APBS
1.4.1
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Class Vpbe methods. More...
#include "vpbe.h"
Go to the source code of this file.
Macros | |
#define | MAX_SPLINE_WINDOW 0.5 |
Functions | |
VPUBLIC Valist * | Vpbe_getValist (Vpbe *thee) |
Get atom list. More... | |
VPUBLIC Vacc * | Vpbe_getVacc (Vpbe *thee) |
Get accessibility oracle. More... | |
VPUBLIC double | Vpbe_getBulkIonicStrength (Vpbe *thee) |
Get bulk ionic strength. More... | |
VPUBLIC double | Vpbe_getTemperature (Vpbe *thee) |
Get temperature. More... | |
VPUBLIC double | Vpbe_getSoluteDiel (Vpbe *thee) |
Get solute dielectric constant. More... | |
VPUBLIC double * | Vpbe_getSoluteCenter (Vpbe *thee) |
Get coordinates of solute center. More... | |
VPUBLIC double | Vpbe_getSolventDiel (Vpbe *thee) |
Get solvent dielectric constant. More... | |
VPUBLIC double | Vpbe_getSolventRadius (Vpbe *thee) |
Get solvent molecule radius. More... | |
VPUBLIC double | Vpbe_getMaxIonRadius (Vpbe *thee) |
Get maximum radius of ion species. More... | |
VPUBLIC double | Vpbe_getXkappa (Vpbe *thee) |
Get Debye-Huckel parameter. More... | |
VPUBLIC double | Vpbe_getDeblen (Vpbe *thee) |
Get Debye-Huckel screening length. More... | |
VPUBLIC double | Vpbe_getZkappa2 (Vpbe *thee) |
Get modified squared Debye-Huckel parameter. More... | |
VPUBLIC double | Vpbe_getZmagic (Vpbe *thee) |
Get charge scaling factor. More... | |
VPUBLIC double | Vpbe_getSoluteRadius (Vpbe *thee) |
Get sphere radius which bounds biomolecule. More... | |
VPUBLIC double | Vpbe_getSoluteXlen (Vpbe *thee) |
Get length of solute in x dimension. More... | |
VPUBLIC double | Vpbe_getSoluteYlen (Vpbe *thee) |
Get length of solute in y dimension. More... | |
VPUBLIC double | Vpbe_getSoluteZlen (Vpbe *thee) |
Get length of solute in z dimension. More... | |
VPUBLIC double | Vpbe_getSoluteCharge (Vpbe *thee) |
Get total solute charge. More... | |
VPUBLIC double | Vpbe_getzmem (Vpbe *thee) |
Get z position of the membrane bottom. More... | |
VPUBLIC double | Vpbe_getLmem (Vpbe *thee) |
Get length of the membrane (A)aauthor Michael Grabe. More... | |
VPUBLIC double | Vpbe_getmembraneDiel (Vpbe *thee) |
Get membrane dielectric constant. More... | |
VPUBLIC double | Vpbe_getmemv (Vpbe *thee) |
Get membrane potential (kT) More... | |
VPUBLIC Vpbe * | Vpbe_ctor (Valist *alist, int ionNum, double *ionConc, double *ionRadii, double *ionQ, double T, double soluteDiel, double solventDiel, double solventRadius, int focusFlag, double sdens, double z_mem, double L, double membraneDiel, double V) |
Construct Vpbe object. More... | |
VPUBLIC int | Vpbe_ctor2 (Vpbe *thee, Valist *alist, int ionNum, double *ionConc, double *ionRadii, double *ionQ, double T, double soluteDiel, double solventDiel, double solventRadius, int focusFlag, double sdens, double z_mem, double L, double membraneDiel, double V) |
FORTRAN stub to construct Vpbe objct. More... | |
VPUBLIC void | Vpbe_dtor (Vpbe **thee) |
Object destructor. More... | |
VPUBLIC void | Vpbe_dtor2 (Vpbe *thee) |
FORTRAN stub object destructor. More... | |
VPUBLIC double | Vpbe_getCoulombEnergy1 (Vpbe *thee) |
Calculate coulombic energy of set of charges. More... | |
VPUBLIC unsigned long int | Vpbe_memChk (Vpbe *thee) |
Return the memory used by this structure (and its contents) in bytes. More... | |
VPUBLIC int | Vpbe_getIons (Vpbe *thee, int *nion, double ionConc[MAXION], double ionRadii[MAXION], double ionQ[MAXION]) |
Get information about the counterion species present. More... | |
Class Vpbe methods.
* * APBS -- Adaptive Poisson-Boltzmann Solver * * Nathan A. Baker (nathan.baker@pnnl.gov) * Pacific Northwest National Laboratory * * Additional contributing authors listed in the code documentation. * * Copyright (c) 2010-2012 Battelle Memorial Institute. Developed at the * Pacific Northwest National Laboratory, operated by Battelle Memorial * Institute, Pacific Northwest Division for the U.S. Department of Energy. * * Portions Copyright (c) 2002-2010, Washington University in St. Louis. * Portions Copyright (c) 2002-2010, Nathan A. Baker. * Portions Copyright (c) 1999-2002, The Regents of the University of * California. * Portions Copyright (c) 1995, Michael Holst. * All rights reserved. * * Redistribution and use in source and binary forms, with or without * modification, are permitted provided that the following conditions are met: * * Redistributions of source code must retain the above copyright notice, this * list of conditions and the following disclaimer. * * Redistributions in binary form must reproduce the above copyright notice, * this list of conditions and the following disclaimer in the documentation * and/or other materials provided with the distribution. * * Neither the name of the developer nor the names of its contributors may be * used to endorse or promote products derived from this software without * specific prior written permission. * * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF * THE POSSIBILITY OF SUCH DAMAGE. * *
Definition in file vpbe.c.