Package schrodinger :: Package application :: Package desmond :: Package packages :: Package msys :: Module atomsel :: Class Atomsel

[frames] | no frames]

Class Atomsel

object --+
         |
        Atomsel

Supports alignment of molecular structures

Instance Methods

[hide private]

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

__len__(self)
number of selected atoms

__str__(self)
str(x)

__repr__(self)
repr(x)

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__, __setattr__, __sizeof__, __subclasshook__

Properties

[hide private]

ids
ids of selected atoms in the parent system

system
parent system

_ids

_ptr

_seltext

Inherited from object: __class__

Method Details

[hide private]

init(self, ptr, seltext)
(Constructor)

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

Overrides: object.__init__

str(self)
(Informal representation operator)

str(x)

Overrides: object.__str__: (inherited documentation)

repr(self)
(Representation operator)

repr(x)

Overrides: object.__repr__: (inherited documentation)

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.

Property Details

[hide private]

ids

ids of selected atoms in the parent system

Get Method:: unreachable.ids(self) - ids of selected atoms in the parent system

system

parent system

Get Method:: unreachable.system(self) - parent system

Class Atomsel

__init__(self, ptr, seltext) (Constructor)

__str__(self) (Informal representation operator)

__repr__(self) (Representation operator)

raw_alignment(self, other)

currentRMSD(self, other)

alignCoordinates(self, other)

ids

system

init(self, ptr, seltext)
(Constructor)

str(self)
(Informal representation operator)

repr(self)
(Representation operator)