def add_disulfides_from_model_metadata(model):
m_id = model.id_string
from chimerax.core.commands import atomspec
metadata = model.metadata
try:
disulfide_list = metadata['SSBOND']
except KeyError:
return
from chimerax.atomic.struct_edit import add_bond
for disulfide in disulfide_list:
sym1 = None
sym2 = None
d = disulfide.split()
chain1, res1 = d[3], d[4]
chain2, res2 = d[6], d[7]
if len(d) > 8:
sym1, sym2 = d[8], d[9]
if sym1 is not None and sym1 != sym2:
# Disulfide across a symmetry interface. Ignore for now.
continue
arg = atomspec.AtomSpecArg('ss')
thearg = '#{}/{}:{}@{}|#{}/{}:{}@{}'.format(m_id, chain1, res1, 'SG',
m_id, chain2, res2, 'SG')
aspec = arg.parse(thearg, model.session)
atoms = aspec[0].evaluate(model.session).atoms
bonds = atoms.intra_bonds
if not len(bonds):
a1, a2 = atoms
add_bond(a1, a2)
def add_bonds_from_template_by_matched_names(residue, template):
from chimerax.atomic.struct_edit import add_bond
amap = {}
for a in residue.atoms:
ta = template.find_atom(a.name)
if ta is not None:
amap[a] = ta
for a, ta in amap.items():
for n in ta.neighbors:
rn = residue.find_atom(n.name)
if rn is not None and rn not in a.neighbors:
add_bond(a, rn)
def run_script(session):
from chimerax.atomic import selected_atoms
from chimerax.core.errors import UserError
sel = selected_atoms(session)
if len(sel) != 2:
raise UserError('Must have exactly two atoms selected!')
us = sel.unique_structures
if len(us) != 1:
raise UserError('Both atoms must be from the same structure!')
m = us[0]
from chimerax.atomic.struct_edit import add_bond
add_bond(*sel)
def add_metal_bonds_from_template(residue, template):
m = residue.structure
metal_atoms = [a for a in template.atoms if a.element.is_metal]
from chimerax.atomic.struct_edit import add_bond
for met in metal_atoms:
rmet = residue.find_atom(met.name)
if rmet is None:
raise TypeError(
'Residue does not have the required metal ion! Use fix_residue_from_template() instead.'
)
for n in met.neighbors:
rn = residue.find_atom(n.name)
if not rn in rmet.neighbors:
add_bond(rmet, rn)
def create_disulfide(cys1, cys2):
from chimerax.core.errors import UserError
if cys1.structure != cys2.structure:
raise UserError('Both cysteine residues must be in the same model!')
structure = cys1.structure
s1 = cys1.find_atom('SG')
s2 = cys2.find_atom('SG')
if s1 is None or s2 is None:
raise UserError(
'Missing SG atom! Are both residues complete cysteines?')
if s2 in s1.neighbors:
raise UserError('These residues are already disulfide bonded!')
for s in (s1, s2):
for a in s.neighbors:
if a.element.name == 'H':
a.delete()
from chimerax.atomic.struct_edit import add_bond
add_bond(s1, s2)
def new_residue_from_template(model,
template,
chain_id,
center,
residue_number=None,
insert_code=' ',
b_factor=50,
precedes=None):
'''
Create a new residue based on a template, and add it to the model.
'''
if residue_number is None:
if chain_id in model.residues.chain_ids:
residue_number = suggest_new_residue_number_for_ligand(
model, chain_id)
else:
residue_number = 0
import numpy
from chimerax.atomic import Atom
t_coords = numpy.array([a.coord for a in template.atoms])
t_center = t_coords.mean(axis=0)
t_coords += numpy.array(center) - t_center
tatom_to_atom = {}
r = model.new_residue(template.name,
chain_id,
residue_number,
insert=insert_code,
precedes=precedes)
from chimerax.atomic.struct_edit import add_bond, add_atom
for i, ta in enumerate(template.atoms):
a = tatom_to_atom[ta] = add_atom(ta.name,
ta.element,
r,
t_coords[i],
bfactor=b_factor)
for tn in ta.neighbors:
n = tatom_to_atom.get(tn, None)
if n is not None:
add_bond(a, n)
return r
def build_next_atom_from_coords(residue, found_neighbors, template_new_atom):
# print('Building next atom {} from aligned coords of {}'.format(template_new_atom.name,
# ','.join([f[0].name for f in found_neighbors])))
bonded_to = [f[0] for f in found_neighbors]
m = residue.structure
n = len(found_neighbors)
found = set(f[0] for f in found_neighbors)
while len(found_neighbors) < 3:
for ra, ta in found_neighbors:
for tn in ta.neighbors:
rn = residue.find_atom(tn.name)
if rn and rn not in found:
found_neighbors.append((rn, tn))
found.add(rn)
if len(found_neighbors) <= n:
residue.session.logger.warning(
"Couldn't find more than two neighbor atoms. Falling back to simple geometry-based addition."
)
return build_next_atom_from_geometry(residue, *found_neighbors[0],
template_new_atom)
n = len(found_neighbors)
from chimerax.geometry import align_points
import numpy
ra_coords = numpy.array([f[0].coord for f in found_neighbors])
ta_coords = numpy.array([f[1].coord for f in found_neighbors])
bfactor = numpy.mean([f[0].bfactor for f in found_neighbors])
occupancy = numpy.mean([f[0].occupancy for f in found_neighbors])
tf, rms = align_points(ta_coords, ra_coords)
from chimerax.atomic.struct_edit import add_atom
ta = template_new_atom
a = add_atom(ta.name,
ta.element,
residue,
tf * ta.coord,
occupancy=occupancy,
bfactor=bfactor)
from chimerax.atomic.struct_edit import add_bond
for b in bonded_to:
add_bond(a, b)
def use_rotamer(session, res, rots, retain=False, log=False, bfactor=None):
"""Takes a Residue instance and either a list or dictionary of rotamers (as returned by get_rotamers,
i.e. with backbone already matched) and swaps the Residue's side chain with the given rotamers.
If the rotamers are a dictionary, then the keys should match the alt locs of the CA atom, and
the corresponding rotamer will be used for that alt loc. If the alt locs are a list, if the list
has only one rotamer then that rotamer will be used for each CA alt loc. If the list has multiple
rotamers, then the CA must have only one alt loc (namely ' ') and all the rotamers will be attached,
using different alt loc characters for each.
If 'retain' is True, existing side chains will be retained. If 'bfactor' is None, then the
current highest existing bfactor in the residue will be used.
"""
N = res.find_atom("N")
CA = res.find_atom("CA")
C = res.find_atom("C")
if not N or not C or not CA:
raise LimitationError(
"N, CA, or C missing from %s: needed for side-chain pruning algorithm"
% res)
import string
alt_locs = string.ascii_uppercase + string.ascii_lowercase + string.digits + string.punctuation
if retain and CA.alt_locs:
raise LimitationError(
"Cannot retain side chains if multiple CA alt locs")
ca_alt_locs = [' '] if not CA.alt_locs else CA.alt_locs
if not isinstance(rots, dict):
# reformat as dictionary
if CA.alt_locs and len(rots) > 1:
raise LimitationError(
"Cannot add multiple rotamers to multi-position backbone")
retained_alt_locs = side_chain_locs(res) if retain else []
num_retained = len(retained_alt_locs)
if len(rots) + num_retained > len(alt_locs):
raise LimitationError("Don't have enough unique alternate "
"location characters to place %d rotamers." %
len(rots))
if len(rots) + num_retained > 1:
rots = {
loc: rot
for loc, rot in zip(
[c for c in alt_locs
if c not in retained_alt_locs][:len(rots)], rots)
}
else:
rots = {alt_loc: rots[0] for alt_loc in ca_alt_locs}
swap_type = list(rots.values())[0].residues[0].name
if retain and res.name != swap_type:
raise LimitationError(
"Cannot retain side chains if rotamers are a different residue type"
)
rot_anchors = {}
for rot in rots.values():
rot_res = rot.residues[0]
rot_N, rot_CA = rot_res.find_atom("N"), rot_res.find_atom("CA")
if not rot_N or not rot_CA:
raise LimitationError(
"N or CA missing from rotamer: cannot matchup with original residue"
)
rot_anchors[rot] = (rot_N, rot_CA)
color_by_element = N.color != CA.color
if color_by_element:
carbon_color = CA.color
else:
uniform_color = N.color
# prune old side chain
bfactor = bfactor_for_res(res, bfactor)
if not retain:
res_atoms = res.atoms
side_atoms = res_atoms.filter(res_atoms.is_side_onlys)
serials = {a.name: a.serial_number for a in side_atoms}
side_atoms.delete()
else:
serials = {}
# for proline, also prune amide hydrogens
if swap_type == "PRO":
for nnb in N.neighbors[:]:
if nnb.element.number == 1:
N.structure.delete_atom(nnb)
tot_prob = sum([r.rotamer_prob for r in rots.values()])
with CA.suppress_alt_loc_change_notifications():
res.name = swap_type
from chimerax.atomic.struct_edit import add_atom, add_bond
for alt_loc, rot in rots.items():
if CA.alt_locs:
CA.alt_loc = alt_loc
if log:
extra = " using alt loc %s" % alt_loc if alt_loc != ' ' else ""
session.logger.info(
"Applying %s rotamer (chi angles: %s) to %s%s" %
(rot_res.name, " ".join(["%.1f" % c
for c in rot.chis]), res, extra))
# add new side chain
rot_N, rot_CA = rot_anchors[rot]
visited = set([N, CA, C])
sprouts = [rot_CA]
while sprouts:
sprout = sprouts.pop()
built_sprout = res.find_atom(sprout.name)
for nb in sprout.neighbors:
built_nb = res.find_atom(nb.name)
if tot_prob == 0.0:
# some rotamers in Dunbrack are zero prob!
occupancy = 1.0 / len(rots)
else:
occupancy = rot.rotamer_prob / tot_prob
if not built_nb:
serial = serials.get(nb.name, None)
built_nb = add_atom(nb.name,
nb.element,
res,
nb.coord,
serial_number=serial,
bonded_to=built_sprout,
alt_loc=alt_loc)
built_nb.occupancy = occupancy
built_nb.bfactor = bfactor
if color_by_element:
if built_nb.element.name == "C":
built_nb.color = carbon_color
else:
from chimerax.atomic.colors import element_color
built_nb.color = element_color(
built_nb.element.number)
else:
built_nb.color = uniform_color
elif built_nb not in visited:
built_nb.set_alt_loc(alt_loc, True)
built_nb.coord = nb.coord
built_nb.occupancy = occupancy
built_nb.bfactor = bfactor
if built_nb not in visited:
sprouts.append(nb)
visited.add(built_nb)
if built_nb not in built_sprout.neighbors:
add_bond(built_sprout, built_nb)
def template_swap_res(res, res_type, *, preserve=False, bfactor=None):
"""change 'res' into type 'res_type'"""
fixed, buds, start, end = get_res_info(res)
if res_type == "HIS":
res_type = "HIP"
if res_type in ["A", "C", "G", "T"
] and res.name in ["DA", "DC", "DT", "DG"]:
res_type = "D" + res_type
from chimerax.atomic import TmplResidue, Atom
tmpl_res = TmplResidue.get_template(res_type, start=start, end=end)
if not tmpl_res:
raise TemplateError("No connectivity template for residue '%s'" %
res_type)
# sanity check: does the template have the bud atoms?
for bud in buds:
if tmpl_res.find_atom(bud) is None:
raise TemplateError("New residue type (%s) not compatible with"
" starting residue type (%s)" %
(res_type, res.name))
color_by_element = False
uniform_color = res.find_atom(buds[0]).color
het = res.find_atom("N") or res.find_atom("O4'")
if het:
carbon = res.find_atom("CA") or res.find_atom("C4'")
if carbon:
color_by_element = het.color != carbon.color
if color_by_element:
carbon_color = carbon.color
else:
uniform_color = het.color
bfactor = bfactor_for_res(res, bfactor)
if preserve:
if "CA" in fixed and res_type not in ['GLY', 'ALA']:
raise TemplateSwapError(
"'preserve' keyword not yet implemented for amino acids")
a1 = res.find_atom("O4'")
a2 = res.find_atom("C1'")
if not a1 or not a2:
preserve_pos = None
else:
dihed_names = {"N9": ["C4", "C8"], "N1": ["C2", "C6"]}
a3 = res.find_atom("N9") or res.find_atom("N1")
if a3:
if a2 not in a3.neighbors:
preserve_pos = None
else:
preserve_pos = a3.coord
else:
preserve_pos = None
if preserve_pos:
p1, p2, p3 = [a.coord for a in (a1, a2, a3)]
preserved_pos = False
prev_name, alt_name = dihed_names[a3.name]
a4 = res.find_atom(prev_name)
if a4 and a3 in a4.neighbors:
p4 = a4.coord
from chimerax.geometry import dihedral
preserve_dihed = dihedral(p1, p2, p3, p4)
else:
preserve_dihed = None
else:
preserve_dihed = None
# prune non-backbone atoms
for a in res.atoms:
if a.name not in fixed:
a.structure.delete_atom(a)
# add new sidechain
new_atoms = []
xf = None
from chimerax.atomic.struct_edit import add_bond
while len(buds) > 0:
bud = buds.pop()
tmpl_bud = tmpl_res.find_atom(bud)
res_bud = res.find_atom(bud)
try:
info = Atom.idatm_info_map[tmpl_bud.idatm_type]
geom = info.geometry
subs = info.substituents
except KeyError:
raise AssertionError(
"Can't determine atom type information for atom %s of residue %s"
% (bud, res))
# use .coord rather than .scene_coord: we want to set the new atom's coord,
# to which the proper xform will then be applied
for a, b in zip(tmpl_bud.neighbors, tmpl_bud.bonds):
if a.element.number == 1:
# don't add hydrogens
continue
if res.find_atom(a.name):
res_bonder = res.find_atom(a.name)
if res_bonder not in res_bud.neighbors:
add_bond(a, res_bonder)
continue
new_atom = None
num_bonded = len(res_bud.bonds)
if num_bonded >= subs:
raise AssertionError(
"Too many atoms bonded to %s of residue %s" % (bud, res))
if num_bonded == 0:
raise AssertionError(
"Atom %s of residue %s has no neighbors after pruning?!?" %
(bud, res))
# since fused ring systems may have distorted bond angles, always use dihedral placement
real1 = res_bud.neighbors[0]
kw = {}
if preserve:
if preserve_pos and not preserved_pos:
kw['pos'] = preserve_pos
preserved_pos = True
preserved_name = a.name
elif preserve_dihed is not None:
prev_name, alt_name = dihed_names[preserved_name]
if a.name == prev_name:
kw['dihed'] = preserve_dihed
elif a.name == alt_name:
kw['dihed'] = preserve_dihed + 180.0
if not kw and xf is not None:
kw['pos'] = xf * a.coord
new_atom = form_dihedral(res_bud, real1, tmpl_res, a, b, **kw)
new_atom.draw_mode = res_bud.draw_mode
new_atom.bfactor = bfactor
if color_by_element:
if new_atom.element.name == "C":
new_atom.color = carbon_color
else:
from chimerax.atomic.colors import element_color
new_atom.color = element_color(new_atom.element.number)
else:
new_atom.color = uniform_color
new_atoms.append(new_atom)
for bonded in a.neighbors:
bond_atom = res.find_atom(bonded.name)
if not bond_atom:
continue
add_bond(new_atom, bond_atom)
buds.append(new_atom.name)
# once we've placed 3 side chain atoms, we use superpositioning to
# place the remainder of the side chain, since dihedrals will
# likely distort ring closures if 'preserve' is true
if buds and not xf and len(new_atoms) >= 3:
placed_positions = []
tmpl_positions = []
for na in new_atoms:
placed_positions.append(na.coord)
tmpl_positions.append(tmpl_res.find_atom(na.name).coord)
import numpy
from chimerax.geometry import align_points
xf = align_points(numpy.array(tmpl_positions),
numpy.array(placed_positions))[0]
res.name = res_type
def get_rotamers(session,
res,
phi=None,
psi=None,
cis=False,
res_type=None,
rot_lib="Dunbrack",
log=False):
"""Takes a Residue instance and optionally phi/psi angles (if different from the Residue), residue
type (e.g. "TYR"), and/or rotamer library name. Returns a list of AtomicStructure instances (sublass of
AtomicStructure). The AtomicStructure are each a single residue (a rotamer) and are in descending
probability order. Each has an attribute "rotamer_prob" for the probability and "chis" for the
chi angles.
"""
res_type = res_type or res.name
if res_type == "ALA" or res_type == "GLY":
raise NoResidueRotamersError("No rotamers for %s" % res_type)
if not isinstance(rot_lib, RotamerLibrary):
rot_lib = session.rotamers.library(rot_lib)
# check that the residue has the n/c/ca atoms needed to position the rotamer
# and to ensure that it is an amino acid
from chimerax.atomic import Residue
match_atoms = {}
for bb_name in Residue.aa_min_backbone_names:
match_atoms[bb_name] = a = res.find_atom(bb_name)
if a is None:
raise LimitationError("%s missing from %s; needed to position CB" %
(bb_name, res))
match_atoms["CB"] = res.find_atom("CB")
if not phi and not psi:
phi, psi = res.phi, res.psi
omega = res.omega
cis = False if omega is None or abs(omega) > 90 else True
if log:
def _info(ang):
if ang is None:
return "none"
return "%.1f" % ang
if match_atoms["CA"].alt_locs:
al_info = " (alt loc %s)" % match_atoms["CA"].alt_loc
else:
al_info = ""
session.logger.info("%s%s: phi %s, psi %s %s" %
(res, al_info, _info(phi), _info(psi),
"cis" if cis else "trans"))
session.logger.status("Retrieving rotamers from %s library" %
rot_lib.display_name)
res_template_func = rot_lib.res_template_func
params = rot_lib.rotamer_params(res_type, phi, psi, cis=cis)
session.logger.status("Rotamers retrieved from %s library" %
rot_lib.display_name)
mapped_res_type = rot_lib.res_name_mapping.get(res_type, res_type)
template = rot_lib.res_template_func(mapped_res_type)
tmpl_N = template.find_atom("N")
tmpl_CA = template.find_atom("CA")
tmpl_C = template.find_atom("C")
tmpl_CB = template.find_atom("CB")
if match_atoms['CB']:
res_match_atoms, tmpl_match_atoms = [
match_atoms[x] for x in ("C", "CA", "CB")
], [tmpl_C, tmpl_CA, tmpl_CB]
else:
res_match_atoms, tmpl_match_atoms = [
match_atoms[x] for x in ("N", "CA", "C")
], [tmpl_N, tmpl_CA, tmpl_C]
from chimerax.geometry import align_points
from numpy import array
xform, rmsd = align_points(array([fa.coord for fa in tmpl_match_atoms]),
array([ta.coord for ta in res_match_atoms]))
n_coord = xform * tmpl_N.coord
ca_coord = xform * tmpl_CA.coord
cb_coord = xform * tmpl_CB.coord
info = Residue.chi_info[mapped_res_type]
bond_cache = {}
angle_cache = {}
from chimerax.atomic.struct_edit import add_atom, add_dihedral_atom, add_bond
structs = []
middles = {}
ends = {}
for i, rp in enumerate(params):
s = AtomicStructure(session, name="rotamer %d" % (i + 1))
structs.append(s)
r = s.new_residue(mapped_res_type, 'A', 1)
registerer = "swap_res get_rotamers"
AtomicStructure.register_attr(session,
"rotamer_prob",
registerer,
attr_type=float)
s.rotamer_prob = rp.p
AtomicStructure.register_attr(session, "chis", registerer)
s.chis = rp.chis
rot_N = add_atom("N", tmpl_N.element, r, n_coord)
rot_CA = add_atom("CA", tmpl_CA.element, r, ca_coord, bonded_to=rot_N)
rot_CB = add_atom("CB", tmpl_CB.element, r, cb_coord, bonded_to=rot_CA)
todo = []
for j, chi in enumerate(rp.chis):
n3, n2, n1, new = info[j]
b_len, angle = _len_angle(new, n1, n2, template, bond_cache,
angle_cache)
n3 = r.find_atom(n3)
n2 = r.find_atom(n2)
n1 = r.find_atom(n1)
new = template.find_atom(new)
a = add_dihedral_atom(new.name,
new.element,
n1,
n2,
n3,
b_len,
angle,
chi,
bonded=True)
todo.append(a)
middles[n1] = [a, n1, n2]
ends[a] = [a, n1, n2]
# if there are any heavy non-backbone atoms bonded to template
# N and they haven't been added by the above (which is the
# case for Richardson proline parameters) place them now
for tnnb in tmpl_N.neighbors:
if r.find_atom(tnnb.name) or tnnb.element.number == 1:
continue
tnnb_coord = xform * tnnb.coord
add_atom(tnnb.name, tnnb.element, r, tnnb_coord, bonded_to=rot_N)
# fill out bonds and remaining heavy atoms
from chimerax.geometry import distance, align_points
done = set([rot_N, rot_CA])
while todo:
a = todo.pop(0)
if a in done:
continue
tmpl_A = template.find_atom(a.name)
for bonded, bond in zip(tmpl_A.neighbors, tmpl_A.bonds):
if bonded.element.number == 1:
continue
rbonded = r.find_atom(bonded.name)
if rbonded is None:
# use middles if possible...
try:
p1, p2, p3 = middles[a]
conn = p3
except KeyError:
p1, p2, p3 = ends[a]
conn = p2
t1 = template.find_atom(p1.name)
t2 = template.find_atom(p2.name)
t3 = template.find_atom(p3.name)
xform = align_points(
array([t.coord for t in [t1, t2, t3]]),
array([p.coord for p in [p1, p2, p3]]))[0]
pos = xform * template.find_atom(bonded.name).coord
rbonded = add_atom(bonded.name,
bonded.element,
r,
pos,
bonded_to=a)
middles[a] = [rbonded, a, conn]
ends[rbonded] = [rbonded, a, conn]
if a not in rbonded.neighbors:
add_bond(a, rbonded)
if rbonded not in done:
todo.append(rbonded)
done.add(a)
return structs
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 fix_residue_from_template(residue,
template,
rename_atoms_only=False,
rename_residue=False,
match_by='name',
template_indices=None):
import numpy
from chimerax.atomic import Atoms
from chimerax.atomic.struct_edit import add_bond
if any([numpy.any(numpy.isnan(a.coord)) for a in template.atoms]):
raise TypeError('Template is missing one or more atom coordinates!')
matched_nodes, residue_extra, template_extra = find_maximal_isomorphous_fragment(
residue,
template,
limit_template_indices=template_indices,
match_by=match_by)
if len(matched_nodes) < 3:
from chimerax.atomic import Residue
if residue.polymer_type == Residue.PT_NONE:
final_string = (
f'Try deleting this residue and replacing it with "isolde add ligand {residue.name} - or have you just forgotten '
f'to add hydrogens?')
elif residue.polymer_type == Residue.PT_AMINO:
final_string = (
f'Try deleting this residue and replacing it with "isolde add aa {residue.name}'
)
else:
final_string = (
'Adding of nucleic acid residues is not currently possible in ISOLDE. To move forward, just delete this residue.'
)
raise UserError(
f'Residue {residue.name} {residue.chain_id}{residue.number}{residue.insertion_code} '
f'has only {len(matched_nodes)} atoms in common with the template. At least 3 are needed to rebuild automatically. '
f'{final_string}')
m = residue.structure
session = m.session
rnames = set(residue.atoms.names)
tnames = set([a.name for a in template.atoms])
# Delete any isolated atoms and rebuild from template
if len(residue_extra):
if rename_atoms_only:
session.logger.warning(
'The following atoms in {} {}{} did not match template {}, and will not be renamed: {}.'
.format(residue.name, residue.chain_id, residue.number,
template.name, ', '.join(residue_extra.names)))
else:
session.logger.info(
'Deleted the following atoms from residue {} {}{}{}: {}'.
format(residue.name, residue.chain_id, residue.number,
residue.insertion_code, ', '.join(residue_extra.names)))
residue_extra.delete()
conn_ratoms = Atoms(matched_nodes.keys())
renamed_atoms = []
for ratom, tatom in matched_nodes.items():
if ratom.name != tatom.name:
renamed_atoms.append((ratom.name, tatom.name))
ratom.name = tatom.name
if len(renamed_atoms):
warn_str = '{} atoms were automatically renamed to match the template: '.format(
len(renamed_atoms))
warn_str += ', '.join(['->'.join(apair) for apair in renamed_atoms])
session.logger.warning(warn_str)
if rename_atoms_only:
return
still_missing = set(template_extra)
remaining = len(still_missing)
found = set()
while remaining:
for ta in still_missing:
found_neighbors = []
for tn in ta.neighbors:
ra = residue.find_atom(tn.name)
if ra:
found_neighbors.append((ra, tn))
if len(found_neighbors) == 0:
continue
else:
ra, tn = found_neighbors[0]
build_next_atom_from_geometry(residue, ra, tn, ta)
found.add(ta)
still_missing = still_missing.difference(found)
if len(still_missing) and not len(found):
raise RuntimeError(
'Failed to add atoms on last iteration for residue {}. Still missing: {}'
.format('{}{}'.format(residue.chain_id, residue.number),
','.join(still_missing)))
# m.session.logger.status('Still missing: {}'.format(
# ','.join([ta.name for ta in still_missing])
# ))
remaining = len(still_missing)
bonds = set()
for a in template.atoms:
bonds.update(set(a.bonds))
for b in bonds:
a1, a2 = [residue.find_atom(a.name) for a in b.atoms]
if a1 is None or a2 is None:
continue
if a2 not in a1.neighbors:
add_bond(a1, a2)
if rename_residue:
residue.name = template.name
def merge_fragment(target_model,
residues,
chain_id=None,
renumber_from=None,
anchor_n=None,
anchor_c=None,
transform=None):
'''
Copy the atoms from a fragment into the current model, optionally reassigning
chain ID and numbers. If alternate conformers are present, only the active
one will be copied.
* Args:
- target_model: the model to copy into
- residues: the residues to be copied. Isotropic B-factors will be
copied, but aniso_u records will be ignored.
- chain_id: if provided, all residues must be from one chain. The copied
residues will be given this chain ID.
- renumber_from: if provided, all residues will be renumbered with an
offset of (lowest residue number - renumber_from)
- anchor_n: an amino acid residue or None. If provided, the first amino
acid residue in the fragment will be linked to this one. Throws an
error if anchor_n has another residue linked at its C-terminus.
- anchor_c: an amino acid residue or None. If provided, the last amino
acid residue in the fragment will be linked to this one. Throws an
error if anchor_c has another residue linked at its C-terminus.
- transform: a Place or None. If provided, the atoms will be placed at
the transformed coordinates.
'''
from chimerax.core.errors import UserError
us = residues.unique_structures
if len(us) != 1:
raise UserError(
'All residues to be copied must be from the same model!')
if (chain_id or anchor_n or anchor_c or (renumber_from is not None)) \
and len(residues.unique_chain_ids) != 1:
raise UserError(
'If reassigning chain ID, renumbering or specifying '
'N- and/or C-terminal anchors, all residues to be copied must be '
'from a single chain!')
from chimerax.atomic import Residue, Residues, Atoms
if (anchor_n or anchor_c):
protein_residues = residues[residues.polymer_types == Residue.PT_AMINO]
if not len(protein_residues):
raise UserError(
'N- and/or C-terminal anchors were specified, but '
'the copied selection does not contain any amino acid residues!'
)
import numpy
fm = us[0]
m = target_model
residues = Residues(
sorted(residues,
key=lambda r: (r.chain_id, r.number, r.insertion_code)))
atoms = residues.atoms
coords = atoms.coords
atom_map = {}
if renumber_from:
offset = residues[0].number - renumber_from
else:
offset = 0
def new_residue_number(r):
if r in residues:
return r.number - offset
return r.number
def new_chain_id(r):
if r in residues and chain_id:
return chain_id
return r.chain_id
merged_residues = m.residues.merge(residues)
merged_residues = Residues(
sorted(merged_residues,
key=lambda r:
(new_chain_id(r), new_residue_number(r), r.insertion_code)))
new_residue_mask = numpy.in1d(merged_residues, residues)
new_residue_indices = numpy.argwhere(new_residue_mask).ravel()
existing_residue_mask = numpy.in1d(merged_residues, m.residues)
existing_residue_indices = numpy.argwhere(existing_residue_mask).ravel()
insertion_point_map = {}
if chain_id is not None:
cids = [chain_id]
else:
cids = residues.unique_chain_ids
for cid in cids:
existing_residues = m.residues[m.residues.chain_ids == cid]
if not len(existing_residues):
insertion_point_map[cid] = None
continue
existing_residue_numbers = numpy.array(
[str(r.number) + r.insertion_code for r in existing_residues])
cres = residues[residues.chain_ids == cid]
new_residue_numbers = numpy.array(
[str(r.number - offset) + r.insertion_code for r in cres])
duplicate_flags = numpy.in1d(new_residue_numbers,
existing_residue_numbers)
if numpy.any(duplicate_flags):
dup_residues = cres[duplicate_flags]
err_str = (
'The requested merge could not be completed because the '
'following residues in chain {} (after applying any renumbering) '
'will have the same residue numbers as existing residues in '
'the target: {}').format(
cid, ', '.join(
str(r.number) + r.insertion_code
for r in dup_residues))
raise UserError(err_str)
chain_mask = (numpy.array([new_chain_id(r)
for r in merged_residues]) == cid)
new_r_in_chain_mask = numpy.logical_and(chain_mask, new_residue_mask)
insertion_point_map[cid] = None
if numpy.any(new_r_in_chain_mask):
last_new_r_index = numpy.argwhere(new_r_in_chain_mask)[-1]
greater_indices = existing_residue_indices[
existing_residue_indices > last_new_r_index]
if len(greater_indices):
insertion_point_map[cid] = merged_residues[greater_indices[0]]
current_residue = None
first_index = new_residue_indices[0]
if first_index > 0:
prev_res = merged_residues[first_index - 1]
else:
prev_res = None
prev_new_res = None
from chimerax.atomic.struct_edit import add_bond
for merged_index, r in zip(new_residue_indices, residues):
if chain_id:
cid = chain_id
else:
cid = r.chain_id
precedes = insertion_point_map[cid]
insertion_code = r.insertion_code
if insertion_code == '':
insertion_code = ' '
nr = m.new_residue(r.name,
cid,
r.number - offset,
insert=insertion_code,
precedes=precedes)
nr.ribbon_hide_backbone = r.ribbon_hide_backbone
nr.ribbon_display = r.ribbon_display
nr.ribbon_color = r.ribbon_color
nr.ss_type = r.ss_type
for a in r.atoms:
na = atom_map[a] = m.new_atom(a.name, a.element)
na.coord = a.coord
na.bfactor = a.bfactor
na.aniso_u6 = a.aniso_u6
na.occupancy = a.occupancy
na.draw_mode = a.draw_mode
na.color = a.color
na.display = a.display
nr.add_atom(na)
for n in a.neighbors:
nn = atom_map.get(n, None)
if nn is not None:
add_bond(na, nn)
if prev_res is not None:
if (r.polymer_type == Residue.PT_AMINO
and prev_res not in nr.neighbors
and prev_res.chain_id == cid
and prev_res.polymer_type == Residue.PT_AMINO):
if precedes is not None:
if precedes.chain_id == cid and precedes.polymer_type == Residue.PT_AMINO:
ratoms = prev_res.atoms.merge(precedes.atoms)
pc = prev_res.find_atom('C')
nn = nr.find_atom('N')
if precedes is not None and precedes.polymer_type == Residue.PT_AMINO and precedes.chain_id == cid:
nc = nr.find_atom('C')
pn = precedes.find_atom('N')
prev_res = nr
new_atoms = Atoms(list(atom_map.values()))
if transform is not None:
# Using Atoms.transform() rather than simply transforming the coords,
# because this also correctly transforms any anisotropic B-factors.
new_atoms.transform(transform)
if anchor_n:
anchor_atom = anchor_n.find_atom('C')
link_atom = atom_map[protein_residues[0].find_atom('N')]
_remove_excess_terminal_atoms(anchor_atom)
_remove_excess_terminal_atoms(link_atom)
add_bond(anchor_atom, link_atom)
for r in new_atoms.unique_residues:
merged_atoms = anchor_n.atoms.merge(r.atoms)
if anchor_c:
anchor_atom = anchor_c.find_atom('N')
link_atom = atom_map[protein_residues[-1].find_atom('C')]
_remove_excess_terminal_atoms(anchor_atom)
_remove_excess_terminal_atoms(link_atom)
add_bond(anchor_atom, link_atom)
new_atoms.displays = True
return new_atoms
def create_merged_residue(residues, base_residue=None, new_name=None):
if base_residue is None:
base_residue = residues[0]
if base_residue not in residues:
raise TypeError('base_residue must be a member of residues!')
if new_name is None:
new_name = base_residue.name
from chimerax.atomic import Residues
from chimerax.atomic.struct_edit import add_atom, add_bond
residues = Residues(residues)
seen = set()
for r in residues:
for n in r.neighbors:
seen.add(n)
if not all([r in seen for r in residues]):
raise TypeError(
'All residues must be connected through covalent bonds!')
atoms = residues.atoms
other_residues = residues.subtract(Residues([base_residue]))
bonds = atoms.intra_bonds
external_bonds = []
for r in seen:
if r not in other_residues:
for n in r.neighbors:
if n in residues:
external_bonds.extend(r.bonds_between(n))
next_atom_number = highest_atom_number(base_residue.atoms) + 1
atom_map = {}
other_atoms = other_residues.atoms
# Do heavy atoms first, so we can assign hydrogen names based on them
other_heavy_atoms = other_atoms[other_atoms.element_names != 'H']
for a in other_heavy_atoms:
name = a.element.name + str(next_atom_number)
next_atom_number += 1
atom_map[a] = add_atom(name,
a.element,
base_residue,
a.coord,
occupancy=a.occupancy,
bfactor=a.bfactor)
# Add the hydrogens
for a, na in atom_map.items():
base_number = na.name[1:]
i = 1
for n in a.neighbors:
if n.element.name == 'H':
name = 'H' + base_number + str(i)
i += 1
add_atom(name,
n.element,
base_residue,
n.coord,
bonded_to=na,
occupancy=n.occupancy,
bfactor=n.bfactor)
# Add all internal bonds
for a, na in atom_map.items():
for n in a.neighbors:
nn = atom_map.get(n, None)
if nn is not None and nn not in na.neighbors:
add_bond(na, nn)
# Now we just need to add the bonds between base_residue and the merged portion, and any
# other bonds between the merged portion and the wider model. To avoid valence errors we'll need
# to first delete the existing bonds.
for b in external_bonds:
atoms = b.atoms
if atoms[1] in atom_map.keys():
atoms = atoms[::-1]
na = atom_map[atoms[0]]
a = atoms[1]
b.delete()
add_bond(na, a)
other_residues.delete()
base_residue.name = new_name