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ForceBalance API
1.3
Automated optimization of force fields and empirical potentials
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ForceBalance API
1.3
Automated optimization of force fields and empirical potentials
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| ►CABCMeta | |
| ►Csrc.target.Target | Base class for all fitting targets |
| Csrc.target.RemoteTarget | |
| ►CBaseClass | |
| Csrc.engine.Engine | Base class for all engines |
| Csrc.ffyapf.FF | Force field class |
| Csrc.forcefield.FF | Force field class |
| Csrc.objective.Objective | Objective function |
| Csrc.optimizer.Optimizer | Optimizer class |
| Csrc.target.Target | Base class for all fitting targets |
| ►Cdict | |
| Csrc.ffyapf.BackedUpDict | |
| Csrc.forcefield.BackedUpDict | |
| ►CException | |
| Csrc._version.NotThisMethod | Exception raised if a method is not valid for the current scenario |
| ►CFileHandler | |
| Csrc.nifty.RawFileHandler | Exactly like FileHandler, except no newline character is printed at the end of each message |
| Csrc.output.CleanFileHandler | File handler that does not write terminal escape codes and carriage returns to files |
| Csrc.output.RawFileHandler | Exactly like output.FileHandler except it does no extra formatting before sending logging messages to the file |
| ►CIOError | |
| Csrc.molecule.ActuallyArcError | |
| ►CLogger | |
| Csrc.output.ForceBalanceLogger | This logger starts out with a default handler that writes to stdout addHandler removes this default the first time another handler is added |
| Csrc.output.ModLogger | |
| Csrc.evaluator_io.Evaluator_SMIRNOFF.OptionsFile | Represents the set of options that a Evaluator_SMIRNOFF target will be run with |
| ►CStreamHandler | |
| Csrc.molecule.RawStreamHandler | Exactly like output.StreamHandler except it does no extra formatting before sending logging messages to the stream |
| Csrc.nifty.RawStreamHandler | Exactly like StreamHandler, except no newline character is printed at the end of each message |
| Csrc.output.CleanStreamHandler | Similar to RawStreamHandler except it does not write terminal escape codes |
| Csrc.output.RawStreamHandler | Exactly like output.StreamHandler except it does no extra formatting before sending logging messages to the stream |
| ►CStructure | |
| Csrc.molecule.MolfileTimestep | Wrapper for the timestep C structure used in molfile plugins |
| Csrc._version.VersioneerConfig | Container for Versioneer configuration parameters |
| ►CAbInitio | |
| Csrc.abinitio_internal.AbInitio_Internal | Subclass of Target for force and energy matching using an internal implementation |
| Csrc.amberio.AbInitio_AMBER | Subclass of Target for force and energy matching using AMBER |
| Csrc.gmxio.AbInitio_GMX | Subclass of AbInitio for force and energy matching using GROMACS |
| Csrc.smirnoffio.AbInitio_SMIRNOFF | Force and energy matching using OpenMM |
| Csrc.tinkerio.AbInitio_TINKER | Subclass of Target for force and energy matching using TINKER |
| ►CBaseReader | |
| Csrc.amberio.FrcMod_Reader | Finite state machine for parsing FrcMod force field file |
| Csrc.amberio.Mol2_Reader | Finite state machine for parsing Mol2 force field file |
| Csrc.custom_io.Gen_Reader | Finite state machine for parsing custom GROMACS force field files |
| Csrc.gmxio.ITP_Reader | Finite state machine for parsing GROMACS force field files |
| Csrc.psi4io.GBS_Reader | Interaction type -> Parameter Dictionary |
| Csrc.psi4io.Grid_Reader | Finite state machine for parsing DVR grid files |
| Csrc.qchemio.QCIn_Reader | Finite state machine for parsing Q-Chem input files |
| Csrc.smirnoffio.SMIRNOFF_Reader | Class for parsing OpenMM force field files |
| Csrc.tinkerio.Tinker_Reader | Finite state machine for parsing TINKER force field files |
| ►CBindingEnergy | |
| Csrc.gmxio.BindingEnergy_GMX | Binding energy matching using Gromacs |
| Csrc.tinkerio.BindingEnergy_TINKER | Binding energy matching using TINKER |
| ►CEngine | |
| Csrc.amberio.AMBER | Engine for carrying out general purpose AMBER calculations |
| Csrc.gmxio.GMX | Derived from Engine object for carrying out general purpose GROMACS calculations |
| Csrc.tinkerio.TINKER | Engine for carrying out general purpose TINKER calculations |
| ►CInteraction | |
| Csrc.amberio.Interaction_AMBER | Subclass of Target for calculating and matching ineraction energies using AMBER |
| Csrc.gmxio.Interaction_GMX | Interaction energy matching using GROMACS |
| Csrc.tinkerio.Interaction_TINKER | Subclass of Target for interaction matching using TINKER |
| ►CLeastSquares | |
| Csrc.psi4io.THCDF_Psi4 | |
| ►CLipid | |
| Csrc.gmxio.Lipid_GMX | |
| ►CLiquid | |
| Csrc.amberio.Liquid_AMBER | Subclass of Target for calculating and matching liquid properties using AMBER |
| Csrc.gmxio.Liquid_GMX | |
| Csrc.smirnoffio.Liquid_SMIRNOFF | Condensed phase property matching using OpenMM |
| Csrc.tinkerio.Liquid_TINKER | Condensed phase property matching using TINKER |
| ►CMoments | |
| Csrc.gmxio.Moments_GMX | Multipole moment matching using GROMACS |
| Csrc.tinkerio.Moments_TINKER | Subclass of Target for multipole moment matching using TINKER |
| ►Cobject | |
| Csrc.amberio.PrmtopLoader | Parsed AMBER prmtop file |
| Csrc.BaseClass | Provides some nifty functions that are common to all ForceBalance classes |
| Csrc.BaseReader | The 'reader' class |
| Csrc.Mol2.mol2 | This is to manage one mol2 series of lines on the form: |
| Csrc.Mol2.mol2_atom | This is to manage mol2 atomic lines on the form: 1 C1 5.4790 42.2880 49.5910 C.ar 1 <1> 0.0424 |
| Csrc.Mol2.mol2_bond | This is to manage mol2 bond lines on the form: 1 1 2 ar |
| Csrc.Mol2.mol2_set | |
| Csrc.molecule.Molecule | Lee-Ping's general file format conversion class |
| Csrc.nifty.LineChunker | |
| Csrc.objective.Penalty | Penalty functions for regularizing the force field optimizer |
| ►Csrc.quantity.Quantity | Base class for thermodynamical quantity used for fitting |
| Csrc.quantity.Quantity_Density | |
| Csrc.quantity.Quantity_H_vap | |
| Csrc.thermo.Point | |
| ►COpenMM | |
| Csrc.smirnoffio.SMIRNOFF | Derived from Engine object for carrying out OpenMM calculations that use the SMIRNOFF force field |
| ►COptGeoTarget | |
| Csrc.smirnoffio.OptGeoTarget_SMIRNOFF | Optimized geometry fitting using SMIRNOFF format powered by OpenMM |
| ►CTarget | |
| Csrc.abinitio.AbInitio | Subclass of Target for fitting force fields to ab initio data |
| Csrc.binding.BindingEnergy | Improved subclass of Target for fitting force fields to binding energies |
| Csrc.counterpoise.Counterpoise | Target subclass for matching the counterpoise correction |
| Csrc.evaluator_io.Evaluator_SMIRNOFF | A custom optimisation target which employs the openff-evaluator package to rapidly estimate a collection of condensed phase physical properties at each optimisation epoch |
| Csrc.hydration.Hydration | Subclass of Target for fitting force fields to hydration free energies |
| Csrc.interaction.Interaction | Subclass of Target for fitting force fields to interaction energies |
| Csrc.leastsq.LeastSquares | Subclass of Target for general least squares fitting |
| Csrc.lipid.Lipid | Subclass of Target for lipid property matching |
| Csrc.liquid.Liquid | Subclass of Target for liquid property matching |
| Csrc.moments.Moments | Subclass of Target for fitting force fields to multipole moments (from experiment or theory) |
| Csrc.opt_geo_target.OptGeoTarget | Subclass of Target for fitting MM optimized geometries to QM optimized geometries |
| Csrc.psi4io.RDVR3_Psi4 | Subclass of Target for R-DVR3 grid fitting |
| Csrc.thermo.Thermo | A target for fitting general experimental data sets |
| Csrc.torsion_profile.TorsionProfileTarget | Subclass of Target for fitting MM optimized geometries to QM optimized geometries |
| Csrc.vibration.Vibration | Subclass of Target for fitting force fields to vibrational spectra (from experiment or theory) |
| ►CThermo | |
| Csrc.gmxio.Thermo_GMX | Thermodynamical property matching using GROMACS |
| ►CTorsionProfileTarget | |
| Csrc.smirnoffio.TorsionProfileTarget_SMIRNOFF | Force and energy matching using SMIRKS native Open Force Field (SMIRNOFF) |
| ►CVibration | |
| Csrc.amberio.Vibration_AMBER | Subclass of Target for calculating and matching vibrational modes using AMBER |
| Csrc.gmxio.Vibration_GMX | Vibrational frequency matching using GROMACS |
| Csrc.smirnoffio.Vibration_SMIRNOFF | Vibrational frequency matching using TINKER |
| Csrc.tinkerio.Vibration_TINKER | Vibrational frequency matching using TINKER |
| ►Cwith_metaclass | |
| Csrc.target.Target | Base class for all fitting targets |
1.8.13