def dbscan(points, epsilon=3, min_points=6):
'''
Simple implementation of the DBSCAN algorithm for clustering points in 3D
space.
'''
import numpy
from chimerax.geometry import find_close_points
core = set()
neighbors = []
for i, p in enumerate(points):
_, close_i = find_close_points([points[i]],
points,
max_distance=epsilon)
neighbors.append(set(close_i))
if len(close_i) > min_points:
core.add(i)
remainder = set(range(len(points)))
clusters = [] # final clusters
# Assign core groups (those with at least min_points points) to clusters
while len(core) > 0:
remainder_old = remainder.copy()
idx = core.pop()
qp = [idx]
remainder.remove(idx)
while len(qp) > 0:
q = qp.pop(0)
nq = neighbors[q]
if len(nq) >= min_points:
delta = nq.intersection(remainder)
qp.extend(delta)
remainder.difference_update(delta)
new_cluster = remainder_old.difference(remainder)
clusters.append(new_cluster)
core.difference_update(new_cluster)
clusters = list(sorted(clusters, key=lambda c: len(c), reverse=True))
# Add remaining points to clusters
for cluster in clusters:
close = [1]
while len(close):
remaining = numpy.array(list(remainder))
rpoints = points[remaining]
idx_map = {i: idx for i, idx in enumerate(remaining)}
cpoints = points[numpy.array(list(cluster))]
_, close = find_close_points(cpoints, rpoints, epsilon)
if len(close):
ci = set([idx_map[i] for i in close])
cluster.update(ci)
remainder.difference_update(ci)
clusters = list(sorted(clusters, key=lambda c: len(c), reverse=True))
clusters = [numpy.array(list(c)) for c in clusters]
noise = numpy.array(list(remainder))
return clusters, noise
def _zone_atoms(atoms, near_atoms, distance):
axyz = atoms.scene_coords
naxyz = near_atoms.scene_coords
from chimerax.geometry import find_close_points
i1,i2 = find_close_points(axyz, naxyz, distance)
za = atoms[i1]
return za
def sidechain_buried_score(residue):
'''
Defines how "buried" a sidechain is by counting the number of heavy atoms
from other residues coming within 4A of any heavy atom from the sidechain.
The returned score is a value ranging from 0 to 1, where 0 indicates no
contact with other atoms, and 1 indicates 3 or more other atoms per
sidechain atoms. The score scales linearly with the number of contacting
atoms in between these values.
'''
from chimerax.geometry import find_close_points
from chimerax.atomic import Residues
import numpy
r = residue
m = r.structure
other_residues = m.residues.subtract(Residues([r]))
sidechain_atoms = r.atoms[numpy.logical_not(
numpy.in1d(r.atoms.names, ['N', 'C', 'CA', 'O']))]
if not len(sidechain_atoms):
return 0
other_atoms = other_residues.atoms
cp = find_close_points(sidechain_atoms.coords, other_atoms.coords, 4.0)[1]
score = (len(cp) / len(sidechain_atoms)) / 3
if score > 1:
score = 1
return score
def apply_restraints(trs, rrs, adjust_for_confidence, confidence_type):
template_as = []
restrained_as = []
for tr, rr in zip(trs, rrs):
ta_names = set(tr.atoms.names).intersection(atom_names)
ra_names = set(rr.atoms.names).intersection(atom_names)
common_names = list(ta_names.intersection(ra_names))
template_as.extend([tr.find_atom(name) for name in common_names])
restrained_as.extend([rr.find_atom(name) for name in common_names])
# template_as.append(tr.atoms[numpy.in1d(tr.atoms.names, common_names)])
# restrained_as.append(rr.atoms[numpy.in1d(rr.atoms.names, common_names)])
from chimerax.atomic import Atoms
template_as = Atoms(template_as)
restrained_as = Atoms(restrained_as)
template_coords = template_as.coords
from math import sqrt
for i, ra1 in enumerate(restrained_as):
query_coord = numpy.array([template_coords[i]])
indices = find_close_points(query_coord, template_coords,
distance_cutoff)[1]
indices = indices[indices != i]
for ind in indices:
ra2 = restrained_as[ind]
if ra1.residue == ra2.residue:
continue
if adjust_for_confidence:
if confidence_type == 'plddt':
scores = [
template_as[i].bfactor * confidence_multiplier,
template_as[ind].bfactor * confidence_multiplier
]
elif confidence_type == 'pae':
scores = [
pae_matrix[template_as[i].residue.number - 1,
template_as[ind].residue.number - 1]
]
kappa_adj, tol_adj, falloff_adj = adjust_distance_restraint_terms_by_confidence(
scores, confidence_type)
if kappa_adj == 0:
continue
else:
kappa_adj = tol_adj = 1
falloff_adj = 0
try:
dr = adrm.add_restraint(ra1, ra2)
except ValueError:
continue
dist = distance(query_coord[0], template_coords[ind])
dr.tolerance = tolerance * dist * tol_adj
dr.target = dist
dr.c = max(sqrt(dist) * well_half_width, 0.1)
#dr.effective_spring_constant = spring_constant
dr.kappa = kappa * kappa_adj
from math import log
dr.alpha = -1 - fall_off * log(
(max(dist - 1, 1))) - falloff_adj
dr.enabled = True
def restrain_ca_distances_to_template(template_residues,
restrained_residues,
distance_cutoff=8,
spring_constant=500):
'''
Creates a "web" of distance restraints between nearby CA atoms, restraining
one set of residues to the same spatial organisation as another.
Args:
* template_residues:
- a :class:`chimerax.atomic.Residues` instance. All residues must be
from a single model, but need no be contiguous
* restrained_residues:
- a :class:`chimerax.atomic.Residues` instance. All residues must be
from a single model (which may or may not be the same model as for
`template_residues`). May be the same array as `template_residues`
(which will just restrain all distances to their current values).
* distance_cutoff (default = 8):
- for each CA atom in `restrained_residues`, a distance restraint
will be created between it and every other CA atom where the
equivalent atom in `template_residues` is within `distance_cutoff`
of its template equivalent.
* spring_constant (default = 500):
- the strength of each restraint, in :math:`kJ mol^{-1} nm^{-2}`
'''
from chimerax.isolde import session_extensions as sx
if len(template_residues) != len(restrained_residues):
raise TypeError(
'Template and restrained residue arrays must be the same length!')
template_us = template_residues.unique_structures
if len(template_us) != 1:
raise TypeError('Template residues must be from a single model!')
restrained_us = restrained_residues.unique_structures
if len(restrained_us) != 1:
raise TypeError('Restrained residues must be from a single model!')
restrained_model = restrained_us[0]
template_cas = template_residues.atoms[template_residues.atoms.names ==
'CA']
restrained_cas = restrained_residues.atoms[restrained_residues.atoms.names
== 'CA']
template_coords = template_cas.coords
drm = sx.get_distance_restraint_mgr(restrained_model)
from chimerax.geometry import find_close_points, distance
for i, rca1 in enumerate(restrained_cas):
query_coord = numpy.array([template_coords[i]])
indices = find_close_points(query_coord, template_coords,
distance_cutoff)[1]
indices = indices[indices != i]
for ind in indices:
rca2 = restrained_cas[ind]
dr = drm.add_restraint(rca1, rca2)
dr.spring_constant = spring_constant
dr.target = distance(query_coord[0], template_coords[ind])
dr.enabled = True
def get_shell_of_residues(model, existing_sel, dist_cutoff):
from chimerax.geometry import find_close_points
from chimerax.atomic import selected_atoms, Atoms, concatenate
selatoms = existing_sel
allatoms = model.atoms
unselected_atoms = allatoms.subtract(selatoms)
selcoords = selatoms.coords
unselcoords = unselected_atoms.coords
ignore, shell_indices = find_close_points(selcoords, unselcoords,
dist_cutoff)
shell_atoms = unselected_atoms[shell_indices].unique_residues.atoms
return shell_atoms
def refmac_distance_restraints(session,
model,
distance_cutoff=4.5,
include_waters=False,
file_name='RESTRAINTS.txt'):
import numpy
m = model
from chimerax.atomic import AtomicStructures
if isinstance(m, AtomicStructures):
if len(m) != 1:
from chimerax.core.errors import UserError
raise UserError('Please specify a single atomic model!')
m = m[0]
residues = m.residues
if not include_waters:
residues = residues[residues.names != 'HOH']
atoms = residues.atoms[residues.atoms.element_names != 'H']
coords = atoms.coords
from chimerax.geometry import find_close_points
seen = set()
with open(file_name, 'wt') as rfile:
rfile.write('# ISOLDE Restraints File\n'
'# \n'
'# Restraints to ISOLDE output geometry\n')
for i, atom in enumerate(atoms):
query_coord = numpy.array([coords[i]])
indices = find_close_points(query_coord, coords,
distance_cutoff)[1]
for ind in indices:
atom2 = atoms[ind]
if atom2 == atom:
continue
# Do not include restraints for neighbors or 1-3 relationships
if any([
atom2 == n or atom2 in n.neighbors
for n in atom.neighbors
]):
continue
# Don't double-count
pair = frozenset((atom, atom2))
if pair in seen:
continue
rfile.write(refmac_distance_restraint(atom, atom2) + '\n')
seen.add(pair)
import os
session.logger.info(
f'Top-out distance restraints file for REFMAC5 written to {file_name}. '
f'This is essentially equivalent to a ProSMART restraints file, restraining '
f'interatomic distances to their current values. Use it in the "External restraints" '
f'section of a Refmac5 job in the CCP-EM GUI, or at the command line as: \n'
f'refmac5 {{all other arguments}} < {file_name}')
def pick_closest_to_line(session,
mx,
my,
atoms,
cutoff,
displayed_only=True,
hydrogens=False):
'''
Pick the atom coming closest to the ray projected from the mouse pointer
away from the camera. Only atoms found between the near and far clipping
planes and within cutoff of the line will be considered. Optionally the
selection can be further limited to include only displayed atoms and/or
exclude hydrogens.
'''
closest = None
if atoms is None:
return None
xyz1, xyz2 = session.main_view.clip_plane_points(mx, my)
import numpy
# Create an array of coordinates with spacing cutoff/2
length = numpy.linalg.norm(xyz2 - xyz1)
numpoints = numpy.ceil(length / cutoff * 2).astype(int)
xvals = numpy.linspace(xyz1[0], xyz2[0], num=numpoints)
yvals = numpy.linspace(xyz1[1], xyz2[1], num=numpoints)
zvals = numpy.linspace(xyz1[2], xyz2[2], num=numpoints)
xyzlist = []
for xyz in zip(xvals, yvals, zvals):
xyzlist.append(xyz)
xyzlist = numpy.array(xyzlist)
if displayed_only:
atoms = atoms.filter(atoms.visibles)
if not hydrogens:
atoms = atoms.filter(atoms.element_names != 'H')
atomic_coords = atoms.scene_coords
from chimerax.geometry import find_close_points
line_indices, atom_indices = find_close_points(xyzlist, atomic_coords,
cutoff)
line_shortlist = xyzlist[line_indices]
ac_shortlist = atomic_coords[atom_indices]
atom_shortlist = atoms[atom_indices]
min_dist = cutoff
for lxyz in line_shortlist:
for axyz, atom in zip(ac_shortlist, atom_shortlist):
d = numpy.linalg.norm(axyz - lxyz)
if d < min_dist:
closest = atom
min_dist = d
return closest
def surface_geometry(triangles, tolerance=1e-5):
from numpy import array, reshape, single as floatc, intc
varray = reshape(triangles, (3 * len(triangles), 3)).astype(floatc)
uindex = {}
unique = []
from chimerax.geometry import find_close_points
for v in range(len(varray)):
if not v in uindex:
i1, i2 = find_close_points(varray[v:v + 1, :], varray, tolerance)
for i in i2:
if not i in uindex:
uindex[i] = len(unique)
unique.append(varray[v])
uvarray = array(unique, floatc)
tlist = [(uindex[3 * t], uindex[3 * t + 1], uindex[3 * t + 2]) for t in range(len(triangles))]
tarray = array(tlist, intc)
return uvarray, tarray
def cluster_unbound_ligands(model, unbound, cutoff=5):
from chimerax.geometry import find_close_points
from chimerax.atomic import Residue, Residues
from collections import defaultdict
import numpy
m = model
chain_ids = m.residues.unique_chain_ids
other_residues = m.residues.subtract(unbound)
#polymeric = m.residues[m.residues.polymer_types!=Residue.PT_NONE]
ligand_atoms = unbound.atoms[unbound.atoms.element_names != 'H']
chain_map = {}
for cid in chain_ids:
cres = other_residues[other_residues.chain_ids == cid]
catoms = cres.atoms[cres.atoms.element_names != 'H']
ci, li = find_close_points(catoms.coords, ligand_atoms.coords, cutoff)
close_ligand_atoms = ligand_atoms[li]
weights = numpy.ones(len(close_ligand_atoms), numpy.double)
weights[close_ligand_atoms.element_names == 'C'] = _carbon_weight
weights[close_ligand_atoms.elements.is_metal] = _metal_weight
chain_map[cid] = Weighted_Counter(
[a.residue for a in close_ligand_atoms], weights)
unclassified = []
closest_chain_map = defaultdict(list)
for r in unbound:
max_atoms = 0
closest = None
for cid in chain_ids:
close = chain_map[cid].get(r, None)
if close is not None:
if close > max_atoms:
closest = cid
max_atoms = close
if closest is not None:
closest_chain_map[closest].append(r)
else:
unclassified.append(r)
return {
cid: Residues(residues)
for cid, residues in closest_chain_map.items()
}, Residues(unclassified)
def get_shell_of_residues(residues, dist_cutoff):
'''
Get a shell of whole residues from the same model as the atoms in residues,
within a user-defined cut-off distance surrounding residues. Expects
all residues to be within the same model.
'''
from chimerax.geometry import find_close_points
from chimerax.atomic import selected_atoms, Atoms, concatenate
us = residues.unique_structures
selatoms = residues.atoms
if len(us) != 1:
raise Exception(
'selection should contain atoms from a single molecule!')
allres = us[0].residues
unsel_residues = allres.subtract(residues)
unselected_atoms = unsel_residues.atoms
selcoords = selatoms.coords
unselcoords = unselected_atoms.coords
ignore, shell_indices = find_close_points(selcoords, unselcoords,
dist_cutoff)
shell_residues = unselected_atoms[shell_indices].unique_residues
return shell_residues
def restrain_small_ligands(model,
distance_cutoff=4,
heavy_atom_limit=3,
spring_constant=5000,
bond_to_carbon=False):
'''
Residues with a small number of heavy atoms can be problematic in MDFF if
unrestrained, since if knocked out of density they tend to simply keep
going. It is best to restrain them with distance restraints to suitable
surrounding atoms or, failing that, to their starting positions.
Args:
* model:
- a :class:`chimerax.atomic.AtomicStructure` instance
* distance_cutoff (default = 3.5):
- radius in Angstroms to look for candidate heavy atoms for distance
restraints. If no candidates are found, a position restraint will
be applied instead.
* heavy_atom_limit (default = 3):
- Only residues with a number of heavy atoms less than or equal to
`heavy_atom_limit` will be restrained
* spring_constant (default = 500):
- strength of each restraint, in :math:`kJ mol^{-1} nm^{-2}`
* bond_to_carbon (default = `False`):
- if `True`, only non-carbon heavy atoms will be restrained using
distance restraints.
'''
from chimerax.atomic import Residue, Residues
residues = model.residues
ligands = residues[residues.polymer_types == Residue.PT_NONE]
small_ligands = Residues([
r for r in ligands
if len(r.atoms[r.atoms.element_names != 'H']) < heavy_atom_limit
])
from .. import session_extensions as sx
drm = sx.get_distance_restraint_mgr(model)
prm = sx.get_position_restraint_mgr(model)
all_heavy_atoms = model.atoms[model.atoms.element_names != 'H']
if not bond_to_carbon:
all_heavy_atoms = all_heavy_atoms[all_heavy_atoms.element_names != 'C']
all_heavy_coords = all_heavy_atoms.coords
from chimerax.geometry import find_close_points, distance
for r in small_ligands:
r_heavy_atoms = r.atoms[r.atoms.element_names != 'H']
if not bond_to_carbon:
r_non_carbon_atoms = r_heavy_atoms[
r_heavy_atoms.element_names != 'C']
if not len(r_non_carbon_atoms):
# No non-carbon heavy atoms. Apply position restraints
prs = prm.get_restraints(r_heavy_atoms)
prs.targets = prs.atoms.coords
prs.spring_constants = spring_constant
prs.enableds = True
continue
r_heavy_atoms = r_non_carbon_atoms
r_indices = all_heavy_atoms.indices(r_heavy_atoms)
r_coords = r_heavy_atoms.coords
applied_drs = False
for ra, ri, rc in zip(r_heavy_atoms, r_indices, r_coords):
_, found_i = find_close_points([rc], all_heavy_coords,
distance_cutoff)
found_i = found_i[found_i != ri]
num_drs = 0
for fi in found_i:
if fi in r_indices:
continue
dr = drm.add_restraint(ra, all_heavy_atoms[fi])
dr.spring_constant = spring_constant
dr.target = distance(rc, all_heavy_coords[fi])
dr.enabled = True
num_drs += 1
# applied_drs = True
if num_drs < 3:
# Really need at least 3 distance restraints (probably 4, actually,
# but we don't want to be *too* restrictive) to be stable in 3D
# space. If we have fewer than that, add position restraints to be
# sure.
prs = prm.add_restraints(r_heavy_atoms)
prs.targets = prs.atoms.coords
prs.spring_constants = spring_constant
prs.enableds = True
def find_clashes(session,
test_atoms,
assumed_max_vdw=2.1,
attr_name=defaults["attr_name"],
bond_separation=defaults["bond_separation"],
clash_threshold=defaults["clash_threshold"],
distance_only=None,
hbond_allowance=defaults["clash_hbond_allowance"],
inter_model=True,
inter_submodel=False,
intra_model=True,
intra_res=False,
intra_mol=True,
res_separation=None,
restrict="any"):
"""Detect steric clashes/contacts
'test_atoms' should be an Atoms collection.
'restrict' can be one of:
- 'any': interactions involving at least one atom from 'test_atoms' will be found
- 'both': interactions involving only atoms from 'test_atoms' will be found
- 'cross': interactions involving exactly one atom from 'test_atoms' will be found
- an Atoms collection : interactions between 'test_atoms' and the 'restrict' atoms will be found
The "clash value" is the sum of the VDW radii minus the distance, which must exceed 'clash_threshold'.
'hbond_allowance' is how much the clash value is reduced if one
atom is a donor and the other an acceptor.
If 'distance_only' is set (in which case it must be a positive numeric
value), then both VDW radii, clash_threshold, and hbond_allowance are
ignored and the center-center distance between the atoms must be <= the given value.
Atom pairs are eliminated from consideration if they are less than
or equal to 'bond_separation' bonds apart.
Intra-residue clashes are ignored unless intra_res is True.
Intra-model clashes are ignored unless intra_model is True.
Intra-molecule (covalently connected fragment) clashes are ignored
unless intra_mol is True.
Inter-(sibling)submodel clashes are ignored unless inter_submodel is True.
Inter-model clashes are ignored unless inter_model is True.
If res_separation is not None, it should be a positive integer -- in which
case for residues in the same chain, clashes/contacts are ignored unless
the residues are at least that far apart in the sequence.
Returns a dictionary keyed on atoms, with values that are
dictionaries keyed on clashing atom with value being the clash value.
"""
from chimerax.atomic import Structure
use_scene_coords = inter_model and len(
[m for m in session.models if isinstance(m, Structure)]) > 1
# use the fast _closepoints module to cut down candidate atoms if we
# can (since _closepoints doesn't know about "non-bonded" it isn't as
# useful as it might otherwise be)
if restrict == "any":
if inter_model:
from chimerax.atomic import all_atoms
search_atoms = all_atoms(session)
else:
from chimerax.atomic import structure_atoms
search_atoms = structure_atoms(test_atoms.unique_structures)
elif restrict == "cross":
if inter_model:
from chimerax.atomic import all_atoms
universe_atoms = all_atoms(session)
else:
from chimerax.atomic import structure_atoms
universe_atoms = structure_atoms(test_atoms.unique_structures)
other_atoms = universe_atoms.subtract(test_atoms)
if distance_only:
cutoff = distance_only
else:
cutoff = 2.0 * assumed_max_vdw - clash_threshold
if use_scene_coords:
test_coords = test_atoms.scene_coords
other_coords = other_atoms.scene_coords
else:
test_coords = test_atoms.coords
other_coords = other_atoms.coords
from chimerax.geometry import find_close_points
t_close, o_close = find_close_points(test_coords, other_coords, cutoff)
test_atoms = test_atoms[t_close]
search_atoms = other_atoms[o_close]
elif not isinstance(restrict, str):
search_atoms = restrict
else:
search_atoms = test_atoms
if res_separation is not None:
chain_pos = {}
for s in test_atoms.unique_structures:
for c in s.chains:
for i, r in enumerate(c.residues):
if r:
chain_pos[r] = i
from chimerax.atom_search import AtomSearchTree
tree = AtomSearchTree(search_atoms, scene_coords=inter_model)
clashes = {}
from chimerax.geometry import distance
intra_mol_map = {}
for a in test_atoms:
if distance_only:
cutoff = distance_only
else:
cutoff = a.radius + assumed_max_vdw - clash_threshold
crd = a.scene_coord if use_scene_coords else a.coord
nearby = tree.search(crd, cutoff)
if not nearby:
continue
need_expansion = [a]
exclusions = set(need_expansion)
for i in range(bond_separation):
next_need = []
for expand in need_expansion:
for n in expand.neighbors:
if n in exclusions:
continue
exclusions.add(n)
next_need.append(n)
need_expansion = next_need
if not intra_mol and a not in intra_mol_map:
connected = set([a])
to_do = list(a.neighbors)
while to_do:
conn = to_do.pop()
connected.add(conn)
for nb in conn.neighbors:
if nb not in connected:
to_do.append(nb)
for ca in connected:
intra_mol_map[ca] = connected
for nb in nearby:
if nb in exclusions:
continue
if not intra_res and a.residue == nb.residue:
continue
if not intra_mol and nb in intra_mol_map[a]:
continue
if not inter_model and a.structure != nb.structure:
continue
if not intra_model and a.structure == nb.structure:
continue
if a in clashes and nb in clashes[a]:
continue
if res_separation is not None:
if a.residue.chain is not None and a.residue.chain == nb.residue.chain:
if abs(chain_pos[a.residue] -
chain_pos[nb.residue]) < res_separation:
continue
if not inter_submodel \
and a.structure.id and nb.structure.id \
and a.structure.id[0] == nb.structure.id[0] \
and a.structure.id[:-1] == nb.structure.id[:-1] \
and a.structure.id[1:] != nb.structure.id[1:]:
continue
if use_scene_coords:
a_crd, nb_crd = a.scene_coord, nb.scene_coord
else:
a_crd, nb_crd = a.coord, nb.coord
if distance_only:
clash = distance_only - distance(a_crd, nb_crd)
else:
clash = a.radius + nb.radius - distance(a_crd, nb_crd)
if hbond_allowance and not distance_only:
if (_donor(a) and _acceptor(nb)) or (_donor(nb)
and _acceptor(a)):
clash -= hbond_allowance
if distance_only:
if clash < 0.0:
continue
elif clash < clash_threshold:
continue
clashes.setdefault(a, {})[nb] = clash
clashes.setdefault(nb, {})[a] = clash
return clashes
