BALL
1.4.79
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Functions | |
BALL_EXPORT TRegularData3D< char > * | BALL::calculateSESGrid (const Vector3 &lower, const Vector3 &upper, float spacing, const System &system, float probe_radius) |
BALL_EXPORT TRegularData3D< char > * | BALL::calculateSASGrid (const Vector3 &lower, const Vector3 &upper, float spacing, const System &system, float probe_radius) |
BALL_EXPORT double | BALL::calculateOoiEnergy (AtomContainer &atoms) |
This chapter contains all relevant information on the use of BALL solvation methods.
Error codes: these are the possible error codes that can be produced by FDPB.
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ERROR__NONE |
No error. |
ERROR__UNKNOWN |
Unknown error. |
ERROR__NOT_IMPLEMENTED |
Not implemented error. Someone has been too lazy to implement the this method. Wait for the next release... |
ERROR__CANNOT_CREATE_ATOM_ARRAY |
Unable to create the atom array/out of memory. FDPB internally creates a dynamic array containing the atoms of the system. If FDPB::setupAtomArray() cannot create this array you normally ran out of virtual memory. |
ERROR__CANNOT_CREATE_SAS_GRID |
Unable to create SAS grid/out of memory. FDPB uses a TRegularData3D<char> (FDPB::SAS_grid) to describe whether a point in space is inside the ion exclusion layer. This grid is created by FDPB::setupSASGrid(). On failure this error code is set. It usually indicates a lack of virtual memory. |
ERROR__CANNOT_CREATE_EPSILON_GRID |
Unable to create dielectric grid/out of memory. FDPB uses a
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ERROR__CANNOT_CREATE_KAPPA_GRID |
Unable to create grid for the modified Debye Hueckel parameter/out of memory. The modified Debye Hueckel parameter
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ERROR__CANNOT_CREATE_CHARGE_GRID |
Unable to create charge grid/out of memory. FDPB::setupQGrid() distributes the charge of the atoms in a grid. This grid is named FDPB::q_grid.
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ERROR__CANNOT_CREATE_PHI_GRID |
Unable to create electrostatic potential grid/out of memory. FDPB::setupPhiGrid() creates a TRegularData3D<float> (FDPB::phi_grid) containing the electrostatic potential as a function of space. If the creation of this grid fails due to a lack of virtual memory, this error code is set. |
ERROR__SAS_GRID_REQUIRED |
Create solvent accessible surface grid first. This error code is set by FDPB::setupKappGrid() if it is called but the ion excluded surface has not been set (usually by calling FDPB::setupSASGrid).
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ERROR__EPSILON_GRID_REQUIRED |
Create dielectric constant grid first. This error code is set by FDPB::setupQGrid(), FDPB::setupKappaGrid(), or FDPB::setupPhiGrid() if it was called, but FDPB::eps_grid was not defined yet (this is usually done by calling FDPB::setupEpsGrid ).
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ERROR__ATOM_ARRAY_REQUIRED |
Create atom array first. This error code is set by FDPB::setupQGrid() or FDPB::setupBoundary() if it was called but FDPB::atom_array was not yet defined (this is usually done by calling FDPB::setupAtomArray()).
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ERROR__PHI_GRID_REQUIRED |
Create electrostatic potential grid first. FDPB::phi_grid contains the electrostatic potential at each point in space. FDPB::setupBoundary() sets this error code if it is called but FDPB::phi_grid has not been set yet. Solution: call FDPB::setupPhiGrid() before calling FDPB::setupBoundary() |
ERROR__OUT_OF_MEMORY |
Not enough virtual memory. This error code is set if FDPB::solve() ran out of virtual memory while creating some internal datastructures. Solution: reduce grid dimensions or increase grid spacing. |
ERROR__UNKNOWN_DIELECTRIC_SMOOTHING_METHOD |
The specified method to smooth the dielectric constant grid is not allowed. FDPB::setupEpsGrid sets this error code, if it cannot identify the method given in FDPB::Option::dielectric_smoothing.
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ERROR__UNKNOWN_CHARGE_DISTRIBUTION_METHOD |
The specified charge distribution is not allowed. FDPB::setupQGrid() sets this error code, if it cannot identify the method given in FDPB::Option::charge_distribution.
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ERROR__UNKNOWN_BOUNDARY_CONDITION_TYPE |
The specified boundary condition type is not allowed. FDPB::setupBoundary() sets this error code, if it cannot identify the boundary condition given in FDPB::Option::boundary.
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ERROR__NOT_A_VECTOR_IN_UPPER_LOWER |
Upper or lower grid coordinates were specified in an incorrect format. This error code is set by FDPB::setupEpsGrid if the string given in FDPB::options (key FDPB::Option::LOWER or FDPB::Option::UPPER) were not in vector format.
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ERROR__ILLEGAL_VALUE_FOR_LOWER_UPPER |
Lower and upper corner of the grid were set to wrong values. Lower and upper corners of the grid given in FDPB::options (key FDPB::Option::LOWER and FDPB::Option::UPPER) must fulfill just one condition: every coordinate of lower hast to be less (not equal!) to the corresponding coordinate of upper.
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ERROR__SETUP_REQUIRED |
Call setup first. This error code is set by FDPB::solve() if FDPB::q_grid or FDPB::phi_grid or FDPB::eps_grid are undefined.
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NUMBER_OF_ERRORS |
Total number of errors defined. |
Definition at line 45 of file poissonBoltzmann.h.
The available methods for integration
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METHOD__UNKNOWN | |
METHOD__ANALYTICAL | |
METHOD__TRAPEZIUM |
Definition at line 89 of file pair6_12RDFIntegrator.h.
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SURFACE__UNKNOWN | |
SURFACE__SAS | |
SURFACE__SES | |
SURFACE__EXTERNAL |
Definition at line 55 of file pair6_12InteractionEnergyProcessor.h.
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SURFACE__UNKNOWN |
Unknown surface. |
SURFACE__SAS |
Solvent assessible surface. |
SURFACE__SES |
Solvent excluding surface. |
SURFACE__EXTERNAL |
Use a surface description from a file. |
Definition at line 63 of file pairExpInteractionEnergyProcessor.h.
BALL_EXPORT double BALL::calculateOoiEnergy | ( | AtomContainer & | atoms | ) |
Calculate the solvation energy after Ooi et al. This function computes the solvation energy using the empirical surface model proposed by Ooi et al.(T. Ooi, M. Oobatake, G. Nemethy, H. A. Scheraga: Accessible surface areas as a measure off the thermodynamic parameters of hydration of peptides, Proc. Natl. Acad. Sci. USA, Vol. 84 (1987), pp. 3086-3090).
The method is parameterized for proteins only. Calling the function with different structures probably yields results of arbitrary meaninglessness.
The energy is returned in units of kJ/mol. Unparametrized atoms are simply ignored, which might lead to unreasonable values.
BALL_EXPORT TRegularData3D<char>* BALL::calculateSASGrid | ( | const Vector3 & | lower, |
const Vector3 & | upper, | ||
float | spacing, | ||
const System & | system, | ||
float | probe_radius | ||
) |
calculateSASGrid