BioSimSpace._SireWrappers.Atom¶
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class
BioSimSpace._SireWrappers.
Atom
(atom)¶ A class for storing an atom.
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__init__
(atom)¶ Constructor.
- Parameters
atom (Sire.Mol.Atom,
Atom
) – A Sire or BioSimSpace Atom object.
Methods
__init__
(atom)Constructor.
charge
([property_map, is_lambda1])Return the charge.
coordinates
([property_map])Return the coordinates of the atom.
copy
()Return a copy of this object.
element
([property_map])Return the element.
getAxisAlignedBoundingBox
([property_map])Get the axis-aligned bounding box enclosing the object.
index
()Return the index of the atom.
Return the number of the molecule to which this atom belongs.
name
()Return the name of the atom.
Convert a single Atom to a Molecule.
translate
(vector[, property_map])Translate the object.
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charge
(property_map={}, is_lambda1=False)¶ Return the charge.
- Parameters
property_map (dict) – A dictionary that maps system “properties” to their user defined values. This allows the user to refer to properties with their own naming scheme, e.g. { “charge” : “my-charge” }
is_lambda1 (bool) – Whether to use the charge at lambda = 1 if the object is peturbable.
- Returns
charge – The charge.
- Return type
-
coordinates
(property_map={})¶ Return the coordinates of the atom.
- Parameters
property_map (dict) – A dictionary that maps system “properties” to their user defined values. This allows the user to refer to properties with their own naming scheme, e.g. { “charge” : “my-charge” }
- Returns
coordinates – The coordinates of the atom.
- Return type
class:
Coordinate
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copy
()¶ Return a copy of this object. The return type is same as the object on which copy is called.
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element
(property_map={})¶ Return the element.
- Parameters
property_map (dict) – A dictionary that maps system “properties” to their user defined values. This allows the user to refer to properties with their own naming scheme, e.g. { “charge” : “my-charge” }
- Returns
element – The element.
- Return type
str
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getAxisAlignedBoundingBox
(property_map={})¶ Get the axis-aligned bounding box enclosing the object.
- Parameters
property_map (dict) – A dictionary that maps system “properties” to their user defined values. This allows the user to refer to properties with their own naming scheme, e.g. { “charge” : “my-charge” }
- Returns
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index
()¶ Return the index of the atom.
- Returns
index – The index of the atom.
- Return type
int
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moleculeNumber
()¶ Return the number of the molecule to which this atom belongs.
- Returns
number – The number of the molecule to which the atom belongs.
- Return type
int
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name
()¶ Return the name of the atom.
- Returns
name – The name of the atom.
- Return type
str
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translate
(vector, property_map={})¶ Translate the object.
- Parameters
vector ([
Length
]) – The translation vector in Angstroms.property_map (dict) – A dictionary that maps system “properties” to their user defined values. This allows the user to refer to properties with their own naming scheme, e.g. { “charge” : “my-charge” }
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