calculate_rmsd_kabsch Namespace Reference

## 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

## Function Documentation

 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
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

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

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.

## Variable Documentation

 calculate_rmsd_kabsch.__doc__ = \
private

Definition at line 2 of file calculate_rmsd_kabsch.py.

 string calculate_rmsd_kabsch.__version__ = '1.2.5'
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.

librealsense2
Author(s): Sergey Dorodnicov , Doron Hirshberg , Mark Horn , Reagan Lopez , Itay Carpis
autogenerated on Mon May 3 2021 02:50:35