Molecule.h File Reference

#include "common.h"
#include "NamdTypes.h"
#include "structures.h"
#include "Vector.h"
#include "UniqueSet.h"
#include "Hydrogen.h"
#include "GromacsTopFile.h"
#include "GridForceGrid.h"
#include "molfile_plugin.h"

Go to the source code of this file.

Classes
class	ObjectArena< Type >
class	ExclusionCheck
class	ResidueLookupElem
struct	go_val
struct	go_pair
struct	seg_resid
class	Molecule
	Molecule stores the structural information for the system. More...

Namespaces
	AmberParm7Reader

Macros
#define	MAX_GO_CHAINS   10
#define	MAX_RESTRICTIONS   10
#define	EXCHCK_FULL   1
#define	EXCHCK_MOD   2
#define	QMLSSMODEDIST   1
#define	QMLSSMODECOM   2
#define	QMFormatORCA   1
#define	QMFormatMOPAC   2
#define	QMFormatUSR   3
#define	QMCHRGNONE   0
#define	QMCHRGMULLIKEN   1
#define	QMCHRGCHELPG   2
#define	QMSCHEMECS   1
#define	QMSCHEMERCD   2
#define	QMSCHEMEZ1   3
#define	QMSCHEMEZ2   4
#define	QMSCHEMEZ3   5
#define	LARGEMOLTH   64

Typedefs
typedef struct go_val	GoValue
typedef struct go_pair	GoPair
typedef struct seg_resid	AtomSegResInfo

Macro Definition Documentation

EXCHCK_FULL

#define EXCHCK_FULL   1

Definition at line 86 of file Molecule.h.

Referenced by Calc_Coul_PairSer().

EXCHCK_MOD

#define EXCHCK_MOD   2

Definition at line 87 of file Molecule.h.

Referenced by Calc_Coul_PairSer().

LARGEMOLTH

#define LARGEMOLTH   64

Definition at line 143 of file Molecule.h.

Referenced by Molecule::build_molecule().

MAX_GO_CHAINS

#define MAX_GO_CHAINS   10

Copyright (c) 1995, 1996, 1997, 1998, 1999, 2000 by The Board of Trustees of the University of Illinois. All rights reserved.

Definition at line 34 of file Molecule.h.

Referenced by Molecule::get_go_cutoff(), Molecule::get_go_epsilon(), Molecule::get_go_epsilonRep(), Molecule::get_go_exp_a(), Molecule::get_go_exp_b(), Molecule::get_go_exp_rep(), Molecule::get_go_sigmaRep(), Molecule::go_restricted(), Molecule::print_go_params(), Molecule::read_go_file(), Molecule::receive_GoMolecule(), and Molecule::send_GoMolecule().

MAX_RESTRICTIONS

#define MAX_RESTRICTIONS   10

Definition at line 35 of file Molecule.h.

Referenced by Molecule::go_restricted(), Molecule::read_go_file(), Molecule::receive_GoMolecule(), and Molecule::send_GoMolecule().

QMCHRGCHELPG

#define QMCHRGCHELPG   2

Definition at line 135 of file Molecule.h.

Referenced by ComputeQMMgr::calcORCA().

QMCHRGMULLIKEN

#define QMCHRGMULLIKEN   1

Definition at line 134 of file Molecule.h.

Referenced by ComputeQMMgr::calcORCA().

QMCHRGNONE

#define QMCHRGNONE   0

Definition at line 133 of file Molecule.h.

Referenced by ComputeQMMgr::calcMOPAC(), ComputeQMMgr::calcORCA(), and ComputeQMMgr::calcUSR().

QMFormatMOPAC

#define QMFormatMOPAC   2

Definition at line 130 of file Molecule.h.

Referenced by Molecule::prepare_qm(), and ComputeQMMgr::recvPntChrg().

QMFormatORCA

#define QMFormatORCA   1

Definition at line 129 of file Molecule.h.

Referenced by Molecule::prepare_qm(), and ComputeQMMgr::recvPntChrg().

QMFormatUSR

#define QMFormatUSR   3

Definition at line 131 of file Molecule.h.

Referenced by ComputeQMMgr::recvPntChrg().

QMLSSMODECOM

#define QMLSSMODECOM   2

Definition at line 127 of file Molecule.h.

Referenced by Molecule::prepare_qm().

QMLSSMODEDIST

#define QMLSSMODEDIST   1

Definition at line 126 of file Molecule.h.

Referenced by Molecule::prepare_qm().

QMSCHEMECS

#define QMSCHEMECS   1

Definition at line 137 of file Molecule.h.

Referenced by Molecule::prepare_qm().

QMSCHEMERCD

#define QMSCHEMERCD   2

Definition at line 138 of file Molecule.h.

Referenced by Molecule::prepare_qm().

QMSCHEMEZ1

#define QMSCHEMEZ1   3

Definition at line 139 of file Molecule.h.

Referenced by Molecule::prepare_qm().

QMSCHEMEZ2

#define QMSCHEMEZ2   4

Definition at line 140 of file Molecule.h.

Referenced by Molecule::prepare_qm().

QMSCHEMEZ3

#define QMSCHEMEZ3   5

Definition at line 141 of file Molecule.h.

Referenced by Molecule::prepare_qm().

Typedef Documentation

AtomSegResInfo

typedef struct seg_resid AtomSegResInfo

GoPair

typedef struct go_pair GoPair

GoValue

typedef struct go_val GoValue