APBS 3.0.0
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valist.c File Reference

Class Valist methods. More...

#include "valist.h"
Include dependency graph for valist.c:

Go to the source code of this file.

Functions

VPUBLIC double Valist_getCenterX (Valist *thee)
 Get x-coordinate of molecule center.
 
VPUBLIC double Valist_getCenterY (Valist *thee)
 Get y-coordinate of molecule center.
 
VPUBLIC double Valist_getCenterZ (Valist *thee)
 Get z-coordinate of molecule center.
 
VPUBLIC VatomValist_getAtomList (Valist *thee)
 Get actual array of atom objects from the list.
 
VPUBLIC int Valist_getNumberAtoms (Valist *thee)
 Get number of atoms in the list.
 
VPUBLIC VatomValist_getAtom (Valist *thee, int i)
 Get pointer to particular atom in list.
 
VPUBLIC unsigned long int Valist_memChk (Valist *thee)
 Get total memory allocated for this object and its members.
 
VPUBLIC ValistValist_ctor ()
 Construct the atom list object.
 
VPUBLIC Vrc_Codes Valist_ctor2 (Valist *thee)
 FORTRAN stub to construct the atom list object.
 
VPUBLIC void Valist_dtor (Valist **thee)
 Destroys atom list object.
 
VPUBLIC void Valist_dtor2 (Valist *thee)
 FORTRAN stub to destroy atom list object.
 
VPRIVATE Vrc_Codes Valist_readPDBSerial (Valist *thee, Vio *sock, int *serial)
 
VPRIVATE Vrc_Codes Valist_readPDBAtomName (Valist *thee, Vio *sock, char atomName[VMAX_ARGLEN])
 
VPRIVATE Vrc_Codes Valist_readPDBResidueName (Valist *thee, Vio *sock, char resName[VMAX_ARGLEN])
 
VPRIVATE Vrc_Codes Valist_readPDBResidueNumber (Valist *thee, Vio *sock, int *resSeq)
 
VPRIVATE Vrc_Codes Valist_readPDBAtomCoord (Valist *thee, Vio *sock, double *coord)
 
VPRIVATE Vrc_Codes Valist_readPDBChargeRadius (Valist *thee, Vio *sock, double *charge, double *radius)
 
VPRIVATE Vrc_Codes Valist_readPDB_throughXYZ (Valist *thee, Vio *sock, int *serial, char atomName[VMAX_ARGLEN], char resName[VMAX_ARGLEN], int *resSeq, double *x, double *y, double *z)
 
VPRIVATE VatomValist_getAtomStorage (Valist *thee, Vatom **plist, int *pnlist, int *pnatoms)
 
VPRIVATE Vrc_Codes Valist_setAtomArray (Valist *thee, Vatom **plist, int nlist, int natoms)
 
VPUBLIC Vrc_Codes Valist_readPDB (Valist *thee, Vparam *param, Vio *sock)
 Fill atom list with information from a PDB file.
 
VPUBLIC Vrc_Codes Valist_readPQR (Valist *thee, Vparam *params, Vio *sock)
 Fill atom list with information from a PQR file.
 
VPUBLIC Vrc_Codes Valist_readXML (Valist *thee, Vparam *params, Vio *sock)
 Fill atom list with information from an XML file.
 
VPUBLIC Vrc_Codes Valist_getStatistics (Valist *thee)
 Load up Valist with various statistics.
 

Variables

VPRIVATE char * Valist_whiteChars = " \t\r\n"
 
VPRIVATE char * Valist_commChars = "#%"
 
VPRIVATE char * Valist_xmlwhiteChars = " \t\r\n<>"
 

Detailed Description

Class Valist methods.

Author
Nathan Baker
Version
$Id$
Attention
*
* 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) 2010-2020 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) 2002-2020, 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 valist.c.

Function Documentation

◆ Valist_getAtomStorage()

VPRIVATE Vatom * Valist_getAtomStorage ( Valist * thee,
Vatom ** plist,
int * pnlist,
int * pnatoms )

Definition at line 424 of file valist.c.

◆ Valist_readPDB_throughXYZ()

VPRIVATE Vrc_Codes Valist_readPDB_throughXYZ ( Valist * thee,
Vio * sock,
int * serial,
char atomName[VMAX_ARGLEN],
char resName[VMAX_ARGLEN],
int * resSeq,
double * x,
double * y,
double * z )

Definition at line 344 of file valist.c.

◆ Valist_readPDBAtomCoord()

VPRIVATE Vrc_Codes Valist_readPDBAtomCoord ( Valist * thee,
Vio * sock,
double * coord )

Definition at line 298 of file valist.c.

◆ Valist_readPDBAtomName()

VPRIVATE Vrc_Codes Valist_readPDBAtomName ( Valist * thee,
Vio * sock,
char atomName[VMAX_ARGLEN] )

Definition at line 206 of file valist.c.

◆ Valist_readPDBChargeRadius()

VPRIVATE Vrc_Codes Valist_readPDBChargeRadius ( Valist * thee,
Vio * sock,
double * charge,
double * radius )

Definition at line 316 of file valist.c.

◆ Valist_readPDBResidueName()

VPRIVATE Vrc_Codes Valist_readPDBResidueName ( Valist * thee,
Vio * sock,
char resName[VMAX_ARGLEN] )

Definition at line 224 of file valist.c.

◆ Valist_readPDBResidueNumber()

VPRIVATE Vrc_Codes Valist_readPDBResidueNumber ( Valist * thee,
Vio * sock,
int * resSeq )

Definition at line 242 of file valist.c.

◆ Valist_readPDBSerial()

VPRIVATE Vrc_Codes Valist_readPDBSerial ( Valist * thee,
Vio * sock,
int * serial )

Definition at line 186 of file valist.c.

◆ Valist_setAtomArray()

VPRIVATE Vrc_Codes Valist_setAtomArray ( Valist * thee,
Vatom ** plist,
int nlist,
int natoms )

Definition at line 480 of file valist.c.

Variable Documentation

◆ Valist_commChars

VPRIVATE char* Valist_commChars = "#%"

Definition at line 61 of file valist.c.

◆ Valist_whiteChars

VPRIVATE char* Valist_whiteChars = " \t\r\n"

Definition at line 60 of file valist.c.

◆ Valist_xmlwhiteChars

VPRIVATE char* Valist_xmlwhiteChars = " \t\r\n<>"

Definition at line 62 of file valist.c.