Geometry
Geometry(parent_molecule_object)
¶
A class containing a few gemoetry functions. Note that numpy should be used for most geometry functions.
Initializes the pymolecule.Geometry class.
parent_molecule_object: The pymolecule.Molecule object associated with this class.
parent_molecule = parent_molecule_object
instance-attribute
¶
angle_between_three_points(pt1, pt2, pt3)
¶
Computes the angle (in radians) formed by three points (np.array objects).
| PARAMETER | DESCRIPTION |
|---|---|
pt1
|
A np.array (x, y, z) representing the first of the three 3D points.
|
pt2
|
A np.array (x, y, z) representing the second of the three 3D points.
|
pt3
|
A np.array (x, y, z) representing the third of the three 3D points.
|
| RETURNS | DESCRIPTION |
|---|---|
|
A float containing the angle between the three points, in radians. |
dihedral_angle(pt1, pt2, pt3, pt4)
¶
Calculates the dihedral angle formed by four points (np.array objects).
| PARAMETER | DESCRIPTION |
|---|---|
pt1
|
A np.array (x, y, z) representing the first 3D point.
|
pt2
|
A np.array (x, y, z) representing the second 3D point.
|
pt3
|
A np.array (x, y, z) representing the third 3D point.
|
pt4
|
A np.array (x, y, z) representing the fourth 3D point.
|
| RETURNS | DESCRIPTION |
|---|---|
|
A float containing the dihedral angle between the four points, in radians. |
is_planar(pt1, pt2, pt3, pt4, planarity_cutoff=0.2)
¶
Checks whether four points (np.array) lie in a common plane.
| PARAMETER | DESCRIPTION |
|---|---|
pt1
|
A np.array (x, y, z) representing a 3D point.
|
pt2
|
A np.array (x, y, z) representing a 3D point.
|
pt3
|
A np.array (x, y, z) representing a 3D point.
|
pt4
|
A np.array (x, y, z) representing a 3D point.
|
planarity_cutoff
|
An optional float. How much the points can deviate (in Angstroms) and still be considered planar. The default is 0.2.
DEFAULT:
|
| RETURNS | DESCRIPTION |
|---|---|
|
A boolean, whether the 4 points can be considered planar. |
planarity_deviation(pt1, pt2, pt3, pt4)
¶
Determines how close four points (np.array objects) come to lying in a common plane.
| PARAMETER | DESCRIPTION |
|---|---|
pt1
|
A np.array (x, y, z) representing a 3D point.
|
pt2
|
A np.array (x, y, z) representing a 3D point.
|
pt3
|
A np.array (x, y, z) representing a 3D point.
|
pt4
|
A np.array (x, y, z) representing a 3D point.
|
| RETURNS | DESCRIPTION |
|---|---|
|
A float, the minimum distance between one point and the plane formed by the other three. |