sel = building.get_nearby_water_selection(
pdb_hierarchy=pdb_in.hierarchy,
xray_structure=pdb_in.input.xray_structure_simple(),
selection=sele)
assert (list(water_sel.iselection()) == [59, 60, 61, 62, 63])
from mmtbx.monomer_library import idealized_aa
from mmtbx.monomer_library import server
mon_lib_srv = server.server()
ideal_dict = idealized_aa.residue_dict()
for resname, hierarchy in ideal_dict.iteritems() :
residue = hierarchy.only_model().only_chain().only_residue_group().only_atom_group()
result = building.generate_sidechain_clusters(residue, mon_lib_srv)
if (len(result) == 0) :
# no side-chain clusters for UNK as well
assert (residue.resname in ["ALA", "GLY", "UNK"]), residue.resname
# show_chain_resseq_ranges
resids = [ (1,''),(2,''),(2,'A'),(4,''),(5,''),(6,''),(10,'B') ]
import iotbx.pdb.hierarchy
chain = iotbx.pdb.hierarchy.chain(id='A')
for (resseq, icode) in resids :
rg = iotbx.pdb.hierarchy.residue_group(resseq="%4d" % resseq, icode=icode)
chain.append_residue_group(rg)
out = StringIO()
building.show_chain_resseq_ranges(chain.residue_groups(), out=out,
prefix=" ")
assert out.getvalue() == """ chain 'A': 1-2A,4-6,10B\n""", out.getvalue()
def extend_residue(residue, target_atom_group, mon_lib_srv):
"""
Rebuild a sidechain by substituting an ideal amino acid and rotating the
sidechain to match the old conformation as closely as possible.
Limited functionality:
1) Amino-acids only, 2) side chain atoms only.
"""
from iotbx.pdb import hierarchy
from mmtbx.building import generate_sidechain_clusters
import mmtbx.refinement.real_space
tmp_residue = residue.detached_copy()
new_residue = hierarchy.substitute_atom_group(current_group=tmp_residue,
new_group=target_atom_group)
clusters = generate_sidechain_clusters(residue=new_residue,
mon_lib_srv=mon_lib_srv)
scorer = conformation_scorer(old_residue=residue, new_residue=new_residue)
mmtbx.refinement.real_space.torsion_search(
scorer=scorer,
clusters=clusters,
sites_cart=new_residue.atoms().extract_xyz(),
start=0,
stop=360,
step=1)
scorer.apply_final()
return new_residue
def exercise_model_utils () :
pdb_in = get_1yjp_pdb()
residue = pdb_in.hierarchy.only_model().chains()[0].residue_groups()[0].only_atom_group()
sele = pdb_in.hierarchy.atom_selection_cache().selection("resname TYR")
water_sel = building.get_nearby_water_selection(
pdb_hierarchy=pdb_in.hierarchy,
xray_structure=pdb_in.input.xray_structure_simple(),
selection=sele)
assert (list(water_sel.iselection()) == [59, 60, 61, 62, 63])
from mmtbx.monomer_library import idealized_aa
from mmtbx.monomer_library import server
mon_lib_srv = server.server()
ideal_dict = idealized_aa.residue_dict()
for resname, hierarchy in ideal_dict.iteritems() :
residue = hierarchy.only_model().only_chain().only_residue_group().only_atom_group()
result = building.generate_sidechain_clusters(residue, mon_lib_srv)
if (len(result) == 0) :
# no side-chain clusters for UNK as well
assert (residue.resname in ["ALA", "GLY", "UNK"]), residue.resname
# show_chain_resseq_ranges
resids = [ (1,''),(2,''),(2,'A'),(4,''),(5,''),(6,''),(10,'B') ]
import iotbx.pdb.hierarchy
chain = iotbx.pdb.hierarchy.chain(id='A')
for (resseq, icode) in resids :
rg = iotbx.pdb.hierarchy.residue_group(resseq="%4d" % resseq, icode=icode)
chain.append_residue_group(rg)
out = StringIO()
building.show_chain_resseq_ranges(chain.residue_groups(), out=out,
prefix=" ")
assert out.getvalue() == """ chain 'A': 1-2A,4-6,10B\n""", out.getvalue()
def __init__(self,
residue,
sites_cart,
mon_lib_srv,
params,
prev_residue=None,
next_residue=None,
next_next_residue=None,
evaluate_backbone_callback=None):
adopt_init_args(self, locals())
from mmtbx.rotamer import rotamer_eval
from mmtbx.rotamer import ramachandran_eval
import iotbx.pdb
from scitbx.array_family import flex
get_class = iotbx.pdb.common_residue_names_get_class
assert get_class(
residue.resname) == "common_amino_acid", residue.resname
self.rotamer_scorer = rotamer_eval.RotamerEval(data_version="8000")
self.ramachandran_scorer = ramachandran_eval.RamachandranEval()
self.sidechain_clusters = generate_sidechain_clusters(
residue=residue, mon_lib_srv=mon_lib_srv)
self.sites_start = sites_cart.deep_copy()
self.i_seqs_residue = residue.atoms().extract_i_seq()
self.i_seqs_sidechain = flex.size_t()
for atom in self.residue.atoms():
if (not atom.name.strip() in ["C", "N", "H", "CA", "CB", "self"]):
self.i_seqs_sidechain.append(atom.i_seq)
self.i_seqs_primary = flex.size_t()
if (not None in [prev_residue, next_residue]):
self.set_up_backrub()
if (next_next_residue is not None):
self.set_up_shear()
for i_seq in self.shear_i_seqs_primary1:
self.i_seqs_primary.append(i_seq)
for i_seq in self.shear_i_seqs_primary2:
self.i_seqs_primary.append(i_seq)
for i_seq in self.shear_i_seqs_middle:
self.i_seqs_primary.append(i_seq)
else:
for i_seq in self.backrub_i_seqs:
self.i_seqs_primary.append(i_seq)
else:
self.i_seqs_primary = self.i_seqs_residue
def __init__ (self,
residue,
sites_cart,
mon_lib_srv,
params,
prev_residue=None,
next_residue=None,
next_next_residue=None,
evaluate_backbone_callback=None) :
adopt_init_args(self, locals())
from mmtbx.rotamer import rotamer_eval
from mmtbx.rotamer import ramachandran_eval
import iotbx.pdb
from scitbx.array_family import flex
get_class = iotbx.pdb.common_residue_names_get_class
assert get_class(residue.resname) == "common_amino_acid", residue.resname
self.rotamer_scorer = rotamer_eval.RotamerEval(data_version="8000")
self.ramachandran_scorer = ramachandran_eval.RamachandranEval()
self.sidechain_clusters = generate_sidechain_clusters(
residue=residue,
mon_lib_srv=mon_lib_srv)
self.sites_start = sites_cart.deep_copy()
self.i_seqs_residue = residue.atoms().extract_i_seq()
self.i_seqs_sidechain = flex.size_t()
for atom in self.residue.atoms() :
if (not atom.name.strip() in ["C","N","H","CA","CB","self"]) :
self.i_seqs_sidechain.append(atom.i_seq)
self.i_seqs_primary = flex.size_t()
if (not None in [prev_residue, next_residue]) :
self.set_up_backrub()
if (next_next_residue is not None) :
self.set_up_shear()
for i_seq in self.shear_i_seqs_primary1 :
self.i_seqs_primary.append(i_seq)
for i_seq in self.shear_i_seqs_primary2 :
self.i_seqs_primary.append(i_seq)
for i_seq in self.shear_i_seqs_middle :
self.i_seqs_primary.append(i_seq)
else:
for i_seq in self.backrub_i_seqs : self.i_seqs_primary.append(i_seq)
else :
self.i_seqs_primary = self.i_seqs_residue
def extend_residue(residue,
ideal_dict,
mon_lib_srv=None,
hydrogens=False,
match_conformation=True):
"""
Rebuild a sidechain by substituting an ideal amino acid and (optionally)
rotating the sidechain to match the old conformation as closely as possible.
"""
from iotbx.pdb import hierarchy
res_key = residue.resname.lower()
if (hydrogens == True): res_key += "_h"
ideal = ideal_dict[res_key]
tmp_residue = residue.detached_copy()
new_residue = hierarchy.substitute_atom_group(
current_group=tmp_residue,
new_group=ideal.only_model().only_chain().only_residue_group().
only_atom_group(),
backbone_only=True,
is_amino_acid=True, # XXX this could probably be smarter...
exclude_hydrogens=False)
assert (new_residue.resname == residue.resname)
if (match_conformation):
from mmtbx.building import generate_sidechain_clusters
import mmtbx.refinement.real_space
assert (mon_lib_srv is not None)
clusters = generate_sidechain_clusters(residue=new_residue,
mon_lib_srv=mon_lib_srv)
scorer = conformation_scorer(old_residue=residue,
new_residue=new_residue)
mmtbx.refinement.real_space.torsion_search(
scorer=scorer,
clusters=clusters,
sites_cart=new_residue.atoms().extract_xyz(),
start=0,
stop=360,
step=1)
scorer.apply_final()
return new_residue
def extend_residue (residue,
ideal_dict,
mon_lib_srv=None,
hydrogens=False,
match_conformation=True) :
"""
Rebuild a sidechain by substituting an ideal amino acid and (optionally)
rotating the sidechain to match the old conformation as closely as possible.
"""
from iotbx.pdb import hierarchy
res_key = residue.resname.lower()
if (hydrogens == True) : res_key += "_h"
ideal = ideal_dict[res_key]
tmp_residue = residue.detached_copy()
new_residue = hierarchy.substitute_atom_group(
current_group=tmp_residue,
new_group=ideal.only_model().only_chain().only_residue_group().only_atom_group(),
backbone_only=True,
is_amino_acid=True, # XXX this could probably be smarter...
exclude_hydrogens=False)
assert (new_residue.resname == residue.resname)
if (match_conformation) :
from mmtbx.building import generate_sidechain_clusters
import mmtbx.refinement.real_space
assert (mon_lib_srv is not None)
clusters = generate_sidechain_clusters(residue=new_residue,
mon_lib_srv=mon_lib_srv)
scorer = conformation_scorer(
old_residue=residue,
new_residue=new_residue)
mmtbx.refinement.real_space.torsion_search(
scorer=scorer,
clusters=clusters,
sites_cart=new_residue.atoms().extract_xyz(),
start=0, stop=360, step=1)
scorer.apply_final()
return new_residue