Parameterisers

Parameterise a given system to be simulated with classical molecular dynamics.

For charging molecule in the system. The default is to use AM1-BCC. An alternative is to use the mlddec charges.

class mdfptools.Parameteriser.BaseParameteriser[source]

Warning

The base class should not be used directly

Attributes
system_pmd

Methods

load_ddec_models([epsilon])

Charging molecule using machine learned charge instead of the default AM1-BCC method.

pmd_generator()

Abstract method

run()

Abstract method

save(file_name[, file_path])

Save to file the parameterised system.

unload_ddec_models(\*\*kwargs)

Unload the machine-learned charge model, which takes over 1 GB of memory.

via_openeye()

Abstract method

via_rdkit()

Abstract method
classmethod via_openeye()[source]

Abstract method

classmethod via_rdkit()[source]

Abstract method

classmethod pmd_generator()[source]

Abstract method

classmethod _rdkit_setter(smiles, **kwargs)[source]

Prepares an rdkit molecule with 3D coordinates.

Parameters

smiles (str) – SMILES string of the solute moleulce

Returns

mol

Return type

rdkit.Chem.Mol

classmethod _rdkit_parameteriser(mol, **kwargs)[source]
classmethod load_ddec_models(epsilon=4, **kwargs)[source]

Charging molecule using machine learned charge instead of the default AM1-BCC method.

Requires first installing the mlddec(https://github.com/rinikerlab/mlddec) package. Parameters are availible for elements : {H,C,N,O,Cl,Br,F}.

Parameters

epsilon (int) – Dielectric constant to be used, polarity of the resulting molecule varies, possible values are {4,78}.

classmethod unload_ddec_models(**kwargs)[source]

Unload the machine-learned charge model, which takes over 1 GB of memory.

classmethod _openeye_setter(smiles, **kwargs)[source]

Prepares an openeye molecule with 3D coordinates.

Parameters

smiles (str) – SMILES string of the solute moleulce

Returns

mol

Return type

oechem.OEMol

classmethod _openeye_parameteriser(mol, **kwargs)[source]

Creates a parameterised system from openeye molecule

Parameters

mol (oechem.OEMol) –

classmethod save(file_name, file_path='./', **kwargs)[source]

Save to file the parameterised system.

Parameters

  • file_name (str) – No file type postfix is necessary

  • file_path (str) – Default to current directory

Returns

path – The absolute path where the trajectory is written to.

Return type

str

classmethod run()

Abstract method

__init__(self, /, *args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

class mdfptools.Parameteriser.LiquidParameteriser[source]

Parameterisation of liquid box, i.e. multiple replicates of the same molecule

Attributes
system_pmd

Methods

load_ddec_models([epsilon])

Charging molecule using machine learned charge instead of the default AM1-BCC method.

pmd_generator()

Abstract method

run(smiles, density[, …])

Parameterisation perfromed via openeye toolkit.

save(file_name[, file_path])

Save to file the parameterised system.

unload_ddec_models(\*\*kwargs)

Unload the machine-learned charge model, which takes over 1 GB of memory.

via_openeye(smiles, density[, …])

Parameterisation perfromed via openeye toolkit.

via_rdkit(smiles, density[, …])

Parameterisation perfromed via rdkit.
classmethod via_openeye(smiles, density, allow_undefined_stereo=False, num_lig=100, **kwargs)[source]

Parameterisation perfromed via openeye toolkit.

Parameters

  • smiles (str) – SMILES string of the molecule to be parametersied

  • density (simtk.unit) – Density of liquid box

  • allow_undefined_stereo (bool) – Flag passed to OpenForceField Molecule object during parameterisation. When set to False an error is returned if SMILES have no/ambiguous steroechemistry. Default to False here as a sanity check for user.

  • num_lig (int) – Number of replicates of the molecule

Returns

system_pmd – The parameterised system as parmed object

Return type

parmed.structure

classmethod via_rdkit(smiles, density, allow_undefined_stereo=False, num_lig=100, **kwargs)[source]

Parameterisation perfromed via rdkit.

Parameters

  • smiles (str) – SMILES string of the molecule to be parametersied

  • density (simtk.unit) – Density of liquid box

  • allow_undefined_stereo (bool) – Flag passed to OpenForceField Molecule object during parameterisation. When set to False an error is returned if SMILES have no/ambiguous steroechemistry. Default to False here as a sanity check for user.

  • num_lig (int) – Number of replicates of the molecule

Returns

system_pmd – The parameterised system as parmed object

Return type

parmed.structure

classmethod _via_helper(density, num_lig, **kwargs)[source]

Helper function for via_rdkit or via_openeye

Parameters

  • density (simtk.unit) – Density of liquid box

  • num_lig (int) – Number of replicates of the molecule

Returns

system_pmd – The parameterised system as parmed object

Return type

parmed.structure

classmethod run(smiles, density, allow_undefined_stereo=False, num_lig=100, **kwargs)

Parameterisation perfromed via openeye toolkit.

Parameters

  • smiles (str) – SMILES string of the molecule to be parametersied

  • density (simtk.unit) – Density of liquid box

  • allow_undefined_stereo (bool) – Flag passed to OpenForceField Molecule object during parameterisation. When set to False an error is returned if SMILES have no/ambiguous steroechemistry. Default to False here as a sanity check for user.

  • num_lig (int) – Number of replicates of the molecule

Returns

system_pmd – The parameterised system as parmed object

Return type

parmed.structure

__init__(self, /, *args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

classmethod _openeye_parameteriser(mol, **kwargs)

Creates a parameterised system from openeye molecule

Parameters

mol (oechem.OEMol) –

classmethod _openeye_setter(smiles, **kwargs)

Prepares an openeye molecule with 3D coordinates.

Parameters

smiles (str) – SMILES string of the solute moleulce

Returns

mol

Return type

oechem.OEMol

classmethod _rdkit_parameteriser(mol, **kwargs)
classmethod _rdkit_setter(smiles, **kwargs)

Prepares an rdkit molecule with 3D coordinates.

Parameters

smiles (str) – SMILES string of the solute moleulce

Returns

mol

Return type

rdkit.Chem.Mol

classmethod load_ddec_models(epsilon=4, **kwargs)

Charging molecule using machine learned charge instead of the default AM1-BCC method.

Requires first installing the mlddec(https://github.com/rinikerlab/mlddec) package. Parameters are availible for elements : {H,C,N,O,Cl,Br,F}.

Parameters

epsilon (int) – Dielectric constant to be used, polarity of the resulting molecule varies, possible values are {4,78}.

classmethod pmd_generator()

Abstract method

classmethod save(file_name, file_path='./', **kwargs)

Save to file the parameterised system.

Parameters

  • file_name (str) – No file type postfix is necessary

  • file_path (str) – Default to current directory

Returns

path – The absolute path where the trajectory is written to.

Return type

str

classmethod unload_ddec_models(**kwargs)

Unload the machine-learned charge model, which takes over 1 GB of memory.

class mdfptools.Parameteriser.SolutionParameteriser[source]

Parameterisation of solution box, i.e. one copy of solute molecule surronded by water.

Parameters

solvent_pmd (parmed.structure) – Parameterised tip3p water as parmed object

Attributes
system_pmd

Methods

load_ddec_models([epsilon])

Charging molecule using machine learned charge instead of the default AM1-BCC method.

pmd_generator()

Abstract method

run(smiles[, allow_undefined_stereo, …])

Parameterisation perfromed via openeye.

save(file_name[, file_path])

Save to file the parameterised system.

unload_ddec_models(\*\*kwargs)

Unload the machine-learned charge model, which takes over 1 GB of memory.

via_openeye(smiles[, …])

Parameterisation perfromed via openeye.

via_rdkit(smiles[, allow_undefined_stereo, …])

Parameterisation perfromed via openeye.
classmethod via_openeye(smiles, allow_undefined_stereo=False, default_padding=Quantity(value=1.25, unit=nanometer), **kwargs)[source]

Parameterisation perfromed via openeye.

Parameters

  • smiles (str) – SMILES string of the solute molecule

  • allow_undefined_stereo (bool) – Flag passed to OpenForceField Molecule object during parameterisation. When set to False an error is returned if SMILES have no/ambiguous steroechemistry. Default to False here as a sanity check for user.

  • default_padding (simtk.unit) – Dictates amount of water surronding the solute. Default is 1.25 nanometers

Returns

system_pmd – The parameterised system as parmed object

Return type

parmed.structure

classmethod via_rdkit(smiles, allow_undefined_stereo=False, default_padding=Quantity(value=1.25, unit=nanometer), **kwargs)[source]

Parameterisation perfromed via openeye.

Parameters

  • smiles (str) – SMILES string of the solute molecule

  • allow_undefined_stereo (bool) – Flag passed to OpenForceField Molecule object during parameterisation. When set to False an error is returned if SMILES have no/ambiguous steroechemistry. Default to False here as a sanity check for user.

  • default_padding (simtk.unit) – Dictates amount of water surronding the solute. Default is 1.25 nanometers

Returns

system_pmd – The parameterised system as parmed object

Return type

parmed.structure

classmethod _via_helper(**kwargs)[source]

Helper function for via_rdkit or via_openeye

Returns

system_pmd – The parameterised system as parmed object

Return type

parmed.structure

classmethod run(smiles, allow_undefined_stereo=False, default_padding=Quantity(value=1.25, unit=nanometer), **kwargs)

Parameterisation perfromed via openeye.

Parameters

  • smiles (str) – SMILES string of the solute molecule

  • allow_undefined_stereo (bool) – Flag passed to OpenForceField Molecule object during parameterisation. When set to False an error is returned if SMILES have no/ambiguous steroechemistry. Default to False here as a sanity check for user.

  • default_padding (simtk.unit) – Dictates amount of water surronding the solute. Default is 1.25 nanometers

Returns

system_pmd – The parameterised system as parmed object

Return type

parmed.structure

__init__(self, /, *args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

classmethod _openeye_parameteriser(mol, **kwargs)

Creates a parameterised system from openeye molecule

Parameters

mol (oechem.OEMol) –

classmethod _openeye_setter(smiles, **kwargs)

Prepares an openeye molecule with 3D coordinates.

Parameters

smiles (str) – SMILES string of the solute moleulce

Returns

mol

Return type

oechem.OEMol

classmethod _rdkit_parameteriser(mol, **kwargs)
classmethod _rdkit_setter(smiles, **kwargs)

Prepares an rdkit molecule with 3D coordinates.

Parameters

smiles (str) – SMILES string of the solute moleulce

Returns

mol

Return type

rdkit.Chem.Mol

classmethod load_ddec_models(epsilon=4, **kwargs)

Charging molecule using machine learned charge instead of the default AM1-BCC method.

Requires first installing the mlddec(https://github.com/rinikerlab/mlddec) package. Parameters are availible for elements : {H,C,N,O,Cl,Br,F}.

Parameters

epsilon (int) – Dielectric constant to be used, polarity of the resulting molecule varies, possible values are {4,78}.

classmethod pmd_generator()

Abstract method

classmethod save(file_name, file_path='./', **kwargs)

Save to file the parameterised system.

Parameters

  • file_name (str) – No file type postfix is necessary

  • file_path (str) – Default to current directory

Returns

path – The absolute path where the trajectory is written to.

Return type

str

classmethod unload_ddec_models(**kwargs)

Unload the machine-learned charge model, which takes over 1 GB of memory.

class mdfptools.Parameteriser.VaccumParameteriser[source]
Attributes
system_pmd

Methods

load_ddec_models([epsilon])

Charging molecule using machine learned charge instead of the default AM1-BCC method.

pmd_generator()

Abstract method

run(smiles[, allow_undefined_stereo])

Parameterisation perfromed via openeye toolkit.

save(file_name[, file_path])

Save to file the parameterised system.

unload_ddec_models(\*\*kwargs)

Unload the machine-learned charge model, which takes over 1 GB of memory.

via_openeye(smiles[, allow_undefined_stereo])

Parameterisation perfromed via openeye toolkit.

via_rdkit(smiles[, allow_undefined_stereo])

Parameterisation perfromed via rdkit toolkit.
classmethod via_openeye(smiles, allow_undefined_stereo=False, **kwargs)[source]

Parameterisation perfromed via openeye toolkit.

Parameters

  • smiles (str) – SMILES string of the molecule to be parametersied

  • allow_undefined_stereo (bool) – Flag passed to OpenForceField Molecule object during parameterisation. When set to False an error is returned if SMILES have no/ambiguous steroechemistry. Default to False here as a sanity check for user.

Returns

system_pmd – The parameterised system as parmed object

Return type

parmed.structure

classmethod via_rdkit(smiles, allow_undefined_stereo=False, **kwargs)[source]

Parameterisation perfromed via rdkit toolkit.

Parameters

  • smiles (str) – SMILES string of the molecule to be parametersied

  • allow_undefined_stereo (bool) – Flag passed to OpenForceField Molecule object during parameterisation. When set to False an error is returned if SMILES have no/ambiguous steroechemistry. Default to False here as a sanity check for user.

Returns

system_pmd – The parameterised system as parmed object

Return type

parmed.structure

__init__(self, /, *args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

classmethod _openeye_parameteriser(mol, **kwargs)

Creates a parameterised system from openeye molecule

Parameters

mol (oechem.OEMol) –

classmethod _openeye_setter(smiles, **kwargs)

Prepares an openeye molecule with 3D coordinates.

Parameters

smiles (str) – SMILES string of the solute moleulce

Returns

mol

Return type

oechem.OEMol

classmethod _rdkit_parameteriser(mol, **kwargs)
classmethod _rdkit_setter(smiles, **kwargs)

Prepares an rdkit molecule with 3D coordinates.

Parameters

smiles (str) – SMILES string of the solute moleulce

Returns

mol

Return type

rdkit.Chem.Mol

classmethod load_ddec_models(epsilon=4, **kwargs)

Charging molecule using machine learned charge instead of the default AM1-BCC method.

Requires first installing the mlddec(https://github.com/rinikerlab/mlddec) package. Parameters are availible for elements : {H,C,N,O,Cl,Br,F}.

Parameters

epsilon (int) – Dielectric constant to be used, polarity of the resulting molecule varies, possible values are {4,78}.

classmethod pmd_generator()

Abstract method

classmethod run(smiles, allow_undefined_stereo=False, **kwargs)

Parameterisation perfromed via openeye toolkit.

Parameters

  • smiles (str) – SMILES string of the molecule to be parametersied

  • allow_undefined_stereo (bool) – Flag passed to OpenForceField Molecule object during parameterisation. When set to False an error is returned if SMILES have no/ambiguous steroechemistry. Default to False here as a sanity check for user.

Returns

system_pmd – The parameterised system as parmed object

Return type

parmed.structure

classmethod save(file_name, file_path='./', **kwargs)

Save to file the parameterised system.

Parameters

  • file_name (str) – No file type postfix is necessary

  • file_path (str) – Default to current directory

Returns

path – The absolute path where the trajectory is written to.

Return type

str

classmethod unload_ddec_models(**kwargs)

Unload the machine-learned charge model, which takes over 1 GB of memory.

class mdfptools.Parameteriser.BaseParameteriser[source]

Warning

The base class should not be used directly

Attributes
system_pmd

Methods

load_ddec_models([epsilon])

Charging molecule using machine learned charge instead of the default AM1-BCC method.

pmd_generator()

Abstract method

run()

Abstract method

save(file_name[, file_path])

Save to file the parameterised system.

unload_ddec_models(\*\*kwargs)

Unload the machine-learned charge model, which takes over 1 GB of memory.

via_openeye()

Abstract method

via_rdkit()

Abstract method
classmethod via_openeye()[source]

Abstract method

classmethod via_rdkit()[source]

Abstract method

classmethod pmd_generator()[source]

Abstract method

classmethod _rdkit_setter(smiles, **kwargs)[source]

Prepares an rdkit molecule with 3D coordinates.

Parameters

smiles (str) – SMILES string of the solute moleulce

Returns

mol

Return type

rdkit.Chem.Mol

classmethod _rdkit_parameteriser(mol, **kwargs)[source]
classmethod load_ddec_models(epsilon=4, **kwargs)[source]

Charging molecule using machine learned charge instead of the default AM1-BCC method.

Requires first installing the mlddec(https://github.com/rinikerlab/mlddec) package. Parameters are availible for elements : {H,C,N,O,Cl,Br,F}.

Parameters

epsilon (int) – Dielectric constant to be used, polarity of the resulting molecule varies, possible values are {4,78}.

classmethod unload_ddec_models(**kwargs)[source]

Unload the machine-learned charge model, which takes over 1 GB of memory.

classmethod _openeye_setter(smiles, **kwargs)[source]

Prepares an openeye molecule with 3D coordinates.

Parameters

smiles (str) – SMILES string of the solute moleulce

Returns

mol

Return type

oechem.OEMol

classmethod _openeye_parameteriser(mol, **kwargs)[source]

Creates a parameterised system from openeye molecule

Parameters

mol (oechem.OEMol) –

classmethod save(file_name, file_path='./', **kwargs)[source]

Save to file the parameterised system.

Parameters

  • file_name (str) – No file type postfix is necessary

  • file_path (str) – Default to current directory

Returns

path – The absolute path where the trajectory is written to.

Return type

str

classmethod run()

Abstract method

__init__(self, /, *args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

class mdfptools.Parameteriser.SolutionParameteriser[source]

Parameterisation of solution box, i.e. one copy of solute molecule surronded by water.

Parameters

solvent_pmd (parmed.structure) – Parameterised tip3p water as parmed object

Attributes
system_pmd

Methods

load_ddec_models([epsilon])

Charging molecule using machine learned charge instead of the default AM1-BCC method.

pmd_generator()

Abstract method

run(smiles[, allow_undefined_stereo, …])

Parameterisation perfromed via openeye.

save(file_name[, file_path])

Save to file the parameterised system.

unload_ddec_models(\*\*kwargs)

Unload the machine-learned charge model, which takes over 1 GB of memory.

via_openeye(smiles[, …])

Parameterisation perfromed via openeye.

via_rdkit(smiles[, allow_undefined_stereo, …])

Parameterisation perfromed via openeye.
classmethod via_openeye(smiles, allow_undefined_stereo=False, default_padding=Quantity(value=1.25, unit=nanometer), **kwargs)[source]

Parameterisation perfromed via openeye.

Parameters

  • smiles (str) – SMILES string of the solute molecule

  • allow_undefined_stereo (bool) – Flag passed to OpenForceField Molecule object during parameterisation. When set to False an error is returned if SMILES have no/ambiguous steroechemistry. Default to False here as a sanity check for user.

  • default_padding (simtk.unit) – Dictates amount of water surronding the solute. Default is 1.25 nanometers

Returns

system_pmd – The parameterised system as parmed object

Return type

parmed.structure

classmethod via_rdkit(smiles, allow_undefined_stereo=False, default_padding=Quantity(value=1.25, unit=nanometer), **kwargs)[source]

Parameterisation perfromed via openeye.

Parameters

  • smiles (str) – SMILES string of the solute molecule

  • allow_undefined_stereo (bool) – Flag passed to OpenForceField Molecule object during parameterisation. When set to False an error is returned if SMILES have no/ambiguous steroechemistry. Default to False here as a sanity check for user.

  • default_padding (simtk.unit) – Dictates amount of water surronding the solute. Default is 1.25 nanometers

Returns

system_pmd – The parameterised system as parmed object

Return type

parmed.structure

classmethod _via_helper(**kwargs)[source]

Helper function for via_rdkit or via_openeye

Returns

system_pmd – The parameterised system as parmed object

Return type

parmed.structure

classmethod run(smiles, allow_undefined_stereo=False, default_padding=Quantity(value=1.25, unit=nanometer), **kwargs)

Parameterisation perfromed via openeye.

Parameters

  • smiles (str) – SMILES string of the solute molecule

  • allow_undefined_stereo (bool) – Flag passed to OpenForceField Molecule object during parameterisation. When set to False an error is returned if SMILES have no/ambiguous steroechemistry. Default to False here as a sanity check for user.

  • default_padding (simtk.unit) – Dictates amount of water surronding the solute. Default is 1.25 nanometers

Returns

system_pmd – The parameterised system as parmed object

Return type

parmed.structure

__init__(self, /, *args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

classmethod _openeye_parameteriser(mol, **kwargs)

Creates a parameterised system from openeye molecule

Parameters

mol (oechem.OEMol) –

classmethod _openeye_setter(smiles, **kwargs)

Prepares an openeye molecule with 3D coordinates.

Parameters

smiles (str) – SMILES string of the solute moleulce

Returns

mol

Return type

oechem.OEMol

classmethod _rdkit_parameteriser(mol, **kwargs)
classmethod _rdkit_setter(smiles, **kwargs)

Prepares an rdkit molecule with 3D coordinates.

Parameters

smiles (str) – SMILES string of the solute moleulce

Returns

mol

Return type

rdkit.Chem.Mol

classmethod load_ddec_models(epsilon=4, **kwargs)

Charging molecule using machine learned charge instead of the default AM1-BCC method.

Requires first installing the mlddec(https://github.com/rinikerlab/mlddec) package. Parameters are availible for elements : {H,C,N,O,Cl,Br,F}.

Parameters

epsilon (int) – Dielectric constant to be used, polarity of the resulting molecule varies, possible values are {4,78}.

classmethod pmd_generator()

Abstract method

classmethod save(file_name, file_path='./', **kwargs)

Save to file the parameterised system.

Parameters

  • file_name (str) – No file type postfix is necessary

  • file_path (str) – Default to current directory

Returns

path – The absolute path where the trajectory is written to.

Return type

str

classmethod unload_ddec_models(**kwargs)

Unload the machine-learned charge model, which takes over 1 GB of memory.

class mdfptools.Parameteriser.LiquidParameteriser[source]

Parameterisation of liquid box, i.e. multiple replicates of the same molecule

Attributes
system_pmd

Methods

load_ddec_models([epsilon])

Charging molecule using machine learned charge instead of the default AM1-BCC method.

pmd_generator()

Abstract method

run(smiles, density[, …])

Parameterisation perfromed via openeye toolkit.

save(file_name[, file_path])

Save to file the parameterised system.

unload_ddec_models(\*\*kwargs)

Unload the machine-learned charge model, which takes over 1 GB of memory.

via_openeye(smiles, density[, …])

Parameterisation perfromed via openeye toolkit.

via_rdkit(smiles, density[, …])

Parameterisation perfromed via rdkit.
classmethod via_openeye(smiles, density, allow_undefined_stereo=False, num_lig=100, **kwargs)[source]

Parameterisation perfromed via openeye toolkit.

Parameters

  • smiles (str) – SMILES string of the molecule to be parametersied

  • density (simtk.unit) – Density of liquid box

  • allow_undefined_stereo (bool) – Flag passed to OpenForceField Molecule object during parameterisation. When set to False an error is returned if SMILES have no/ambiguous steroechemistry. Default to False here as a sanity check for user.

  • num_lig (int) – Number of replicates of the molecule

Returns

system_pmd – The parameterised system as parmed object

Return type

parmed.structure

classmethod via_rdkit(smiles, density, allow_undefined_stereo=False, num_lig=100, **kwargs)[source]

Parameterisation perfromed via rdkit.

Parameters

  • smiles (str) – SMILES string of the molecule to be parametersied

  • density (simtk.unit) – Density of liquid box

  • allow_undefined_stereo (bool) – Flag passed to OpenForceField Molecule object during parameterisation. When set to False an error is returned if SMILES have no/ambiguous steroechemistry. Default to False here as a sanity check for user.

  • num_lig (int) – Number of replicates of the molecule

Returns

system_pmd – The parameterised system as parmed object

Return type

parmed.structure

classmethod _via_helper(density, num_lig, **kwargs)[source]

Helper function for via_rdkit or via_openeye

Parameters

  • density (simtk.unit) – Density of liquid box

  • num_lig (int) – Number of replicates of the molecule

Returns

system_pmd – The parameterised system as parmed object

Return type

parmed.structure

classmethod run(smiles, density, allow_undefined_stereo=False, num_lig=100, **kwargs)

Parameterisation perfromed via openeye toolkit.

Parameters

  • smiles (str) – SMILES string of the molecule to be parametersied

  • density (simtk.unit) – Density of liquid box

  • allow_undefined_stereo (bool) – Flag passed to OpenForceField Molecule object during parameterisation. When set to False an error is returned if SMILES have no/ambiguous steroechemistry. Default to False here as a sanity check for user.

  • num_lig (int) – Number of replicates of the molecule

Returns

system_pmd – The parameterised system as parmed object

Return type

parmed.structure

__init__(self, /, *args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

classmethod _openeye_parameteriser(mol, **kwargs)

Creates a parameterised system from openeye molecule

Parameters

mol (oechem.OEMol) –

classmethod _openeye_setter(smiles, **kwargs)

Prepares an openeye molecule with 3D coordinates.

Parameters

smiles (str) – SMILES string of the solute moleulce

Returns

mol

Return type

oechem.OEMol

classmethod _rdkit_parameteriser(mol, **kwargs)
classmethod _rdkit_setter(smiles, **kwargs)

Prepares an rdkit molecule with 3D coordinates.

Parameters

smiles (str) – SMILES string of the solute moleulce

Returns

mol

Return type

rdkit.Chem.Mol

classmethod load_ddec_models(epsilon=4, **kwargs)

Charging molecule using machine learned charge instead of the default AM1-BCC method.

Requires first installing the mlddec(https://github.com/rinikerlab/mlddec) package. Parameters are availible for elements : {H,C,N,O,Cl,Br,F}.

Parameters

epsilon (int) – Dielectric constant to be used, polarity of the resulting molecule varies, possible values are {4,78}.

classmethod pmd_generator()

Abstract method

classmethod save(file_name, file_path='./', **kwargs)

Save to file the parameterised system.

Parameters

  • file_name (str) – No file type postfix is necessary

  • file_path (str) – Default to current directory

Returns

path – The absolute path where the trajectory is written to.

Return type

str

classmethod unload_ddec_models(**kwargs)

Unload the machine-learned charge model, which takes over 1 GB of memory.