Index

A

align() (angstrom.molecule.Molecule method) align_vectors() (in module angstrom.geometry.geometry) angstrom.geometry.geometry (module) angstrom.molecule.bonds (module) angstrom.molecule.read (module) angstrom.molecule.write (module) angstrom.trajectory.read (module)

angstrom.trajectory.write (module) angstrom.visualize.render (module) angstrom.visualize.render_settings (module) angstrom.visualize.show (module) angstrom.visualize.tools (module) arrange_molecules() (in module angstrom.visualize.tools) arrange_positions() (in module angstrom.visualize.tools)

C

calculate_edges() (angstrom.molecule.Cell method) calculate_vectors() (angstrom.molecule.Cell method) calculate_vertices() (angstrom.molecule.Cell method)

calculate_volume() (angstrom.molecule.Cell method) car2frac() (angstrom.molecule.Cell method) Cell (class in angstrom.molecule) center() (angstrom.molecule.Molecule method)

F

frac2car() (angstrom.molecule.Cell method)

G

get_blender_settings() (in module angstrom.visualize.render_settings) get_bonds() (angstrom.molecule.Molecule method) (in module angstrom.molecule.bonds) get_center() (angstrom.geometry.Plane method) (angstrom.molecule.Molecule method) (angstrom.trajectory.Trajectory method)

get_molecular_weight() (angstrom.molecule.Molecule method) get_molecule_center() (in module angstrom.geometry.geometry) grid() (angstrom.geometry.Plane method)

I

inv() (angstrom.geometry.Quaternion method)

M

Molecule (class in angstrom.molecule)

N

np() (angstrom.geometry.Quaternion method)

O

openbabel_settings (in module angstrom.visualize.render_settings)

P

Plane (class in angstrom.geometry)

Q

Quaternion (class in angstrom.geometry)

R

read() (angstrom.molecule.Molecule method) (angstrom.trajectory.Trajectory method) read_xyz() (in module angstrom.molecule.read) read_xyz_traj() (in module angstrom.trajectory.read) reflect() (angstrom.geometry.Plane method) (angstrom.molecule.Molecule method)

render() (in module angstrom.visualize.render) render_blender() (in module angstrom.visualize.render) render_openbabel() (in module angstrom.visualize.render) render_vmd() (in module angstrom.visualize.render) replicate() (angstrom.molecule.Molecule method) rotate() (angstrom.molecule.Molecule method) rotation() (angstrom.geometry.Quaternion method)

S

set_cell() (angstrom.molecule.Molecule method)

show() (in module angstrom.visualize.show) supercell() (angstrom.molecule.Cell method)

T

to_list() (angstrom.molecule.Cell method)

Trajectory (class in angstrom.trajectory) translate() (angstrom.molecule.Molecule method)

W

write() (angstrom.molecule.Molecule method) (angstrom.trajectory.Trajectory method) write_cif() (in module angstrom.molecule.write)

write_molecule() (in module angstrom.molecule.write) write_pdb() (in module angstrom.molecule.write) write_xyz() (in module angstrom.molecule.write) write_xyz_traj() (in module angstrom.trajectory.write)

X

xyz() (angstrom.geometry.Quaternion method)