#include <BALL/SOLVATION/poissonBoltzmann.h>
Static Public Attributes | |
static const String | VERBOSITY |
static const String | PRINT_TIMING |
static const String | SPACING |
static const String | BORDER |
static const String | IONIC_STRENGTH |
static const String | SOLUTE_DC |
static const String | SOLVENT_DC |
static const String | PROBE_RADIUS |
static const String | ION_RADIUS |
static const String | TEMPERATURE |
static const String | BOUNDARY |
static const String | CHARGE_DISTRIBUTION |
static const String | DIELECTRIC_SMOOTHING |
static const String | OFFSET |
static const String | RMS_CRITERION |
static const String | MAX_CRITERION |
static const String | CHECK_AFTER_ITERATIONS |
static const String | MAX_ITERATIONS |
static const String | LOWER |
static const String | UPPER |
static const String | BOUNDING_BOX_LOWER |
static const String | BOUNDING_BOX_UPPER |
Symbolic names for option keys. This struct contains a symbolic name for each recognized key in FDPB::options.
const String BALL::FDPB::Option::BORDER [static] |
The border of the system. Use this option to define the aumount of space left between the bounding box of the solute and the border of the cubic grid in every direction. Use units of Angstrom with this option. The default is 4 A.
border | float |
const String BALL::FDPB::Option::BOUNDARY [static] |
Boundary condition for solving the differential equation. This parameter defines the type of boundary condition will be used for initializing the equation solver. Possible options are: zero, Debye, Coulomb, dipole and focusing. Default is dipole.
boundary_condition | String |
const String BALL::FDPB::Option::BOUNDING_BOX_LOWER [static] |
The lower corner of the bounding box of the solute molecule. This option works like
bounding_box_lower | Vector3 |
const String BALL::FDPB::Option::BOUNDING_BOX_UPPER [static] |
The upper corner of the bounding box of the solute molecule. This is the analogous option to
bounding_box_upper | Vector3 |
const String BALL::FDPB::Option::CHARGE_DISTRIBUTION [static] |
Charge distribution of the system. This parameter chooses the method used for distributing charges oiver grid points. Possible methods are: trilinear and uniform. The default is uniform.
border | float |
const String BALL::FDPB::Option::CHECK_AFTER_ITERATIONS [static] |
Checking frequency. This option defines the number of iterations which will be performed without checking the criterions. The default is 10.
check_after_iterations | int |
const String BALL::FDPB::Option::DIELECTRIC_SMOOTHING [static] |
Smoothing the dielectric constant. With this option you can choose a smoothing function for the dielectric thus permitting a smooth transition from the inside of the molecule (usually dc = 2.0) to the surrounding solvent (78.5). You have the followin options: none, uniform and harmonic. Default is none. different dielectric constant
dielectric_smoothing | String |
const String BALL::FDPB::Option::ION_RADIUS [static] |
const String BALL::FDPB::Option::IONIC_STRENGTH [static] |
The ionic strength of the salt solution This parameter defines the ionic strength of the salt solution in which the Poisson-Boltzmann calculation takes place. This parameter is given in units of mol/l. The default is 0, i. e. only a Poisson equation will be calculated.
ionic_strength | float |
const String BALL::FDPB::Option::LOWER [static] |
The lower corner of the grid. This option contains the lower corner of the grid. It can be used to fix it before setting up the solver. If this option was not used for initializing the solver gtrid it contains the automatically computed lower corner after the calculation. Use a vector of Angstroms with this option.
lower | Vector3 |
const String BALL::FDPB::Option::MAX_CRITERION [static] |
Define the MAX criterion. This option defines the upper limit for the residuals. If the maximum residuals are below this value and the RMS lies below rms_criterion, the iteration terminates. The default is 1e-4.
max_criterion | float |
const String BALL::FDPB::Option::MAX_ITERATIONS [static] |
The upper limit of iterations. Use this option to define the maximum number of iterations to be performed. If the solver does not terminate when this number of iterations is reached, the calculation did not converge. The default is 500 interations.
max_iterations | int |
const String BALL::FDPB::Option::OFFSET [static] |
Use an offset. This option allows to offset the wohle system by the vector defined in thos option. The calculation does not use an offset by default. Use threedimensional vectors in units of Angstrom with this option.
offset | Vector3 |
const String BALL::FDPB::Option::PRINT_TIMING [static] |
Print the timing for each step.
This prints the timing (if Option::verbosity > 1) of each setup routine and the time needed to solve the equations.
print_timing | bool |
const String BALL::FDPB::Option::PROBE_RADIUS [static] |
The probe radius used for calculating the SAS of the molecule. This parameter defaults to 1.4 A (water).
probe_radius | float |
const String BALL::FDPB::Option::RMS_CRITERION [static] |
Define the RMS criterion. This option defines the RMS criterion in Angstrom used for terminating the iteration of the solver. If the RMS lies below rms_criterion and the maximum residuals are below max_criterion, the iteration terminates. The default is 1e-5 Angstrom.
rms_criterion | float |
const String BALL::FDPB::Option::SOLUTE_DC [static] |
The dielectric constant of the solute. This parameter derfaults to 2.0.
solute_dielectric_constant | float |
const String BALL::FDPB::Option::SOLVENT_DC [static] |
The dielectric constant of the solvent. This parameter defaults to 78.0.
solvent_dielectric_constant | float |
const String BALL::FDPB::Option::SPACING [static] |
The grid spacing in Angstrom. Use this option to define the distance between a grid point and its closest neighbour in units o Angstrom. The default spacing is 0.6 A.
spacing | float |
const String BALL::FDPB::Option::TEMPERATURE [static] |
The temperature of the system. This parameter needs values in units of K. The default temperature is 298.15 K = 25.15 deg C.
temperature | float |
const String BALL::FDPB::Option::UPPER [static] |
The upper corner of the grid. This is the analogous option to
upper | Vector3 |
const String BALL::FDPB::Option::VERBOSITY [static] |
The verbosity level. Use integer values with this option. 0 = terse
verbosity | integer |