Class Atomsel

object --+
         |
        Atomsel

Instance Methods

[hide private]

__init__(self, ptr, ids)
don't use directly - use System.atomsel()

__len__(self)
number of selected atoms

ids(self)
ids of selected atoms in the parent system

system(self)
parent system

getPositions(self)

_positions(self, other)

raw_alignment(self, other)
Compute alignment to other object.

currentRMSD(self, other)
compute RMS distance to other object, which may be Atomsel or an array of positions.

alignedRMSD(self, other)
Return the aligned rmsd to other.

alignCoordinates(self, other)
If other is an Atomsel instance, align the coordinates of other's System with self.

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

init(self, ptr, ids)
(Constructor)

don't use directly - use System.atomsel()

Overrides: object.__init__

ids(self)

ids of selected atoms in the parent system

Decorators:

@property

system(self)

parent system

Decorators:

@property

raw_alignment(self, other)

Compute alignment to other object. Compute and return aligned rmsd, and rotational and translational transformations.

currentRMSD(self, other)

compute RMS distance to other object, which may be Atomsel or an array of positions. In either it must be the case that len(other) equals len(self) or len(self.system)

alignCoordinates(self, other)

If other is an Atomsel instance, align the coordinates of other's System with self. If other is a numpy array, align the array with self, using corresponding indices.

In either case, return the aligned RMSD.

Class Atomsel

__init__(self, ptr, ids) (Constructor)

ids(self)

system(self)

raw_alignment(self, other)

currentRMSD(self, other)

alignCoordinates(self, other)

init(self, ptr, ids)
(Constructor)