Index

_

__init__() (mdfptools.Composer.BaseComposer method), [1], [2] (mdfptools.Composer.LiquidComposer method), [1], [2] (mdfptools.Composer.MDFP method), [1], [2] (mdfptools.Composer.SolutionComposer method), [1], [2] (mdfptools.Composer.SolutionLiquidComposer class method), [1], [2] (mdfptools.Extractor.BaseExtractor method), [1], [2] (mdfptools.Extractor.LiquidExtractor method), [1], [2] (mdfptools.Extractor.SolutionExtractor method), [1], [2] (mdfptools.Extractor.TrialSolutionExtractor method), [1] (mdfptools.Extractor.WaterExtractor method), [1] (mdfptools.Parameteriser.BaseParameteriser method), [1], [2] (mdfptools.Parameteriser.LiquidParameteriser method), [1], [2] (mdfptools.Parameteriser.SolutionParameteriser method), [1], [2] (mdfptools.Parameteriser.VaccumParameteriser method), [1] (mdfptools.Simulator.BaseSimulator method), [1], [2] (mdfptools.Simulator.LiquidSimulator method), [1], [2] (mdfptools.Simulator.SolutionSimulator method), [1], [2] _extract_energies_helper() (mdfptools.Extractor.BaseExtractor class method), [1], [2] (mdfptools.Extractor.LiquidExtractor class method), [1], [2] (mdfptools.Extractor.SolutionExtractor class method), [1], [2] (mdfptools.Extractor.TrialSolutionExtractor class method), [1] (mdfptools.Extractor.WaterExtractor class method), [1] _get_2d_descriptors() (mdfptools.Composer.BaseComposer class method), [1], [2] (mdfptools.Composer.LiquidComposer class method), [1], [2] (mdfptools.Composer.SolutionComposer class method), [1], [2] (mdfptools.Composer.SolutionLiquidComposer class method), [1], [2] _get_all_exception_atom_pairs() (mdfptools.Extractor.BaseExtractor class method), [1], [2] (mdfptools.Extractor.LiquidExtractor class method), [1], [2] (mdfptools.Extractor.SolutionExtractor class method), [1], [2] (mdfptools.Extractor.TrialSolutionExtractor class method), [1] (mdfptools.Extractor.WaterExtractor class method), [1]

_get_relevant_properties() (mdfptools.Composer.BaseComposer class method), [1], [2] (mdfptools.Composer.LiquidComposer class method), [1], [2] (mdfptools.Composer.SolutionComposer class method), [1], [2] (mdfptools.Composer.SolutionLiquidComposer class method), [1], [2] _get_statistical_moments() (mdfptools.Composer.BaseComposer class method), [1], [2] (mdfptools.Composer.LiquidComposer class method), [1], [2] (mdfptools.Composer.SolutionComposer class method), [1], [2] (mdfptools.Composer.SolutionLiquidComposer class method), [1], [2] _openeye_parameteriser() (mdfptools.Parameteriser.BaseParameteriser class method), [1], [2] (mdfptools.Parameteriser.LiquidParameteriser class method), [1], [2] (mdfptools.Parameteriser.SolutionParameteriser class method), [1], [2] (mdfptools.Parameteriser.VaccumParameteriser class method), [1] _openeye_setter() (mdfptools.Parameteriser.BaseParameteriser class method), [1], [2] (mdfptools.Parameteriser.LiquidParameteriser class method), [1], [2] (mdfptools.Parameteriser.SolutionParameteriser class method), [1], [2] (mdfptools.Parameteriser.VaccumParameteriser class method), [1] _rdkit_parameteriser() (mdfptools.Parameteriser.BaseParameteriser class method), [1], [2] (mdfptools.Parameteriser.LiquidParameteriser class method), [1], [2] (mdfptools.Parameteriser.SolutionParameteriser class method), [1], [2] (mdfptools.Parameteriser.VaccumParameteriser class method), [1] _rdkit_setter() (mdfptools.Parameteriser.BaseParameteriser class method), [1], [2] (mdfptools.Parameteriser.LiquidParameteriser class method), [1], [2] (mdfptools.Parameteriser.SolutionParameteriser class method), [1], [2] (mdfptools.Parameteriser.VaccumParameteriser class method), [1] _solute_solvent_split() (mdfptools.Extractor.BaseExtractor class method), [1], [2] (mdfptools.Extractor.LiquidExtractor class method), [1], [2] (mdfptools.Extractor.SolutionExtractor class method), [1], [2] (mdfptools.Extractor.TrialSolutionExtractor class method), [1] (mdfptools.Extractor.WaterExtractor class method), [1] _via_helper() (mdfptools.Parameteriser.LiquidParameteriser class method), [1], [2] (mdfptools.Parameteriser.SolutionParameteriser class method), [1], [2]

B

BaseComposer (class in mdfptools.Composer), [1], [2] BaseExtractor (class in mdfptools.Extractor), [1], [2]

BaseParameteriser (class in mdfptools.Parameteriser), [1], [2] BaseSimulator (class in mdfptools.Simulator), [1], [2]

C

canonical_smiles_from_smiles() (in module mdfptools.utils), [1]

E

equil_steps (mdfptools.Simulator.BaseSimulator attribute) (mdfptools.Simulator.LiquidSimulator attribute) (mdfptools.Simulator.SolutionSimulator attribute) extract_dipole() (mdfptools.Extractor.SolutionExtractor class method), [1], [2] (mdfptools.Extractor.TrialSolutionExtractor class method), [1] (mdfptools.Extractor.WaterExtractor class method), [1] extract_dipole_magnitude() (mdfptools.Extractor.LiquidExtractor class method), [1], [2] extract_energies() (mdfptools.Extractor.BaseExtractor class method), [1], [2] (mdfptools.Extractor.LiquidExtractor class method), [1], [2] (mdfptools.Extractor.SolutionExtractor class method), [1], [2] (mdfptools.Extractor.TrialSolutionExtractor class method), [1] (mdfptools.Extractor.WaterExtractor class method), [1]

extract_h_bonds() (mdfptools.Extractor.LiquidExtractor class method), [1], [2] extract_rgyr() (mdfptools.Extractor.BaseExtractor class method), [1], [2] (mdfptools.Extractor.LiquidExtractor class method), [1], [2] (mdfptools.Extractor.SolutionExtractor class method), [1], [2] (mdfptools.Extractor.TrialSolutionExtractor class method), [1] (mdfptools.Extractor.WaterExtractor class method), [1] extract_sasa() (mdfptools.Extractor.BaseExtractor class method), [1], [2] (mdfptools.Extractor.LiquidExtractor class method), [1], [2] (mdfptools.Extractor.SolutionExtractor class method), [1], [2] (mdfptools.Extractor.TrialSolutionExtractor class method), [1] (mdfptools.Extractor.WaterExtractor class method), [1]

G

get_data_filename() (in module mdfptools.utils), [1]

get_mdfp() (mdfptools.Composer.MDFP method), [1], [2]

H

hashing() (in module mdfptools.utils), [1]

L

LiquidComposer (class in mdfptools.Composer), [1], [2] LiquidExtractor (class in mdfptools.Extractor), [1], [2] LiquidParameteriser (class in mdfptools.Parameteriser), [1], [2] LiquidSimulator (class in mdfptools.Simulator), [1], [2]

load_ddec_models() (mdfptools.Parameteriser.BaseParameteriser class method), [1], [2] (mdfptools.Parameteriser.LiquidParameteriser class method), [1], [2] (mdfptools.Parameteriser.SolutionParameteriser class method), [1], [2] (mdfptools.Parameteriser.VaccumParameteriser class method), [1]

M

MDFP (class in mdfptools.Composer), [1], [2] mdfptools (module) mdfptools.Composer (module), [1] mdfptools.Extractor (module), [1]

mdfptools.Parameteriser (module), [1] mdfptools.Simulator (module), [1] mdfptools.tests (module) mdfptools.utils (module), [1]

P

pmd_generator() (mdfptools.Parameteriser.BaseParameteriser class method), [1], [2] (mdfptools.Parameteriser.LiquidParameteriser class method), [1], [2] (mdfptools.Parameteriser.SolutionParameteriser class method), [1], [2] (mdfptools.Parameteriser.VaccumParameteriser class method), [1]

pressure (mdfptools.Simulator.BaseSimulator attribute) (mdfptools.Simulator.LiquidSimulator attribute) (mdfptools.Simulator.SolutionSimulator attribute)

R

run() (mdfptools.Composer.BaseComposer class method), [1], [2] (mdfptools.Composer.LiquidComposer class method), [1], [2] (mdfptools.Composer.SolutionComposer class method), [1], [2] (mdfptools.Composer.SolutionLiquidComposer class method), [1], [2] (mdfptools.Parameteriser.BaseParameteriser class method), [1], [2] (mdfptools.Parameteriser.LiquidParameteriser class method), [1], [2] (mdfptools.Parameteriser.SolutionParameteriser class method), [1], [2] (mdfptools.Parameteriser.VaccumParameteriser class method), [1] (mdfptools.Simulator.BaseSimulator class method), [1], [2] (mdfptools.Simulator.LiquidSimulator class method), [1], [2] (mdfptools.Simulator.SolutionSimulator class method), [1], [2]

S

save() (mdfptools.Parameteriser.BaseParameteriser class method), [1], [2] (mdfptools.Parameteriser.LiquidParameteriser class method), [1], [2] (mdfptools.Parameteriser.SolutionParameteriser class method), [1], [2] (mdfptools.Parameteriser.VaccumParameteriser class method), [1] screen_organic() (in module mdfptools.utils), [1] SolutionComposer (class in mdfptools.Composer), [1], [2] SolutionExtractor (class in mdfptools.Extractor), [1], [2] SolutionLiquidComposer (class in mdfptools.Composer), [1], [2] SolutionParameteriser (class in mdfptools.Parameteriser), [1], [2]

SolutionSimulator (class in mdfptools.Simulator), [1], [2] string_identifier (mdfptools.Extractor.BaseExtractor attribute) (mdfptools.Extractor.LiquidExtractor attribute) (mdfptools.Extractor.SolutionExtractor attribute) (mdfptools.Extractor.TrialSolutionExtractor attribute) (mdfptools.Extractor.WaterExtractor attribute) system_pmd (mdfptools.Parameteriser.BaseParameteriser attribute) (mdfptools.Parameteriser.LiquidParameteriser attribute) (mdfptools.Parameteriser.SolutionParameteriser attribute) (mdfptools.Parameteriser.VaccumParameteriser attribute)

T

temperature (mdfptools.Simulator.BaseSimulator attribute) (mdfptools.Simulator.LiquidSimulator attribute) (mdfptools.Simulator.SolutionSimulator attribute)

time_step (mdfptools.Simulator.BaseSimulator attribute) (mdfptools.Simulator.LiquidSimulator attribute) (mdfptools.Simulator.SolutionSimulator attribute) TrialSolutionExtractor (class in mdfptools.Extractor), [1]

U

unload_ddec_models() (mdfptools.Parameteriser.BaseParameteriser class method), [1], [2] (mdfptools.Parameteriser.LiquidParameteriser class method), [1], [2] (mdfptools.Parameteriser.SolutionParameteriser class method), [1], [2] (mdfptools.Parameteriser.VaccumParameteriser class method), [1]

V

VaccumParameteriser (class in mdfptools.Parameteriser), [1] via_gromacs() (mdfptools.Simulator.BaseSimulator class method), [1], [2] (mdfptools.Simulator.LiquidSimulator class method), [1], [2] (mdfptools.Simulator.SolutionSimulator class method), [1], [2] via_openeye() (mdfptools.Parameteriser.BaseParameteriser class method), [1], [2] (mdfptools.Parameteriser.LiquidParameteriser class method), [1], [2] (mdfptools.Parameteriser.SolutionParameteriser class method), [1], [2] (mdfptools.Parameteriser.VaccumParameteriser class method), [1]

via_openmm() (mdfptools.Simulator.BaseSimulator class method), [1], [2] (mdfptools.Simulator.LiquidSimulator class method), [1], [2] (mdfptools.Simulator.SolutionSimulator class method), [1], [2] via_rdkit() (mdfptools.Parameteriser.BaseParameteriser class method), [1], [2] (mdfptools.Parameteriser.LiquidParameteriser class method), [1], [2] (mdfptools.Parameteriser.SolutionParameteriser class method), [1], [2] (mdfptools.Parameteriser.VaccumParameteriser class method), [1]

W

WaterExtractor (class in mdfptools.Extractor), [1]