| __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 | |
1.8.13
