vpbe.c File Reference
Class Vpbe methods. More...
#include "apbscfg.h"#include "apbs/vpbe.h"
Include dependency graph for vpbe.c:
Functions | |
| VPUBLIC Valist * | Vpbe_getValist (Vpbe *thee) |
| Get atom list. | |
| VPUBLIC Vacc * | Vpbe_getVacc (Vpbe *thee) |
| Get accessibility oracle. | |
| VPUBLIC double | Vpbe_getBulkIonicStrength (Vpbe *thee) |
| Get bulk ionic strength. | |
| VPUBLIC double | Vpbe_getTemperature (Vpbe *thee) |
| Get temperature. | |
| VPUBLIC double | Vpbe_getSoluteDiel (Vpbe *thee) |
| Get solute dielectric constant. | |
| VPUBLIC double * | Vpbe_getSoluteCenter (Vpbe *thee) |
| Get coordinates of solute center. | |
| VPUBLIC double | Vpbe_getSolventDiel (Vpbe *thee) |
| Get solvent dielectric constant. | |
| VPUBLIC double | Vpbe_getSolventRadius (Vpbe *thee) |
| Get solvent molecule radius. | |
| VPUBLIC double | Vpbe_getMaxIonRadius (Vpbe *thee) |
| Get maximum radius of ion species. | |
| VPUBLIC double | Vpbe_getXkappa (Vpbe *thee) |
| Get Debye-Huckel parameter. | |
| VPUBLIC double | Vpbe_getDeblen (Vpbe *thee) |
| Get Debye-Huckel screening length. | |
| VPUBLIC double | Vpbe_getZkappa2 (Vpbe *thee) |
| Get modified squared Debye-Huckel parameter. | |
| VPUBLIC double | Vpbe_getZmagic (Vpbe *thee) |
| Get charge scaling factor. | |
| VPUBLIC double | Vpbe_getSoluteRadius (Vpbe *thee) |
| Get sphere radius which bounds biomolecule. | |
| VPUBLIC double | Vpbe_getSoluteXlen (Vpbe *thee) |
| Get length of solute in x dimension. | |
| VPUBLIC double | Vpbe_getSoluteYlen (Vpbe *thee) |
| Get length of solute in y dimension. | |
| VPUBLIC double | Vpbe_getSoluteZlen (Vpbe *thee) |
| Get length of solute in z dimension. | |
| VPUBLIC double | Vpbe_getSoluteCharge (Vpbe *thee) |
| Get total solute charge. | |
| VPUBLIC double | Vpbe_getzmem (Vpbe *thee) |
| Get z position of the membrane bottom. | |
| VPUBLIC double | Vpbe_getLmem (Vpbe *thee) |
| Get length of the membrane (A)aauthor Michael Grabe. | |
| VPUBLIC double | Vpbe_getmembraneDiel (Vpbe *thee) |
| Get membrane dielectric constant. | |
| VPUBLIC double | Vpbe_getmemv (Vpbe *thee) |
| Get membrane potential (kT). | |
| 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. | |
| 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. | |
| VPUBLIC void | Vpbe_dtor (Vpbe **thee) |
| Object destructor. | |
| VPUBLIC void | Vpbe_dtor2 (Vpbe *thee) |
| FORTRAN stub object destructor. | |
| VPUBLIC double | Vpbe_getCoulombEnergy1 (Vpbe *thee) |
| Calculate coulombic energy of set of charges. | |
| VPUBLIC unsigned long int | Vpbe_memChk (Vpbe *thee) |
| Return the memory used by this structure (and its contents) in bytes. | |
| VPUBLIC int | Vpbe_getIons (Vpbe *thee, int *nion, double ionConc[MAXION], double ionRadii[MAXION], double ionQ[MAXION]) |
| Get information about the counterion species present. | |
Detailed Description
Class Vpbe methods.
- Version:
- Id
- vpbe.c 1389 2009-08-19 17:21:23Z sdg0919
- Attention:
* * APBS -- Adaptive Poisson-Boltzmann Solver * * Nathan A. Baker (baker@biochem.wustl.edu) * Dept. of Biochemistry and Molecular Biophysics * Center for Computational Biology * Washington University in St. Louis * * Additional contributing authors listed in the code documentation. * * Copyright (c) 2002-2009, Washington University in St. Louis. * Portions Copyright (c) 2002-2009. 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 Washington University in St. Louis 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. * *
