def make_fmet_from_met(session, residue):
err_string = "make_fmet_from_met() is only applicable to N-terminal methionine residues!"
if residue.name != 'MET':
raise TypeError(err_string)
n = residue.find_atom('N')
if n is None:
raise TypeError('Missing N atom! Is your residue complete?')
for nb in n.neighbors:
if nb.residue != residue:
raise TypeError(err_string)
if nb.element.name == 'H':
nb.delete()
from chimerax.mmcif import find_template_residue
import numpy
fme = find_template_residue(session, 'FME')
ref_atoms = ('C', 'CA', 'N')
r_coords = numpy.array([residue.find_atom(a).coord for a in ref_atoms])
t_coords = numpy.array([fme.find_atom(a).coord for a in ref_atoms])
from chimerax.geometry import align_points
tf, rms = align_points(t_coords, r_coords)
from chimerax.atomic.struct_edit import add_atom
atom_pairs = (('N', 'H'), ('N', 'CN'), ('CN', 'O1'), ('CN', 'HCN'))
for (bname, aname) in atom_pairs:
ta = fme.find_atom(aname)
add_atom(aname,
ta.element,
residue,
tf * ta.coord,
bonded_to=residue.find_atom(bname))
residue.name = 'FME'
def get_ccd_template_and_name(session, tname):
from ..openmm.amberff.template_utils import template_name_to_ccd_name
from chimerax import mmcif
ccd_name, extra_info = template_name_to_ccd_name(tname)
if ccd_name is None:
return (None, '')
try:
tmpl = mmcif.find_template_residue(session, ccd_name)
except ValueError:
return (None, "No CCD template found")
description = tmpl.description
if extra_info is not None:
description += ', ' + extra_info
return (tmpl, description)
def match_ff_templates_to_ccd_templates(session, forcefield, ccd_names):
'''
For each template in the MD forcefield, try to find the CCD template that
most closely matches it. This will take a long time!
'''
from chimerax.isolde.graph import make_graph_from_residue_template
from chimerax import mmcif
ff_templates = forcefield._templates
best_matches = {}
ccd_graphs = {}
small_ccd_templates = []
for name in ccd_names:
ccd_template = mmcif.find_template_residue(session, name)
if len(ccd_template.atoms) > 2:
ccd_graphs[name] = make_graph_from_residue_template(ccd_template)
else:
small_ccd_templates.append(ccd_template)
for tname, template in ff_templates.items():
best_score = -1000
if len(template.atoms) < 4:
best_match, score = match_small_ff_template_to_ccd_templates(
template, small_ccd_templates)
best_matches[tname] = (best_match, score)
continue
tgraph = template.graph
num_heavy_atoms = len(tgraph.labels[tgraph.labels != 1])
for ccd_name, ccd_graph in ccd_graphs.items():
ccd_heavy_atoms = len(ccd_graph.labels[ccd_graph.labels != 1])
if abs(ccd_heavy_atoms - num_heavy_atoms) > 2:
continue
fti, cti, _ = tgraph.maximum_common_subgraph(ccd_graph)
score = len(fti) * 3 - len(tgraph.labels) - len(ccd_graph.labels)
if score > best_score:
best_matches[tname] = ([ccd_name], score)
best_score = score
elif score == best_score:
best_matches[tname][0].append(ccd_name)
print('Best matches for {}: {}'.format(
tname, ', '.join(best_matches[tname][0])),
flush=True)
return best_matches
def fix_residue_to_match_md_template(session,
residue,
md_template,
cif_template=None,
rename=False):
'''
For the given residue, add/remove atoms as necessary to match the given MD
template. If no explicit cif_template argument is given, an attempt will be
made to find a match using ISOLDE's database. If no CIF template is found,
corrections to the residue will be limited to deleting excess atoms.
'''
import numpy
from chimerax.isolde.openmm.amberff.template_utils import (
template_name_to_ccd_name, match_template_atoms_to_ccd_atoms)
if cif_template is None:
ccd_name, _ = template_name_to_ccd_name(md_template.name)
if ccd_name is not None:
from chimerax import mmcif
try:
cif_template = mmcif.find_template_residue(session, ccd_name)
except ValueError:
pass
else:
ccd_name = cif_template.name
if cif_template is None:
return trim_residue_to_md_template(residue, md_template)
template_indices, ccd_indices = match_template_atoms_to_ccd_atoms(
session, md_template, ccd_name)
fix_residue_from_template(residue,
cif_template,
template_indices=ccd_indices)
from chimerax.atomic import Atoms
ratoms = Atoms(
[residue.find_atom(cif_template.atoms[i].name) for i in ccd_indices])
residue_indices = residue.atoms.indices(ratoms)
#template_extra_atoms = [md_template.atoms[i] for i in template_extra_indices]
add_missing_md_template_atoms(session, residue, md_template,
residue_indices, template_indices)
def match_template_atoms_to_ccd_atoms(session,
template,
ccd_name=None,
timeout=5):
if ccd_name is None:
ccd_name, _ = template_name_to_ccd_name(template.name)
if ccd_name is None:
raise TypeError('MD template {} has no match in the CCD!'.format(
template.name))
matches = _template_atom_to_ccd_atom_cache.get((template.name, ccd_name))
if matches is not None:
return matches
from chimerax import mmcif
ccd_template = mmcif.find_template_residue(session, ccd_name)
if len(template.atoms) > 2:
# Try by name first (typically very fast)
from chimerax.isolde.graph import make_graph_from_residue_template
tgraph = template.graph
ccd_graph = make_graph_from_residue_template(ccd_template)
ti, ci, timed_out = tgraph.maximum_common_subgraph(ccd_graph,
big_first=True,
timeout=timeout)
if timed_out:
ti_2, ci_2, to_2 = tgraph.maximum_common_subgraph(ccd_graph,
timeout=timeout)
if len(ti_2) > len(ti):
ti = ti_2
ci = ci_2
if to_2:
warn_str = (
'Graph matching of MD template {} to CCD template {}'
' timed out. Match may not be optimal').format(
template.name, ccd_name)
session.logger.warning(warn_str)
_template_atom_to_ccd_atom_cache[(template.name, ccd_name)] = (ti, ci)
return ti, ci
import numpy
ti = []
ci = []
for i, a in enumerate(template.atoms):
ti.append(i)
candidates = []
for j, ca in enumerate(ccd_template.atoms):
if j not in ci:
if ca.element.number == a.element.atomic_number:
candidates.append((j, ca))
if not len(candidates):
raise TypeError(
'MD Template {} does not match CCD template {}!'.format(
template.name, ccd_template.name))
elif len(candidates) == 1:
ci.append(candidates[0][0])
else:
# Check to see if we can distinguish by name
name_match = False
for j, ca in candidates:
if ca.name == a.name:
name_match = True
candidates.append(j)
break
if not name_match:
# Just pick the first
ci.append(candidates[0][0])
ti = numpy.array(ti)
ci = numpy.array(ci)
_template_atom_to_ccd_atom_cache[(template.name, ccd_name)] = (ti, ci)
return ti, ci
def replace_residue(session, residue, new_residue_name):
block_if_sim_running(session)
from chimerax.core.errors import UserError
from chimerax.isolde.cmd import isolde_start
isolde_start(session)
from chimerax.atomic import Residues
if isinstance(residue, Residues):
if len(residue) != 1:
raise UserError('Must have a single residue selected!')
residue = residue[0]
if len(residue.neighbors):
raise UserError(
'Replacement by graph matching is currently only '
'supported for ligands with no covalent bonds to other residues!')
from ..template_utils import (fix_residue_from_template,
fix_residue_to_match_md_template)
from chimerax import mmcif
try:
cif_template = mmcif.find_template_residue(session, new_residue_name)
except:
err_str = (
'Could not find a mmCIF template for residue name {}. '
'For novel residues not in the Chemical Components Dictionary, '
'you will need to provide this first.').format(new_residue_name)
raise UserError(err_str)
fix_residue_from_template(residue,
cif_template,
rename_residue=True,
match_by='element')
ff = session.isolde.forcefield_mgr[session.isolde.sim_params.forcefield]
ligand_db = session.isolde.forcefield_mgr.ligand_db(
session.isolde.sim_params.forcefield)
from chimerax.isolde.openmm.openmm_interface import find_residue_templates
from chimerax.atomic import Residues
tdict = find_residue_templates(Residues([residue]),
ff,
ligand_db=ligand_db,
logger=session.logger)
md_template_name = tdict.get(0)
if md_template_name is not None:
fix_residue_to_match_md_template(session,
residue,
ff._templates[md_template_name],
cif_template=cif_template)
from chimerax.atomic import Atoms, Atom
chiral_centers = Atoms(
[a for a in residue.atoms if residue.ideal_chirality(a.name) != 'N'])
if len(chiral_centers):
warn_str = (
'Rebuilt ligand {} has chiral centres at atoms {} '
'(highlighted). Since the current algorithm used to match topologies '
'is not chirality aware, you should check these sites carefully to '
'ensure they are sensible. If in doubt, it is best to delete with '
'"del #{}/{}:{}{}" and replace with "isolde add ligand {}".'
).format(residue.name, ','.join(chiral_centers.names),
residue.structure.id_string, residue.chain_id, residue.number,
residue.insertion_code, residue.name)
session.selection.clear()
chiral_centers.selected = True
chiral_centers.draw_modes = Atom.BALL_STYLE
from chimerax.isolde.view import focus_on_selection
focus_on_selection(session, chiral_centers)
session.logger.warning(warn_str)
def _prep_add(session,
structures,
unknowns_info,
template,
need_all=False,
**prot_schemes):
global _serial
_serial = None
atoms = []
type_info_for_atom = {}
naming_schemas = {}
idatm_type = {} # need this later; don't want a recomp
hydrogen_totals = {}
# add missing OXTs of "real" C termini;
# delete hydrogens of "fake" N termini after protonation
# and add a single "HN" back on, using same dihedral as preceding residue;
# delete extra hydrogen of "fake" C termini after protonation
logger = session.logger
real_N, real_C, fake_N, fake_C = determine_termini(session, structures)
logger.info("Chain-initial residues that are actual N"
" termini: %s" % ", ".join([str(r) for r in real_N]))
logger.info("Chain-initial residues that are not actual N"
" termini: %s" % ", ".join([str(r) for r in fake_N]))
logger.info("Chain-final residues that are actual C"
" termini: %s" % ", ".join([str(r) for r in real_C]))
logger.info("Chain-final residues that are not actual C"
" termini: %s" % ", ".join([str(r) for r in fake_C]))
for rc in real_C:
complete_terminal_carboxylate(session, rc)
# ensure that N termini are protonated as N3+ (since Npl will fail)
from chimerax.atomic import Sequence
for nter in real_N + fake_N:
n = nter.find_atom("N")
if not n:
continue
# if residue wasn't templated, leave atom typing alone
if Sequence.protein3to1(n.residue.name) == 'X':
continue
if not (n.residue.name == "PRO" and n.num_bonds >= 2):
n.idatm_type = "N3+"
coordinations = {}
for struct in structures:
pbg = struct.pseudobond_group(struct.PBG_METAL_COORDINATION,
create_type=None)
if not pbg:
continue
for pb in pbg.pseudobonds:
for a in pb.atoms:
if not need_all and a.structure not in structures:
continue
if not a.element.is_metal:
coordinations.setdefault(a, []).append(pb.other_atom(a))
remaining_unknowns = {}
type_info_class = type_info['H'].__class__
from chimerax.atomic import Residue
for struct in structures:
for atom in struct.atoms:
if atom.element.number == 0:
res = atom.residue
struct.delete_atom(atom)
idatm_lookup = {}
if template:
template_lookup = {}
from chimerax.atomic import TmplResidue
get_template = TmplResidue.get_template
for res in struct.residues:
if get_template(res.name):
continue
try:
exemplar = template_lookup[res.name]
except KeyError:
from chimerax.mmcif import find_template_residue
tmpl = find_template_residue(session, res.name)
if not tmpl:
continue
from chimerax.atomic import AtomicStructure
s = AtomicStructure(session)
r = exemplar = template_lookup[res.name] = s.new_residue(
res.name, 'A', 1)
atom_map = {}
for ta in tmpl.atoms:
if ta.element.number > 1:
a = s.new_atom(ta.name, ta.element)
a.coord = ta.coord
r.add_atom(a)
atom_map[ta] = a
for tnb in ta.neighbors:
if tnb in atom_map:
s.new_bond(a, atom_map[tnb])
for a in res.atoms:
ea = exemplar.find_atom(a.name)
if ea:
a.idatm_type = ea.idatm_type
for r in template_lookup.values():
r.structure.delete()
template_lookup.clear()
for atom in struct.atoms:
atom_type = atom.idatm_type
idatm_type[atom] = atom_type
if atom_type in type_info:
# don't want to ask for idatm_type in middle
# of hydrogen-adding loop (since that will
# force a recomp), so remember here
type_info_for_atom[atom] = type_info[atom_type]
# if atom is in standard residue but has missing bonds to
# heavy atoms, skip it instead of incorrectly protonating
# (or possibly throwing an error if e.g. it's planar)
# also
# UNK/N residues will be missing some or all of their side-chain atoms, so
# skip atoms that would otherwise be incorrectly protonated due to their
# missing neighbors
truncated = \
atom.is_missing_heavy_template_neighbors(no_template_okay=True) \
or \
(atom.residue.name in ["UNK", "N"] and atom.residue.polymer_type != Residue.PT_NONE
and unk_atom_truncated(atom)) \
or \
(atom.residue.polymer_type == Residue.PT_NUCLEIC and atom.name == "P"
and atom.num_explicit_bonds < 4)
if truncated:
session.logger.warning(
"Not adding hydrogens to %s because it is missing heavy-atom"
" bond partners" % atom)
type_info_for_atom[atom] = type_info_class(
4, atom.num_bonds, atom.name)
else:
atoms.append(atom)
# sulfonamide nitrogens coordinating a metal
# get an additional hydrogen stripped
if coordinations.get(atom, []) and atom.element.name == "N":
if "Son" in [nb.idatm_type for nb in atom.neighbors]:
orig_ti = type_info[atom_type]
type_info_for_atom[atom] = orig_ti.__class__(
orig_ti.geometry, orig_ti.substituents - 1,
orig_ti.description)
continue
if atom in unknowns_info:
type_info_for_atom[atom] = unknowns_info[atom]
atoms.append(atom)
continue
remaining_unknowns.setdefault(atom.residue.name,
set()).add(atom.name)
# leave remaining unknown atoms alone
type_info_for_atom[atom] = type_info_class(4, atom.num_bonds,
atom.name)
for rname, atom_names in remaining_unknowns.items():
names_text = ", ".join([nm for nm in atom_names])
atom_text, obj_text = ("atoms",
"them") if len(atom_names) > 1 else ("atom",
"it")
logger.warning(
"Unknown hybridization for %s (%s) of residue type %s;"
" not adding hydrogens to %s" %
(atom_text, names_text, rname, obj_text))
naming_schemas.update(
determine_naming_schemas(struct, type_info_for_atom))
if need_all:
from chimerax.atomic import AtomicStructure
for struct in [
m for m in session.models if isinstance(m, AtomicStructure)
]:
if struct in structures:
continue
for atom in struct.atoms:
idatm_type[atom] = atom.idatm_type
if atom.idatm_type in type_info:
type_info_for_atom[atom] = type_info[atom.idatm_type]
for atom in atoms:
if atom not in type_info_for_atom:
continue
bonding_info = type_info_for_atom[atom]
total_hydrogens = bonding_info.substituents - atom.num_bonds
for bonded in atom.neighbors:
if bonded.element.number == 1:
total_hydrogens += 1
hydrogen_totals[atom] = total_hydrogens
schemes = {}
# HIS and CYS treated as 'unspecified'; use built-in typing
for scheme_type, res_names, res_check, typed_atoms in [
('his', ["HID", "HIE", "HIP"], None, []),
('asp', asp_res_names, _asp_check, asp_prot_names),
('glu', glu_res_names, _glu_check, glu_prot_names),
('lys', ["LYS", "LYN"], _lys_check, ["NZ"]),
('cys', ["CYM"], _cys_check, ["SG"])
]:
scheme = prot_schemes.get(scheme_type + '_scheme', None)
if scheme is None:
by_name = True
scheme = {}
else:
by_name = False
if not scheme:
for s in structures:
for r in s.residues:
if r.name in res_names and res_check and res_check(r):
if by_name:
scheme[r] = r.name
elif scheme_type != 'his':
scheme[r] = res_names[0]
# unset any explicit typing...
for ta in typed_atoms:
a = r.find_atom(ta)
if a:
a.idatm_type = None
else:
for r in scheme.keys():
if res_check and not res_check(r, scheme[r]):
del scheme[r]
schemes[scheme_type] = scheme
# create dictionary keyed on histidine residue with value of another
# dictionary keyed on the nitrogen atoms with boolean values: True
# equals should be protonated
his_Ns = {}
for r, protonation in schemes["his"].items():
delta = r.find_atom("ND1")
epsilon = r.find_atom("NE2")
if delta is None or epsilon is None:
# find the ring, etc.
rings = r.structure.rings()
for ring in rings:
if r in rings.atoms.residues:
break
else:
continue
# find CG by locating CB-CG bond
ring_bonds = ring.bonds
for ra in ring.atoms:
if ra.element.name != "C":
continue
for ba, b in zip(ra.neighbors, ra.bonds):
if ba.element.name == "C" and b not in ring_bonds:
break
else:
continue
break
else:
continue
nitrogens = [a for a in ring.atoms if a.element.name == "N"]
if len(nitrogens) != 2:
continue
if ra in nitrogens[0].neighbors:
delta, epsilon = nitrogens
else:
epsilon, delta = nitrogens
if protonation == "HID":
his_Ns.update({delta: True, epsilon: False})
elif protonation == "HIE":
his_Ns.update({delta: False, epsilon: True})
elif protonation == "HIP":
his_Ns.update({delta: True, epsilon: True})
else:
continue
for n, do_prot in his_Ns.items():
if do_prot:
type_info_for_atom[n] = type_info["Npl"]
n.idatm_type = idatm_type[n] = "Npl"
else:
type_info_for_atom[n] = type_info["N2"]
n.idatm_type = idatm_type[n] = "N2"
for r, protonation in schemes["asp"].items():
_handle_acid_protonation_scheme_item(r, protonation, asp_res_names,
asp_prot_names, type_info,
type_info_for_atom)
for r, protonation in schemes["glu"].items():
_handle_acid_protonation_scheme_item(r, protonation, glu_res_names,
glu_prot_names, type_info,
type_info_for_atom)
for r, protonation in schemes["lys"].items():
nz = r.find_atom("NZ")
if protonation == "LYS":
it = 'N3+'
else:
it = 'N3'
ti = type_info[it]
if nz is not None:
type_info_for_atom[nz] = ti
# avoid explicitly setting type if possible
if nz.idatm_type != it:
nz.idatm_type = it
for r, protonation in schemes["cys"].items():
sg = r.find_atom("SG")
if protonation == "CYS":
it = 'S3'
else:
it = 'S3-'
ti = type_info[it]
if sg is not None:
type_info_for_atom[sg] = ti
# avoid explicitly setting type if possible
if sg.idatm_type != it:
sg.idatm_type = it
return atoms, type_info_for_atom, naming_schemas, idatm_type, \
hydrogen_totals, his_Ns, coordinations, fake_N, fake_C
def add_amino_acid_residue(model,
resname,
prev_res=None,
next_res=None,
chain_id=None,
number=None,
center=None,
insertion_code=' ',
add_b_factor=0,
occupancy=1,
phi=-135,
psi=135):
session = model.session
if (not chain_id or not number or center is None) and (not prev_res
and not next_res):
raise TypeError('If no anchor residues are specified, chain ID, '
'number and center must be provided!')
if prev_res and next_res:
raise TypeError('Cannot specify both previous and next residues!')
other_atom = None
insertion_point = None
import numpy
if prev_res:
ref_res = prev_res
b_factor = prev_res.atoms[numpy.in1d(
prev_res.atoms.names,
('N', 'CA', 'C', 'O', 'CB'))].bfactors.mean() + add_b_factor
pri = model.residues.index(prev_res)
if pri > 0 and pri < len(model.residues) - 1:
insertion_point = model.residues[pri + 1]
catom = prev_res.find_atom('C')
for n in catom.neighbors:
if n.residue != prev_res:
raise TypeError(
'This residue already has another bonded to its '
'C terminus!')
if chain_id is not None:
session.logger.warning(
'AddAA: chain_id argument is ignored when adding to an existing residue.'
)
chain_id = prev_res.chain_id
oxt = prev_res.find_atom('OXT')
if oxt is not None:
oxt.delete()
elif next_res:
ref_res = next_res
b_factor = next_res.atoms[numpy.in1d(
next_res.atoms.names,
('N', 'CA', 'C', 'O', 'CB'))].bfactors.mean() + add_b_factor
insertion_point = next_res
natom = next_res.find_atom('N')
for n in natom.neighbors:
if n.residue != next_res:
raise TypeError(
'This residue already has another bonded to its '
'N terminus!')
if chain_id is not None:
session.logger.warning(
'AddAA: chain_id argument is ignored when adding to an existing residue.'
)
chain_id = next_res.chain_id
for hname in ('H2', 'H3'):
h = next_res.find_atom(hname)
if h is not None:
h.delete()
h = next_res.find_atom('H1')
if h is not None:
h.name = 'H'
if next_res.name == 'PRO':
h = next_res.find_atom('H')
if h:
h.delete()
if number is None:
if prev_res:
number = prev_res.number + 1
elif next_res:
number = next_res.number - 1
from chimerax import mmcif
tmpl = mmcif.find_template_residue(session, resname)
from .place_ligand import new_residue_from_template
import numpy
# delete extraneous atoms
r = new_residue_from_template(model,
tmpl,
chain_id, [0, 0, 0],
number,
insert_code=insertion_code,
b_factor=b_factor,
precedes=insertion_point)
r.atoms[numpy.in1d(r.atoms.names,
['OXT', 'HXT', 'H2', 'H1', 'HN1', 'HN2'])].delete()
# Translate and rotate residue to (roughly) match the desired position
if not next_res and not prev_res:
r.atoms.coords += numpy.array(center) - r.atoms.coords.mean(axis=0)
b_factor = max(add_b_factor, 5)
else:
from chimerax.geometry import align_points
from chimerax.atomic.struct_edit import add_bond
if prev_res:
correct_o_position(prev_res, psi)
add_bond(r.find_atom('N'), prev_res.find_atom('C'))
n_pos = _find_next_N_position(prev_res)
ca_pos = _find_next_CA_position(n_pos, prev_res)
c_pos = _find_next_C_position(ca_pos, n_pos, prev_res, phi)
target_coords = numpy.array([n_pos, ca_pos, c_pos])
align_coords = numpy.array(
[r.find_atom(a).coord for a in ['N', 'CA', 'C']])
elif next_res:
add_bond(r.find_atom('C'), next_res.find_atom('N'))
c_pos = _find_prev_C_position(next_res, psi)
ca_pos = _find_prev_CA_position(c_pos, next_res)
#o_pos = _find_prev_O_position(c_pos, next_res)
n_pos = _find_prev_N_position(c_pos, ca_pos, next_res, psi)
target_coords = numpy.array([c_pos, ca_pos, n_pos])
align_coords = numpy.array(
[r.find_atom(a).coord for a in ['C', 'CA', 'N']])
tf = align_points(align_coords, target_coords)[0]
r.atoms.coords = tf * r.atoms.coords
correct_o_position(r, psi)
if r.name in ('GLU', 'ASP'):
fix_amino_acid_protonation_state(r)
if r.name == 'PRO':
r.atoms[r.atoms.names == 'H'].delete()
r.atoms.bfactors = b_factor
r.atoms.occupancies = occupancy
from . import copy_atom_style_from
copy_atom_style_from(session, r.atoms, ref_res)
model.atoms.selecteds = False
r.atoms.selecteds = True
return r
def find_incorrect_residues(session, model, heavy_atoms_only=True):
from chimerax.atomic import Residue, TmplResidue
from chimerax import mmcif
residues = model.residues
questionable = []
for r in residues:
pt = r.polymer_type
tmpl = None
if pt in (Residue.PT_AMINO, Residue.PT_NUCLEIC):
start = True
end = True
if pt == Residue.PT_AMINO:
fa = r.find_atom('N')
la = r.find_atom('C')
else:
fa = r.find_atom('P')
la = r.find_atom("O3'")
if fa is not None:
for fn in fa.neighbors:
if fn.residue != r:
start = False
break
if la is not None:
for ln in la.neighbors:
if ln.residue != r:
end = False
break
try:
tmpl = TmplResidue.get_template(r.name, start=start, end=end)
except ValueError:
tmpl = None
if tmpl is None:
if r.name not in _fetched_templates:
session.logger.info(
'Fetching CCD definition for residue {} {}{}'.format(
r.name, r.chain_id, r.number))
try:
tmpl = mmcif.find_template_residue(session, r.name)
_fetched_templates.add(r.name)
except ValueError:
session.logger.warning(
'Template {} not found in the Chemical Components Dictionary'
.format(r.name))
continue
if heavy_atoms_only:
ra_names = set(r.atoms[r.atoms.element_names != 'H'].names)
ta_names = set(
[a.name for a in tmpl.atoms if a.element.name != 'H'])
else:
ra_names = set(r.atoms.names)
ta_names = set([a.name for a in tmpl.atoms])
ra_residuals = ra_names.difference(ta_names)
ta_residuals = ta_names.difference(ra_names)
if len(ta_residuals):
if end:
if pt == Residue.PT_AMINO:
print(
'C-terminal residue {} {}{}; ra_residuals: {}; ta_residuals: {}'
.format(r.name, r.chain_id, r.number, ra_residuals,
ta_residuals))
if pt == Residue.PT_AMINO and not len(
ra_residuals) and ta_residuals == set(('OXT', )):
# Dangling C-terminal peptide. Allow.
continue
elif pt == Residue.PT_NUCLEIC and not heavy_atoms_only and not len(
ra_residuals) and ta_residuals == set(("HO5'", )):
# Dangling 5' end. Allow
continue
if start and not heavy_atoms_only:
if pt == Residue.PT_AMINO and ta_residuals == set(
('H', )) and ra_residuals == set(('H1', 'H2', 'H3')):
# Dangling N-terminal peptide. Allow
continue
elif pt == Residue.PT_NUCLEIC and ta_residuals == set(
("HO3'", )):
# Dangling 3' end. Allow.
continue
questionable.append(r)
return questionable
def place_ligand(session,
ligand_id,
model=None,
position=None,
bfactor=None,
chain=None,
distance_cutoff=8.0,
sim_settle=False,
use_md_template=True,
md_template_name=None):
'''
Place a ligand at the given position, or the current centre of
rotation if no :attr:`position` is specified. If the :attr:`bfactor` or
:attr:`chain` arguments are not specified, the water will be assigned the
missing properties based on the nearest residue within
:attr:`distance_cutoff` of :attr:`position`, with the assigned B-factor
being (average B-factor of nearest residue)+5. If :attr:`sim_settle` is
True, a small local simulation will automatically start to settle the
ligand into position.
For residues of more than three atoms, if you have loaded an MD template for
the residue (with matching residue name), any mis-matches between atoms in
the CIF and MD templates will be automatically corrected as long as the
changes only involve removing atoms from the CIF template and/or adding
atoms that are directly connected to a single atom in the CIF template. The
most common scenario where this arises is where the protonation state of the
CIF template is different from that of the MD template.
Note that at this stage no attempt is made at a preliminary fit to the
density, or to avoid clashes: the ligand is simply placed at the given
position with coordinates defined by the template in the Chemical
Components Dictionary. Except for small, rigid ligands the use of
:attr:`sim_settle`=True is inadvisable. If the ligand as placed clashes
badly with the existing model, the best approach is to run the command
`isolde ignore ~selAtoms` then start a simulation (which will involve *only*
the new residue) to pull it into position (you may want to use pins where
necessary). Once satisfied that there are no severe clashes, stop the
simulation and run `isolde ~ignore` to reinstate all atoms for simulation
purposes, and continue with your model building.
'''
from chimerax.geometry import find_closest_points
from chimerax import mmcif
from chimerax.core.errors import UserError
if hasattr(session, 'isolde') and session.isolde.simulation_running:
raise UserError('Cannot add atoms when a simulation is running!')
if model is None:
if hasattr(session,
'isolde') and session.isolde.selected_model is not None:
model = session.isolde.selected_model
else:
raise UserError(
'If model is not specified, ISOLDE must be started '
'with a model loaded')
if position is None:
position = session.view.center_of_rotation
matoms = model.atoms
if bfactor is None or chain is None:
_, _, i = find_closest_points([position], matoms.coords,
distance_cutoff)
if not len(i):
err_str = (
'No existing atoms found within the given distance cutoff '
'of the target position. You may repeat with a larger cutoff or '
'explicitly specify the B-factor and chain ID')
if ligand_id == 'HOH':
err_str += (
', but keep in mind that placing waters outside of '
'H-bonding distance to the model is generally inadvisable.'
)
else:
err_str += '.'
raise UserError(err_str)
na = matoms[i[0]]
if chain is None:
chain = na.residue.chain_id
if bfactor is None:
bfactor = na.residue.atoms.bfactors.mean() + 5
tmpl = mmcif.find_template_residue(session, ligand_id)
r = new_residue_from_template(model,
tmpl,
chain,
position,
b_factor=bfactor)
if use_md_template and len(r.atoms) > 3:
ff = session.isolde.forcefield_mgr[
session.isolde.sim_params.forcefield]
if md_template_name is None:
from chimerax.isolde.openmm.amberff.template_utils import ccd_to_known_template
md_template_name = ccd_to_known_template.get(ligand_id, None)
if md_template_name is None:
ligand_db = session.isolde.forcefield_mgr.ligand_db(
session.isolde.sim_params.forcefield)
from chimerax.isolde.openmm.openmm_interface import find_residue_templates
from chimerax.atomic import Residues
tdict = find_residue_templates(Residues([r]),
ff,
ligand_db=ligand_db,
logger=session.logger)
md_template_name = tdict.get(0)
md_template = None
if md_template_name is not None:
md_template = ff._templates.get(md_template_name, None)
if md_template is None:
session.logger.warning(
'place_ligand() was called with use_md_template=True, '
'but no suitable template was found. This command has been ignored.'
)
return
from ..template_utils import fix_residue_to_match_md_template
fix_residue_to_match_md_template(session,
r,
md_template,
cif_template=tmpl)
matoms.selected = False
r.atoms.selected = True
if sim_settle:
if not hasattr(session, 'isolde'):
session.logger.warning(
'ISOLDE is not running. sim_settle argument ignored.')
elif model != session.isolde.selected_model:
session.logger.warning(
"New ligand was not added to ISOLDE's "
"selected model. sim_settle argument ignored.")
else:
# defer the simulation starting until after the new atoms have been
# drawn, to make sure their styling "sticks"
def do_run(*_, session=session):
from chimerax.core.commands import run
run(session, 'isolde sim start sel')
from chimerax.core.triggerset import DEREGISTER
return DEREGISTER
session.triggers.add_handler('frame drawn', do_run)
return r