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.show module angstrom.visualize.tools module append() (angstrom.trajectory.Trajectory method) 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)

D

delete() (angstrom.molecule.Molecule method)

F

frac2car() (angstrom.molecule.Cell method)

G

get_angles() (angstrom.molecule.Molecule method) 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_chemical_formula() (angstrom.molecule.Molecule method) get_dihedrals() (angstrom.molecule.Molecule method) get_impropers() (angstrom.molecule.Molecule method) get_molecular_weight() (angstrom.molecule.Molecule method) get_molecule_center() (in module angstrom.geometry.geometry) get_topology() (angstrom.molecule.Molecule method) grid() (angstrom.geometry.Plane method)

I

inv() (angstrom.geometry.Quaternion method)

M

module angstrom.geometry.geometry angstrom.molecule.bonds angstrom.molecule.read angstrom.molecule.write angstrom.trajectory.read angstrom.trajectory.write angstrom.visualize.render angstrom.visualize.show angstrom.visualize.tools

Molecule (class in angstrom.molecule)

N

np() (angstrom.geometry.Quaternion method)

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_image() (in module angstrom.visualize.render) render_video() (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)