#include "maloc/maloc.h"
#include "apbs/apbs.h"
#include "isim/various.h"
#include "isim/ionlist.h"
#include "apbs/valist.h"
#include "apbs/vatom.h"
#include "apbs/vacc.h"
#include "apbs/vpbe.h"
#include "apbs/vopot.h"
Go to the source code of this file.
Compounds | |
| struct | macromolecule |
| Class for generic representation of macromolecules. More... | |
Defines | |
| #define | _MACROMOLECULE_H_ 1 |
| Environment variable for 'macromolecule.h'. | |
Typedefs | |
| typedef macromolecule | macromolecule |
Functions | |
| macromolecule * | macromolecule_ctor (char id) |
| Constructor for the macromolecule object. More... | |
| void | macromolecule_dtor (macromolecule *thee, char id) |
| Destructor for the macromolecule object. More... | |
| double | Born_vol (macromolecule *thee) |
| Volume calculation for Born ion. More... | |
| int | Born_is_at (macromolecule *thee, double *xyz, double rad) |
| Accessibility check for a specified point (Born ion). More... | |
| double | Born_total_steric (macromolecule *thee, int types, ionlist *ions, char mode) |
| Get value for total steric energy due to interaction of Born ion with explicit ions. More... | |
| double | Born_total_steric2 (macromolecule *thee, int types, ionlist *ions, char mode, double *coordsnew[]) |
| Get value for total steric energy due to interaction of Born ion with explicit ions. More... | |
| double | Born_one_steric (macromolecule *thee, ionlist *ions, int type, int pos, char mode) |
| Get value for steric energy due to interaction of Born ion with specified ion. More... | |
| double | Born_total_estatic (macromolecule *thee, int types, ionlist *ions) |
| Get value for total electrostatic energy due to interaction of Born ion with explicit ions. More... | |
| double | Born_total_estatic2 (macromolecule *thee, int types, ionlist *ions, double *coordsnew[]) |
| Get value for total electrostatic energy due to interaction of Born ion with explicit ions. More... | |
| double | Born_point_pot (macromolecule *thee, double *point) |
| Get value for electrostatic potential due to Born ion at given point. More... | |
| void | Born_reference (macromolecule *thee, ionlist *ions, int types, double rad, int res, double KB_T, double KB_T_IN_J) |
| Writes out some reference knowledge for the Born ion problem based on the work by Debye and Hückel . More... | |
| double | PQR_vol (macromolecule *thee) |
| Volume calculation for PQR-file macromolecule. More... | |
| int | PQR_is_at (macromolecule *thee, double *xyz, double rad) |
| Accessibility check for a specified point (van-der-Waals surface of a PQR-file macromolecule). More... | |
| void | PQR_rotate (macromolecule *thee) |
| Rotates PQR-based macromolecule in case of cylindrical simulation systems. More... | |
| double | PQR_total_steric (macromolecule *thee, int types, ionlist *ions, char mode) |
| Get value for total steric energy due to interaction of PQR-based macromolecule with explicit ions. More... | |
| double | PQR_total_steric2 (macromolecule *thee, int types, ionlist *ions, char mode, double *coordsnew[]) |
| Get value for total steric energy due to interaction of PQR-based macromolecule with explicit ions. More... | |
| double | PQR_one_steric (macromolecule *thee, ionlist *ions, int type, int pos, char mode) |
| Get value for steric energy due to interaction of PQR-based macromolecule with specified ion. More... | |
| double | PQR_total_estatic (macromolecule *thee, int types, ionlist *ions) |
| Get value for total electrostatic energy due to interaction of PQR-based macromolecule with explicit ions. More... | |
| double | PQR_total_estatic2 (macromolecule *thee, int types, ionlist *ions, double *coordsnew[]) |
| Get value for total electrostatic energy due to interaction of PQR-based macromolecule with explicit ions. More... | |
| double | PQR_point_pot (macromolecule *thee, double *point) |
| Get value for electrostatic potential due to PQR-based macromolecule at given point. More... | |
| double | PQR_sphere_maxradius (macromolecule *thee) |
| Gives maximum spherical radius of a PQR-based macromolecule for a sphere centered at {0.0,0.0,0.0}. More... | |
| double | PQR_cylinder_maxradius (macromolecule *thee) |
| Gives maximum cylindrical radius of a PQR-based macromolecule for a cylinder centered at {0.0,0.0,0.0}. More... | |
| void | Born_shift (macromolecule *thee, double xshift, double yshift, double zshift) |
| Shifts center coordinates of Born ion by specified vector. More... | |
| void | PQR_shift (macromolecule *thee, double xshift, double yshift, double zshift) |
| Shifts coordinates in atom list of a PQR-based macromolecule by specified vector. More... | |
| double | CYL_vol (macromolecule *thee) |
| Volume calculation for cylinder. More... | |
| int | CYL_is_at (macromolecule *thee, double *xyz, double rad) |
| Accessibility check for a specified point (charged cylinder). More... | |
| double | CYL_total_steric (macromolecule *thee, int types, ionlist *ions, char mode) |
| Get value for total steric energy due to interaction of charged cylinder with explicit ions. More... | |
| double | CYL_total_steric2 (macromolecule *thee, int types, ionlist *ions, char mode, double *coordsnew[]) |
| Get value for total steric energy due to interaction of charged cylinder with explicit ions. More... | |
| double | CYL_one_steric (macromolecule *thee, ionlist *ions, int type, int pos, char mode) |
| Get value for steric energy due to interaction of charged cylinder with specified ion. More... | |
| double | CYL_total_estatic (macromolecule *thee, int types, ionlist *ions) |
| Get value for total electrostatic energy due to interaction of charged cylinder with explicit ions. More... | |
| double | CYL_total_estatic2 (macromolecule *thee, int types, ionlist *ions, double *coordsnew[]) |
| Get value for total electrostatic energy due to interaction of charged cylinder with explicit ions. More... | |
| double | CYL_point_pot (macromolecule *thee, double *point) |
| Get value for electrostatic potential due to charged cylinder at given point. More... | |
The file depends on 'ionlist.h' for interface purposes and on some APBS ('vatom.h', 'valist.h', 'vacc.h', 'vopot.h', 'vpbe.h') files to support PDB/PQR-files
In the source code ignore data members and functions within comments
* * ISIM (simulation of explicit ions in the GCE) * * * Dept. of Chemistry and Biochemistry * University of California, San Diego * * Contributing authors listed in the code documentation. * * Copyright (c) 1999-2002. The Regents of the University of California * (Regents). All Rights Reserved. * * Permission to use, copy, modify, and distribute this software and its * documentation for educational, research, and not-for-profit purposes, * without fee and without a signed licensing agreement, is hereby granted, * provided that the above copyright notice, this paragraph and the * following two paragraphs appear in all copies, modifications, and * distributions. * * IN NO EVENT SHALL REGENTS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, * SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, * ARISING OUT OF THE USE OF THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF * REGENTS HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. * * REGENTS SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A * PARTICULAR PURPOSE. THE SOFTWARE AND ACCOMPANYING DOCUMENTATION, IF * ANY, PROVIDED HEREUNDER IS PROVIDED "AS IS". REGENTS HAS NO OBLIGATION * TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR * MODIFICATIONS. * *
1.2.14 written by Dimitri van Heesch,
© 1997-2002