The ihm.geometry
Python module¶
Classes for handling geometry.
Geometric objects (see GeometricObject
) are usually
used in GeometricRestraint
objects.

class
ihm.geometry.
Center
(x, y, z)[source]¶ Define the center of a geometric object in Cartesian space.
Parameters:  x (float) – x coordinate
 y (float) – y coordinate
 z (float) – z coordinate

class
ihm.geometry.
Transformation
(rot_matrix, tr_vector)[source]¶ Rotation and translation applied to an object.
Transformation objects are typically used in subclasses of
GeometricObject
, or byihm.dataset.TransformedDataset
.Parameters:  rot_matrix – Rotation matrix (as a 3x3 array of floats) that places the object in its final position.
 tr_vector – Translation vector (as a 3element float list) that places the object in its final position.

class
ihm.geometry.
GeometricObject
(name=None, description=None)[source]¶ A generic geometric object. See also
Sphere
,Torus
,Axis
,Plane
.Geometric objects are typically assigned to one or more
GeometricRestraint
objects.Parameters:  name (str) – A short userprovided name.
 description (str) – A brief description of the object.

class
ihm.geometry.
Sphere
(center, radius, transformation=None, name=None, description=None)[source]¶ A sphere in Cartesian space.
Parameters:  center (
Center
) – Coordinates of the center of the sphere.  radius – Radius of the sphere.
 transformation (
Transformation
) – Rotation and translation that moves the sphere from the original center to its final location, if any.  name (str) – A short userprovided name.
 description (str) – A brief description of the object.
 center (

class
ihm.geometry.
Torus
(center, major_radius, minor_radius, transformation=None, name=None, description=None)[source]¶ A torus in Cartesian space.
Parameters:  center (
Center
) – Coordinates of the center of the torus.  major_radius – The major radius  the distance from the center of the tube to the center of the torus.
 minor_radius – The minor radius  the radius of the tube.
 transformation (
Transformation
) – Rotation and translation that moves the torus (which by default lies in the xy plane) from the original center to its final location, if any.  name (str) – A short userprovided name.
 description (str) – A brief description of the object.
 center (

class
ihm.geometry.
HalfTorus
(center, major_radius, minor_radius, thickness, transformation=None, inner=None, name=None, description=None)[source]¶ A section of a
Torus
. This is defined as a surface over part of the torus with a given thickness, and is often used to represent a membrane.Parameters:  thickness – The thickness of the surface.
 inner – True if the surface is the ‘inner’ half of the torus (i.e. closer to the center), False for the outer surface, or None for some other section (described in description).
See
Torus
for a description of the other parameters.

class
ihm.geometry.
Axis
(transformation=None, name=None, description=None)[source]¶ One of the three Cartesian axes  see
XAxis
,YAxis
,ZAxis
.Parameters:  transformation (
Transformation
) – Rotation and translation that moves the axis from the original Cartesian axis to its final location, if any.  name (str) – A short userprovided name.
 description (str) – A brief description of the object.
 transformation (

class
ihm.geometry.
XAxis
(transformation=None, name=None, description=None)[source]¶ The x Cartesian axis.
See
GeometricObject
for a description of the parameters.

class
ihm.geometry.
YAxis
(transformation=None, name=None, description=None)[source]¶ The y Cartesian axis.
See
GeometricObject
for a description of the parameters.

class
ihm.geometry.
ZAxis
(transformation=None, name=None, description=None)[source]¶ The z Cartesian axis.
See
GeometricObject
for a description of the parameters.

class
ihm.geometry.
Plane
(transformation=None, name=None, description=None)[source]¶ A plane in Cartesian space  see
XYPlane
,YZPlane
,XZPlane
.Parameters:  transformation (
Transformation
) – Rotation and translation that moves the plane from the original position to its final location, if any.  name (str) – A short userprovided name.
 description (str) – A brief description of the object.
 transformation (

class
ihm.geometry.
XYPlane
(transformation=None, name=None, description=None)[source]¶ The xy plane in Cartesian space.
See
GeometricObject
for a description of the parameters.

class
ihm.geometry.
YZPlane
(transformation=None, name=None, description=None)[source]¶ The yz plane in Cartesian space.
See
GeometricObject
for a description of the parameters.

class
ihm.geometry.
XZPlane
(transformation=None, name=None, description=None)[source]¶ The xz plane in Cartesian space.
See
GeometricObject
for a description of the parameters.