BioSimSpace._SireWrappers.Bond¶
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class
BioSimSpace._SireWrappers.Bond(bond)¶ A class for storing a bond.
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__init__(bond)¶ Constructor.
- Parameters
bond (Sire.MM.Bond,
Bond) – A Sire or BioSimSpace Bond object.
Methods
__init__(bond)Constructor.
atom0()Return the first atom in the bond.
atom1()Return the first atom in the bond.
charge([property_map, is_lambda1])Return the charge.
coordinates([property_map])Return the coordinates of the atoms in the bond.
copy()Return a copy of this object.
energy()Return the energy of the bond.
getAtoms()Return a list containing all of the atoms in the bond.
getAxisAlignedBoundingBox([property_map])Get the axis-aligned bounding box enclosing the object.
length()Return the length of the bond.
Return the number of the molecule to which this bond belongs.
nAtoms()Return the number of atoms in the bond.
name()Return the name of the bond.
search(query[, property_map])Search the bond for atoms and bonds.
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 bond.
- 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 bond.
- 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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energy()¶ Return the energy of the bond. This assumes that an energy expression has been assigned to this bond.
- Returns
energy – The energy of the bond
- Return type
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getAtoms()¶ Return a list containing all of the atoms in the bond.
- Returns
atoms – The list of atoms in the bond.
- 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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moleculeNumber()¶ Return the number of the molecule to which this bond belongs.
- Returns
number – The number of the molecule to which the bond belongs.
- Return type
int
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nAtoms()¶ Return the number of atoms in the bond.
- Returns
num_atoms – The number of atoms in the system.
- Return type
int
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name()¶ Return the name of the bond.
- Returns
name – The name of the bond.
- Return type
str
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search(query, property_map={})¶ Search the bond for atoms and bonds.
- 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 = bond.search("element oxygen or element hydrogen")
Search for atom index 23.
>>> result = bond.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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