def get_chimera(self, session, coordsets=False, filereader=None):
"""returns a chimerax equivalent of self"""
struc = AtomicStructure(session, name=self.name)
struc.comment = self.comment
self.update_chix(struc)
if coordsets and filereader is not None and filereader.all_geom is not None:
#make a trajectory
#each list of atoms in filereader.all_geom is a frame in the trajectory
#replace previous coordinates
#this matters when a filereader is given because the
#geometry created from a filereader (which was probably passed as geom)
#is the last geometry in the log or xyz file
xyzs = self.all_geom_coordsets(filereader)
struc.add_coordsets(xyzs, replace=True)
struc.active_coordset_id = len(xyzs)
# if it's a frequency file, draw TS bonds for imaginary modes
if filereader is not None and "frequency" in filereader.other:
for mode in filereader.other["frequency"].data:
if mode.frequency < 0:
max_disp = max(np.linalg.norm(x) for x in mode.vector)
cur_coords = self.coords
coord_forward = self.coords + (0.2 /
max_disp) * mode.vector
coord_reverse = self.coords - (0.2 /
max_disp) * mode.vector
forward_connectivity = np.zeros(
(len(self.atoms), len(self.atoms)))
reverse_connectivity = np.zeros(
(len(self.atoms), len(self.atoms)))
self.update_geometry(coord_forward)
self.refresh_connected()
for i, atom1 in enumerate(self.atoms):
for j, atom2 in enumerate(self.atoms[:i]):
if atom1 in atom2.connected:
forward_connectivity[i, j] = 1
forward_connectivity[j, i] = 1
self.update_geometry(coord_reverse)
self.refresh_connected()
for i, atom1 in enumerate(self.atoms):
for j, atom2 in enumerate(self.atoms[:i]):
if atom1 in atom2.connected:
reverse_connectivity[i, j] = 1
reverse_connectivity[j, i] = 1
changes = forward_connectivity - reverse_connectivity
for i, atom1 in enumerate(self.atoms):
for j, atom1 in enumerate(self.atoms[:i]):
if changes[i, j] != 0:
sel = _FauxAtomSelection(
atoms=(struc.atoms[i], struc.atoms[j]))
tsbond(session, sel)
self.update_geometry(cur_coords)
return struc
def _read_block(session, stream):
# First line should be an integer count of the number of
# atoms in the block. Each block gets turned into an
# AtomicStructure instance.
count_line = stream.readline()
if not count_line:
return None
try:
count = int(count_line)
except ValueError:
# XXX: Should emit an error message
return None
from chimerax.atomic import AtomicStructure
s = AtomicStructure(session)
# Next line is a comment line
s.comment = stream.readline().strip()
# There should be "count" lines of atoms.
from numpy import array, float64
residue = s.new_residue("UNK", 'A', 1)
element_count = {}
for n in range(count):
atom_line = stream.readline()
if not atom_line:
# XXX: Should emit an error message
return None
parts = atom_line.split()
if len(parts) != 4:
# XXX: Should emit an error message
return None
# Extract available data
element = parts[0]
xyz = [float(v) for v in parts[1:]]
# Convert to required initializers
# XXX: May need to convert element to usable form
n = element_count.get(element, 0) + 1
name = element + str(n)
element_count[element] = n
# Create atom
atom = s.new_atom(name, element)
atom.coord = array(xyz, dtype=float64)
residue.add_atom(atom)
s.connect_structure()
s.new_atoms() # tell structure it needs to update
return s
def _read_block(session, stream, line_number):
# XYZ files are stored in blocks, with each block representing
# a set of atoms. This function reads a single block
# and builds a ChimeraX AtomStructure instance containing
# the atoms listed in the block.
# First line should be an integer count of the number of
# atoms in the block.
count_line = stream.readline()
if not count_line:
# Reached EOF, normal termination condition
return None, line_number
line_number += 1
try:
count = int(count_line)
except ValueError:
session.logger.error("line %d: atom count missing" % line_number)
return None, line_number
# Create the AtomicStructure instance for atoms in this block.
# All atoms in the structure are placed in one residue
# since XYZ format does not partition atoms into groups.
from chimerax.atomic import AtomicStructure
from numpy import array, float64
s = AtomicStructure(session)
residue = s.new_residue("UNK", 'A', 1)
# XYZ format supplies the atom element type only, but
# ChimeraX keeps track of both the element type and
# a unique name for each atom. To construct the unique
# atom name, the # 'element_count' dictionary is used
# to track the number of atoms of each element type so far,
# and the current count is used to build unique atom names.
element_count = {}
# Next line is a comment line
s.comment = stream.readline().strip()
line_number += 1
# There should be "count" lines of atoms.
for n in range(count):
atom_line = stream.readline()
if not atom_line:
session.logger.error("line %d: atom data missing" % line_number)
return None, line_number
line_number += 1
# Extract available data
parts = atom_line.split()
if len(parts) != 4:
session.logger.error("line %d: atom data malformatted" %
line_number)
return None, line_number
# Convert to required parameters for creating atom.
# Since XYZ format only required atom element, we
# create a unique atom name by putting a number after
# the element name.
xyz = [float(v) for v in parts[1:]]
element = parts[0]
n = element_count.get(element, 0) + 1
name = element + str(n)
element_count[element] = n
# Create atom in AtomicStructure instance 's',
# set its coordinates, and add to residue
atom = s.new_atom(name, element)
atom.coord = array(xyz, dtype=float64)
residue.add_atom(atom)
# Use AtomicStructure method to add bonds based on interatomic distances
s.connect_structure()
# Updating state such as atom types while adding atoms iteratively
# is unnecessary (and generally incorrect for partial structures).
# When all atoms have been added, the instance is notified to
# tell it to update internal state.
s.new_atoms()
# Return AtomicStructure instance and current line number
return s, line_number
def get_chimera(self, session, coordsets=False, filereader=None):
"""returns a chimerax equivalent of self"""
struc = AtomicStructure(session, name=self.name)
struc.comment = self.comment
self.update_chix(struc)
if coordsets and filereader is not None and filereader.all_geom is not None:
#make a trajectory
#each list of atoms in filereader.all_geom is a frame in the trajectory
#replace previous coordinates
#this matters when a filereader is given because the
#geometry created from a filereader (which was probably passed as geom)
#is the last geometry in the log or xyz file
xyzs = self.all_geom_coordsets(filereader)
struc.add_coordsets(xyzs, replace=True)
struc.active_coordset_id = len(xyzs)
# if it's a frequency file, draw TS bonds for imaginary modes
if filereader is not None and "frequency" in filereader.other:
for mode in filereader.other["frequency"].data:
if mode.frequency < 0:
max_disp = max(np.linalg.norm(x) for x in mode.vector)
cur_coords = self.coords
coord_forward = self.coords + (0.2 /
max_disp) * mode.vector
coord_reverse = self.coords - (0.2 /
max_disp) * mode.vector
forward_connectivity = np.zeros(
(len(self.atoms), len(self.atoms)))
reverse_connectivity = np.zeros(
(len(self.atoms), len(self.atoms)))
self.update_geometry(coord_forward)
self.refresh_connected()
for i, atom1 in enumerate(self.atoms):
for j, atom2 in enumerate(self.atoms[:i]):
if atom1 in atom2.connected:
forward_connectivity[i, j] = 1
forward_connectivity[j, i] = 1
self.update_geometry(coord_reverse)
self.refresh_connected()
for i, atom1 in enumerate(self.atoms):
for j, atom2 in enumerate(self.atoms[:i]):
if atom1 in atom2.connected:
reverse_connectivity[i, j] = 1
reverse_connectivity[j, i] = 1
changes = forward_connectivity - reverse_connectivity
for i, atom1 in enumerate(self.atoms):
for j, atom1 in enumerate(self.atoms[:i]):
if changes[i, j] != 0:
sel = _FauxAtomSelection(
atoms=(struc.atoms[i], struc.atoms[j]))
tsbond(session, sel)
self.update_geometry(cur_coords)
if filereader is not None and "Mulliken Charges" in filereader.other:
for atom, charge in zip(struc.atoms,
filereader.other["Mulliken Charges"]):
atom.mullikenCharge = charge
atom.charge = charge
if not any(attr[0] == "mullikenCharge"
for attr in atom.custom_attrs):
atom.register_attr(session,
"mullikenCharge",
"seqcrow ResidueCollection.get_chimera",
attr_type=float)
if not any(attr[0] == "charge" for attr in atom.custom_attrs):
atom.register_attr(session,
"charge",
"seqcrow ResidueCollection.get_chimera",
attr_type=float)
if filereader is not None and "NPA Charges" in filereader.other:
for atom, charge in zip(struc.atoms,
filereader.other["NPA Charges"]):
atom.npaCharge = charge
atom.charge = charge
if not any(attr[0] == "npaCharge"
for attr in atom.custom_attrs):
atom.register_attr(session,
"npaCharge",
"seqcrow ResidueCollection.get_chimera",
attr_type=float)
if not any(attr[0] == "charge" for attr in atom.custom_attrs):
atom.register_attr(session,
"charge",
"seqcrow ResidueCollection.get_chimera",
attr_type=float)
if filereader is not None and "Nuclear ZEff" in filereader.other:
for atom, zeff in zip(struc.atoms,
filereader.other["Nuclear ZEff"]):
atom.Zeff = zeff
if not any(attr[0] == "Zeff" for attr in atom.custom_attrs):
atom.register_attr(session,
"Zeff",
"seqcrow ResidueCollection.get_chimera",
attr_type=float)
if filereader is not None and "Nuclear spins" in filereader.other:
for atom, spin in zip(struc.atoms,
filereader.other["Nuclear spins"]):
atom.nuclearSpin = spin
if not any(attr[0] == "nuclearSpin"
for attr in atom.custom_attrs):
atom.register_attr(session,
"nuclearSpin",
"seqcrow ResidueCollection.get_chimera",
attr_type=int)
if filereader is not None:
if any(attr[0] == "aarontools_filereader"
for attr in struc.custom_attrs):
struc.register_attr(
session,
"filereader",
"SEQCROW",
attr_type=FileReader,
)
struc.filereader = filereader
return struc