Index

A

add_atoms() (gimbal.molecule.BaseMolecule method) add_molecules() (gimbal.molecule.MoleculeBundle method) add_subs() (gimbal.substitute.SubLib method) align_axis() (in module gimbal.displace) align_pos() (in module gimbal.displace)

angax() (in module gimbal.displace) angunits (in module gimbal.constants) arccos() (in module gimbal.constants) assign_rotor() (in module gimbal.symmetry) axes (gimbal.displace.VectorParser attribute)

B

BaseMolecule (class in gimbal.molecule) bend() (in module gimbal.measure) bnadd (gimbal.displace.VectorParser attribute)

bnmul (gimbal.displace.VectorParser attribute) bnop (gimbal.displace.VectorParser attribute) build_adjmat() (in module gimbal.bonding)

C

cart_jumble() (in module gimbal.symmetry) centre_mass() (gimbal.molecule.Molecule method) (in module gimbal.displace) comment (gimbal.molecule.BaseMolecule attribute), [1] (gimbal.molecule.Molecule attribute)

conv() (in module gimbal.constants) convert() (in module gimbal.fileio) copy() (gimbal.molecule.BaseMolecule method) (gimbal.molecule.Molecule method) (gimbal.molecule.MoleculeBundle method) covrad (in module gimbal.constants)

E

edgetors() (in module gimbal.measure) elem (gimbal.molecule.BaseMolecule attribute), [1] (gimbal.molecule.Molecule attribute) (gimbal.substitute.SubLib attribute)

eneunits (in module gimbal.constants) expr (gimbal.displace.VectorParser attribute)

G

generate_parser() (gimbal.displace.VectorParser method) get_centremass() (in module gimbal.displace) get_covrad() (in module gimbal.constants) get_formula() (gimbal.molecule.Molecule method) get_mass() (gimbal.molecule.Molecule method) (in module gimbal.constants) get_num() (in module gimbal.constants) get_optarg() (in module gimbal.fileio) get_sub() (gimbal.substitute.SubLib method)

gimbal (module) gimbal.bonding (module) gimbal.constants (module) gimbal.displace (module) gimbal.fileio (module) gimbal.kabsch (module) gimbal.measure (module) gimbal.molecule (module) gimbal.substitute (module) gimbal.symmetry (module)

I

import_bundle() (in module gimbal.molecule)

import_molecule() (in module gimbal.molecule) import_sub() (in module gimbal.substitute)

K

kabsch() (in module gimbal.kabsch)

L

lenunits (in module gimbal.constants)

M

map_onto() (in module gimbal.kabsch) mass (in module gimbal.constants) masunits (in module gimbal.constants) match_to_ref() (gimbal.molecule.Molecule method) (gimbal.molecule.MoleculeBundle method)

measure() (gimbal.molecule.Molecule method) (gimbal.molecule.MoleculeBundle method) Molecule (class in gimbal.molecule) MoleculeBundle (class in gimbal.molecule) molecules (gimbal.molecule.MoleculeBundle attribute), [1]

N

natm (gimbal.molecule.BaseMolecule attribute) (gimbal.molecule.Molecule attribute)

nmol (gimbal.molecule.MoleculeBundle attribute) num_loops() (in module gimbal.bonding) num_neighbours() (in module gimbal.bonding)

O

oop() (in module gimbal.measure) opt_multi() (in module gimbal.kabsch)

opt_permute() (in module gimbal.kabsch) opt_ref() (in module gimbal.kabsch)

P

path_len() (in module gimbal.bonding) planeang() (in module gimbal.measure) planetors() (in module gimbal.measure)

power() (in module gimbal.bonding) principal_axes() (in module gimbal.symmetry) print_vec (gimbal.molecule.BaseMolecule attribute) (gimbal.molecule.Molecule attribute)

R

read() (gimbal.molecule.Molecule method) (gimbal.molecule.MoleculeBundle method) read_auto() (in module gimbal.fileio) read_col() (in module gimbal.fileio) read_gdat() (in module gimbal.fileio) read_multiple() (in module gimbal.fileio) read_single() (in module gimbal.fileio) read_traj() (in module gimbal.fileio) read_xyz() (in module gimbal.fileio) read_zmt() (in module gimbal.fileio)

rearrange() (gimbal.molecule.BaseMolecule method) (gimbal.molecule.Molecule method) (gimbal.molecule.MoleculeBundle method) revert() (gimbal.molecule.BaseMolecule method) (gimbal.molecule.MoleculeBundle method) rm_atoms() (gimbal.molecule.BaseMolecule method) rm_molecules() (gimbal.molecule.MoleculeBundle method) rmsd() (in module gimbal.kabsch) rotate() (gimbal.molecule.Molecule method) (in module gimbal.displace) rotmat() (in module gimbal.displace)

S

save() (gimbal.molecule.BaseMolecule method) (gimbal.molecule.MoleculeBundle method) save_comment (gimbal.molecule.BaseMolecule attribute) save_elem (gimbal.molecule.BaseMolecule attribute) save_molecules (gimbal.molecule.MoleculeBundle attribute) save_print_vec (gimbal.molecule.BaseMolecule attribute) save_vec (gimbal.molecule.BaseMolecule attribute) save_xyz (gimbal.molecule.BaseMolecule attribute)

saved (gimbal.molecule.BaseMolecule attribute) (gimbal.molecule.MoleculeBundle attribute) stre() (in module gimbal.measure) SubLib (class in gimbal.substitute) subst() (gimbal.molecule.Molecule method) (in module gimbal.substitute) sym (in module gimbal.constants) symmetrize() (in module gimbal.symmetry) syn (gimbal.substitute.SubLib attribute)

T

timunits (in module gimbal.constants) tors() (in module gimbal.measure)

translate() (gimbal.molecule.Molecule method) (in module gimbal.displace)

U

unit_vec() (in module gimbal.constants)

unop (gimbal.displace.VectorParser attribute)

V

vec (gimbal.molecule.BaseMolecule attribute), [1] (gimbal.molecule.Molecule attribute)

VectorParser (class in gimbal.displace)

W

write() (gimbal.molecule.Molecule method) (gimbal.molecule.MoleculeBundle method) write_auto() (in module gimbal.fileio) write_col() (in module gimbal.fileio) write_gdat() (in module gimbal.fileio)

write_multiple() (in module gimbal.fileio) write_single() (in module gimbal.fileio) write_traj() (in module gimbal.fileio) write_xyz() (in module gimbal.fileio) write_zmt() (in module gimbal.fileio) write_zmtvar() (in module gimbal.fileio)

X

xyz (gimbal.displace.VectorParser attribute), [1] (gimbal.molecule.BaseMolecule attribute), [1] (gimbal.molecule.Molecule attribute) (gimbal.substitute.SubLib attribute)