src.molecule.Molecule Member List

This is the complete list of members for src.molecule.Molecule, including all inherited members.

__add__(self, other)	src.molecule.Molecule
__deepcopy__(self, memo)	src.molecule.Molecule
__delitem__(self, key)	src.molecule.Molecule
__getattr__(self, key)	src.molecule.Molecule
__getitem__(self, key)	src.molecule.Molecule
__iadd__(self, other)	src.molecule.Molecule
__init__(self, fnm=None, ftype=None, top=None, ttype=None, kwargs)	src.molecule.Molecule
__iter__(self)	src.molecule.Molecule
__len__(self)	src.molecule.Molecule
__setattr__(self, key, value)	src.molecule.Molecule
add_quantum(self, other)	src.molecule.Molecule
add_virtual_site(self, idx, kwargs)	src.molecule.Molecule
align(self, smooth=False, center=True, center_mass=False, atom_select=None)	src.molecule.Molecule
align_by_moments(self)	src.molecule.Molecule
align_center(self)	src.molecule.Molecule
aliphatic_hydrogens(self)	src.molecule.Molecule
all_pairwise_rmsd(self)	src.molecule.Molecule
append(self, other)	src.molecule.Molecule
atom_select(self, atomslice, build_topology=True)	src.molecule.Molecule
atom_stack(self, other)	src.molecule.Molecule
atomname	src.molecule.Molecule
boxes	src.molecule.Molecule
build_bonds(self)	src.molecule.Molecule
build_topology(self, force_bonds=True, kwargs)	src.molecule.Molecule
built_bonds	src.molecule.Molecule
center(self, center_mass=False)	src.molecule.Molecule
center_of_mass(self)	src.molecule.Molecule
charge	src.molecule.Molecule
comms	src.molecule.Molecule
Data	src.molecule.Molecule
distance_displacement(self)	src.molecule.Molecule
distance_matrix(self, pbc=True)	src.molecule.Molecule
edit_qcrems(self, in_dict, subcalc=None)	src.molecule.Molecule
find_angles(self)	src.molecule.Molecule
find_clashes(self, thre=0.0, pbc=True, groups=None)	src.molecule.Molecule
find_dihedrals(self)	src.molecule.Molecule
find_rings(self, max_size=6)	src.molecule.Molecule
fout	src.molecule.Molecule
Funnel	src.molecule.Molecule
get_populations(self)	src.molecule.Molecule
get_reaxff_atom_types(self)	src.molecule.Molecule
load_frames(self, fnm, ftype=None, kwargs)	src.molecule.Molecule
load_popxyz(self, fnm)	src.molecule.Molecule
measure_angles(self, i, j, k)	src.molecule.Molecule
measure_dihedrals(self, i, j, k, l)	src.molecule.Molecule
measure_distances(self, i, j)	src.molecule.Molecule
molecules	src.molecule.Molecule
mult	src.molecule.Molecule
openmm_boxes(self)	src.molecule.Molecule
openmm_positions(self)	src.molecule.Molecule
order_by_connectivity(self, m, i, currList, max_min_path)	src.molecule.Molecule
pathwise_rmsd(self, align=True)	src.molecule.Molecule
positive_resid	src.molecule.Molecule
qm_mulliken_charges	src.molecule.Molecule
qm_mulliken_spins	src.molecule.Molecule
radius_of_gyration(self)	src.molecule.Molecule
read_arc(self, fnm, kwargs)	src.molecule.Molecule
read_charmm(self, fnm, kwargs)	src.molecule.Molecule
read_com(self, fnm, kwargs)	src.molecule.Molecule
read_comm_charge_mult(self, verbose=False)	src.molecule.Molecule
read_dcd(self, fnm, kwargs)	src.molecule.Molecule
read_gro(self, fnm, kwargs)	src.molecule.Molecule
read_inpcrd(self, fnm, kwargs)	src.molecule.Molecule
read_mdcrd(self, fnm, kwargs)	src.molecule.Molecule
read_mol2(self, fnm, kwargs)	src.molecule.Molecule
read_pdb(self, fnm, kwargs)	src.molecule.Molecule
read_qcesp(self, fnm, kwargs)	src.molecule.Molecule
read_qcin(self, fnm, kwargs)	src.molecule.Molecule
read_qcout(self, fnm, errok=None, kwargs)	src.molecule.Molecule
read_qcschema(self, schema, kwargs)	src.molecule.Molecule
read_qdata(self, fnm, kwargs)	src.molecule.Molecule
Read_Tab	src.molecule.Molecule
read_xyz(self, fnm, kwargs)	src.molecule.Molecule
read_xyz0(self, fnm, kwargs)	src.molecule.Molecule
ref_rmsd(self, i, align=True)	src.molecule.Molecule
reorder_according_to(self, other)	src.molecule.Molecule
reorder_indices(self, other)	src.molecule.Molecule
repair(self, key, klast)	src.molecule.Molecule
replace_peratom(self, key, orig, want)	src.molecule.Molecule
replace_peratom_conditional(self, key1, cond, key2, orig, want)	src.molecule.Molecule
require(self, args)	src.molecule.Molecule
require_boxes(self)	src.molecule.Molecule
require_resid(self)	src.molecule.Molecule
require_resname(self)	src.molecule.Molecule
resid	src.molecule.Molecule
resname	src.molecule.Molecule
rigid_water(self)	src.molecule.Molecule
rotate_bond(self, frame, aj, ak, increment=15)	src.molecule.Molecule
rotate_check_clash(self, frame, rotate_index, thresh_hyd=1.4, thresh_hvy=1.8, printLevel=1)	src.molecule.Molecule
split(self, fnm=None, ftype=None, method="chunks", num=None)	src.molecule.Molecule
top_settings	src.molecule.Molecule
topology	src.molecule.Molecule
without(self, args)	src.molecule.Molecule
write(self, fnm=None, ftype=None, append=False, selection=None, kwargs)	src.molecule.Molecule
write_arc(self, selection, kwargs)	src.molecule.Molecule
write_dcd(self, selection, kwargs)	src.molecule.Molecule
write_gro(self, selection, kwargs)	src.molecule.Molecule
write_inpcrd(self, selection, sn=None, kwargs)	src.molecule.Molecule
write_lammps_data(self, selection, kwargs)	src.molecule.Molecule
write_mdcrd(self, selection, kwargs)	src.molecule.Molecule
write_molproq(self, selection, kwargs)	src.molecule.Molecule
write_pdb(self, selection, kwargs)	src.molecule.Molecule
write_qcin(self, selection, kwargs)	src.molecule.Molecule
write_qdata(self, selection, kwargs)	src.molecule.Molecule
Write_Tab	src.molecule.Molecule
write_xyz(self, selection, kwargs)	src.molecule.Molecule
xyzs	src.molecule.Molecule