PyFrag
qmworks.plams.core.basemol.Molecule Member List

This is the complete list of members for qmworks.plams.core.basemol.Molecule, including all inherited members.

__add__(self, other)qmworks.plams.core.basemol.Molecule
__copy__(self) (defined in qmworks.plams.core.basemol.Molecule)qmworks.plams.core.basemol.Molecule
__getitem__(self, key)qmworks.plams.core.basemol.Molecule
__iadd__(self, other)qmworks.plams.core.basemol.Molecule
__init__(self, filename=None, inputformat=None, geometry=1, other) (defined in qmworks.plams.core.basemol.Molecule)qmworks.plams.core.basemol.Molecule
__iter__(self)qmworks.plams.core.basemol.Molecule
__len__(self)qmworks.plams.core.basemol.Molecule
__str__(self)qmworks.plams.core.basemol.Molecule
add_atom(self, atom, adjacent=None)qmworks.plams.core.basemol.Molecule
add_bond(self, arg1, arg2=None, order=1)qmworks.plams.core.basemol.Molecule
as_dict(self)qmworks.plams.core.basemol.Molecule
atoms (defined in qmworks.plams.core.basemol.Molecule)qmworks.plams.core.basemol.Molecule
bonds (defined in qmworks.plams.core.basemol.Molecule)qmworks.plams.core.basemol.Molecule
closest_atom(self, point, unit='angstrom')qmworks.plams.core.basemol.Molecule
copy(self, atoms=None)qmworks.plams.core.basemol.Molecule
delete_all_bonds(self)qmworks.plams.core.basemol.Molecule
delete_atom(self, atom)qmworks.plams.core.basemol.Molecule
delete_bond(self, arg1, arg2=None)qmworks.plams.core.basemol.Molecule
distance_to_mol(self, other, result_unit='angstrom', return_atoms=False)qmworks.plams.core.basemol.Molecule
distance_to_point(self, point, unit='angstrom', result_unit='angstrom')qmworks.plams.core.basemol.Molecule
find_bond(self, atom1, atom2)qmworks.plams.core.basemol.Molecule
from_dict(cls, atomBlock, bondBlock, properties)qmworks.plams.core.basemol.Molecule
get_center_of_mass(self, unit='angstrom')qmworks.plams.core.basemol.Molecule
get_formula(self)qmworks.plams.core.basemol.Molecule
get_mass(self)qmworks.plams.core.basemol.Molecule
guess_bonds(self)qmworks.plams.core.basemol.Molecule
lattice (defined in qmworks.plams.core.basemol.Molecule)qmworks.plams.core.basemol.Molecule
neighbors(self, atom)qmworks.plams.core.basemol.Molecule
properties (defined in qmworks.plams.core.basemol.Molecule)qmworks.plams.core.basemol.Molecule
read(self, filename, inputformat=None, frame=1)qmworks.plams.core.basemol.Molecule
readmol(self, f, frame) (defined in qmworks.plams.core.basemol.Molecule)qmworks.plams.core.basemol.Molecule
readmol2(self, f, frame) (defined in qmworks.plams.core.basemol.Molecule)qmworks.plams.core.basemol.Molecule
readpdb(self, f, frame) (defined in qmworks.plams.core.basemol.Molecule)qmworks.plams.core.basemol.Molecule
readxyz(self, f, frame) (defined in qmworks.plams.core.basemol.Molecule)qmworks.plams.core.basemol.Molecule
rotate(self, matrix)qmworks.plams.core.basemol.Molecule
rotate_bond(self, bond, atom, angle, unit='radian')qmworks.plams.core.basemol.Molecule
separate(self)qmworks.plams.core.basemol.Molecule
set_atoms_id(self)qmworks.plams.core.basemol.Molecule
translate(self, vector, unit='angstrom')qmworks.plams.core.basemol.Molecule
unset_atoms_id(self)qmworks.plams.core.basemol.Molecule
wrap(self, length, angle=2 *math.pi, length_unit='angstrom', angle_unit='radian')qmworks.plams.core.basemol.Molecule
write(self, filename, outputformat=None)qmworks.plams.core.basemol.Molecule
writemol(self, f) (defined in qmworks.plams.core.basemol.Molecule)qmworks.plams.core.basemol.Molecule
writemol2(self, f) (defined in qmworks.plams.core.basemol.Molecule)qmworks.plams.core.basemol.Molecule
writepdb(self, f) (defined in qmworks.plams.core.basemol.Molecule)qmworks.plams.core.basemol.Molecule
writexyz(self, f) (defined in qmworks.plams.core.basemol.Molecule)qmworks.plams.core.basemol.Molecule