Main Page | Namespace List | Class Hierarchy | Alphabetical List | Class List | File List | Class Members | File Members

structures.h File Reference

#include "common.h"
#include <vector>

Go to the source code of this file.

Classes

struct  atom_name_info
struct  atom_constants
struct  bond
struct  angle
struct  dihedral
struct  improper
struct  crossterm
struct  drude_constants
struct  lphost
struct  aniso
struct  thole
class  Exclusion
class  TupleSignature
class  AtomSignature
struct  AtomNameIdx
struct  AtomCstInfo
struct  ExclusionSignature

Defines

#define UnknownAtom   0x00
#define HydrogenAtom   0x01
#define OxygenAtom   0x02
#define HBDonorAtom   0x04
#define HBAcceptorAtom   0x08
#define HBAntecedentAtom   0x10
#define HBHydrogenAtom   0x20
#define LonepairAtom   0x40
#define DrudeAtom   0x80
#define CMPSIGS(TUPLE)

Typedefs

typedef int Index
typedef atom_name_info AtomNameInfo
typedef atom_constants Atom
typedef bond Bond
typedef angle Angle
typedef dihedral Dihedral
typedef improper Improper
typedef crossterm Crossterm
typedef drude_constants DrudeConst
typedef lphost Lphost
typedef aniso Aniso
typedef thole Thole

Enumerations

enum  TupleSigType {
  BOND = 0, ANGLE, DIHEDRAL, IMPROPER,
  DONOR, ACCEPTOR, CROSSTERM, EXCLUSION
}

Functions

unsigned int circShift (unsigned int h, unsigned int by)


Define Documentation

#define CMPSIGS TUPLE   ) 
 

Value:

for(int i=0; i<sig.TUPLE##Cnt; i++){ \
            if(!(TUPLE##Sigs[i]==sig.TUPLE##Sigs[i])) return 0; \
        } \

Referenced by AtomSignature::operator==().

#define DrudeAtom   0x80
 

Definition at line 23 of file structures.h.

#define HBAcceptorAtom   0x08
 

Definition at line 19 of file structures.h.

#define HBAntecedentAtom   0x10
 

Definition at line 20 of file structures.h.

#define HBDonorAtom   0x04
 

Definition at line 18 of file structures.h.

#define HBHydrogenAtom   0x20
 

Definition at line 21 of file structures.h.

#define HydrogenAtom   0x01
 

Definition at line 16 of file structures.h.

#define LonepairAtom   0x40
 

Definition at line 22 of file structures.h.

#define OxygenAtom   0x02
 

Definition at line 17 of file structures.h.

#define UnknownAtom   0x00
 

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

Definition at line 15 of file structures.h.


Typedef Documentation

typedef struct angle Angle
 

Referenced by AngleElem::AngleElem(), Parameters::assign_angle_index(), Molecule::atoms_1to4(), buildAngleData(), ComputeAngles::ComputeAngles(), ComputeSelfAngles::ComputeSelfAngles(), dumpbench(), Molecule::get_angle(), AForcingAngleRestraint::Get_dU_dLambda(), Molecule::getAllAngles(), ARestraint::GetDihe(), ADiheRestraint::GetE(), AnAngleRestraint::GetE(), ABoundAngleRestraint::GetEnergy(), AnAngleRestraint::GetGrad(), ABoundAngleRestraint::GetGradient(), AngleElem::getMoleculePointers(), AnAngleRestraint::PrintInfo(), Molecule::receive_Molecule(), Molecule::send_Molecule(), ABoundDiheRestraint::SetIntervalAngle(), ABoundDiheRestraint::SetLowerAngle(), AFixedDiheRestraint::SetRefAngle(), ABoundAngleRestraint::SetRefAngle(), AFixedAngleRestraint::SetRefAngle(), AForcingDiheRestraint::SetStartAngle(), AForcingAngleRestraint::SetStartAngle(), AForcingDiheRestraint::SetStopAngle(), AForcingAngleRestraint::SetStopAngle(), and ABoundDiheRestraint::SetUpperAngle().

typedef struct aniso Aniso
 

Referenced by AnisoElem::AnisoElem(), ComputeAniso::ComputeAniso(), ComputeSelfAniso::ComputeSelfAniso(), AnisoElem::getMoleculePointers(), Molecule::receive_Molecule(), and Molecule::send_Molecule().

typedef struct atom_constants Atom
 

Referenced by AddAtom(), Parameters::assign_vdw_index(), buildAtomData(), Molecule::getAtoms(), outputCompressedFile(), Molecule::receive_Molecule(), and Molecule::send_Molecule().

typedef struct atom_name_info AtomNameInfo
 

Referenced by buildAtomData(), and Molecule::getAtomNames().

typedef struct bond Bond
 

Referenced by Parameters::assign_bond_index(), Molecule::atoms_1to4(), BondElem::BondElem(), buildBondData(), ComputeBonds::ComputeBonds(), ComputeSelfBonds::ComputeSelfBonds(), dumpbench(), Molecule::get_acceptor(), Molecule::get_bond(), Molecule::get_donor(), Molecule::getAllAcceptors(), Molecule::getAllBonds(), Molecule::getAllDonors(), BondElem::getMoleculePointers(), Molecule::receive_Molecule(), and Molecule::send_Molecule().

typedef struct crossterm Crossterm
 

Referenced by Parameters::assign_crossterm_index(), buildCrosstermData(), ComputeCrossterms::ComputeCrossterms(), ComputeSelfCrossterms::ComputeSelfCrossterms(), CrosstermElem::CrosstermElem(), Molecule::get_crossterm(), Molecule::getAllCrossterms(), CrosstermElem::getMoleculePointers(), Molecule::receive_Molecule(), and Molecule::send_Molecule().

typedef struct dihedral Dihedral
 

Referenced by Parameters::assign_dihedral_index(), Molecule::atoms_1to4(), buildDihedralData(), ComputeDihedrals::ComputeDihedrals(), ComputeSelfDihedrals::ComputeSelfDihedrals(), DihedralElem::DihedralElem(), dumpbench(), Molecule::get_dihedral(), Molecule::getAllDihedrals(), DihedralElem::getMoleculePointers(), ADiheRestraint::PrintInfo(), Molecule::receive_Molecule(), and Molecule::send_Molecule().

typedef struct drude_constants DrudeConst
 

Referenced by Molecule::receive_Molecule(), and Molecule::send_Molecule().

typedef struct improper Improper
 

Referenced by Parameters::assign_improper_index(), buildImproperData(), ComputeImpropers::ComputeImpropers(), ComputeSelfImpropers::ComputeSelfImpropers(), dumpbench(), Molecule::get_improper(), Molecule::getAllImpropers(), ImproperElem::getMoleculePointers(), ImproperElem::ImproperElem(), Molecule::receive_Molecule(), and Molecule::send_Molecule().

typedef int Index
 

Definition at line 26 of file structures.h.

Referenced by Molecule::atomvdwtype(), dumpbench(), Molecule::get_atom_from_name(), Parameters::get_table_pair_params(), Parameters::get_vdw_pair_params(), ARestraintManager::operator[](), ALambdaManager::operator[](), AGroup::operator[](), and ARestraintManager::PrintPreInfo().

typedef struct lphost Lphost
 

Referenced by Molecule::get_lphost(), Molecule::getAllLphosts(), Molecule::receive_Molecule(), and Molecule::send_Molecule().

typedef struct thole Thole
 

Referenced by ComputeSelfThole::ComputeSelfThole(), ComputeThole::ComputeThole(), TholeElem::getMoleculePointers(), and TholeElem::TholeElem().


Enumeration Type Documentation

enum TupleSigType
 

Enumeration values:
BOND 
ANGLE 
DIHEDRAL 
IMPROPER 
DONOR 
ACCEPTOR 
CROSSTERM 
EXCLUSION 

Definition at line 165 of file structures.h.

00165 {BOND=0, ANGLE, DIHEDRAL, IMPROPER, DONOR, ACCEPTOR, CROSSTERM, EXCLUSION};


Function Documentation

unsigned int circShift unsigned int  h,
unsigned int  by
[inline]
 

Definition at line 167 of file structures.h.

Referenced by ExclusionSignature::hash(), TupleSignature::hash(), and ExclSigInfo::hash().

00167                                                                {
00168   const unsigned int intBits=8*sizeof(unsigned int);
00169   by%=intBits;
00170   return (h<<by)|(h>>(intBits-by));
00171 }


Generated on Fri May 25 04:07:19 2012 for NAMD by  doxygen 1.3.9.1