Index

A

add_transformation() (render_molecules.geometry.Geometry method) adjust_settings() (in module render_molecules.blender_utils) AMU_TO_KG (in module render_molecules.constants) angle_between() (in module render_molecules.geometry)

ANGSTROM_TO_BOHR (in module render_molecules.constants) ANGSTROM_TO_METERS (in module render_molecules.constants) assign_isosurface_material_based_on_sign() (in module render_molecules.blender_utils) Atom (class in render_molecules.atom)

B

Background BOHR_TO_ANGSTROM (in module render_molecules.constants)

BOHR_TO_METERS (in module render_molecules.constants) Bond (class in render_molecules.bond)

C

calculate_isosurface() (render_molecules.structure.CUBEfile method) check_3d_vector() (in module render_molecules.geometry) check_4x4_matrix() (in module render_molecules.geometry) color_srgb_to_scene_linear() (in module render_molecules.other_utils) Community Guidelines create_animation() (render_molecules.trajectory.Trajectory method) create_atoms() (render_molecules.structure.Structure method) create_bonds() (render_molecules.structure.Structure method) create_cylinder() (in module render_molecules.blender_utils)

create_hydrogen_bonds() (render_molecules.structure.Structure method) create_isosurface() (in module render_molecules.blender_utils) create_material() (in module render_molecules.blender_utils) create_mesh_of_atoms() (in module render_molecules.blender_utils) create_structure() (render_molecules.structure.Structure method) create_uv_sphere() (in module render_molecules.blender_utils) CUBEfile (class in render_molecules.structure) CYLINDER_LENGTH_FRACTION (in module render_molecules.constants) CYLINDER_LENGTH_FRACTION_SPLIT (in module render_molecules.constants)

D

delete_all_materials() (in module render_molecules.blender_utils) delete_all_objects() (in module render_molecules.blender_utils)

deselect_all_selected() (in module render_molecules.blender_utils) displace_atoms() (render_molecules.structure.Structure method)

E

Examples

F

find_all_string_in_list_of_strings() (in module render_molecules.other_utils) find_bonds_from_distances() (render_molecules.structure.Structure method) find_first_string_in_list_of_strings() (in module render_molecules.other_utils) from_cube_string() (render_molecules.atom.Atom class method) from_orca() (render_molecules.trajectory.Trajectory class method) from_sdf() (render_molecules.structure.Structure class method)

from_sdf_string() (render_molecules.atom.Atom class method) from_xsf() (render_molecules.structure.Structure class method) (render_molecules.trajectory.Trajectory class method) from_xyz() (render_molecules.structure.Structure class method) (render_molecules.trajectory.Trajectory class method) from_xyz_string() (render_molecules.atom.Atom class method)

G

generate_bond_order_bond() (render_molecules.structure.Structure method) Geometry (class in render_molecules.geometry) get_affine_matrix() (render_molecules.geometry.Geometry method) get_all_materials() (in module render_molecules.blender_utils) get_atom1_index() (render_molecules.bond.Bond method) get_atom1_position() (render_molecules.bond.Bond method) get_atom2_index() (render_molecules.bond.Bond method) get_atom2_position() (render_molecules.bond.Bond method) get_atom_positions() (render_molecules.structure.Structure method) get_atomic_number() (render_molecules.atom.Atom method) get_atomic_number_from_element() (in module render_molecules.element_data) get_atoms() (render_molecules.structure.Structure method) get_axis_angle_with_z() (render_molecules.bond.Bond method) get_bond_type() (render_molecules.bond.Bond method) get_bonds() (render_molecules.structure.Structure method) get_center_of_mass() (render_molecules.structure.Structure method) get_charge() (render_molecules.atom.Atom method) get_direction() (render_molecules.bond.Bond method) get_element() (render_molecules.atom.Atom method) get_element_from_atomic_number() (in module render_molecules.element_data) get_frame() (render_molecules.trajectory.Trajectory method) get_frames() (render_molecules.trajectory.Trajectory method)

get_inertia_tensor() (render_molecules.structure.Structure method) get_interatomic_vector() (render_molecules.bond.Bond method) get_length() (render_molecules.bond.Bond method) get_mass() (render_molecules.atom.Atom method) get_midpoint() (render_molecules.bond.Bond method) get_name() (render_molecules.bond.Bond method) get_nframes() (render_molecules.trajectory.Trajectory method) get_nr_electrons() (render_molecules.structure.Structure method) get_object_by_name() (in module render_molecules.blender_utils) get_position() (render_molecules.atom.Atom method) get_principal_moments_of_inertia() (render_molecules.structure.Structure method) get_render_molecules_dir() (in module render_molecules.other_utils) get_total_charge() (render_molecules.structure.Structure method) get_vdw_radius() (render_molecules.atom.Atom method) get_vdw_weighted_cylinder_midpoints() (render_molecules.bond.Bond method) get_vdw_weighted_midpoint() (render_molecules.bond.Bond method) get_volumetric_axis_vectors() (render_molecules.structure.CUBEfile method) get_volumetric_data() (render_molecules.structure.CUBEfile method) get_volumetric_origin_vector() (render_molecules.structure.CUBEfile method) get_x() (render_molecules.atom.Atom method) get_y() (render_molecules.atom.Atom method) get_z() (render_molecules.atom.Atom method)

H

hex2rgbtuple() (in module render_molecules.other_utils)

HYDROGEN_BOND_ANGLE (in module render_molecules.constants) HYDROGEN_BOND_LENGTH (in module render_molecules.constants)

I

Installation

is_radical() (render_molecules.structure.Structure method)

J

join_bonds() (render_molecules.structure.Structure method) join_cylinders() (in module render_molecules.blender_utils)

join_two_cylinders() (in module render_molecules.blender_utils) JSONfile (class in render_molecules.structure)

K

KG_TO_AMU (in module render_molecules.constants)

KGM2_TO_AMU_ANGSTROM2 (in module render_molecules.constants)

L

load_ply() (in module render_molecules.blender_utils)

M

material_exists() (in module render_molecules.blender_utils) METERS_TO_ANGSTROM (in module render_molecules.constants) METERS_TO_BOHR (in module render_molecules.constants) module render_molecules.atom render_molecules.blender_utils render_molecules.bond render_molecules.constants render_molecules.element_data render_molecules.geometry render_molecules.other_utils render_molecules.structure render_molecules.trajectory

O

orbit_camera() (in module render_molecules.blender_utils)

outline_in_render() (in module render_molecules.blender_utils)

P

position_bohr_to_angstrom() (render_molecules.atom.Atom method)

put_cap_on_cylinder() (in module render_molecules.blender_utils)

R

read_volumetric_data() (render_molecules.structure.CUBEfile method) render_molecules.atom module render_molecules.blender_utils module render_molecules.bond module render_molecules.constants module render_molecules.element_data module render_molecules.geometry module

render_molecules.other_utils module render_molecules.structure module render_molecules.trajectory module rotate_around_axis() (render_molecules.geometry.Geometry method) (render_molecules.structure.Structure method) (render_molecules.trajectory.Trajectory method) rotate_around_x() (render_molecules.geometry.Geometry method) rotate_around_y() (render_molecules.geometry.Geometry method) rotate_around_z() (render_molecules.geometry.Geometry method) rotation_matrix() (in module render_molecules.geometry)

S

scale_vertices() (in module render_molecules.blender_utils) select_object_by_name() (in module render_molecules.blender_utils) set_affine_matrix() (render_molecules.geometry.Geometry method) set_average_position() (render_molecules.structure.Structure method) set_background_color() (in module render_molecules.blender_utils) set_background_transparency() (in module render_molecules.blender_utils) set_center_of_mass() (render_molecules.structure.Structure method) (render_molecules.trajectory.Trajectory method)

set_frame_end() (in module render_molecules.blender_utils) set_frame_step() (in module render_molecules.blender_utils) set_midpoint() (render_molecules.bond.Bond method) set_name() (render_molecules.bond.Bond method) set_position() (render_molecules.atom.Atom method) SPHERE_SCALE (in module render_molecules.constants) Structure (class in render_molecules.structure)

T

Trajectory (class in render_molecules.trajectory) translate() (render_molecules.geometry.Geometry method) (render_molecules.structure.Structure method) (render_molecules.trajectory.Trajectory method)

try_autosmooth() (in module render_molecules.blender_utils)

U

user_interface

W

write_ply() (render_molecules.structure.CUBEfile method)