BioSimSpace._SireWrappers.Molecule¶
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class
BioSimSpace._SireWrappers.Molecule(molecule)¶ A container class for storing a molecule.
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__init__(molecule)¶ Constructor.
- Parameters
molecule (Sire.Mol.Molecule, Molecule
Molecule) – A Sire or BioSimSpace Molecule object.
Methods
__init__(molecule)Constructor.
charge([property_map, is_lambda1])Return the charge.
copy()Return a copy of this object
getAtoms()Return a list containing the atoms in the molecule.
Return a list containing the residues in the molecule.
isMerged()Whether this molecule has been merged with another.
isWater()Whether this is a water molecule.
Return the component of the merged molecule at lambda = 0.
Return the component of the merged molecule at lambda = 1.
nAtoms()Return the number of atoms in the molecule.
nChains()Return the number of chains in the molecule.
Return the number of residues in the molecule.
number()Return the number of the molecule.
search(query)Search the molecule for atoms and residues.
toSystem()Convert a single Molecule to a System.
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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copy()¶ Return a copy of this object
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getAtoms()¶ Return a list containing the atoms in the molecule.
- Returns
atoms – The list of atoms in the molecule.
- Return type
[
Atom]
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getResidues()¶ Return a list containing the residues in the molecule.
- Returns
residues – The list of residues in the molecule.
- Return type
[
Residue]
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isMerged()¶ Whether this molecule has been merged with another.
- Returns
is_merged – Whether the molecule has been merged.
- Return type
bool
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isWater()¶ Whether this is a water molecule.
- Returns
is_water – Whether this is a water molecule.
- Return type
bool
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molecule0()¶ Return the component of the merged molecule at lambda = 0.
- Returns
molecule – The component of the merged molecule at lambda = 0. Returns None if this isn’t a merged molecule.
- Return type
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molecule1()¶ Return the component of the merged molecule at lambda = 1.
- Returns
molecule – The component of the merged molecule at lambda = 1. Returns None if this isn’t a merged molecule.
- Return type
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nAtoms()¶ Return the number of atoms in the molecule.
- Returns
num_atoms – The number of atoms in the molecule.
- Return type
int
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nChains()¶ Return the number of chains in the molecule.
- Returns
num_chains – The number of chains in the molecule.
- Return type
int
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nResidues()¶ Return the number of residues in the molecule.
- Returns
num_residues – The number of residues in the molecule.
- Return type
int
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number()¶ Return the number of the molecule. Each molecule has a unique identification number.
- Returns
mol_num – The unique number of the molecule.
- Return type
int
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search(query)¶ Search the molecule for atoms and residues. Search results will be reduced to their minimal representation, i.e. a residue containing a single atom will be returned as a atom.
- Parameters
query (str) – The search query.
- Returns
results – A list of objects matching the search query.
- Return type
Examples
Search for all residues named ALA.
>>> result = molecule.search("resname ALA")
Search for all oxygen or hydrogen atoms.
>>> result = molecule.search("element oxygen or element hydrogen")
Search for atom index 23.
>>> result = molecule.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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