Functions | |
| def | centroid (X) |
| def | get_coordinates (filename, fmt) |
| def | get_coordinates_pdb (filename) |
| def | get_coordinates_xyz (filename) |
| def | kabsch (P, Q) |
| def | kabsch_rmsd (P, Q) |
| def | kabsch_rotate (P, Q) |
| def | main () |
| def | makeQ (r1, r2, r3, r4=0) |
| def | makeW (r1, r2, r3, r4=0) |
| def | quaternion_rmsd (P, Q) |
| def | quaternion_rotate (X, Y) |
| def | quaternion_transform (r) |
| def | rmsd (V, W) |
| def | write_coordinates (atoms, V, title="") |
Variables | |
| __doc__ = \ | |
| string | __version__ = '1.2.5' |
| range = xrange | |
| def calculate_rmsd_kabsch.centroid | ( | X | ) |
Calculate the centroid from a vectorset X.
https://en.wikipedia.org/wiki/Centroid
Centroid is the mean position of all the points in all of the coordinate
directions.
C = sum(X)/len(X)
Parameters
----------
X : array
(N,D) matrix, where N is points and D is dimension.
Returns
-------
C : float
centeroid
Definition at line 221 of file calculate_rmsd_kabsch.py.
| def calculate_rmsd_kabsch.get_coordinates | ( | filename, | |
| fmt | |||
| ) |
Get coordinates from filename in format fmt. Supports XYZ and PDB.
Parameters
----------
filename : string
Filename to read
fmt : string
Format of filename. Either xyz or pdb.
Returns
-------
atoms : list
List of atomic types
V : array
(N,3) where N is number of atoms
Definition at line 297 of file calculate_rmsd_kabsch.py.
| def calculate_rmsd_kabsch.get_coordinates_pdb | ( | filename | ) |
Get coordinates from the first chain in a pdb file
and return a vectorset with all the coordinates.
Parameters
----------
filename : string
Filename to read
Returns
-------
atoms : list
List of atomic types
V : array
(N,3) where N is number of atoms
Definition at line 323 of file calculate_rmsd_kabsch.py.
| def calculate_rmsd_kabsch.get_coordinates_xyz | ( | filename | ) |
Get coordinates from filename and return a vectorset with all the
coordinates, in XYZ format.
Parameters
----------
filename : string
Filename to read
Returns
-------
atoms : list
List of atomic types
V : array
(N,3) where N is number of atoms
Definition at line 405 of file calculate_rmsd_kabsch.py.
| def calculate_rmsd_kabsch.kabsch | ( | P, | |
| Q | |||
| ) |
The optimal rotation matrix U is calculated and then used to rotate matrix
P unto matrix Q so the minimum root-mean-square deviation (RMSD) can be
calculated.
Using the Kabsch algorithm with two sets of paired point P and Q, centered
around the centroid. Each vector set is represented as an NxD
matrix, where D is the the dimension of the space.
The algorithm works in three steps:
- a translation of P and Q
- the computation of a covariance matrix C
- computation of the optimal rotation matrix U
http://en.wikipedia.org/wiki/Kabsch_algorithm
Parameters
----------
P : array
(N,D) matrix, where N is points and D is dimension.
Q : array
(N,D) matrix, where N is points and D is dimension.
Returns
-------
U : matrix
Rotation matrix (D,D)
Example
-----
TODO
Definition at line 77 of file calculate_rmsd_kabsch.py.
| def calculate_rmsd_kabsch.kabsch_rmsd | ( | P, | |
| Q | |||
| ) |
Rotate matrix P unto Q using Kabsch algorithm and calculate the RMSD.
Parameters
----------
P : array
(N,D) matrix, where N is points and D is dimension.
Q : array
(N,D) matrix, where N is points and D is dimension.
Returns
-------
rmsd : float
root-mean squared deviation
Definition at line 32 of file calculate_rmsd_kabsch.py.
| def calculate_rmsd_kabsch.kabsch_rotate | ( | P, | |
| Q | |||
| ) |
Rotate matrix P unto matrix Q using Kabsch algorithm.
Parameters
----------
P : array
(N,D) matrix, where N is points and D is dimension.
Q : array
(N,D) matrix, where N is points and D is dimension.
Returns
-------
P : array
(N,D) matrix, where N is points and D is dimension,
rotated
Definition at line 52 of file calculate_rmsd_kabsch.py.
| def calculate_rmsd_kabsch.main | ( | void | ) |
Definition at line 463 of file calculate_rmsd_kabsch.py.
| def calculate_rmsd_kabsch.makeQ | ( | r1, | |
| r2, | |||
| r3, | |||
r4 = 0 |
|||
| ) |
matrix involved in quaternion rotation
Definition at line 181 of file calculate_rmsd_kabsch.py.
| def calculate_rmsd_kabsch.makeW | ( | r1, | |
| r2, | |||
| r3, | |||
r4 = 0 |
|||
| ) |
matrix involved in quaternion rotation
Definition at line 169 of file calculate_rmsd_kabsch.py.
| def calculate_rmsd_kabsch.quaternion_rmsd | ( | P, | |
| Q | |||
| ) |
Rotate matrix P unto Q and calculate the RMSD
based on doi:10.1016/1049-9660(91)90036-O
Parameters
----------
P : array
(N,D) matrix, where N is points and D is dimension.
P : array
(N,D) matrix, where N is points and D is dimension.
Returns
-------
rmsd : float
Definition at line 135 of file calculate_rmsd_kabsch.py.
| def calculate_rmsd_kabsch.quaternion_rotate | ( | X, | |
| Y | |||
| ) |
Calculate the rotation
Parameters
----------
X : array
(N,D) matrix, where N is points and D is dimension.
Y: array
(N,D) matrix, where N is points and D is dimension.
Returns
-------
rot : matrix
Rotation matrix (D,D)
Definition at line 193 of file calculate_rmsd_kabsch.py.
| def calculate_rmsd_kabsch.quaternion_transform | ( | r | ) |
Get optimal rotation note: translation will be zero when the centroids of each molecule are the same
Definition at line 157 of file calculate_rmsd_kabsch.py.
| def calculate_rmsd_kabsch.rmsd | ( | V, | |
| W | |||
| ) |
Calculate Root-mean-square deviation from two sets of vectors V and W.
Parameters
----------
V : array
(N,D) matrix, where N is points and D is dimension.
W : array
(N,D) matrix, where N is points and D is dimension.
Returns
-------
rmsd : float
Root-mean-square deviation
Definition at line 246 of file calculate_rmsd_kabsch.py.
| def calculate_rmsd_kabsch.write_coordinates | ( | atoms, | |
| V, | |||
title = "" |
|||
| ) |
Print coordinates V with corresponding atoms to stdout in XYZ format.
Parameters
----------
atoms : list
List of atomic types
V : array
(N,3) matrix of atomic coordinates
title : string (optional)
Title of molecule
Definition at line 271 of file calculate_rmsd_kabsch.py.
|
private |
Definition at line 2 of file calculate_rmsd_kabsch.py.
|
private |
Definition at line 17 of file calculate_rmsd_kabsch.py.
| calculate_rmsd_kabsch.range = xrange |
Definition at line 27 of file calculate_rmsd_kabsch.py.