Index

A | B | C | D | E | F | G | I | L | M | N | O | P | Q | R | S | T | U | V | W | X

A

AbstractRenderer (class in chemlab.graphics.renderers)
add() (chemlab.core.System method)
add_renderer() (chemlab.graphics.QtTrajectoryViewer method)
(chemlab.graphics.QtViewer method)
add_ui() (chemlab.graphics.QtTrajectoryViewer method)
(chemlab.graphics.QtViewer method)
affine_matrix_from_points() (in module chemlab.graphics.transformations)
angle_between_vectors() (in module chemlab.graphics.transformations)
Arcball (class in chemlab.graphics.transformations)
arcball_constrain_to_axis() (in module chemlab.graphics.transformations)
arcball_map_to_sphere() (in module chemlab.graphics.transformations)
arcball_nearest_axis() (in module chemlab.graphics.transformations)
aspectratio (Camera attribute)
Atom (class in chemlab.core)
atom_export_array (Molecule attribute)
(System attribute)
AtomRenderer (class in chemlab.graphics.renderers)

B

background_color (QChemlabWidget attribute)
box_vectors (System attribute)
BoxRenderer (class in chemlab.graphics.renderers)

C

Camera (class in chemlab.graphics.camera)
camera (QChemlabWidget attribute)
can_read (IOHandler attribute)
can_write (IOHandler attribute)
center_of_mass (Molecule attribute)
check_feature() (chemlab.io.handlers.IOHandler method)
chemlab.graphics.transformations (module)
clip_matrix() (in module chemlab.graphics.transformations)
compose_matrix() (in module chemlab.graphics.transformations)
concatenate_matrices() (in module chemlab.graphics.transformations)
copy() (chemlab.core.Atom method)
(chemlab.core.Molecule method)
crystal() (in module chemlab.core)
CylinderRenderer (class in chemlab.graphics.renderers)

D

datafile() (in module chemlab.io)
decompose_matrix() (in module chemlab.graphics.transformations)
DefaultRenderer (class in chemlab.graphics.renderers)
display_system() (in module chemlab.graphics)
display_trajectory() (in module chemlab.graphics)
distance() (in module chemlab.graphics.transformations)
down() (chemlab.graphics.transformations.Arcball method)
drag() (chemlab.graphics.transformations.Arcball method)
draw() (chemlab.graphics.renderers.AbstractRenderer method)
draw_vertices() (chemlab.graphics.renderers.DefaultRenderer method)
(chemlab.graphics.renderers.ShaderBaseRenderer method)

E

EdrIO (class in chemlab.io.handlers)
empty() (chemlab.core.System class method)
euler_from_matrix() (in module chemlab.graphics.transformations)
euler_from_quaternion() (in module chemlab.graphics.transformations)
euler_matrix() (in module chemlab.graphics.transformations)
export (Atom attribute)
(Molecule attribute)

F

fields (Atom attribute)
filename (IOHandler attribute)
formula (Molecule attribute)
from_arrays() (chemlab.core.Molecule class method)
(chemlab.core.System class method)
from_fields() (chemlab.core.Atom class method)

G

geometric_center (Molecule attribute)
get_molecule() (chemlab.core.System method)
getconstrain() (chemlab.graphics.transformations.Arcball method)
GromacsIO (class in chemlab.io.handlers)

I

identity_matrix() (in module chemlab.graphics.transformations)
inverse_matrix() (in module chemlab.graphics.transformations)
IOHandler (class in chemlab.io.handlers)
is_same_transform() (in module chemlab.graphics.transformations)

L

light_dir (QChemlabWidget attribute)
LineRenderer (class in chemlab.graphics.renderers)

M

m_array (Molecule attribute)
(System attribute)
mass (Atom attribute)
(Molecule attribute)
matrix (Camera attribute)
matrix() (chemlab.graphics.transformations.Arcball method)
merge_systems() (in module chemlab.core)
mol_export (System attribute)
mol_indices (System attribute)
mol_n_atoms (System attribute)
mol_to_atom_indices() (chemlab.core.System method)
Molecule (class in chemlab.core)
mouse_rotate() (chemlab.graphics.camera.Camera method)
mouse_zoom() (chemlab.graphics.camera.Camera method)
move_to() (chemlab.core.Molecule method)

N

n_atoms (Molecule attribute)
(System attribute)
n_mol (System attribute)
next() (chemlab.graphics.transformations.Arcball method)
normalized() (in module chemlab.graphics.transformations)

O

orbit_x() (chemlab.graphics.camera.Camera method)
orbit_y() (chemlab.graphics.camera.Camera method)
orthogonalization_matrix() (in module chemlab.graphics.transformations)

P

paintGL() (chemlab.graphics.QChemlabWidget method)
PdbIO (class in chemlab.io.handlers)
pivot (Camera attribute)
place() (chemlab.graphics.transformations.Arcball method)
PointRenderer (class in chemlab.graphics.renderers)
position (Camera attribute)
projection (Camera attribute)
projection_from_matrix() (in module chemlab.graphics.transformations)
projection_matrix() (in module chemlab.graphics.transformations)

Q

QChemlabWidget (class in chemlab.graphics)
QtTrajectoryViewer (class in chemlab.graphics)
QtViewer (class in chemlab.graphics)
quaternion_about_axis() (in module chemlab.graphics.transformations)
quaternion_conjugate() (in module chemlab.graphics.transformations)
quaternion_from_euler() (in module chemlab.graphics.transformations)
quaternion_from_matrix() (in module chemlab.graphics.transformations)
quaternion_imag() (in module chemlab.graphics.transformations)
quaternion_inverse() (in module chemlab.graphics.transformations)
quaternion_matrix() (in module chemlab.graphics.transformations)
quaternion_multiply() (in module chemlab.graphics.transformations)
quaternion_real() (in module chemlab.graphics.transformations)
quaternion_slerp() (in module chemlab.graphics.transformations)

R

r (Atom attribute)
r_array (Molecule attribute)
(System attribute)
random_quaternion() (in module chemlab.graphics.transformations)
random_rotation_matrix() (in module chemlab.graphics.transformations)
random_vector() (in module chemlab.graphics.transformations)
read() (chemlab.io.handlers.IOHandler method)
(EdrIO method), [1], [2], [3]
(GromacsIO method)
(PdbIO method), [1]
(XtcIO method)
(XyzIO method)
reflection_from_matrix() (in module chemlab.graphics.transformations)
reflection_matrix() (in module chemlab.graphics.transformations)
renderers (QChemlabWidget attribute)
rotation_from_matrix() (in module chemlab.graphics.transformations)
rotation_matrix() (in module chemlab.graphics.transformations)
run() (chemlab.graphics.QtViewer method)

S

scale (Camera attribute)
scale_from_matrix() (in module chemlab.graphics.transformations)
scale_matrix() (in module chemlab.graphics.transformations)
schedule() (chemlab.graphics.QtViewer method)
set_text() (chemlab.graphics.QtTrajectoryViewer method)
set_ticks() (chemlab.graphics.QtTrajectoryViewer method)
setaxes() (chemlab.graphics.transformations.Arcball method)
setconstrain() (chemlab.graphics.transformations.Arcball method)
ShaderBaseRenderer (class in chemlab.graphics.renderers)
shear_from_matrix() (in module chemlab.graphics.transformations)
shear_matrix() (in module chemlab.graphics.transformations)
simple_clip_matrix() (in module chemlab.graphics.transformations)
sort() (chemlab.core.System method)
SphereImpostorRenderer (class in chemlab.graphics.renderers)
SphereRenderer (class in chemlab.graphics.renderers)
subsystem_from_atoms() (in module chemlab.core)
subsystem_from_molecules() (in module chemlab.core)
superimposition_matrix() (in module chemlab.graphics.transformations)
System (class in chemlab.core)

T

TextUI (class in chemlab.graphics.uis)
translation_from_matrix() (in module chemlab.graphics.transformations)
translation_matrix() (in module chemlab.graphics.transformations)
TriangleRenderer (class in chemlab.graphics.renderers)
type (Atom attribute)
type_array (System attribute)

U

unit_vector() (in module chemlab.graphics.transformations)
unproject() (chemlab.graphics.camera.Camera method)
update() (chemlab.graphics.renderers.BoxRenderer method)
update_bounds() (chemlab.graphics.renderers.CylinderRenderer method)
update_colors() (chemlab.graphics.renderers.LineRenderer method)
(chemlab.graphics.renderers.PointRenderer method)
(chemlab.graphics.renderers.TriangleRenderer method)
update_function() (chemlab.graphics.QtTrajectoryViewer method)
update_normals() (chemlab.graphics.renderers.TriangleRenderer method)
update_positions() (chemlab.graphics.renderers.AtomRenderer method)
(chemlab.graphics.renderers.LineRenderer method)
(chemlab.graphics.renderers.PointRenderer method)
(chemlab.graphics.renderers.SphereRenderer method)
update_vertices() (chemlab.graphics.renderers.TriangleRenderer method)

V

vector_norm() (in module chemlab.graphics.transformations)
vector_product() (in module chemlab.graphics.transformations)

W

write() (chemlab.io.handlers.IOHandler method)
(GromacsIO method)
(XyzIO method)

X

XtcIO (class in chemlab.io.handlers)
XyzIO (class in chemlab.io.handlers)

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