 |
ForceBalance API
1.3
Automated optimization of force fields and empirical potentials
|
|
ForceBalance API
1.3
Automated optimization of force fields and empirical potentials
|
| ▼Nforcebalance | |
| ▼Nsrc | |
| ►N_version | |
| CNotThisMethod | Exception raised if a method is not valid for the current scenario |
| CVersioneerConfig | Container for Versioneer configuration parameters |
| ►Nabinitio | |
| CAbInitio | Subclass of Target for fitting force fields to ab initio data |
| ►Nabinitio_internal | |
| CAbInitio_Internal | Subclass of Target for force and energy matching using an internal implementation |
| ►Namberio | |
| CAbInitio_AMBER | Subclass of Target for force and energy matching using AMBER |
| CAMBER | Engine for carrying out general purpose AMBER calculations |
| CFrcMod_Reader | Finite state machine for parsing FrcMod force field file |
| CInteraction_AMBER | Subclass of Target for calculating and matching ineraction energies using AMBER |
| CLiquid_AMBER | Subclass of Target for calculating and matching liquid properties using AMBER |
| CMol2_Reader | Finite state machine for parsing Mol2 force field file |
| CPrmtopLoader | Parsed AMBER prmtop file |
| CVibration_AMBER | Subclass of Target for calculating and matching vibrational modes using AMBER |
| ►Nbinding | |
| CBindingEnergy | Improved subclass of Target for fitting force fields to binding energies |
| ►Ncounterpoise | |
| CCounterpoise | Target subclass for matching the counterpoise correction |
| ►Ncustom_io | |
| CGen_Reader | Finite state machine for parsing custom GROMACS force field files |
| ►Nengine | |
| CEngine | Base class for all engines |
| ►Nevaluator_io | |
| ►CEvaluator_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 |
| COptionsFile | Represents the set of options that a Evaluator_SMIRNOFF target will be run with |
| ►Nffyapf | |
| CBackedUpDict | |
| CFF | Force field class |
| ►Nforcefield | |
| CBackedUpDict | |
| CFF | Force field class |
| ►Ngmxio | |
| CAbInitio_GMX | Subclass of AbInitio for force and energy matching using GROMACS |
| CBindingEnergy_GMX | Binding energy matching using Gromacs |
| CGMX | Derived from Engine object for carrying out general purpose GROMACS calculations |
| CInteraction_GMX | Interaction energy matching using GROMACS |
| CITP_Reader | Finite state machine for parsing GROMACS force field files |
| CLipid_GMX | |
| CLiquid_GMX | |
| CMoments_GMX | Multipole moment matching using GROMACS |
| CThermo_GMX | Thermodynamical property matching using GROMACS |
| CVibration_GMX | Vibrational frequency matching using GROMACS |
| ►Nhydration | |
| CHydration | Subclass of Target for fitting force fields to hydration free energies |
| ►Ninteraction | |
| CInteraction | Subclass of Target for fitting force fields to interaction energies |
| ►Nleastsq | |
| CLeastSquares | Subclass of Target for general least squares fitting |
| ►Nlipid | |
| CLipid | Subclass of Target for lipid property matching |
| ►Nliquid | |
| CLiquid | Subclass of Target for liquid property matching |
| ►NMol2 | |
| Cmol2 | This is to manage one mol2 series of lines on the form: |
| Cmol2_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 |
| Cmol2_bond | This is to manage mol2 bond lines on the form: 1 1 2 ar |
| Cmol2_set | |
| ►Nmolecule | |
| CActuallyArcError | |
| CMolecule | Lee-Ping's general file format conversion class |
| CMolfileTimestep | Wrapper for the timestep C structure used in molfile plugins |
| CRawStreamHandler | Exactly like output.StreamHandler except it does no extra formatting before sending logging messages to the stream |
| ►Nmoments | |
| CMoments | Subclass of Target for fitting force fields to multipole moments (from experiment or theory) |
| ►Nnifty | |
| CLineChunker | |
| CRawFileHandler | Exactly like FileHandler, except no newline character is printed at the end of each message |
| CRawStreamHandler | Exactly like StreamHandler, except no newline character is printed at the end of each message |
| ►Nobjective | |
| CObjective | Objective function |
| CPenalty | Penalty functions for regularizing the force field optimizer |
| ►Nopt_geo_target | |
| COptGeoTarget | Subclass of Target for fitting MM optimized geometries to QM optimized geometries |
| ►Noptimizer | |
| COptimizer | Optimizer class |
| ►Noutput | |
| CCleanFileHandler | File handler that does not write terminal escape codes and carriage returns to files |
| CCleanStreamHandler | Similar to RawStreamHandler except it does not write terminal escape codes |
| CForceBalanceLogger | This logger starts out with a default handler that writes to stdout addHandler removes this default the first time another handler is added |
| CModLogger | |
| CRawFileHandler | Exactly like output.FileHandler except it does no extra formatting before sending logging messages to the file |
| CRawStreamHandler | Exactly like output.StreamHandler except it does no extra formatting before sending logging messages to the stream |
| ►Npsi4io | |
| CGBS_Reader | Interaction type -> Parameter Dictionary |
| CGrid_Reader | Finite state machine for parsing DVR grid files |
| CRDVR3_Psi4 | Subclass of Target for R-DVR3 grid fitting |
| CTHCDF_Psi4 | |
| ►Nqchemio | |
| CQCIn_Reader | Finite state machine for parsing Q-Chem input files |
| ►Nquantity | |
| CQuantity | Base class for thermodynamical quantity used for fitting |
| CQuantity_Density | |
| CQuantity_H_vap | |
| ►Nsmirnoffio | |
| CAbInitio_SMIRNOFF | Force and energy matching using OpenMM |
| CLiquid_SMIRNOFF | Condensed phase property matching using OpenMM |
| COptGeoTarget_SMIRNOFF | Optimized geometry fitting using SMIRNOFF format powered by OpenMM |
| CSMIRNOFF | Derived from Engine object for carrying out OpenMM calculations that use the SMIRNOFF force field |
| CSMIRNOFF_Reader | Class for parsing OpenMM force field files |
| CTorsionProfileTarget_SMIRNOFF | Force and energy matching using SMIRKS native Open Force Field (SMIRNOFF) |
| CVibration_SMIRNOFF | Vibrational frequency matching using TINKER |
| ►Ntarget | |
| CRemoteTarget | |
| CTarget | Base class for all fitting targets |
| ►Nthermo | |
| CPoint | |
| CThermo | A target for fitting general experimental data sets |
| ►Ntinkerio | |
| CAbInitio_TINKER | Subclass of Target for force and energy matching using TINKER |
| CBindingEnergy_TINKER | Binding energy matching using TINKER |
| CInteraction_TINKER | Subclass of Target for interaction matching using TINKER |
| CLiquid_TINKER | Condensed phase property matching using TINKER |
| CMoments_TINKER | Subclass of Target for multipole moment matching using TINKER |
| CTINKER | Engine for carrying out general purpose TINKER calculations |
| CTinker_Reader | Finite state machine for parsing TINKER force field files |
| CVibration_TINKER | Vibrational frequency matching using TINKER |
| ►Ntorsion_profile | |
| CTorsionProfileTarget | Subclass of Target for fitting MM optimized geometries to QM optimized geometries |
| ►Nvibration | |
| CVibration | Subclass of Target for fitting force fields to vibrational spectra (from experiment or theory) |
| CBaseClass | Provides some nifty functions that are common to all ForceBalance classes |
| CBaseReader | The 'reader' class |
1.8.13