HaMolSet Class Reference

Class to describe a collection of molecules - Central Class of HARLEM. More...

#include <hamolset.h>

Inheritance diagram for HaMolSet:

List of all members.

Axxiliary classes:
typedef BondIteratorMolSet	BondIterator
typedef ResidueIteratorMolSet	ResidueIterator
Chemical(Functional) Groups:
typedef list< ChemGroup >	ChemGroupsType
int	GetNChemGroups () const
	Get total number of chemical groups.
ChemGroup *	AddBlankChemGroup (const HaString &gid="")
	Add an empty chemical groups.
bool	DeleteChemGroup (const HaString &gid)
	Delete Chemical group.
bool	DeleteChemGroupPtr (ChemGroup *grp_ptr)
	Delete Chemical Group if pointer is known.
bool	SetChemGrpSelected (const HaString &gid)
	Set Selected Atoms to a chemical group.
ChemGroup &	GetChemGroupByIdx (int index)
	Get Chemical Group by index.
ChemGroup *	GetChemGroupByID (const HaString &gid)
	Get Chemical Group by id.
ChemGroup *	GetChemGroupByAtom (const HaAtom *aptr)
	Get Chemical Group containg atom.
bool	SetStdChemGroups ()
	Set Standard Chemical Group for a molecular set.
void	RenumberGrp ()
bool	CheckUniqChemGrpID (const HaString &gid)
HaString	GetUniqChemGrpID (int buf_reg_flag)
list< ChemGroup >	ChemGroups
	Chemical Functional Groups.
VecPtr	chemg_idx
Named Atom Groups:
typedef list< AtomList >	NamedAtomListsType
AtomList *	AddAtomList (const char *id="")
	Add New Atom List with ID.
AtomList *	GetAtomListByID (const char *id)
	Get Atom List By ID.
AtomList *	SetAtomListFromSelection (const HaString &id)
	Set Atom List with id by selected atoms of the molset (create list if needed).
bool	DeleteAtomList (const HaString &gid)
	Delete Atom List with id.
bool	DeleteAtomListPtr (AtomList *alist_ptr)
	Delete Atom List if pointer is known.
list< AtomList >	NamedAtomLists
	Named Atom Lists.
Debug Control
enum	DEBUG_FLAG_PARAMS { file_reading_debug = 0x0001 }
bool	Print_info (ostream &sout, const int level)
	Print molecular set info.
int	debug_flag
Input/Output geometry from/to files
enum	MOL_SAVE_FLAG { SAVE_SELECTED = 0x0001, SAVE_AS_ONE_MOL = 0x0002, SAVE_TRANSFORMED = 0x0004 }
int	FetchFile (int format, const char *file_name)
	Load file in a given format (FormatPDB,FormatHarlem etc..).
bool	LoadHarlemFile (const char *fname)
	Load Molecules from file in HARLEM (*.HLM) format.
int	LoadAmberPrepFile (const char *fname)
	Load Molecule in AMBER PREP (*.IN) format.
int	LoadRWFMolecule (const char *fname)
	Load structure in binary Gaussian checkpoint (*.rwf, *.chk) format.
int	LoadPDBFile (const char *fname, int flag=0)
	Load molecule in PDB format (flag = 1 - NMR extension).
int	LoadMol2File (const char *fname)
	Load molecule in TRIPOS *.mol format.
int	LoadMDLFile (const char *fname)
	Load molecule in TRIPOS *.mdl format.
int	LoadXYZFile (const char *fname)
	Load molecule in XYZ format ( iat,x,y,z).
int	SavePDBFile (const char *filename)
	Save molecules into a file in PDB format.
int	SaveHarlemFile (const char *filename)
	Save molecules into a file in HARLEM format.
int	SaveXYZFile (const char *filename)
	Save molecule into a XYZ file (elem_no,x,y,z).
int	SaveXYZRadFile (const char *filename)
	Save file with lines (x,y,z, atom_radius) for MSMS input.
int	m_unique_atom_names_flag
	flag to assign unique atom names in the atoms of the molecules during reading
int	m_save_connect
	Flag to save connectivity information.
int	m_save_transform
	Flag to save transformed atom coordinates.
int	m_save_selected
	Flag to save only Selected Atoms.
HaString	m_save_mol_name
enum HaMolSet::MOL_SAVE_FLAG	save_flags
int	m_calc_bonds_flag = True
	the flag to calculate bonds from atom distance criteria
void	ProcessPDBAtom (int heta, IntPtrMap &id_at_map, HaMolecule *pMol)
Constructors and Destructors:
	HaMolSet (const HaString &new_name)
RASMOL-type Text Command Processing:
int	ExecuteCommand (CmdParser &cmd_pr)
int	ExecuteShowCommand (CmdParser &cmd_pr)
Superimpose molecules functions:
double	OverlapMol (AtomList &fmolatset, AtomList &smolatset)
	Superimpose two molecules containing atom sets fmolatset and smolatset.
double	AlignOverlapMol (AtomList &fmolatset, HaMolecule *pMol2, PtrPtrMap *fit=NULL, HaVec_double *p_trans=NULL, HaMat_double *p_rot=NULL)
	Align Sequences and Overlap two molecules containing atom sets fmolatset and smolatset, return RMS of atoms.
Molecular Structure Modifications
HaMolecule *	CreateMolecule ()
	function to create a new molecule in the set
HaMolecule *	GetFirstMolecule ()
	Get First Molecule in the set.
HaMolecule *	GetMoleculeNum (int imol)
	Get Molecule number imol (0-based).
void	DeleteAll ()
	Delete all the contents of the molecular set.
bool	DeleteMol (HaMolecule *pMol)
	Delete molecule.
bool	DeleteAtomWithRef (const char *atref)
	Delete Atom identified by reference.
bool	DeleteAtom (HaAtom *aptr)
	Delete Atom.
bool	DeleteAtoms (AtomCollection &atset)
	Delete Atoms.
int	MergeMolecules (HaMolecule *pMol1, HaMolecule *pMol2)
	Merge molecule 2 into molecule 1.
int	add_molset_copies (int nx, int ny, int nz)
int	solvate ()
	solvate the molecular set
int	place_to_orig ()
	place the molecular set to the center of origin;
HaMolecule *	CreateTransAlk (const int nunit, const HaString name="ALK")
	Create trans-alkane with the length of nunit.
HaMolecule *	CreateSurf (const int num_layers, const HaString name="GOLD")
	Create Several layers of the metal surface.
bool	Create2DMolArray (HaMolecule *pMol_ref, const double deltx, const double delty, const int nx, const int ny, const double alpha, const double tilt)
	Create two-dimensional layer of molecules.
void	DeleteExtraAtoms ()
	Delete atoms not found in residues templates.
void	AddMissingAtoms ()
	Add Missing atoms in the the structure using residue templates.
void	AddHydrogens ()
	Add hydrogens.
void	AddPolarHydrogens ()
	Add Polar hydrogens involved in hydrogen-bonding.
void	AddHydrogensHybrid ()
	Add Hydrogens using atom hybridization information.
bool	AddElectrSurf (int add_surf_below_flag, int add_surf_top_flag, int add_atom_top_flag, int add_atom_below_flag)
	Add molecular surface or a single donor/acceptor atom to the structure.
int	SetBondDist (HaAtom *aptr1, HaAtom *aptr2, double new_dist)
	Set bond distance between atoms to a new value.
int	SetAngle (HaAtom *aptr1, HaAtom *aptr2, HaAtom *aptr3, double ang_new)
	Set Valence angle (in rad).
int	SetTorsion (HaAtom *aptr1, HaAtom *aptr2, HaAtom *aptr3, HaAtom *aptr4, double tors_new)
	Set Dihedral angle (in rad).
vector< HaMolecule * >	HostMolecules
	Molecules in the molecular set.
HaString	solv_name
	Solvent to solvate molecular set.
int	solv_buffer_dist
	thickness of the solvent buffer around the solute when the molecules solvated
Molecular Structure Info
int	GetNMol () const
	Get the number of Molecules in the molecular set.
int	GetNRes () const
	Get the number of Residues in the molecular set.
int	GetNChains () const
	Get the number of chains in the molecular set.
int	GetNAtoms () const
	Get the total number of atoms in the molecule set.
int	GetNBonds () const
	Get the total number of bonds in the molecule set.
int	GetSeqNumOfAtom (const HaAtom *aptr) const
	Get a linear index of the atom in the molecular set.
double	FindClosestContact (HaAtom *atc1, HaAtom *atc2)
	Find closest Atom in the molecular Set.
HaResidue *	GetResByRef (const char *res_ref)
	get a residue by reference
HaAtom *	GetAtomByRef (const char *at_ref)
	get a single atom by reference
bool	GetAtomsByRef (const char *at_ref, AtomList &at_set)
	get a group of atoms by reference
HaMolecule *	GetMolByName (const char *mol_name)
	Get a moleculae by its name.
bool	GetMinMaxCrd (double &MinX_v, double &MinY_v, double &MinZ_v, double &MaxX_v, double &MaxY_v, double &MaxZ_v)
	Get Min and Max Coordinates of the atoms in the Molecular Set.
bool	GetMinMaxCrdSelected (double &MinX_v, double &MinY_v, double &MinZ_v, double &MaxX_v, double &MaxY_v, double &MaxZ_v)
	Get Min and Max Coordinates of selected atoms.
bool	set_min_max
	flag to indicate that Min and Max coordinates have been set
Selection functions:
void	SelectAllAtoms ()
	Select all atoms in the set.
void	UnSelectAllAtoms ()
	Unselest all atoms in the set.
void	ReverseAtomSelection ()
	Reverse atom selection, Select all unselected atoms and unselect all selected atoms.
void	SelectOnly (AtomCollection *atom_coll)
	Select Atoms of the Atom collection and Unselect other atoms.
void	SelectZone (int mask)
	Select Atoms with flags satisfying mask.
void	SelectZoneExpr (Expr *expr)
	Select Atoms satisfying expression.
void	DisplaySelectCount ()
	Print the number of selected atoms.
H-Bonds Manipulation:
int	AreHBonded (HaAtom *src, HaAtom *dst) const
	check if atoms are H-Bonded (src - H-donor and dst H-acceptor
bool	CalcHBonds (bool recalc=false)
int	m_calc_s_hbonds_flag = False
	Flag if to find H-bonds involving S-atoms.
Names of Molecules and Molecular Set
void	SetName (const char *new_name)
	Set the name of the molecular set.
const char *	GetName ()
	Get the name of the molecular set.
HaString	GetUniqueMolName (const HaString suggest_name)
	Modify a suggested name of the molecule to avoid a conflict with the existing names of the molecules in the set.
HaString	name
	the name of the molecular set
molecular surfaces manipulations
HaDisplayedSurface *	CalcMolSurface ()
	Calculate Molecular Surface.
HaDisplayedSurface *	CalcMolSurfDens ()
	Calculate Molecular Surface computing isosurface of density.
pH dependence. pKa and redox-potentials calculations:
void	SetStdResPK ()
	Set Standard pKa values for protonation and deprotonation of residues.
void	SetStdResPK_G1 ()
	Set Standard pKa values for most activily protonatable residues(HIS,HEM, terminal groups, etc).
void	CalcPKsForSelection ()
	Calc PK for residues in the selected part using interaction matricies.
int	CalcSCFPK (VecPtr &act_chem_st, HaMat_double &inter_mat)
	Calculate self-consistenly average pKs of the alt states.
void	SetAltStatesActive (int set_flag)
	Set Alternative Residue states active (or inactive) for selected residues.
bool	SetChargesForPH (double pH_val)
	Set Atomic charges for a certain pH.
bool	SetChargesForCurrentPH ()
	Set Atomic charged corresponding to a current pH.
void	SetPH (double new_ph)
	Set current pH value in the system.
double	GetPH () const
	Get current pH value in the system.
double	ph
	Current pH value in the system.
Atomic Parameters (charges. force-field symbols etc):
bool	SetStdAtomicParams (const int at_params_type)
	Set atomic parameters according to flag at_params_type.
double	CalculatePotential (double x, double y, double z)
bool	CalcDipole ()
	Calculate and print charge and dipole of selected atoms of mol set.
bool	SetVdwRadii ()
	Set atomic radii to Standard Vdw Radii.
bool	SetParseRadii ()
	Set atomic radii to PARSE radii set.
MatPoint_double_map *	GetChargeMapByName (const char *map_name)
	Get a atom-charge map by the name.
MatPoint_double_map *	CreateChargeMap (const char *map_name)
	Create an atom-charge map with a given name.
int	SetChargeMapByCurrentCharges (const char *map_name)
	Set a atom-charge name by the current atomic chagres of the molecular set.
int	SetChargesFromChargeMap (MatPoint_double_map *charge_map)
	Set atomic charges from the atom-charge map.
vector< MatPoint_double_map >	ChargeMaps
	The vector of atom-charge maps that.
Fragmentation:
HaMolSet *	GetLastFragment ()
HaMolSet *	set_fragment_selected (const char *frag_name)
list< HaMolSet * >	Fragments
Computational Modules:
HaQCMod *	GetQCMod (const bool create_module=false)
	Get Quantum Chemical module associated with the molecular set.
ETCoupl *	GetETCouplMod (const bool create_module=false)
	Get Electron Transfer computational module associated with the molecular set.
HaGaussian *	GetGaussMod (const bool create_module=false)
	Get Gaussian qchem package interaction module associated with the molecular set.
HaDalton *	GetDaltonMod (const bool create_module=false)
	Get Dalton qchem package interaction module associated with the molecular set.
ElectrostMod *	GetElectrostMod (const bool create_module=false)
	Get Continuum Electrostatic computational module associated with the molecular set.
HaInterMolMod *	GetInterMolMod (const bool create_module=false)
	Get Intermolecular interaction module associated with the molecular set.
HaMolMechMod *	GetMolMechMod (const bool create_module=false)
	Get Molecular Mechanics module associated with the molecular set.
HaScatterMod *	GetScatterMod (const bool create_module=false)
	Get the Electron Scattering module associated with the molecular set.
StmMod *	GetSTMMod (const bool create_module=false)
	Get the Electron Scattering module associated with the molecular set.
NuclAcidMod *	GetNuclAcidMod (const bool create_module=false)
	Get Nucleic Acid modeling module.
HaCompMod *	GetCompModule (const int mtype, const bool create_module=false)
	Get a computational module of a given type associated with the molecular set.
void	ResetETModule ()
	clear ET module associated with the molset
list< HaCompMod * >	CompModules
	List of Computational modulles associated with the molecular set.
Molecular Display functions:
virtual int	AnnounceGeomChange ()
	Call to update views to reflect changes in the molecular geometry.
void	RefreshAllViews (long lHint=0L)
	Refresh Molecular Views associated with the molecular set.
HaMolView *	GetActiveMolView ()
	Get Active HaMolView object associated with the MolSet.
bool	AddObject3D (Object3D *new_view_object)
	Add a new 3D object to the list.
bool	DeleteObject3D (Object3D *pobj)
	Delete 3D object from the list using the pointer.
bool	DeleteObject3D (const HaString obj_name)
	Delete 3D object from the list using its name.
void	ClearPickedAtoms ()
	Clear Picked Atoms Set.
HaMolView *	mset_pview
	A pointer to the Moleculular View object associated with the molecular set.
HaMolSetDoc *	pmsetdoc
	A pointer to the MFC Molecular Set Document associated with the molecular set.
list< Object3D * >	ViewObjects
	the list of 3D objects
AtomList	picked_atoms
StrVec	info_str
	vector of string to display on the screen
Periodical Boundary Conditions:
HaString	spacegroup
double	pbox_x
double	pbox_y
double	pbox_z
	Unit Cell sizes for periodical boundary conditions (Bohrs).
double	pbox_alpha
double	pbox_beta
double	pbox_gamma
	Unit Cell Parameters for periodical boundary conditions (radians).
Public Types
Friends
class	MolSetParDlg

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Detailed Description

Class to describe a collection of molecules - Central Class of HARLEM.

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Member Function Documentation

double HaMolSet::OverlapMol (  AtomList &  fmolatset, AtomList &  smolatset )

Superimpose two molecules containing atom sets fmolatset and smolatset. Superimpose the two structures such that chosen set of atoms Parameters: firstatset  atom group of the first molecule secatset  atom group of the second molecule corresponding to firstatset of the first molecule Returns: eps(Ang) - atom RMS deviation in superimposed structures -1.0 on error

double HaMolSet::AlignOverlapMol (  AtomList &  atset1, HaMolecule *  pMol2, PtrPtrMap *  fit = NULL, HaVec_double *  p_trans = NULL, HaMat_double *  p_rot = NULL )

Align Sequences and Overlap two molecules containing atom sets fmolatset and smolatset, return RMS of atoms. Input Parameters: atset1 - list of atoms of the molecule1 that will be superimposed by the corresponding atoms of the molecule 2 Corresponding atoms of two molecules are found using graph matching algorithm finding the best match between two molecules molecules 1 and 2 should have the same number of atoms. Return: eps - best RMS to fit atset1 by corresponding atoms of molecule 2 Optional parameters: fit - map of atom pointers of two molecules in the best fit trans,rot - translation vector and rotational matrix to superimpose molecule 2 to molecule 1

int HaMolSet::add_molset_copies (  int  nx, int  ny, int  nz )

add to the molset its copies obtained < using periodical boundary conditions

int HaMolSet::SetBondDist (  HaAtom *  aptr1, HaAtom *  aptr2, double  new_dist )

Set bond distance between atoms to a new value. Atoms moved are aptr2 and all atoms reachable from aptr2 by a graph of covalent bonds

int HaMolSet::SetAngle (  HaAtom *  aptr1, HaAtom *  aptr2, HaAtom *  aptr3, double  ang_new )

Set Valence angle (in rad). Atoms moved are aptr3 and all atoms reachable from aptr3 by a graph of covalent bonds Also moved atoms conected to aptr2 by 1/2 of ang_new

int HaMolSet::SetTorsion (  HaAtom *  aptr1, HaAtom *  aptr2, HaAtom *  aptr3, HaAtom *  aptr4, double  tors_new )

Set Dihedral angle (in rad). Atoms moved are aptr4 and all atoms reachable from aptr4 by a graph of covalent bonds

double HaMolSet::CalculatePotential (  double  x, double  y, double  z )

calculate electrostatic potential < in a point from atomic point charges and eps=10.0

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The documentation for this class was generated from the following files:

• hamolset.h
• hamolsetdoc.cpp
• command.cpp
• hamolset.cpp
• infile.cpp

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