class mdfptools.Composer.MDFP(mdfp_dict)

A MDFP object contains a set of features for a molecule, obtaining from a simulation or a set of simulations.

Methods

get_mdfp(self)

returns

__init__(self, mdfp_dict)

Parameters

fp_dict (dict) –

Keys are each of the type features a given Extractor obtains, e.g. “2d_count” are the 2D topological features obtained from molecule SMILES, “intra_lj” are the intra-molecular LJ energies obtained from simulation.

Values are the corresponding set of numerics, stored as lists.

get_mdfp(self)

Returns

Return type

a list of floating values, i.e. the mdfp feature vector

class mdfptools.Composer.BaseComposer

The BaseComposer class containing functions that can be used by different composers for different types of simulations

Methods

run(smiles)

param smiles SMILES string of the solute molecule

classmethod run(smiles)

Parameters

smiles (str) – SMILES string of the solute molecule

classmethod _get_relevant_properties()

Where the set of features to be included in the final MDFP are defined

classmethod _get_2d_descriptors()

Obtain those 2D topological features as described in the original publication.

classmethod _get_statistical_moments(property_extractor, statistical_moments=[<function mean at 0x7f3b88a77730>, <function std at 0x7f3b88a778c8>, <function median at 0x7f3b8892d950>], **kwargs)

Performs statistical weighting of the numerical properties (e.g. LJ and electrostatics energies) obtained from each frame of simulation.

Parameters

• property_extractor (mdfptools.Extractor) – The particular type of Extractor methodclass used to obtain the various properties from simulation.

• statistical_moments (list) – The list of statistical weighting to be performed to each properties from all the frames. Default list of weighting are the mean, standard deviation and median.

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

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

class mdfptools.Composer.SolutionComposer

Composer used to extract features from solution simulations, namely one copy of solute in water solvent. This generates fingerprint most akin to that from the original publication.

Methods

run(mdtraj_obj, parmed_obj[, smiles])

param mdtraj_obj The simulated trajectory

classmethod run(mdtraj_obj, parmed_obj, smiles=None, **kwargs)

Parameters

• mdtraj_obj (mdtraj.trajectory) – The simulated trajectory

• parmed_obj (parmed.structure) – Parmed object of the fully parameterised simulated system.

• smiles (str) – SMILES string of the solute. If mdfptools.Parameteriser was used during parameterisation, then smiles is automatically obtained from the parmed_obj.

classmethod _get_relevant_properties()

Where the set of features to be included in the final MDFP are defined

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

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

classmethod _get_2d_descriptors()

Obtain those 2D topological features as described in the original publication.

classmethod _get_statistical_moments(property_extractor, statistical_moments=[<function mean at 0x7f3b88a77730>, <function std at 0x7f3b88a778c8>, <function median at 0x7f3b8892d950>], **kwargs)

Performs statistical weighting of the numerical properties (e.g. LJ and electrostatics energies) obtained from each frame of simulation.

Parameters

• property_extractor (mdfptools.Extractor) – The particular type of Extractor methodclass used to obtain the various properties from simulation.

• statistical_moments (list) – The list of statistical weighting to be performed to each properties from all the frames. Default list of weighting are the mean, standard deviation and median.

class mdfptools.Composer.LiquidComposer

Composer used to extract features from liquid simulations, namely a box containing replicates of the same molecule.

Methods

run(mdtraj_obj, parmed_obj[, smiles])

param mdtraj_obj The simulated trajectory

classmethod run(mdtraj_obj, parmed_obj, smiles=None, **kwargs)

Parameters

• mdtraj_obj (mdtraj.trajectory) – The simulated trajectory

• parmed_obj (parmed.structure) – Parmed object of the fully parameterised simulated system.

• smiles (str) – SMILES string of one copy of the solute. If mdfptools.Parameteriser was used during parameterisation, then smiles is automatically obtained from the parmed_obj.

classmethod _get_relevant_properties()

Where the set of features to be included in the final MDFP are defined

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

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

classmethod _get_2d_descriptors()

Obtain those 2D topological features as described in the original publication.

classmethod _get_statistical_moments(property_extractor, statistical_moments=[<function mean at 0x7f3b88a77730>, <function std at 0x7f3b88a778c8>, <function median at 0x7f3b8892d950>], **kwargs)

Performs statistical weighting of the numerical properties (e.g. LJ and electrostatics energies) obtained from each frame of simulation.

Parameters

• property_extractor (mdfptools.Extractor) – The particular type of Extractor methodclass used to obtain the various properties from simulation.

• statistical_moments (list) – The list of statistical weighting to be performed to each properties from all the frames. Default list of weighting are the mean, standard deviation and median.

class mdfptools.Composer.SolutionLiquidComposer(solv_mdtraj_obj, solv_parmed_obj, liq_mdtraj_obj, liq_parmed_obj, smiles=None, **kwargs)

Composer used to extract features from pairs of solution and liquid simulations.

Methods

run(smiles)

param smiles SMILES string of the solute molecule

classmethod __init__(solv_mdtraj_obj, solv_parmed_obj, liq_mdtraj_obj, liq_parmed_obj, smiles=None, **kwargs)

Parameters

• solv_mdtraj_obj (mdtraj.trajectory) – The simulated solution trajectory

• solv_parmed_obj (parmed.structure) – Parmed object of the fully parameterised simulated solution system.

• liq_mdtraj_obj (mdtraj.trajectory) – The simulated liquid trajectory

• liq_parmed_obj (parmed.structure) – Parmed object of the fully parameterised simulated liquid system.

• smiles (str) – SMILES string of one copy of the solute. If mdfptools.Parameteriser was used during parameterisation, then smiles is automatically obtained from the parmed_obj.

classmethod _get_2d_descriptors()

Obtain those 2D topological features as described in the original publication.

classmethod _get_statistical_moments(property_extractor, statistical_moments=[<function mean at 0x7f3b88a77730>, <function std at 0x7f3b88a778c8>, <function median at 0x7f3b8892d950>], **kwargs)

Performs statistical weighting of the numerical properties (e.g. LJ and electrostatics energies) obtained from each frame of simulation.

Parameters

• property_extractor (mdfptools.Extractor) – The particular type of Extractor methodclass used to obtain the various properties from simulation.

• statistical_moments (list) – The list of statistical weighting to be performed to each properties from all the frames. Default list of weighting are the mean, standard deviation and median.

classmethod run(smiles)

Parameters

smiles (str) – SMILES string of the solute molecule

classmethod _get_relevant_properties()

Where the set of features to be included in the final MDFP are defined

MDFP

Molecular Dynamics Fingerprint (MDFP) Object

class mdfptools.Composer.MDFP(mdfp_dict)

A MDFP object contains a set of features for a molecule, obtaining from a simulation or a set of simulations.

Methods

get_mdfp(self)

returns

__init__(self, mdfp_dict)

Parameters

fp_dict (dict) –

Keys are each of the type features a given Extractor obtains, e.g. “2d_count” are the 2D topological features obtained from molecule SMILES, “intra_lj” are the intra-molecular LJ energies obtained from simulation.

Values are the corresponding set of numerics, stored as lists.

get_mdfp(self)

Returns

Return type

a list of floating values, i.e. the mdfp feature vector

Composers

Post-processing of simulation trajectories to form (compose) molecular dynamic fingerprints (MDFPs)

class mdfptools.Composer.BaseComposer

The BaseComposer class containing functions that can be used by different composers for different types of simulations

Methods

run(smiles)

param smiles SMILES string of the solute molecule

classmethod run(smiles)

Parameters

smiles (str) – SMILES string of the solute molecule

classmethod _get_relevant_properties()

Where the set of features to be included in the final MDFP are defined

classmethod _get_2d_descriptors()

Obtain those 2D topological features as described in the original publication.

classmethod _get_statistical_moments(property_extractor, statistical_moments=[<function mean at 0x7f3b88a77730>, <function std at 0x7f3b88a778c8>, <function median at 0x7f3b8892d950>], **kwargs)

Performs statistical weighting of the numerical properties (e.g. LJ and electrostatics energies) obtained from each frame of simulation.

Parameters

• property_extractor (mdfptools.Extractor) – The particular type of Extractor methodclass used to obtain the various properties from simulation.

• statistical_moments (list) – The list of statistical weighting to be performed to each properties from all the frames. Default list of weighting are the mean, standard deviation and median.

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

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

class mdfptools.Composer.SolutionComposer

Composer used to extract features from solution simulations, namely one copy of solute in water solvent. This generates fingerprint most akin to that from the original publication.

Methods

run(mdtraj_obj, parmed_obj[, smiles])

param mdtraj_obj The simulated trajectory

classmethod run(mdtraj_obj, parmed_obj, smiles=None, **kwargs)

Parameters

• mdtraj_obj (mdtraj.trajectory) – The simulated trajectory

• parmed_obj (parmed.structure) – Parmed object of the fully parameterised simulated system.

• smiles (str) – SMILES string of the solute. If mdfptools.Parameteriser was used during parameterisation, then smiles is automatically obtained from the parmed_obj.

classmethod _get_relevant_properties()

Where the set of features to be included in the final MDFP are defined

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

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

classmethod _get_2d_descriptors()

Obtain those 2D topological features as described in the original publication.

classmethod _get_statistical_moments(property_extractor, statistical_moments=[<function mean at 0x7f3b88a77730>, <function std at 0x7f3b88a778c8>, <function median at 0x7f3b8892d950>], **kwargs)

Performs statistical weighting of the numerical properties (e.g. LJ and electrostatics energies) obtained from each frame of simulation.

Parameters

• property_extractor (mdfptools.Extractor) – The particular type of Extractor methodclass used to obtain the various properties from simulation.

• statistical_moments (list) – The list of statistical weighting to be performed to each properties from all the frames. Default list of weighting are the mean, standard deviation and median.

class mdfptools.Composer.LiquidComposer

Composer used to extract features from liquid simulations, namely a box containing replicates of the same molecule.

Methods

run(mdtraj_obj, parmed_obj[, smiles])

param mdtraj_obj The simulated trajectory

classmethod run(mdtraj_obj, parmed_obj, smiles=None, **kwargs)

Parameters

• mdtraj_obj (mdtraj.trajectory) – The simulated trajectory

• parmed_obj (parmed.structure) – Parmed object of the fully parameterised simulated system.

• smiles (str) – SMILES string of one copy of the solute. If mdfptools.Parameteriser was used during parameterisation, then smiles is automatically obtained from the parmed_obj.

classmethod _get_relevant_properties()

Where the set of features to be included in the final MDFP are defined

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

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

classmethod _get_2d_descriptors()

Obtain those 2D topological features as described in the original publication.

classmethod _get_statistical_moments(property_extractor, statistical_moments=[<function mean at 0x7f3b88a77730>, <function std at 0x7f3b88a778c8>, <function median at 0x7f3b8892d950>], **kwargs)

Performs statistical weighting of the numerical properties (e.g. LJ and electrostatics energies) obtained from each frame of simulation.

Parameters

• property_extractor (mdfptools.Extractor) – The particular type of Extractor methodclass used to obtain the various properties from simulation.

• statistical_moments (list) – The list of statistical weighting to be performed to each properties from all the frames. Default list of weighting are the mean, standard deviation and median.

class mdfptools.Composer.SolutionLiquidComposer(solv_mdtraj_obj, solv_parmed_obj, liq_mdtraj_obj, liq_parmed_obj, smiles=None, **kwargs)

Composer used to extract features from pairs of solution and liquid simulations.

Methods

run(smiles)

param smiles SMILES string of the solute molecule

classmethod __init__(solv_mdtraj_obj, solv_parmed_obj, liq_mdtraj_obj, liq_parmed_obj, smiles=None, **kwargs)

Parameters

• solv_mdtraj_obj (mdtraj.trajectory) – The simulated solution trajectory

• solv_parmed_obj (parmed.structure) – Parmed object of the fully parameterised simulated solution system.

• liq_mdtraj_obj (mdtraj.trajectory) – The simulated liquid trajectory

• liq_parmed_obj (parmed.structure) – Parmed object of the fully parameterised simulated liquid system.

• smiles (str) – SMILES string of one copy of the solute. If mdfptools.Parameteriser was used during parameterisation, then smiles is automatically obtained from the parmed_obj.

classmethod _get_2d_descriptors()

Obtain those 2D topological features as described in the original publication.

classmethod _get_statistical_moments(property_extractor, statistical_moments=[<function mean at 0x7f3b88a77730>, <function std at 0x7f3b88a778c8>, <function median at 0x7f3b8892d950>], **kwargs)

Performs statistical weighting of the numerical properties (e.g. LJ and electrostatics energies) obtained from each frame of simulation.

Parameters

• property_extractor (mdfptools.Extractor) – The particular type of Extractor methodclass used to obtain the various properties from simulation.

• statistical_moments (list) – The list of statistical weighting to be performed to each properties from all the frames. Default list of weighting are the mean, standard deviation and median.

classmethod run(smiles)

Parameters

smiles (str) – SMILES string of the solute molecule

classmethod _get_relevant_properties()

Where the set of features to be included in the final MDFP are defined