__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 | |