#include <electrostmod.h>
Inheritance diagram for ElectrostMod:
Public Member Functions | |
| ElectrostMod (HaMolSet *new_phost_mset=NULL) | |
| void | clear () |
| Clear data and set default parameters of the module. | |
| bool | SetStdParam () |
| Set default parameters of the module. | |
| bool | SaveParamFile () |
| Save input parameter file for DELPHI. | |
| bool | SaveChargeFile () |
| Save file of atomic charges for DELPHI. | |
| bool | SaveRadiusFile () |
| Save atomic radii file for DELPHI. | |
| bool | SaveCoordFile () |
| Save atomic coordinates file for DELPHI. | |
| bool | RunDelphi (RunMode rmode) |
| Run Delphi calculations with saved parameters. | |
| bool | run (RunMode rmode) |
| Run continuum electrostatics caclulations with current parameters. | |
| bool | CalcETReorgEne () |
| Calculate outer-sphere Electron Transfer reorganization energy. | |
| bool | CalcAltStatePK (AltChemState *alt_res_st, AtomList *active_atoms=NULL) |
| Calculate pK value of tht alternative state, if active atoms not equal NULL only they assumed to be present. | |
| bool | CalcRedoxPotShft () |
| Calculate the redox-potential shift of the donor due to solvation. | |
| double | CalcAvgPotOn (PointCollection *ptlist) |
| Calculate Average potential on points. | |
| bool | ReadTotEne (double &tot_ene, const char *fname="DELPHI_RES.OUT") |
| Read Total Energy From DELPHI_RES.OUT file. | |
| int | LoadElPotFromFile (int format=HLM_F3D_BIN) |
| Load Electrostatic potential from file. | |
| bool | BuildPotIsoSurface () |
| bool | CalcIndCharge () |
| Calculate charges induced on the dielectric boundary between the molecule and the solvent. | |
| bool | PlotIndCharge () |
| Plot the distribution of the solvent induced charges. | |
| bool | FillChargeMap () |
| distribute atom point charges on 3D grid charge_map | |
| bool | BuildPotVdwDots () |
| bool | ColorMolSurfElPot () |
| Color the molecular surface by the electrostatic potential. | |
| bool | AddBoundaryAtoms () |
| Add Ficticious Atoms to the coordinate file to mark specified boundaries. | |
| bool | SetBoundaryAtoms (const double xmin, const double ymin, const double zmin, const double xmax, const double ymax, const double zmax) |
| Set boundaries of the molecule in the calculations. | |
| bool | ClearBoundaryAtoms () |
| Clear boundary atoms. | |
Public Attributes | |
| Vec3D | min_coord |
| Point marking minimal x,y,z coordinates for the calculations. | |
| Vec3D | max_coord |
| Point marking maximal x,y,z coordinates for the calculations. | |
| HaString | param_file_title |
| Title of the DELPHI job. | |
| int | nx |
| int | ny |
| int | nz |
| dimensions of the grid, default = 65 | |
| double | perfil |
| percent of the grid occupied by the molecule, default = 60.0 | |
| double | offset [3] |
| dimensions of the box, or scale, default =0.0 | |
| double | epsi |
| double | epsout |
| internal and external dielectric constant, default espi = 4.0, epsout = 81.0 | |
| double | rionst |
| ionic strength , default = 0.0 | |
| double | exrad |
| double | radprb |
| Ion exclusion radius, and probe radius, default exrad = 2.0, radprb = 1.4. | |
| int | boundary |
| Boundary: 0=Zero,1=Apprx Coul,2=Focus,3=Coul , default = 0. | |
| int | iper [3] |
| periodic boundary flags | |
| int | nlit |
| number of linear Poisson-Boltz. iterations, default = -1 | |
| int | nnit |
| number of non-linear Poisson-Boltz. iterations, default = 0 | |
| int | iconc |
| int | ibios |
| potential output control | |
| int | isite |
| flag to print electric field at spec. points | |
| int | iatout |
| flag to to write modif. pdb | |
| HaString | toplbl |
| title of the job | |
| int | isph |
| flag for spherical charge distrib | |
| int | ipdbwrt |
| flag for writing pf pdb file | |
| int | ifrcwrt |
| flag for writing frc file | |
| HaString | enc |
| energy print control flags | |
| int | igraph |
| int | ipotent |
| int | icon1 |
| int | icon2 |
| int | imem |
| flag to model membrane | |
| int | phiwrt |
| flag to write potential map | |
| int | ihs |
| int | isen |
| int | ish |
| double | elpot_low_val |
| low and high value of the electrostatic potential | |
| double | elpot_high_val |
| for coloring of the molecular surface (in kT) | |
| HaString | param_file_name |
| Delphi input parameters file name. | |
| HaString | charge_file_name |
| Delphi atomic charges file name. | |
| HaString | radius_file_name |
| Delphi atomic radii file name. | |
| HaString | coord_file_name |
| Delphi atomic coordinates file name. | |
| HaString | log_file_name |
| Delphi log file name. | |
| HaString | elfield_fname |
| name of the file with electrostatic field | |
| float | pot_isolevel |
| value of potential for isosurface plot | |
| int | dots_number |
| number of dots for dot_surface plot | |
| double | tot_ene |
| Current total electrostatic energy of the system (in KT). | |
| HaField3D | el_pot_map |
| Electrostatic poteintial Map on 3D Grid. | |
| list< HaSurface * > | Surfaces |
| int | fill_charge_mode |
| Mode to spread atomic charges on the grid (FILL_CHARGE_NEAREST_PT = 1, FILL_CHARGE_CUBE=2). | |
| HaField3D | charge_map |
| Charges of atoms on 3D Grid. | |
| HaField3D | ind_charge_map |
| Induced charges on 3D Grid. | |
| int | rdx_shft_mode |
| reference state to compute redox-potential shift of the donor: RDX_SHFT_VS_VAC, RDX_SHFT_VS_SOLV | |
| double | rdx_shift |
| Value of the calculated redox-potential shift. | |
| HaVec_double | axx_ene |
| Axxiliary arrays of energies to return intermediate energies from some functions. | |
|
|
flags to write expanded surface data file, < surface energy file and surface charge file |
1.3.6