hamolecule.h File Reference

#include "hastring.h"
#include "hastl.h"
#include "halinalg.h"
#include "gaufile.h"
#include "haatom.h"
#include "habond.h"
#include "haatgroup.h"
#include "object3d.h"
#include "command.h"

Go to the source code of this file.

Classes
class	FeatEntry
class	AtomNode
	Axxiliary class for attaching missing atoms. More...
class	HaMolecule
	Class to define a single Molecule object. More...
class	AtomIteratorMolecule
	Atom iterator class to browse atoms of the molecule. More...
class	BondIteratorMolecule
	Bond iterator class to browse bonds of the molecule. More...
class	ResidueIteratorMolecule
	Residue iterator class to browse residues of the molecule. More...
Defines
#define	SourceNone   0
#define	SourcePDB   1
#define	SourceCalc   2
#define	FeatHelix   1
#define	FeatSheet   2
#define	FeatTurn   3
#define	SerNoFlag   0x01
#define	ResNoFlag   0x02
#define	ForEachChain_HAMOL   for(chain=GetFirstChain();chain;chain=GetNextChain())
#define	ForEachResidue_HAMOL
#define	ForEachBack_HAMOL
Typedefs
typedef list< HaAtom >	AtomsType
typedef set< HaBond, less< HaBond > >	BondsType
Enumerations
enum	ADD_ATOM_TYPE { ADD_ALL_ATOMS = 0x0, ADD_HYDROGENS = 0x1, ADD_POLAR_HYDROGENS = 0x2, ADD_HEAVY_ATOMS = 0x4 }
	Atom Types to add.
Variables
const int	START_TERM_ATOM_ID = 50000
const int	SelectFlag = 0x01
const int	DrawBondFlag = 0x0e
const int	AllAtomFlag = 0x1c
const int	HelixFlag = 0x03
const int	DrawKnotFlag = 0x7e
const int	WideKnotFlag = 0x0e
const int	WireFlag = 0x02
	Depth-cued wireframe.
const int	DashFlag = 0x04
	Dashed Depth-cued wireframe.
const int	CylinderFlag = 0x08
	Line/Cylinder representation.
const int	HydrBondFlag = 0x00
	Hydrogen bond [place keeper].
const int	NormBondFlag = 0x10
const int	DoubBondFlag = 0x20
const int	TripBondFlag = 0x40
const int	AromBondFlag = 0x80
const int	CystineFlag = 0x01
	Disulphide bonded cysteine /.
const int	StrandFlag = 0x02
	Strands representation.
const int	DashStrandFlag = 0x04
	Dash Strands representation.
const int	RibbonFlag = 0x08
	Solid Ribbon representation.
const int	TraceFlag = 0x10
	Smooth trace representation.
const int	CartoonFlag = 0x20
	Richardson protein cartoon.
const int	DotsFlag = 0x40
	Dotted trace representation.
const int	Helix3Flag = 0x01
	3,10-Helix structure
const int	Helix4Flag = 0x02
	Alpha Helix structure.
const int	Helix5Flag = 0x03
	5-Helix structure
const int	SheetFlag = 0x04
	Beta Sheet structure.
const int	TurnFlag = 0x08
	Turn Secondary structure.

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Detailed Description

Classes to define a molecule object in HARLEM.

Author:

Igor Kurnikov

Date:

1997-2002

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Define Documentation

#define ForEachResidue_HAMOL

Value: for(chain=GetFirstChain();chain;chain=GetNextChain()) \ for( group=chain->GetFirstRes(); group; group=chain->GetNextRes() )

#define ForEachBack_HAMOL

Value: for(chain=GetFirstChain();chain;chain=GetNextChain()) \ for(bptr=chain->GetFirstBackB();bptr;bptr=chain->GetNextBackB())

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