hamolset.h File Reference

#include "hastl.h"
#include "command.h"
#include "haatgroup.h"
#include "object3d.h"

Go to the source code of this file.

Classes
class	HaMolSet
	Class to describe a collection of molecules - Central Class of HARLEM. More...
class	AtomIteratorMolSet
	Atom iterator class to browse atoms of the molecular set. More...
class	ResidueIteratorMolSet
	Residue iterator class to browse residues of the molecular set. More...
class	ChemGroupIterator
	Iterator class to browse Chemical Groups of the molecular set. More...
class	AtomListIteratorMolSet
	Iterator class to browse Named Atom lists of the molecular set. More...
class	BondIteratorMolSet
	Bond iterator class to browse bonds of the molecular set. More...
class	HBondIteratorMolSet
	Bond iterator class to browse Hydrogen Bonds of the molecular set. More...
class	AtomIteratorMolSet_const
	Const Atom iterator class to browse atoms of the molecular set. More...
Defines
#define	HAMOLSET_H
#define	ForEachMolInSet   for( mol_itr=HostMolecules.begin(); mol_itr != HostMolecules.end(); mol_itr++)
#define	ForEachResidueInSet
#define	ForEachChainInSet
#define	ForEachChainInMolInSet   for( chain= (*mol_itr)->GetFirstChain();chain; chain= (*mol_itr)->GetNextChain())
Typedefs
typedef vector< HaMolecule * >	MoleculesType
Enumerations
enum	AtomParams {   BACKBONE_CHRG = 0x0001, PROT_CHARGED_GROUPS_CHRG = 0x0002, ZERO_CHRG = 0x00010, AMBER_ALL_ATOM_CHRGS = 0x00020,   AMBER_ALL_ATOM_FF_SYMBOLS = 0x0100, AMBER_ALL_ATOM_MASSES = 0x0200, ATOM_MASSES_ELEMENT = 0x400, ATOM_HBOND_DA_STATUS = 0x800 }
	constants to specify different types of atom parameters to set More...
Functions
HaMolSet *	GetCurMolSet ()
Variables
list< HaAtom >::const_iterator	aitrm
MoleculesType::const_iterator	mol_itr
const HaMolSet *	pmset
HaMolSet *	CurMolSet

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Detailed Description

Class to define set of molecules in HARLEM and accompaniing iterator classes

Author:

Igor Kurnikov

Date:

1999-2002

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Define Documentation

#define ForEachResidueInSet

Value: for( mol_itr=HostMolecules.begin(); mol_itr != HostMolecules.end(); mol_itr++) \ for( chain= (*mol_itr)->GetFirstChain();chain; chain= (*mol_itr)->GetNextChain()) \ for( group=chain->GetFirstRes(); group; group=chain->GetNextRes() )

#define ForEachChainInSet

Value: for( mol_itr=HostMolecules.begin(); mol_itr != HostMolecules.end(); mol_itr++) \ for( chain= (*mol_itr)->GetFirstChain();chain; chain= (*mol_itr)->GetNextChain())

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Enumeration Type Documentation

enum AtomParams

constants to specify different types of atom parameters to set Enumeration values: BACKBONE_CHRG  Set backbone charges. PROT_CHARGED_GROUPS_CHRG  Set charged residues chareges. ZERO_CHRG  Set all charges zero. AMBER_ALL_ATOM_CHRGS  Set All Atom Amber Force field charges. AMBER_ALL_ATOM_FF_SYMBOLS  Set All Atom Amber Force field atom symbols. AMBER_ALL_ATOM_MASSES  Set All Atom Amber Force fieldAtomic Masses. ATOM_MASSES_ELEMENT  Set Atomic Masses corresponding to elements. ATOM_HBOND_DA_STATUS  Set H-Bond Donor/Acceptor status for atoms.

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