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
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	CMPSIGS(TUPLE)
Typedefs
typedef unsigned short	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
Enumerations
enum	TupleSigType {   BOND = 0, ANGLE, DIHEDRAL, IMPROPER,   DONOR, ACCEPTOR, CROSSTERM, EXCLUSION }

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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 HBAcceptorAtom   0x08

Definition at line 20 of file structures.h.

#define HBAntecedentAtom   0x10

Definition at line 21 of file structures.h.

#define HBDonorAtom   0x04

Definition at line 19 of file structures.h.

#define HBHydrogenAtom   0x20

Definition at line 22 of file structures.h.

#define HydrogenAtom   0x01

Definition at line 17 of file structures.h.

#define LonepairAtom   0x40

Definition at line 23 of file structures.h.

#define OxygenAtom   0x02

Definition at line 18 of file structures.h.

#define UnknownAtom   0x00

Definition at line 16 of file structures.h.

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Typedef Documentation

typedef struct angle Angle

Referenced by AngleElem::AngleElem(), Parameters::assign_angle_index(), Molecule::build_extra_bonds(), ComputeAngles::ComputeAngles(), ComputeSelfAngles::ComputeSelfAngles(), dumpbench(), Molecule::get_angle(), AForcingAngleRestraint::Get_dU_dLambda(), getAngleData(), ARestraint::GetDihe(), ADiheRestraint::GetE(), AnAngleRestraint::GetE(), ABoundAngleRestraint::GetEnergy(), getExtraBonds(), AnAngleRestraint::GetGrad(), ABoundAngleRestraint::GetGradient(), AngleElem::getMoleculePointers(), AnAngleRestraint::PrintInfo(), Molecule::read_parm(), 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 atom_constants Atom

Referenced by AddAtom(), Parameters::assign_vdw_index(), AtomsDisInfo::AtomsDisInfo(), Molecule::getAtoms(), Molecule::read_parm(), Molecule::receive_Molecule(), AtomsDisInfo::recvStaticInfo(), SELF(), and Molecule::send_Molecule().

typedef struct atom_name_info AtomNameInfo

Referenced by Molecule::read_parm().

typedef struct bond Bond

Referenced by Parameters::assign_bond_index(), BondElem::BondElem(), Molecule::build_extra_bonds(), ComputeBonds::ComputeBonds(), ComputeSelfBonds::ComputeSelfBonds(), dumpbench(), Molecule::get_acceptor(), Molecule::get_bond(), Molecule::get_donor(), getAcceptorData(), getBondData(), getDonorData(), getExtraBonds(), BondElem::getMoleculePointers(), Molecule::print_bonds(), Molecule::read_parm(), Molecule::receive_Molecule(), and Molecule::send_Molecule().

typedef struct crossterm Crossterm

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

typedef struct dihedral Dihedral

Referenced by Parameters::assign_dihedral_index(), Molecule::build_extra_bonds(), ComputeDihedrals::ComputeDihedrals(), ComputeSelfDihedrals::ComputeSelfDihedrals(), DihedralElem::DihedralElem(), dumpbench(), Molecule::get_dihedral(), getDihedralData(), getExtraBonds(), DihedralElem::getMoleculePointers(), ADiheRestraint::PrintInfo(), Molecule::read_parm(), Molecule::receive_Molecule(), and Molecule::send_Molecule().

typedef struct improper Improper

Referenced by Parameters::assign_improper_index(), Molecule::build_extra_bonds(), ComputeImpropers::ComputeImpropers(), ComputeSelfImpropers::ComputeSelfImpropers(), dumpbench(), Molecule::get_improper(), getExtraBonds(), getImproperData(), ImproperElem::getMoleculePointers(), ImproperElem::ImproperElem(), Molecule::receive_Molecule(), and Molecule::send_Molecule().

typedef unsigned short Index

Definition at line 26 of file structures.h. Referenced by Molecule::atomvdwtype(), dumpbench(), Molecule::get_atom_from_name(), Parameters::get_vdw_pair_params(), ARestraintManager::operator[](), ALambdaManager::operator[](), AGroup::operator[](), ARestraintManager::PrintPreInfo(), Molecule::receive_Molecule(), and Molecule::send_Molecule().

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Enumeration Type Documentation

enum TupleSigType

Enumeration values: BOND  ANGLE  DIHEDRAL  IMPROPER  DONOR  ACCEPTOR  CROSSTERM  EXCLUSION  Definition at line 123 of file structures.h. {BOND=0, ANGLE, DIHEDRAL, IMPROPER, DONOR, ACCEPTOR, CROSSTERM, EXCLUSION};

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