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 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