Extractors

Going through each from of the simulation trajectory and extract the relevant features. Used by Composers under the hood.

class mdfptools.Extractor.BaseExtractor

Warning

The base class should not be used directly

Methods

extract_energies(mdtraj_obj, parmed_obj[, …])	Extracting the various energetic components described in the original publication from each frame of simulation.
extract_rgyr(mdtraj_obj, \*\*kwargs)	Extracting radius of gyration from each frame of simulation.
extract_sasa(mdtraj_obj, \*\*kwargs)	Extracting solvent accessible surface area from each frame of simulation.

classmethod _solute_solvent_split(topology)

Abstract method

classmethod _get_all_exception_atom_pairs(system, topology)

Abstract method

classmethod _extract_energies_helper(mdtraj_obj, parmed_obj, platform='CPU', **kwargs)

Helper function for extracting the various energetic components described in the original publication from each frame of simulation. OpenMM.CustomNonbondedForces are used. Specifically, the reaction field defintion is taken from GROMOS96 manual.

Parameters

• mdtraj_obj (mdtraj.trajectory) – The simulated trajectory

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

• platform (str) – The computing architecture to do the calculation, default to CPU, CUDA, OpenCL is also possible.

Returns

• context (Openmm.Context)

• integrator (Openmm.Integrator)

classmethod extract_energies(mdtraj_obj, parmed_obj, platform='CPU', **kwargs)

Extracting the various energetic components described in the original publication from each frame of simulation.

Parameters

• mdtraj_obj (mdtraj.trajectory) – The simulated trajectory

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

• platform (str) – The computing architecture to do the calculation, default to CPU, CUDA, OpenCL is also possible.

Returns

df – Keys are each of the energetic type features. e.g. “intra_lj” are the intra-molecular LJ energies obtained from simulation.

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

Return type

dict

classmethod extract_rgyr(mdtraj_obj, **kwargs)

Extracting radius of gyration from each frame of simulation. Assumes the first residue in the system is the solute.

Parameters

mdtraj_obj (mdtraj.trajectory) – The simulated trajectory

Returns

df – Key is prefix_rgyr, where prefix changes depending on the type of Extractor class used. Values are the corresponding set of numerics, stored as lists.

Return type

dict

classmethod extract_sasa(mdtraj_obj, **kwargs)

Extracting solvent accessible surface area from each frame of simulation. Assumes the first residue in the system is the solute.

Parameters

mdtraj_obj (mdtraj.trajectory) – The simulated trajectory

Returns

df – Key is prefix_sasa, where prefix changes depending on the type of Extractor class used. Values are the corresponding set of numerics, stored as lists.

Return type

dict

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

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

class mdfptools.Extractor.SolutionExtractor

Extraction from condensed phase simulation where the system is composed of one solute molecule surronded by solvents

Parameters

string_identifier (str) – The string identifier tagged as prefix to all values extracted in this class.

Methods

extract_dipole(mdtraj_obj, parmed_obj, …)	Extracting dipole moment from each frame of simulation.
extract_energies(mdtraj_obj, parmed_obj[, …])	Extracting the various energetic components described in the original publication from each frame of simulation.
extract_rgyr(mdtraj_obj, \*\*kwargs)	Extracting radius of gyration from each frame of simulation.
extract_sasa(mdtraj_obj, \*\*kwargs)	Extracting solvent accessible surface area from each frame of simulation.

classmethod _solute_solvent_split(topology)

Distinguish solutes from solvents, used in _extract_energies_helper()

The following is assumed:

• there are only two type of residues

• the residue that is lesser in number is the solute

Parameters

topology (parmed.topology) –

Returns

• solute_atoms (set) – set of solute_atoms indices

• solvent_atoms (set) – set of solvent_atoms indices

classmethod _get_all_exception_atom_pairs(system, topology)

Using the parametersied system to obtain the exception and exclusion pairs, used in _extract_energies_helper(). This is inferred purely from the parameterised system and connectivity.

Parameters

• system (OpenMM.System) –

• topology (parmed.topology) –

Returns

• solute_1_4_pairs (set)

• solvent_1_4_pairs (set)

• solute_excluded_pairs (set)

• solvent_excluded_pairs (set)

• solute_self_pairs (set)

• solvent_self_pairs (set)

classmethod extract_dipole(mdtraj_obj, parmed_obj, **kwargs)

Extracting dipole moment from each frame of simulation. Assumes the first residue in the system is the solute.

Parameters

• mdtraj_obj (mdtraj.trajectory) – The simulated trajectory

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

Returns

df – Key is prefix_dipole_postfix, where prefix changes depending on the type of Extractor class used, postfix can be {x,y,z,magnitude}. Values are the corresponding set of numerics, stored as lists.

Return type

dict

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

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

classmethod _extract_energies_helper(mdtraj_obj, parmed_obj, platform='CPU', **kwargs)

Helper function for extracting the various energetic components described in the original publication from each frame of simulation. OpenMM.CustomNonbondedForces are used. Specifically, the reaction field defintion is taken from GROMOS96 manual.

Parameters

• mdtraj_obj (mdtraj.trajectory) – The simulated trajectory

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

• platform (str) – The computing architecture to do the calculation, default to CPU, CUDA, OpenCL is also possible.

Returns

• context (Openmm.Context)

• integrator (Openmm.Integrator)

classmethod extract_energies(mdtraj_obj, parmed_obj, platform='CPU', **kwargs)

Extracting the various energetic components described in the original publication from each frame of simulation.

Parameters

• mdtraj_obj (mdtraj.trajectory) – The simulated trajectory

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

• platform (str) – The computing architecture to do the calculation, default to CPU, CUDA, OpenCL is also possible.

Returns

df – Keys are each of the energetic type features. e.g. “intra_lj” are the intra-molecular LJ energies obtained from simulation.

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

Return type

dict

classmethod extract_rgyr(mdtraj_obj, **kwargs)

Extracting radius of gyration from each frame of simulation. Assumes the first residue in the system is the solute.

Parameters

mdtraj_obj (mdtraj.trajectory) – The simulated trajectory

Returns

df – Key is prefix_rgyr, where prefix changes depending on the type of Extractor class used. Values are the corresponding set of numerics, stored as lists.

Return type

dict

classmethod extract_sasa(mdtraj_obj, **kwargs)

Extracting solvent accessible surface area from each frame of simulation. Assumes the first residue in the system is the solute.

Parameters

mdtraj_obj (mdtraj.trajectory) – The simulated trajectory

Returns

df – Key is prefix_sasa, where prefix changes depending on the type of Extractor class used. Values are the corresponding set of numerics, stored as lists.

Return type

dict

class mdfptools.Extractor.TrialSolutionExtractor

Methods

extract_dipole(mdtraj_obj, parmed_obj, …)	Extracting dipole moment from each frame of simulation.
extract_energies(mdtraj_obj, parmed_obj[, …])	Extracting the various energetic components described in the original publication from each frame of simulation.
extract_rgyr(mdtraj_obj, \*\*kwargs)	Extracting radius of gyration from each frame of simulation.
extract_sasa(mdtraj_obj, \*\*kwargs)	Extracting solvent accessible surface area from each frame of simulation.

classmethod extract_energies(mdtraj_obj, parmed_obj, platform='CPU', **kwargs)

Extracting the various energetic components described in the original publication from each frame of simulation.

Parameters

• mdtraj_obj (mdtraj.trajectory) – The simulated trajectory

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

• platform (str) – The computing architecture to do the calculation, default to CPU, CUDA, OpenCL is also possible.

Returns

df – Keys are each of the energetic type features. e.g. “intra_lj” are the intra-molecular LJ energies obtained from simulation.

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

Return type

dict

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

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

classmethod _extract_energies_helper(mdtraj_obj, parmed_obj, platform='CPU', **kwargs)

Helper function for extracting the various energetic components described in the original publication from each frame of simulation. OpenMM.CustomNonbondedForces are used. Specifically, the reaction field defintion is taken from GROMOS96 manual.

Parameters

• mdtraj_obj (mdtraj.trajectory) – The simulated trajectory

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

• platform (str) – The computing architecture to do the calculation, default to CPU, CUDA, OpenCL is also possible.

Returns

• context (Openmm.Context)

• integrator (Openmm.Integrator)

classmethod _get_all_exception_atom_pairs(system, topology)

Using the parametersied system to obtain the exception and exclusion pairs, used in _extract_energies_helper(). This is inferred purely from the parameterised system and connectivity.

Parameters

• system (OpenMM.System) –

• topology (parmed.topology) –

Returns

• solute_1_4_pairs (set)

• solvent_1_4_pairs (set)

• solute_excluded_pairs (set)

• solvent_excluded_pairs (set)

• solute_self_pairs (set)

• solvent_self_pairs (set)

classmethod _solute_solvent_split(topology)

Distinguish solutes from solvents, used in _extract_energies_helper()

The following is assumed:

• there are only two type of residues

• the residue that is lesser in number is the solute

Parameters

topology (parmed.topology) –

Returns

• solute_atoms (set) – set of solute_atoms indices

• solvent_atoms (set) – set of solvent_atoms indices

classmethod extract_dipole(mdtraj_obj, parmed_obj, **kwargs)

Extracting dipole moment from each frame of simulation. Assumes the first residue in the system is the solute.

Parameters

• mdtraj_obj (mdtraj.trajectory) – The simulated trajectory

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

Returns

df – Key is prefix_dipole_postfix, where prefix changes depending on the type of Extractor class used, postfix can be {x,y,z,magnitude}. Values are the corresponding set of numerics, stored as lists.

Return type

dict

classmethod extract_rgyr(mdtraj_obj, **kwargs)

Extracting radius of gyration from each frame of simulation. Assumes the first residue in the system is the solute.

Parameters

mdtraj_obj (mdtraj.trajectory) – The simulated trajectory

Returns

df – Key is prefix_rgyr, where prefix changes depending on the type of Extractor class used. Values are the corresponding set of numerics, stored as lists.

Return type

dict

classmethod extract_sasa(mdtraj_obj, **kwargs)

Extracting solvent accessible surface area from each frame of simulation. Assumes the first residue in the system is the solute.

Parameters

mdtraj_obj (mdtraj.trajectory) – The simulated trajectory

Returns

df – Key is prefix_sasa, where prefix changes depending on the type of Extractor class used. Values are the corresponding set of numerics, stored as lists.

Return type

dict

class mdfptools.Extractor.WaterExtractor

Synonyms class as SolutionExtractor

Parameters

string_identifier (str) – The string identifier tagged as prefix to all values extracted in this class.

Methods

extract_dipole(mdtraj_obj, parmed_obj, …)	Extracting dipole moment from each frame of simulation.
extract_energies(mdtraj_obj, parmed_obj[, …])	Extracting the various energetic components described in the original publication from each frame of simulation.
extract_rgyr(mdtraj_obj, \*\*kwargs)	Extracting radius of gyration from each frame of simulation.
extract_sasa(mdtraj_obj, \*\*kwargs)	Extracting solvent accessible surface area from each frame of simulation.

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

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

classmethod _extract_energies_helper(mdtraj_obj, parmed_obj, platform='CPU', **kwargs)

Helper function for extracting the various energetic components described in the original publication from each frame of simulation. OpenMM.CustomNonbondedForces are used. Specifically, the reaction field defintion is taken from GROMOS96 manual.

Parameters

• mdtraj_obj (mdtraj.trajectory) – The simulated trajectory

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

• platform (str) – The computing architecture to do the calculation, default to CPU, CUDA, OpenCL is also possible.

Returns

• context (Openmm.Context)

• integrator (Openmm.Integrator)

classmethod _get_all_exception_atom_pairs(system, topology)

Using the parametersied system to obtain the exception and exclusion pairs, used in _extract_energies_helper(). This is inferred purely from the parameterised system and connectivity.

Parameters

• system (OpenMM.System) –

• topology (parmed.topology) –

Returns

• solute_1_4_pairs (set)

• solvent_1_4_pairs (set)

• solute_excluded_pairs (set)

• solvent_excluded_pairs (set)

• solute_self_pairs (set)

• solvent_self_pairs (set)

classmethod _solute_solvent_split(topology)

Distinguish solutes from solvents, used in _extract_energies_helper()

The following is assumed:

• there are only two type of residues

• the residue that is lesser in number is the solute

Parameters

topology (parmed.topology) –

Returns

• solute_atoms (set) – set of solute_atoms indices

• solvent_atoms (set) – set of solvent_atoms indices

classmethod extract_dipole(mdtraj_obj, parmed_obj, **kwargs)

Extracting dipole moment from each frame of simulation. Assumes the first residue in the system is the solute.

Parameters

• mdtraj_obj (mdtraj.trajectory) – The simulated trajectory

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

Returns

df – Key is prefix_dipole_postfix, where prefix changes depending on the type of Extractor class used, postfix can be {x,y,z,magnitude}. Values are the corresponding set of numerics, stored as lists.

Return type

dict

classmethod extract_energies(mdtraj_obj, parmed_obj, platform='CPU', **kwargs)

Extracting the various energetic components described in the original publication from each frame of simulation.

Parameters

• mdtraj_obj (mdtraj.trajectory) – The simulated trajectory

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

• platform (str) – The computing architecture to do the calculation, default to CPU, CUDA, OpenCL is also possible.

Returns

df – Keys are each of the energetic type features. e.g. “intra_lj” are the intra-molecular LJ energies obtained from simulation.

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

Return type

dict

classmethod extract_rgyr(mdtraj_obj, **kwargs)

Extracting radius of gyration from each frame of simulation. Assumes the first residue in the system is the solute.

Parameters

mdtraj_obj (mdtraj.trajectory) – The simulated trajectory

Returns

df – Key is prefix_rgyr, where prefix changes depending on the type of Extractor class used. Values are the corresponding set of numerics, stored as lists.

Return type

dict

classmethod extract_sasa(mdtraj_obj, **kwargs)

Extracting solvent accessible surface area from each frame of simulation. Assumes the first residue in the system is the solute.

Parameters

mdtraj_obj (mdtraj.trajectory) – The simulated trajectory

Returns

df – Key is prefix_sasa, where prefix changes depending on the type of Extractor class used. Values are the corresponding set of numerics, stored as lists.

Return type

dict

class mdfptools.Extractor.LiquidExtractor

Extraction from condensed phase simulation where the system is composed of one kind of molecule only.

Parameters

string_identifier (str) – The string identifier tagged as prefix to all values extracted in this class.

Methods

extract_dipole_magnitude(mdtraj_obj, …)	Extracting dipole moment magnitude from each frame of simulation.
extract_energies(mdtraj_obj, parmed_obj[, …])	Extracting the various energetic components described in the original publication from each frame of simulation.
extract_h_bonds(mdtraj_obj, \*\*kwargs)	http://mdtraj.org/1.8.0/api/generated/mdtraj.baker_hubbard.html#mdtraj.baker_hubbar
extract_rgyr(mdtraj_obj, \*\*kwargs)	Extracting radius of gyration from each frame of simulation.
extract_sasa(mdtraj_obj, \*\*kwargs)	Extracting solvent accessible surface area from each frame of simulation.

classmethod extract_h_bonds(mdtraj_obj, **kwargs)

http://mdtraj.org/1.8.0/api/generated/mdtraj.baker_hubbard.html#mdtraj.baker_hubbar

classmethod extract_dipole_magnitude(mdtraj_obj, parmed_obj, **kwargs)

Extracting dipole moment magnitude from each frame of simulation. Assumes the first residue in the system is the solute.

Parameters

• mdtraj_obj (mdtraj.trajectory) – The simulated trajectory

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

Returns

df – Key is prefix_dipole_magnitude, where prefix changes depending on the type of Extractor class used. Values are the corresponding set of numerics, stored as lists.

Return type

dict

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

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

classmethod _extract_energies_helper(mdtraj_obj, parmed_obj, platform='CPU', **kwargs)

Helper function for extracting the various energetic components described in the original publication from each frame of simulation. OpenMM.CustomNonbondedForces are used. Specifically, the reaction field defintion is taken from GROMOS96 manual.

Parameters

• mdtraj_obj (mdtraj.trajectory) – The simulated trajectory

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

• platform (str) – The computing architecture to do the calculation, default to CPU, CUDA, OpenCL is also possible.

Returns

• context (Openmm.Context)

• integrator (Openmm.Integrator)

classmethod _solute_solvent_split(topology)

Distinguish solutes from solvents, used in _extract_energies_helper()

The following is assumed:

• the first residue is the ‘solute’ , else ‘solvent’

Parameters

topology (parmed.topology) –

Returns

• solute_atoms (set) – set of solute_atoms indices

• solvent_atoms (set) – set of solvent_atoms indices

classmethod extract_energies(mdtraj_obj, parmed_obj, platform='CPU', **kwargs)

Extracting the various energetic components described in the original publication from each frame of simulation.

Parameters

• mdtraj_obj (mdtraj.trajectory) – The simulated trajectory

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

• platform (str) – The computing architecture to do the calculation, default to CPU, CUDA, OpenCL is also possible.

Returns

df – Keys are each of the energetic type features. e.g. “intra_lj” are the intra-molecular LJ energies obtained from simulation.

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

Return type

dict

classmethod extract_rgyr(mdtraj_obj, **kwargs)

Extracting radius of gyration from each frame of simulation. Assumes the first residue in the system is the solute.

Parameters

mdtraj_obj (mdtraj.trajectory) – The simulated trajectory

Returns

df – Key is prefix_rgyr, where prefix changes depending on the type of Extractor class used. Values are the corresponding set of numerics, stored as lists.

Return type

dict

classmethod extract_sasa(mdtraj_obj, **kwargs)

Extracting solvent accessible surface area from each frame of simulation. Assumes the first residue in the system is the solute.

Parameters

mdtraj_obj (mdtraj.trajectory) – The simulated trajectory

Returns

df – Key is prefix_sasa, where prefix changes depending on the type of Extractor class used. Values are the corresponding set of numerics, stored as lists.

Return type

dict

classmethod _get_all_exception_atom_pairs(system, topology)

Using the parametersied system to obtain the exception and exclusion pairs, used in _extract_energies_helper(). This is inferred purely from the parameterised system and connectivity.

Parameters

• system (OpenMM.System) –

• topology (parmed.topology) –

Returns

• solute_1_4_pairs (set)

• solvent_1_4_pairs (set)

• solute_excluded_pairs (set)

• solvent_excluded_pairs (set)

• solute_self_pairs (set)

• solvent_self_pairs (set)

class mdfptools.Extractor.BaseExtractor

Warning

The base class should not be used directly

Methods

extract_energies(mdtraj_obj, parmed_obj[, …])	Extracting the various energetic components described in the original publication from each frame of simulation.
extract_rgyr(mdtraj_obj, \*\*kwargs)	Extracting radius of gyration from each frame of simulation.
extract_sasa(mdtraj_obj, \*\*kwargs)	Extracting solvent accessible surface area from each frame of simulation.

classmethod _solute_solvent_split(topology)

Abstract method

classmethod _get_all_exception_atom_pairs(system, topology)

Abstract method

classmethod _extract_energies_helper(mdtraj_obj, parmed_obj, platform='CPU', **kwargs)

Helper function for extracting the various energetic components described in the original publication from each frame of simulation. OpenMM.CustomNonbondedForces are used. Specifically, the reaction field defintion is taken from GROMOS96 manual.

Parameters

• mdtraj_obj (mdtraj.trajectory) – The simulated trajectory

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

• platform (str) – The computing architecture to do the calculation, default to CPU, CUDA, OpenCL is also possible.

Returns

• context (Openmm.Context)

• integrator (Openmm.Integrator)

classmethod extract_energies(mdtraj_obj, parmed_obj, platform='CPU', **kwargs)

Extracting the various energetic components described in the original publication from each frame of simulation.

Parameters

• mdtraj_obj (mdtraj.trajectory) – The simulated trajectory

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

• platform (str) – The computing architecture to do the calculation, default to CPU, CUDA, OpenCL is also possible.

Returns

df – Keys are each of the energetic type features. e.g. “intra_lj” are the intra-molecular LJ energies obtained from simulation.

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

Return type

dict

classmethod extract_rgyr(mdtraj_obj, **kwargs)

Extracting radius of gyration from each frame of simulation. Assumes the first residue in the system is the solute.

Parameters

mdtraj_obj (mdtraj.trajectory) – The simulated trajectory

Returns

df – Key is prefix_rgyr, where prefix changes depending on the type of Extractor class used. Values are the corresponding set of numerics, stored as lists.

Return type

dict

classmethod extract_sasa(mdtraj_obj, **kwargs)

Extracting solvent accessible surface area from each frame of simulation. Assumes the first residue in the system is the solute.

Parameters

mdtraj_obj (mdtraj.trajectory) – The simulated trajectory

Returns

df – Key is prefix_sasa, where prefix changes depending on the type of Extractor class used. Values are the corresponding set of numerics, stored as lists.

Return type

dict

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

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

class mdfptools.Extractor.SolutionExtractor

Extraction from condensed phase simulation where the system is composed of one solute molecule surronded by solvents

Parameters

string_identifier (str) – The string identifier tagged as prefix to all values extracted in this class.

Methods

extract_dipole(mdtraj_obj, parmed_obj, …)	Extracting dipole moment from each frame of simulation.
extract_energies(mdtraj_obj, parmed_obj[, …])	Extracting the various energetic components described in the original publication from each frame of simulation.
extract_rgyr(mdtraj_obj, \*\*kwargs)	Extracting radius of gyration from each frame of simulation.
extract_sasa(mdtraj_obj, \*\*kwargs)	Extracting solvent accessible surface area from each frame of simulation.

classmethod _solute_solvent_split(topology)

Distinguish solutes from solvents, used in _extract_energies_helper()

The following is assumed:

• there are only two type of residues

• the residue that is lesser in number is the solute

Parameters

topology (parmed.topology) –

Returns

• solute_atoms (set) – set of solute_atoms indices

• solvent_atoms (set) – set of solvent_atoms indices

classmethod _get_all_exception_atom_pairs(system, topology)

Using the parametersied system to obtain the exception and exclusion pairs, used in _extract_energies_helper(). This is inferred purely from the parameterised system and connectivity.

Parameters

• system (OpenMM.System) –

• topology (parmed.topology) –

Returns

• solute_1_4_pairs (set)

• solvent_1_4_pairs (set)

• solute_excluded_pairs (set)

• solvent_excluded_pairs (set)

• solute_self_pairs (set)

• solvent_self_pairs (set)

classmethod extract_dipole(mdtraj_obj, parmed_obj, **kwargs)

Extracting dipole moment from each frame of simulation. Assumes the first residue in the system is the solute.

Parameters

• mdtraj_obj (mdtraj.trajectory) – The simulated trajectory

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

Returns

df – Key is prefix_dipole_postfix, where prefix changes depending on the type of Extractor class used, postfix can be {x,y,z,magnitude}. Values are the corresponding set of numerics, stored as lists.

Return type

dict

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

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

classmethod _extract_energies_helper(mdtraj_obj, parmed_obj, platform='CPU', **kwargs)

Helper function for extracting the various energetic components described in the original publication from each frame of simulation. OpenMM.CustomNonbondedForces are used. Specifically, the reaction field defintion is taken from GROMOS96 manual.

Parameters

• mdtraj_obj (mdtraj.trajectory) – The simulated trajectory

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

• platform (str) – The computing architecture to do the calculation, default to CPU, CUDA, OpenCL is also possible.

Returns

• context (Openmm.Context)

• integrator (Openmm.Integrator)

classmethod extract_energies(mdtraj_obj, parmed_obj, platform='CPU', **kwargs)

Extracting the various energetic components described in the original publication from each frame of simulation.

Parameters

• mdtraj_obj (mdtraj.trajectory) – The simulated trajectory

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

• platform (str) – The computing architecture to do the calculation, default to CPU, CUDA, OpenCL is also possible.

Returns

df – Keys are each of the energetic type features. e.g. “intra_lj” are the intra-molecular LJ energies obtained from simulation.

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

Return type

dict

classmethod extract_rgyr(mdtraj_obj, **kwargs)

Extracting radius of gyration from each frame of simulation. Assumes the first residue in the system is the solute.

Parameters

mdtraj_obj (mdtraj.trajectory) – The simulated trajectory

Returns

df – Key is prefix_rgyr, where prefix changes depending on the type of Extractor class used. Values are the corresponding set of numerics, stored as lists.

Return type

dict

classmethod extract_sasa(mdtraj_obj, **kwargs)

Extracting solvent accessible surface area from each frame of simulation. Assumes the first residue in the system is the solute.

Parameters

mdtraj_obj (mdtraj.trajectory) – The simulated trajectory

Returns

df – Key is prefix_sasa, where prefix changes depending on the type of Extractor class used. Values are the corresponding set of numerics, stored as lists.

Return type

dict

class mdfptools.Extractor.LiquidExtractor

Extraction from condensed phase simulation where the system is composed of one kind of molecule only.

Parameters

string_identifier (str) – The string identifier tagged as prefix to all values extracted in this class.

Methods

extract_dipole_magnitude(mdtraj_obj, …)	Extracting dipole moment magnitude from each frame of simulation.
extract_energies(mdtraj_obj, parmed_obj[, …])	Extracting the various energetic components described in the original publication from each frame of simulation.
extract_h_bonds(mdtraj_obj, \*\*kwargs)	http://mdtraj.org/1.8.0/api/generated/mdtraj.baker_hubbard.html#mdtraj.baker_hubbar
extract_rgyr(mdtraj_obj, \*\*kwargs)	Extracting radius of gyration from each frame of simulation.
extract_sasa(mdtraj_obj, \*\*kwargs)	Extracting solvent accessible surface area from each frame of simulation.

classmethod extract_h_bonds(mdtraj_obj, **kwargs)

http://mdtraj.org/1.8.0/api/generated/mdtraj.baker_hubbard.html#mdtraj.baker_hubbar

classmethod extract_dipole_magnitude(mdtraj_obj, parmed_obj, **kwargs)

Extracting dipole moment magnitude from each frame of simulation. Assumes the first residue in the system is the solute.

Parameters

• mdtraj_obj (mdtraj.trajectory) – The simulated trajectory

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

Returns

df – Key is prefix_dipole_magnitude, where prefix changes depending on the type of Extractor class used. Values are the corresponding set of numerics, stored as lists.

Return type

dict

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

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

classmethod _extract_energies_helper(mdtraj_obj, parmed_obj, platform='CPU', **kwargs)

Helper function for extracting the various energetic components described in the original publication from each frame of simulation. OpenMM.CustomNonbondedForces are used. Specifically, the reaction field defintion is taken from GROMOS96 manual.

Parameters

• mdtraj_obj (mdtraj.trajectory) – The simulated trajectory

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

• platform (str) – The computing architecture to do the calculation, default to CPU, CUDA, OpenCL is also possible.

Returns

• context (Openmm.Context)

• integrator (Openmm.Integrator)

classmethod _solute_solvent_split(topology)

Distinguish solutes from solvents, used in _extract_energies_helper()

The following is assumed:

• the first residue is the ‘solute’ , else ‘solvent’

Parameters

topology (parmed.topology) –

Returns

• solute_atoms (set) – set of solute_atoms indices

• solvent_atoms (set) – set of solvent_atoms indices

classmethod extract_energies(mdtraj_obj, parmed_obj, platform='CPU', **kwargs)

Extracting the various energetic components described in the original publication from each frame of simulation.

Parameters

• mdtraj_obj (mdtraj.trajectory) – The simulated trajectory

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

• platform (str) – The computing architecture to do the calculation, default to CPU, CUDA, OpenCL is also possible.

Returns

df – Keys are each of the energetic type features. e.g. “intra_lj” are the intra-molecular LJ energies obtained from simulation.

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

Return type

dict

classmethod extract_rgyr(mdtraj_obj, **kwargs)

Extracting radius of gyration from each frame of simulation. Assumes the first residue in the system is the solute.

Parameters

mdtraj_obj (mdtraj.trajectory) – The simulated trajectory

Returns

df – Key is prefix_rgyr, where prefix changes depending on the type of Extractor class used. Values are the corresponding set of numerics, stored as lists.

Return type

dict

classmethod extract_sasa(mdtraj_obj, **kwargs)

Extracting solvent accessible surface area from each frame of simulation. Assumes the first residue in the system is the solute.

Parameters

mdtraj_obj (mdtraj.trajectory) – The simulated trajectory

Returns

df – Key is prefix_sasa, where prefix changes depending on the type of Extractor class used. Values are the corresponding set of numerics, stored as lists.

Return type

dict

classmethod _get_all_exception_atom_pairs(system, topology)

Using the parametersied system to obtain the exception and exclusion pairs, used in _extract_energies_helper(). This is inferred purely from the parameterised system and connectivity.

Parameters

• system (OpenMM.System) –

• topology (parmed.topology) –

Returns

• solute_1_4_pairs (set)

• solvent_1_4_pairs (set)

• solute_excluded_pairs (set)

• solvent_excluded_pairs (set)

• solute_self_pairs (set)

• solvent_self_pairs (set)