BioSimSpace._SireWrappers.Molecule¶
-
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
) – A Sire or BioSimSpace Molecule object.
Methods
__init__
(molecule)Constructor.
charge
([property_map, is_lambda1])Return the charge.
coordinates
([property_map])Return the coordinates of the atoms in the molecule.
copy
()Return a copy of this Molecule.
extract
(indices[, renumber, property_map])Extract atoms at the specified indices from the molecule to create a new molecule.
getAtoms
()Return a list containing the atoms in the molecule.
getAxisAlignedBoundingBox
([property_map])Get the axis-aligned bounding box enclosing the object.
Return a list containing the residues in the molecule.
isAmberWater
([property_map])Whether this is an AMBER format water molecule.
isGromacsWater
([property_map])Whether this is a GROMACS format water molecule.
Whether this molecule is perturbable, i.e.
isWater
([property_map])Whether this is a water molecule.
makeCompatibleWith
(molecule[, property_map, …])Make this molecule compatible with passed one, i.e.
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.
repartitionHydrogenMass
([factor, water, …])Redistrubute mass of heavy atoms connected to bonded hydrogens into the hydrogen atoms.
search
(query[, property_map])Search the molecule for atoms and residues.
toSystem
()Convert a single Molecule to a System.
translate
(vector[, property_map])Translate each molecule in the container.
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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 atoms in the molecule.
- 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 molecule.
- Return type
[class:
Coordinate
]
-
copy
()¶ Return a copy of this Molecule.
- Returns
molecule – A copy of the object.
- Return type
-
extract
(indices, renumber=False, property_map={})¶ Extract atoms at the specified indices from the molecule to create a new molecule.
- Parameters
indices ([ int ]) – The indices of the atoms to extract.
renumber (bool) – Whether the returned molecule has the same number as the original.
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
molecule – The extracted molecule.
- Return type
-
getAtoms
()¶ Return a list containing the atoms in the molecule.
- Returns
atoms – The list of atoms in the molecule.
- Return type
[
Atom
]
-
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
-
getResidues
()¶ Return a list containing the residues in the molecule.
- Returns
residues – The list of residues in the molecule.
- Return type
[
Residue
]
-
isAmberWater
(property_map={})¶ Whether this is an AMBER format water molecule.
- 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
is_amber_water – Whether this molecule is an AMBER format water.
- Return type
bool
-
isGromacsWater
(property_map={})¶ Whether this is a GROMACS format water molecule.
- 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
- Returns
is_gromacs_water – Whether this molecule is a GROMACS format water.
- Return type
bool
-
isPerturbable
()¶ Whether this molecule is perturbable, i.e. it can be used in a free-energy perturbation simulation.
- Returns
is_perturbable – Whether the molecule is perturbable.
- Return type
bool
-
isWater
(property_map={})¶ Whether this is a water molecule.
- 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
is_water – Whether this is a water molecule.
- Return type
bool
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makeCompatibleWith
(molecule, property_map={}, overwrite=True, rename_atoms=False, verbose=False)¶ Make this molecule compatible with passed one, i.e. match atoms and add all additional properties from the passed molecule while preserving the topology and naming/numbering convention of this molecule.
- Parameters
molecule (Sire.Mol.Molecule,
Molecule
, Sire.System.System,System
) – The molecule, or system of molecules, to match with.property_map (dict) – A map between property names and user supplied names.
overwrite (bool) – Whether to overwrite any duplicate properties.
rename_atoms (bool) – Whether to rename atoms if they have changed.
verbose (bool) – Whether to report status updates to stdout.
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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
-
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
-
nAtoms
()¶ Return the number of atoms in the molecule.
- Returns
num_atoms – The number of atoms in the molecule.
- Return type
int
-
nChains
()¶ Return the number of chains in the molecule.
- Returns
num_chains – The number of chains in the molecule.
- Return type
int
-
nResidues
()¶ Return the number of residues in the molecule.
- Returns
num_residues – The number of residues in the molecule.
- Return type
int
-
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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repartitionHydrogenMass
(factor=4, water='no', use_coordinates=False, property_map={})¶ Redistrubute mass of heavy atoms connected to bonded hydrogens into the hydrogen atoms. This allows the use of larger simulation integration time steps without encountering instabilities related to high-frequency hydrogen motion.
- Parameters
factor (float) – The repartioning scale factor. Hydrogen masses are scaled by this amount.
water (str) – Whether to repartition masses for water molecules. Options are “yes”, “no”, and “exclusive”, which can be used to repartition masses for water molecules only.
use_coordinates (bool) – Whether to use the current molecular coordinates to work out the connectivity before repartitioning. If False, the information from the molecular topology, e.g. force field, will be used, if present.
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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search
(query, property_map={})¶ 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.
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
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 each molecule in the container.
- 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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