def info_atoms(session, atoms=None, attribute="idatm_type"):
if atoms is None:
from chimerax.core.commands import atomspec
atoms = atomspec.everything(session)
results = atoms.evaluate(session)
residues = results.atoms.unique_residues
report_atoms(session.logger, results.atoms, attribute)
def info_distmat(session, atoms):
from scipy.spatial.distance import pdist, squareform
if atoms is None:
from chimerax.core.commands import atomspec
atoms = atomspec.everything(session)
results = atoms.evaluate(session)
atoms = results.atoms
coords = atoms.scene_coords
distmat = pdist(coords, "euclidean")
report_distmat(session.logger, atoms, distmat)
def info_models(session, atoms=None, type_=None, attribute="name"):
if atoms is None:
from chimerax.core.commands import atomspec
atoms = atomspec.everything(session)
results = atoms.evaluate(session)
if type_ is not None:
type_ = type_.lower()
models = [
m for m in results.models
if type_ is None or type(m).__name__.lower() == type_
]
report_models(session.logger, models, attribute)
def info_chains(session, atoms=None, attribute="chain_id"):
if atoms is None:
from chimerax.core.commands import atomspec
atoms = atomspec.everything(session)
results = atoms.evaluate(session)
chains = []
for m in results.models:
try:
chains.extend(m.chains)
except AttributeError:
# No chains, no problem
pass
report_chains(session.logger, chains, attribute)
def info_polymers(session, atoms=None):
if atoms is None:
from chimerax.core.commands import atomspec
atoms = atomspec.everything(session)
results = atoms.evaluate(session)
polymers = []
residues = results.atoms.unique_residues
from chimerax.atomic import AtomicStructure
for m in results.atoms.unique_structures:
try:
for p, ptype in m.polymers(AtomicStructure.PMS_TRACE_CONNECTS,
False):
if p.intersects(residues):
polymers.append(p)
except AttributeError:
# No chains, no problem
pass
report_polymers(session.logger, polymers)
def findclash(session,
spec=None,
make_pseudobonds=False,
log=True,
naming_style="command",
overlap_cutoff=0.6,
hbond_allowance=0.4,
bond_separation=4,
test="other",
intra_residue=False):
from chimerax.core.errors import LimitationError
from chimerax.atomic import Atoms
from chimerax.core.commands import atomspec
from chimerax.atomic.settings import settings
if test != "self":
raise LimitationError("findclash test \"%s\" not implemented" % test)
if hbond_allowance != 0:
session.logger.warning("Hydrogen bond finding is not implemented. "
"Setting hbond_allowance to 0.0.")
hbond_allowance = 0
if naming_style != "command" and naming_style != "command-line":
raise LimitationError("findclash naming style \"%s\" not implemented" %
naming_style)
if make_pseudobonds:
raise LimitationError("findclash make pseudobonds not implemented")
if spec is None:
spec = atomspec.everything(session)
results = spec.evaluate(session)
atoms = results.atoms
neighbors = _find_neighbors(atoms, bond_separation)
clashes = []
for i in range(len(atoms) - 1):
a = atoms[i]
if intra_residue:
# Want intra-residue contacts, so check all atoms
others = atoms[i + 1:]
else:
# Do not want intra-residue contacts, so remove atoms from residue
from numpy import logical_not
others = atoms[i + 1:]
residues = others.residues
# Generate mask for atoms from same residue
mask = others.residues.mask(Atoms([a.residue]))
others = others.filter(logical_not(mask))
# Remove atoms within "separation" bonds of this atom
others -= neighbors[a]
if len(others) > 0:
clashes.extend(
_find_clash_self(a, others, overlap_cutoff, hbond_allowance))
if log:
session.logger.info("Allowed overlap: %g" % overlap_cutoff)
session.logger.info("H-bond overlap reduction: %g" % hbond_allowance)
session.logger.info("Ignored contact between atoms separated by %d "
"bonds or less" % bond_separation)
session.logger.info("%d contacts" % len(clashes))
session.logger.info("atom1\tatom2\toverlap\tdistance")
save = settings.atomspec_contents
settings.atomspec_contents = "command"
msgs = ["%s\t%s\t%.3f\t%.3f" % c for c in clashes]
settings.atomspec_contents = save
session.logger.info('\n'.join(msgs))
session.logger.info("%d contacts" % len(clashes))