BioSimSpace._SireWrappers.Residue¶
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class
BioSimSpace._SireWrappers.Residue(residue)¶ A class for storing a residue.
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__init__(residue)¶ Constructor.
- Parameters
residue (Sire.Mol.Residue,
Residue) – A Sire or BioSimSpace Residue object.
Methods
__init__(residue)Constructor.
charge([property_map, is_lambda1])Return the charge.
coordinates([property_map])Return the coordinates of the atoms in the residue.
copy()Return a copy of this object.
getAtoms()Return a list containing all of the atoms in the residue.
getAxisAlignedBoundingBox([property_map])Get the axis-aligned bounding box enclosing the object.
index()Return the index of the residue.
Return the number of the molecule to which this residue belongs.
nAtoms()Return the number of atoms in the residue.
name()Return the name of the residue.
search(query[, property_map])Search the residue for atoms and residues.
Convert a single Residue 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
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coordinates(property_map={})¶ Return the coordinates of the atoms in the residue.
- 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 atoms in the residue.
- 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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getAtoms()¶ Return a list containing all of the atoms in the residue.
- Returns
atoms – The list of atoms in the residue.
- Return type
[
Atoms]
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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 residue.
- Returns
index – The index of the residue.
- Return type
int
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moleculeNumber()¶ Return the number of the molecule to which this residue belongs.
- Returns
number – The number of the molecule to which the residue belongs.
- Return type
int
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nAtoms()¶ Return the number of atoms in the residue.
- Returns
num_atoms – The number of atoms in the system.
- Return type
int
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name()¶ Return the name of the residue.
- Returns
name – The name of the residue.
- Return type
str
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search(query, property_map={})¶ Search the residue for atoms and residues.
- Parameters
query (str) – The search query.
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
results – A list of objects matching the search query.
- Return type
[
Atom]
Examples
Search for all oxygen or hydrogen atoms.
>>> result = residue.search("element oxygen or element hydrogen")
Search for atom index 23.
>>> result = residue.search("atomidx 23")
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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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