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 total molecular charge.
copy()Create a copy of this 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.
toSystem()Convert a single Molecule to a System.
translate(vector[, property_map])Translate the molecule.
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charge(property_map={}, is_lambda1=False)¶ Return the total molecular 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 molecule is merged.
- Returns
charge – The molecular charge.
- Return type
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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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translate(vector, property_map={})¶ Translate the molecule.
- Parameters
vector ([
Length]) – The translation vector.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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