Index

A

atom_counts (pympfit.mpfit.solvers.ConstrainedMPFITState attribute)

atomtype (pympfit.mpfit.solvers.ConstrainedMPFITState attribute)

B

basis (pympfit.gdma._gdma.GDMASettings attribute) (pympfit.gdma.storage.db.DBGDMASettings attribute) (pympfit.mbis._mbis.MBISSettings attribute) (pympfit.mbis.storage.db.DBMBISSettings attribute)

build_A_matrix() (in module pympfit.mpfit.core) build_A_matrix_torch() (in module pympfit.mpfit.core) build_b_vector() (in module pympfit.mpfit.core) build_quse_matrix() (in module pympfit.mpfit.solvers)

C

CARTESIAN (pympfit.mbis._mbis.MultipoleFormat attribute) cartesian_multipoles_to_flat() (in module pympfit.mbis.multipole_transform) cartesian_to_spherical_dipole() (in module pympfit.mbis.multipole_transform) cartesian_to_spherical_multipoles() (in module pympfit.mbis.multipole_transform) cartesian_to_spherical_octupole() (in module pympfit.mbis.multipole_transform) cartesian_to_spherical_quadrupole() (in module pympfit.mbis.multipole_transform) compute_objective_terms() (pympfit.optimize._optimize.MPFITObjective class method) conformer (pympfit.gdma.storage.MoleculeGDMARecord attribute) (pympfit.mbis.storage.MoleculeMBISRecord attribute) conformer_quantity (pympfit.gdma.storage.MoleculeGDMARecord property) (pympfit.mbis.storage.MoleculeMBISRecord property)

conformers (pympfit.gdma.storage.db.DBMoleculeRecord attribute) (pympfit.mbis.storage.db.DBMoleculeRecord attribute) ConstrainedMPFITSolver (class in pympfit.mpfit.solvers) ConstrainedMPFITState (class in pympfit.mpfit.solvers) ConstrainedSciPySolver (class in pympfit.mpfit.solvers) coordinates (pympfit.gdma.storage.db.DBConformerRecord attribute) (pympfit.mbis.storage.db.DBConformerRecord attribute) count_parameters() (in module pympfit.mpfit.solvers) createdkaisq() (in module pympfit.mpfit.solvers)

D

d_convergence (pympfit.mbis._mbis.MBISSettings attribute) (pympfit.mbis.storage.db.DBMBISSettings attribute) db_to_instance() (pympfit.gdma.storage.db.DBGDMASettings class method) (pympfit.mbis.storage.db.DBMBISSettings class method) db_version (pympfit.gdma.storage.MoleculeGDMAStore property) (pympfit.mbis.storage.MoleculeMBISStore property) DBConformerRecord (class in pympfit.gdma.storage.db) (class in pympfit.mbis.storage.db) DBGDMASettings (class in pympfit.gdma.storage.db) DBGeneralProvenance (class in pympfit.gdma.storage.db) (class in pympfit.mbis.storage.db)

DBInformation (class in pympfit.gdma.storage.db) (class in pympfit.mbis.storage.db) DBMBISSettings (class in pympfit.mbis.storage.db) DBMoleculeRecord (class in pympfit.gdma.storage.db) (class in pympfit.mbis.storage.db) DBSoftwareProvenance (class in pympfit.gdma.storage.db) (class in pympfit.mbis.storage.db) dft_radial_points (pympfit.mbis._mbis.MBISSettings attribute) (pympfit.mbis.storage.db.DBMBISSettings attribute) dft_spherical_points (pympfit.mbis._mbis.MBISSettings attribute) (pympfit.mbis.storage.db.DBMBISSettings attribute)

E

e_convergence (pympfit.mbis._mbis.MBISSettings attribute) (pympfit.mbis.storage.db.DBMBISSettings attribute)

expandcharge() (in module pympfit.mpfit.solvers) extract_arrays() (pympfit.optimize._optimize.MPFITObjective class method) extract_mbis_charges() (in module pympfit.mbis._mbis)

F

flat_to_cartesian_multipoles() (in module pympfit.mbis.multipole_transform)

from_molecule() (pympfit.gdma.storage.MoleculeGDMARecord class method) (pympfit.mbis.storage.MoleculeMBISRecord class method)

G

gdma_settings (pympfit.gdma.storage.db.DBConformerRecord attribute) (pympfit.gdma.storage.MoleculeGDMARecord attribute) gdma_settings_id (pympfit.gdma.storage.db.DBConformerRecord attribute) GDMAGenerator (class in pympfit.gdma._gdma) GDMASettings (class in pympfit.gdma._gdma) general_provenance (pympfit.gdma.storage.db.DBInformation attribute) (pympfit.gdma.storage.MoleculeGDMAStore property) (pympfit.mbis.storage.db.DBInformation attribute) (pympfit.mbis.storage.MoleculeMBISStore property)

generate() (pympfit.gdma._gdma.GDMAGenerator class method) (pympfit.mbis._mbis.MBISGenerator class method) generate_constrained_mpfit_charge_parameter() (in module pympfit.mpfit._mpfit) generate_global_atom_type_labels() (in module pympfit.mpfit._mpfit) generate_mpfit_charge_parameter() (in module pympfit.mpfit._mpfit) guess (pympfit.mbis._mbis.MBISSettings attribute) (pympfit.mbis.storage.db.DBMBISSettings attribute)

I

id (pympfit.gdma.storage.db.DBConformerRecord attribute) (pympfit.gdma.storage.db.DBGDMASettings attribute) (pympfit.mbis.storage.db.DBConformerRecord attribute) (pympfit.mbis.storage.db.DBMBISSettings attribute)

initial_guess() (pympfit.mpfit.solvers.ConstrainedMPFITSolver method)

J

jacobian() (pympfit.mpfit.solvers.ConstrainedMPFITSolver class method)

K

key (pympfit.gdma.storage.db.DBGeneralProvenance attribute) (pympfit.gdma.storage.db.DBSoftwareProvenance attribute) (pympfit.mbis.storage.db.DBGeneralProvenance attribute) (pympfit.mbis.storage.db.DBSoftwareProvenance attribute)

L

limit (pympfit.gdma._gdma.GDMASettings attribute) (pympfit.gdma.storage.db.DBGDMASettings attribute) (pympfit.mbis._mbis.MBISSettings attribute) (pympfit.mbis.storage.db.DBMBISSettings attribute)

list() (pympfit.gdma.storage.MoleculeGDMAStore method) (pympfit.mbis.storage.MoleculeMBISStore method) lmax (pympfit.mpfit.solvers.ConstrainedMPFITState attribute) loss() (pympfit.mpfit.solvers.ConstrainedMPFITSolver class method)

M

max_moment (pympfit.mbis._mbis.MBISSettings attribute) (pympfit.mbis.storage.db.DBMBISSettings attribute) max_radial_moment (pympfit.mbis._mbis.MBISSettings attribute) (pympfit.mbis.storage.db.DBMBISSettings attribute) maxl (pympfit.mpfit.solvers.ConstrainedMPFITState attribute) mbis_d_convergence (pympfit.mbis._mbis.MBISSettings attribute) (pympfit.mbis.storage.db.DBMBISSettings attribute) mbis_radial_points (pympfit.mbis._mbis.MBISSettings attribute) (pympfit.mbis.storage.db.DBMBISSettings attribute) mbis_settings (pympfit.mbis.storage.db.DBConformerRecord attribute) (pympfit.mbis.storage.MoleculeMBISRecord attribute) mbis_settings_id (pympfit.mbis.storage.db.DBConformerRecord attribute) mbis_spherical_points (pympfit.mbis._mbis.MBISSettings attribute) (pympfit.mbis.storage.db.DBMBISSettings attribute) MBISGenerator (class in pympfit.mbis._mbis) MBISSettings (class in pympfit.mbis._mbis) method (pympfit.gdma._gdma.GDMASettings attribute) (pympfit.gdma.storage.db.DBGDMASettings attribute) (pympfit.mbis._mbis.MBISSettings attribute) (pympfit.mbis.storage.db.DBMBISSettings attribute) model_config (pympfit.gdma._gdma.GDMASettings attribute) (pympfit.gdma.storage.MoleculeGDMARecord attribute) (pympfit.mbis._mbis.MBISSettings attribute) (pympfit.mbis.storage.MoleculeMBISRecord attribute) module pympfit.gdma pympfit.gdma._gdma pympfit.gdma.psi4 pympfit.gdma.storage pympfit.gdma.storage.db pympfit.mbis._mbis pympfit.mbis.multipole_transform pympfit.mbis.psi4 pympfit.mbis.storage pympfit.mbis.storage.db pympfit.mpfit pympfit.mpfit._mpfit pympfit.mpfit.core pympfit.mpfit.solvers pympfit.optimize pympfit.optimize._optimize

molecule_charges (pympfit.mpfit.solvers.ConstrainedMPFITState attribute) molecule_to_mpfit_library_charge() (in module pympfit.mpfit._mpfit) MoleculeGDMARecord (class in pympfit.gdma.storage) MoleculeGDMAStore (class in pympfit.gdma.storage) MoleculeMBISRecord (class in pympfit.mbis.storage) MoleculeMBISStore (class in pympfit.mbis.storage) mpfit_atom_radius (pympfit.gdma._gdma.GDMASettings attribute) (pympfit.mbis._mbis.MBISSettings attribute) (pympfit.mbis.storage.db.DBMBISSettings attribute) mpfit_inner_radius (pympfit.gdma._gdma.GDMASettings attribute) (pympfit.mbis._mbis.MBISSettings attribute) (pympfit.mbis.storage.db.DBMBISSettings attribute) mpfit_outer_radius (pympfit.gdma._gdma.GDMASettings attribute) (pympfit.mbis._mbis.MBISSettings attribute) (pympfit.mbis.storage.db.DBMBISSettings attribute) MPFITObjective (class in pympfit.optimize._optimize) MPFITObjectiveTerm (class in pympfit.optimize._optimize) MPFITSolver (class in pympfit.mpfit.solvers) MPFITSolverError MPFITSVDSolver (class in pympfit.mpfit.solvers) multipole_format (pympfit.mbis._mbis.MBISSettings attribute) (pympfit.mbis.storage.db.DBMBISSettings attribute) multipole_units (pympfit.gdma._gdma.GDMASettings attribute) (pympfit.gdma.storage.db.DBGDMASettings attribute) (pympfit.mbis._mbis.MBISSettings attribute) (pympfit.mbis.storage.db.DBMBISSettings attribute) MultipoleFormat (class in pympfit.mbis._mbis) multipoles (pympfit.gdma.storage.db.DBConformerRecord attribute) (pympfit.gdma.storage.MoleculeGDMARecord attribute) (pympfit.mbis.storage.db.DBConformerRecord attribute) (pympfit.mbis.storage.MoleculeMBISRecord attribute) (pympfit.mpfit.solvers.ConstrainedMPFITState attribute) multipoles_quantity (pympfit.gdma.storage.MoleculeGDMARecord property) (pympfit.mbis.storage.MoleculeMBISRecord property)

P

parent_id (pympfit.gdma.storage.db.DBConformerRecord attribute) (pympfit.gdma.storage.db.DBGeneralProvenance attribute) (pympfit.gdma.storage.db.DBSoftwareProvenance attribute) (pympfit.mbis.storage.db.DBConformerRecord attribute) (pympfit.mbis.storage.db.DBGeneralProvenance attribute) (pympfit.mbis.storage.db.DBSoftwareProvenance attribute) predict() (pympfit.optimize._optimize.MPFITObjectiveTerm method) predict_from_free_charges() (pympfit.optimize._optimize.MPFITObjectiveTerm method) Psi4GDMAGenerator (class in pympfit.gdma.psi4) Psi4MBISGenerator (class in pympfit.mbis.psi4) pympfit.gdma module pympfit.gdma._gdma module pympfit.gdma.psi4 module pympfit.gdma.storage module pympfit.gdma.storage.db module pympfit.mbis._mbis module

pympfit.mbis.multipole_transform module pympfit.mbis.psi4 module pympfit.mbis.storage module pympfit.mbis.storage.db module pympfit.mpfit module pympfit.mpfit._mpfit module pympfit.mpfit.core module pympfit.mpfit.solvers module pympfit.optimize module pympfit.optimize._optimize module

Q

quse (pympfit.mpfit.solvers.ConstrainedMPFITState attribute)

R

r1 (pympfit.mpfit.solvers.ConstrainedMPFITState attribute) r2 (pympfit.mpfit.solvers.ConstrainedMPFITState attribute) radius (pympfit.gdma._gdma.GDMASettings attribute) (pympfit.gdma.storage.db.DBGDMASettings attribute)

retrieve() (pympfit.gdma.storage.MoleculeGDMAStore method) (pympfit.mbis.storage.MoleculeMBISStore method) rvdw (pympfit.mpfit.solvers.ConstrainedMPFITState attribute)

S

set_provenance() (pympfit.gdma.storage.MoleculeGDMAStore method) (pympfit.mbis.storage.MoleculeMBISStore method) smiles (pympfit.gdma.storage.db.DBMoleculeRecord attribute) (pympfit.mbis.storage.db.DBMoleculeRecord attribute) software_provenance (pympfit.gdma.storage.db.DBInformation attribute) (pympfit.gdma.storage.MoleculeGDMAStore property) (pympfit.mbis.storage.db.DBInformation attribute) (pympfit.mbis.storage.MoleculeMBISStore property) solve() (pympfit.mpfit.solvers.ConstrainedMPFITSolver method) (pympfit.mpfit.solvers.MPFITSolver method) (pympfit.mpfit.solvers.MPFITSVDSolver method)

SPHERICAL (pympfit.mbis._mbis.MultipoleFormat attribute) spherical_to_cartesian_dipole() (in module pympfit.mbis.multipole_transform) spherical_to_cartesian_multipoles() (in module pympfit.mbis.multipole_transform) spherical_to_cartesian_octupole() (in module pympfit.mbis.multipole_transform) spherical_to_cartesian_quadrupole() (in module pympfit.mbis.multipole_transform) store() (pympfit.gdma.storage.MoleculeGDMAStore method) (pympfit.mbis.storage.MoleculeMBISStore method) switch (pympfit.gdma._gdma.GDMASettings attribute) (pympfit.gdma.storage.db.DBGDMASettings attribute)

T

tagged_smiles (pympfit.gdma.storage.db.DBConformerRecord attribute) (pympfit.gdma.storage.MoleculeGDMARecord attribute) (pympfit.mbis.storage.db.DBConformerRecord attribute) (pympfit.mbis.storage.MoleculeMBISRecord attribute)

V

value (pympfit.gdma.storage.db.DBGeneralProvenance attribute) (pympfit.gdma.storage.db.DBSoftwareProvenance attribute) (pympfit.mbis.storage.db.DBGeneralProvenance attribute) (pympfit.mbis.storage.db.DBSoftwareProvenance attribute)

version (pympfit.gdma.storage.db.DBInformation attribute) (pympfit.mbis.storage.db.DBInformation attribute)

X

xyzcharge (pympfit.mpfit.solvers.ConstrainedMPFITState attribute)

xyzmult (pympfit.mpfit.solvers.ConstrainedMPFITState attribute)