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BaseMolecule Class Reference

Base class for all molecules, without display-specific information. This portion of a molecule contains the structural data, and all routines to find the structure (backbone, residues, etc). It contains the animation list as well. More...

#include <BaseMolecule.h>

Inheritance diagram for BaseMolecule:

List of all members.

Public Methods
float *	radius ()
float *	mass ()
float *	charge ()
float *	beta ()
float *	occupancy ()
float *	bondorders ()
	number of electron pairs, also fractional. More...
void	setbondorder (int atom, int bond, float order)
float	getbondorder (int atom, int bond)
int	has_structure () const
	has structure information already been loaded for this molecule? More...
void	clear_bonds (void)
	clear the entire bond list for all atoms. More...
int	count_bonds (void)
	return the number of unique bonds in the molecule. More...
	BaseMolecule (int)
	constructor takes molecule ID. More...
virtual	~BaseMolecule (void)
	destructor. More...
int	init_atoms (int n)
	Try to set the number of atoms to n. n must be positive. May be called more than once with the same n. Return success. More...
void	find_bonds_from_timestep ()
	compute molecule's bonds using distance bond search from 1st timestep. More...
void	find_unique_bonds_from_timestep ()
int	add_atom (char name, char type, int atomicnumber, char resname, int resid, const char chainid, const char segname, char insertion=(char )"", const char altloc="")
	add a new atom; return it's index. More...
int	add_bond (int, int, float, int=ATOMNORMAL)
	add a new bond from a to b; return total number of bonds added so far. More...
int	add_bond_dupcheck (int, int, float)
	add a bond after checking for duplicates. More...
void	analyze (void)
	find higher level constructs given the atom/bond information. More...
int	id (void) const
	return id number of this molecule. More...
const char *	molname () const
	return molecule name. More...
MolAtom *	atom (int n)
	return Nth atom. More...
Residue *	residue (int)
	return Nth residue. More...
Fragment *	fragment (int)
	return Nth fragment. More...
Residue *	atom_residue (int)
	return residue atom is in. More...
Fragment *	atom_fragment (int)
	return fragment atom is in. More...
void	add_volume_data (const char name, const float o, const float xa, const float ya, const float za, int x, int y, int z, float voldata)
	add volumetric data to a molecule. More...
int	num_volume_data ()
	return number of volume data sets in molecule. More...
const VolumetricData *	get_volume_data (int)
	return requested data set. More...
void	compute_volume_gradient (VolumetricData *)
	compute negated normalized volume gradient map. More...

int	find_atom_in_residue (int atomnameindex, int residue)
	find first occurance of an atom name in the residue, returns -3 not found. More...
int	find_atom_in_residue (const char *atomname, int residue)
	find first occurance of an atom name in the residue, returns -3 not found. More...

float	default_charge (char *)
	return 'default' charge, mass, occupancy value and beta value. More...
float	default_mass (char *)
	return 'default' charge, mass, occupancy value and beta value. More...
float	default_radius (char *)
	return 'default' charge, mass, occupancy value and beta value. More...
float	default_occup (void)
	return 'default' charge, mass, occupancy value and beta value. More...
float	default_beta (void)
	return 'default' charge, mass, occupancy value and beta value. More...
Public Attributes
int	nAtoms
	number of atoms. More...
int	nResidues
	number of residues. More...
int	nWaters
	number of waters. More...
int	nSegments
	number of segments. More...
int	nFragments
	total number of fragments. More...
int	nProteinFragments
	number of protein fragments. More...
int	nNucleicFragments
	number of nucleic fragments. More...
NameList< int >	atomNames
	list of unique atom names. More...
NameList< int >	atomTypes
	list of unique atom types. More...
NameList< int >	resNames
	list of unique residue names. More...
NameList< int >	chainNames
	list of unique chain names. More...
NameList< int >	segNames
	list of unique segment names. More...
NameList< int >	altlocNames
	list of alternate location names. More...
ResizeArray< Residue * >	residueList
	residue connectivity list. More...
ResizeArray< Fragment * >	fragList
	list of connected residues. More...
ResizeArray< Fragment * >	pfragList
	list of connected protein residues this is a single chain from N to C. More...
ResizeArray< int >	pfragCyclic
	flag indicating cyclic fragment. More...
ResizeArray< Fragment * >	nfragList
	ditto for nuc; from 5' to 3'. More...
ResizeArray< int >	nfragCyclic
	flag indicating cyclic fragment. More...
NameList< float * >	extra
Protected Attributes
char *	moleculename
	name of the molcule. More...
int	need_find_bonds
	whether to compute bonds from the first timestep. More...
ResizeArray< VolumetricData * >	volumeList
	array of volume data sets. More...

Detailed Description

Definition at line 57 of file BaseMolecule.h.

Constructor & Destructor Documentation

BaseMolecule::BaseMolecule ( int )

constructor takes molecule ID.

Definition at line 43 of file BaseMolecule.C.
References moleculename, nAtoms, nfragList, NULL, and pfragList.

BaseMolecule::~BaseMolecule ( void ) [virtual]

destructor.

Definition at line 62 of file BaseMolecule.C.
References NameList< float * >::data, extra, fragList, nfragList, NameList< float * >::num, ResizeArray< VolumetricData * >::num, ResizeArray< Fragment * >::num, ResizeArray< Residue * >::num, pfragList, residueList, and volumeList.

Member Function Documentation

int BaseMolecule::add_atom ( char * name,

char * type,

int atomicnumber,

char * resname,

int resid,

const char * chainid,

const char * segname,

char * insertion = (char *)"",

const char * altloc = ""

)

add a new atom; return it's index.

Definition at line 145 of file BaseMolecule.C.
References NameList< int >::add_name, MolAtom::altlocindex, altlocNames, atom, MolAtom::atomicnumber, atomNames, atomTypes, MolAtom::chainindex, chainNames, MolAtom::init, MolAtom::nameindex, nAtoms, NameList< int >::num, MolAtom::resnameindex, resNames, MolAtom::segnameindex, segNames, and MolAtom::typeindex.
Referenced by MolFilePlugin::read_structure.

int BaseMolecule::add_bond ( int ,

int ,

float ,

int = ATOMNORMAL

)

add a new bond from a to b; return total number of bonds added so far.

Definition at line 209 of file BaseMolecule.C.
References MolAtom::add_bond, atom, MolAtom::bonds, MAXBONDERRORS, nAtoms, and setbondorder.
Referenced by add_bond_dupcheck, PickModeAddBond::pick_molecule_end, MolFilePlugin::read_optional_structure, MolFilePlugin::read_structure, and vmd_bond_search.

int BaseMolecule::add_bond_dupcheck ( int ,

int ,

float

)

add a bond after checking for duplicates.

Definition at line 263 of file BaseMolecule.C.
References add_bond, atom, MolAtom::bonds, MolAtom::bondTo, and nAtoms.
Referenced by MolFilePlugin::read_structure, and vmd_bond_search.

void BaseMolecule::add_volume_data ( const char * name,

const float * o,

const float * xa,

const float * ya,

const float * za,

int x,

int y,

int z,

float * voldata

)

add volumetric data to a molecule.

Definition at line 1971 of file BaseMolecule.C.
References ResizeArray< VolumetricData * >::append, VolumetricData::compute_volume_gradient, data, VolumetricData::datamax, VolumetricData::datamin, VolumetricData::name, and volumeList.
Referenced by VMDApp::molecule_add_volumetric, and MolFilePlugin::read_volumetric.

void BaseMolecule::analyze ( void )

find higher level constructs given the atom/bond information.

Definition at line 438 of file BaseMolecule.C.
References atom, ATOMHYDROGEN, atomNames, ATOMNORMAL, MolAtom::atomType, ResizeArray< int >::clear, ResizeArray< Fragment * >::clear, ResizeArray< Residue * >::clear, count_bonds, fragList, IS_HYDROGEN, NameList< int >::name, MolAtom::nameindex, nAtoms, need_find_bonds, nfragCyclic, nfragList, nFragments, nNucleicFragments, nProteinFragments, nResidues, nSegments, ResizeArray< Fragment * >::num, nWaters, pfragCyclic, pfragList, residueList, MolAtom::residueType, RESNUCLEIC, and RESPROTEIN.
Referenced by VMDApp::molecule_load, VMDApp::molecule_reanalyze, and MolFilePlugin::read_optional_structure.

MolAtom* BaseMolecule::atom ( int n ) [inline]

return Nth atom.

Definition at line 305 of file BaseMolecule.h.
Referenced by access_tcl_atomsel, add_atom, add_bond, add_bond_dupcheck, analyze, assign_atoms, GeometryMol::atom_formatted_name, atom_fragment, atom_residue, GeometryMol::atom_short_name, atomsel_altloc, atomsel_backbonetype, atomsel_element, atomsel_fragment, atomsel_name, atomsel_residuetype, atomsel_resname, atomsel_set_altloc, atomsel_set_element, atomsel_type, contacts, AtomColor::find, find_atom_in_residue, getbondorder, getbonds, PickModeAddBond::pick_molecule_end, print_atom_info, MolFilePlugin::read_optional_structure, setbondorder, setbonds, vmd_bond_search, vmd_measure_contacts, vmd_measure_hbonds, write_stride_record, and MolFilePlugin::write_structure.

Fragment * BaseMolecule::atom_fragment ( int )

return fragment atom is in.

Definition at line 343 of file BaseMolecule.C.
References atom, fragment, Residue::fragment, NULL, residue, and MolAtom::uniq_resid.
Referenced by PickModeForceFragment::pick_molecule_move, PickModeForceFragment::pick_molecule_start, PickModeMoveFragment::rotate, and PickModeMoveFragment::translate.

Residue * BaseMolecule::atom_residue ( int )

return residue atom is in.

Definition at line 332 of file BaseMolecule.C.
References atom, NULL, residue, and MolAtom::uniq_resid.
Referenced by PickModeForceResidue::pick_molecule_move, PickModeForceResidue::pick_molecule_start, PickModeMoveResidue::rotate, and PickModeMoveResidue::translate.

float* BaseMolecule::beta ( ) [inline]

Definition at line 114 of file BaseMolecule.h.
References NameList::data.
Referenced by AtomColor::find, MolFilePlugin::read_optional_structure, MolFilePlugin::read_structure, and MolFilePlugin::write_structure.

float* BaseMolecule::bondorders ( ) [inline]

number of electron pairs, also fractional.

Definition at line 118 of file BaseMolecule.h.
References NameList::data.

float* BaseMolecule::charge ( ) [inline]

Definition at line 113 of file BaseMolecule.h.
References NameList::data.
Referenced by GeometryMol::atom_formatted_name, compute_elect_energy, VolMapCreateSlowEnergy::compute_frame, AtomColor::find, measure_dipole, MolFilePlugin::read_optional_structure, MolFilePlugin::read_structure, and MolFilePlugin::write_structure.

void BaseMolecule::clear_bonds ( void )

clear the entire bond list for all atoms.

Definition at line 426 of file BaseMolecule.C.
References MolAtom::bonds, and nAtoms.
Referenced by DrawMolecule::recalc_bonds.

void BaseMolecule::compute_volume_gradient ( VolumetricData * )

compute negated normalized volume gradient map.

int BaseMolecule::count_bonds ( void )

return the number of unique bonds in the molecule.

Definition at line 409 of file BaseMolecule.C.
References MolAtom::bonds, MolAtom::bondTo, and nAtoms.
Referenced by analyze, and DrawMolecule::recalc_bonds.

float BaseMolecule::default_beta ( void ) [inline]

return 'default' charge, mass, occupancy value and beta value.

Definition at line 333 of file BaseMolecule.h.
Referenced by MolFilePlugin::read_structure.

float BaseMolecule::default_charge ( char * )

return 'default' charge, mass, occupancy value and beta value.

Definition at line 400 of file BaseMolecule.C.
Referenced by MolFilePlugin::read_structure.

float BaseMolecule::default_mass ( char * )

return 'default' charge, mass, occupancy value and beta value.

Definition at line 376 of file BaseMolecule.C.
Referenced by MolFilePlugin::read_structure.

float BaseMolecule::default_occup ( void ) [inline]

return 'default' charge, mass, occupancy value and beta value.

Definition at line 332 of file BaseMolecule.h.
Referenced by MolFilePlugin::read_structure.

float BaseMolecule::default_radius ( char * )

return 'default' charge, mass, occupancy value and beta value.

Definition at line 353 of file BaseMolecule.C.
Referenced by MolFilePlugin::read_structure.

int BaseMolecule::find_atom_in_residue ( const char * atomname,

int residue

)

find first occurance of an atom name in the residue, returns -3 not found.

Definition at line 967 of file BaseMolecule.C.
References atomNames, find_atom_in_residue, residue, and NameList< int >::typecode.

int BaseMolecule::find_atom_in_residue ( int atomnameindex,

int residue

) [inline]

find first occurance of an atom name in the residue, returns -3 not found.

Definition at line 315 of file BaseMolecule.h.
References atom, Residue::atoms, MolAtom::nameindex, ResizeArray::num, and num.
Referenced by find_atom_in_residue.

void BaseMolecule::find_bonds_from_timestep ( ) [inline]

compute molecule's bonds using distance bond search from 1st timestep.

Definition at line 278 of file BaseMolecule.h.
References need_find_bonds.
Referenced by MolFilePlugin::read_structure.

void BaseMolecule::find_unique_bonds_from_timestep ( ) [inline]

Definition at line 279 of file BaseMolecule.h.
References need_find_bonds.
Referenced by MolFilePlugin::read_structure.

Fragment * BaseMolecule::fragment ( int )

return Nth fragment.

Definition at line 325 of file BaseMolecule.C.
References fragList.
Referenced by atom_fragment.

const VolumetricData * BaseMolecule::get_volume_data ( int )

return requested data set.

Definition at line 2004 of file BaseMolecule.C.
References id, NULL, ResizeArray< VolumetricData * >::num, and volumeList.
Referenced by atomsel_gridindex_array, atomsel_interp_volume_array, atomsel_volume_array, AtomColor::find, SaveTrajectoryFltkMenu::molchooser_activate_selection, GraphicsFltkMenu::update_molchooser, and GraphicsFltkMenu::volindex_update.

float BaseMolecule::getbondorder ( int atom,

int bond

)

Definition at line 306 of file BaseMolecule.C.
References atom, NameList< float * >::data, extra, MAXATOMBONDS, and NULL.
Referenced by access_tcl_atomsel, assign_atoms, and MolFilePlugin::write_structure.

int BaseMolecule::has_structure ( ) const [inline]

has structure information already been loaded for this molecule?

Definition at line 123 of file BaseMolecule.h.
Referenced by VMDApp::molecule_load, and MolFilePlugin::write_structure.

int BaseMolecule::id ( void ) const [inline]

return id number of this molecule.

Definition at line 300 of file BaseMolecule.h.
Referenced by GraphicsFltkMenu::act_on_command, MoleculeList::add_color_names, MoleculeList::add_molecule, MoleculeList::add_rep, GeometryMol::atom_full_name, atomsel_new, atomsel_set, atomselect, DrawMolecule::change_ts, IMDMgr::check_event, create, MoleculeList::del_molecule, AtomColor::find, find_molecule, get_nearby_atom, Molecule::get_new_frames, get_volume_data, graphics_tcl, DrawMolecule::highlighted_rep, VMDApp::imd_connected, VMDApp::imd_disconnect, imdconnect, make_tcl_atomsel, MoleculeList::make_top, VMDApp::molecule_delete_all, VMDApp::molecule_id, VMDApp::molecule_load, VMDApp::molecule_new, VMDApp::molecule_rename, molecule_tcl, VMDApp::molecule_top, molinfo_set, Molecule::next_frame, DrawMolecule::notify, PickList::pick_check, PickModeUser::pick_molecule_end, PickModeMolLabel::pick_molecule_end, PickModeAddBond::pick_molecule_end, PickModeUser::pick_molecule_start, PickModeMolLabel::pick_molecule_start, PickModeAddBond::pick_molecule_start, print_atom_info, py_write, sel_from_py, GraphicsFltkMenu::set_pbc, Tool::target, text_cmd_imd, MolBrowser::update, and Molecule::~Molecule.

int BaseMolecule::init_atoms ( int n )

Try to set the number of atoms to n. n must be positive. May be called more than once with the same n. Return success.

Definition at line 101 of file BaseMolecule.C.
References NameList< float * >::add_name, NameList< float * >::data, data, extra, nAtoms, NULL, and NameList< float * >::num.
Referenced by VMDApp::molecule_load, and MolFilePlugin::read_structure.

float* BaseMolecule::mass ( ) [inline]

Definition at line 112 of file BaseMolecule.h.
References NameList::data.
Referenced by Tool::assign_rep, center_of_mass, AtomColor::find, measure_inertia, MolFilePlugin::read_optional_structure, MolFilePlugin::read_structure, Tool::target, Tool::tug, and MolFilePlugin::write_structure.

const char* BaseMolecule::molname ( ) const [inline]

return molecule name.

Definition at line 301 of file BaseMolecule.h.
References moleculename.
Referenced by VMDApp::molecule_name, molinfo_get, and MolBrowser::update.

int BaseMolecule::num_volume_data ( )

return number of volume data sets in molecule.

Definition at line 2000 of file BaseMolecule.C.
References ResizeArray< VolumetricData * >::num, and volumeList.
Referenced by AtomColor::find, SaveTrajectoryFltkMenu::molchooser_activate_selection, VMDApp::molecule_load, VMDApp::molecule_savetrajectory, MolBrowser::update, GraphicsFltkMenu::update_molchooser, and GraphicsFltkMenu::volindex_update.

float* BaseMolecule::occupancy ( ) [inline]

Definition at line 115 of file BaseMolecule.h.
References NameList::data.
Referenced by VolMapCreateSlowEnergy::compute_frame, AtomColor::find, MolFilePlugin::read_optional_structure, MolFilePlugin::read_structure, and MolFilePlugin::write_structure.

float* BaseMolecule::radius ( ) [inline]

Definition at line 111 of file BaseMolecule.h.
References NameList::data.
Referenced by VolMapCreateSlowEnergy::compute_frame, MolFilePlugin::read_optional_structure, MolFilePlugin::read_structure, vmd_bond_search, and MolFilePlugin::write_structure.

Residue * BaseMolecule::residue ( int )

return Nth residue.

Definition at line 319 of file BaseMolecule.C.
References residueList.
Referenced by atom_fragment, atom_residue, atomsel_fragment, AtomColor::find, find_atom_in_residue, PickModeForceFragment::pick_molecule_move, PickModeForceFragment::pick_molecule_start, PickModeMoveFragment::rotate, and PickModeMoveFragment::translate.

void BaseMolecule::setbondorder ( int atom,

int bond,

float order

)

Definition at line 286 of file BaseMolecule.C.
References NameList< float * >::add_name, atom, NameList< float * >::data, extra, MAXATOMBONDS, nAtoms, and NULL.
Referenced by access_tcl_atomsel, and add_bond.

Member Data Documentation

NameList<int> BaseMolecule::altlocNames

list of alternate location names.

Definition at line 75 of file BaseMolecule.h.
Referenced by add_atom, MoleculeList::add_color_names, atomsel_altloc, atomsel_set_altloc, AtomColor::find, vmd_bond_search, and MolFilePlugin::write_structure.

NameList<int> BaseMolecule::atomNames

list of unique atom names.

Definition at line 70 of file BaseMolecule.h.
Referenced by add_atom, MoleculeList::add_color_names, analyze, GeometryMol::atom_formatted_name, GeometryMol::atom_short_name, atomsel_name, AtomColor::find, find_atom_in_residue, print_atom_info, vmd_bond_search, write_stride_record, and MolFilePlugin::write_structure.

NameList<int> BaseMolecule::atomTypes

list of unique atom types.

Definition at line 71 of file BaseMolecule.h.
Referenced by add_atom, MoleculeList::add_color_names, atomsel_type, AtomColor::find, print_atom_info, and MolFilePlugin::write_structure.

NameList<int> BaseMolecule::chainNames

list of unique chain names.

Definition at line 73 of file BaseMolecule.h.
Referenced by add_atom, MoleculeList::add_color_names, AtomColor::find, print_atom_info, and MolFilePlugin::write_structure.

NameList<float *> BaseMolecule::extra

Definition at line 107 of file BaseMolecule.h.
Referenced by VolMapCreate::calculate_max_radius, VolMapCreateCoulombPotential::compute_frame, VolMapCreateFastEnergy::compute_frame, VolMapCreateDistance::compute_frame, VolMapCreateOccupancy::compute_frame, VolMapCreateDensity::compute_frame, getbondorder, init_atoms, minmax, sasa, setbondorder, vmd_measure_minmax, vmd_measure_sasa, and ~BaseMolecule.

ResizeArray<Fragment *> BaseMolecule::fragList

list of connected residues.

Definition at line 78 of file BaseMolecule.h.
Referenced by analyze, fragment, and ~BaseMolecule.

char* BaseMolecule::moleculename [protected]

name of the molcule.

Definition at line 255 of file BaseMolecule.h.
Referenced by BaseMolecule, Molecule::Molecule, molname, Molecule::rename, and Molecule::~Molecule.

int BaseMolecule::nAtoms

number of atoms.

Definition at line 62 of file BaseMolecule.h.
Referenced by access_tcl_atomsel, add_atom, add_bond, add_bond_dupcheck, analyze, DrawMolItem::atom_displayed, DrawMolecule::atom_displayed, atomselect, BaseMolecule, AtomSel::change, IMDMgr::check_event, check_mol, GeometryMol::check_mol, clear_bonds, cmd_gettimestep, cmd_rawtimestep, CoorPluginData::CoorPluginData, count_bonds, DrawMolItem::do_color_rgb_changed, DrawMolItem::DrawMolItem, DrawMolecule::duplicate_frame, AtomColor::find, get, Molecule::get_new_frames, getbonds, init_atoms, label_add, VMDApp::molecule_load, VMDApp::molecule_numatoms, VMDApp::molecule_savetrajectory, molinfo_get, print_atom_info, MolFilePlugin::read_optional_structure, PickModeMoveMolecule::rotate, sel_from_py, set, setbondorder, setbonds, PickModeMoveMolecule::translate, MolBrowser::update, vmd_bond_search, write_stride_record, and MolFilePlugin::write_structure.

int BaseMolecule::need_find_bonds [protected]

whether to compute bonds from the first timestep.

Definition at line 256 of file BaseMolecule.h.
Referenced by analyze, DrawMolecule::append_frame, DrawMolecule::DrawMolecule, find_bonds_from_timestep, and find_unique_bonds_from_timestep.

ResizeArray<int> BaseMolecule::nfragCyclic

flag indicating cyclic fragment.

Definition at line 90 of file BaseMolecule.h.
Referenced by analyze.

ResizeArray<Fragment *> BaseMolecule::nfragList

ditto for nuc; from 5' to 3'.

Definition at line 89 of file BaseMolecule.h.
Referenced by analyze, BaseMolecule, and ~BaseMolecule.

int BaseMolecule::nFragments

total number of fragments.

Definition at line 66 of file BaseMolecule.h.
Referenced by analyze.

int BaseMolecule::nNucleicFragments

number of nucleic fragments.

Definition at line 68 of file BaseMolecule.h.
Referenced by analyze.

int BaseMolecule::nProteinFragments

number of protein fragments.

Definition at line 67 of file BaseMolecule.h.
Referenced by analyze.

int BaseMolecule::nResidues

number of residues.

Definition at line 63 of file BaseMolecule.h.
Referenced by analyze.

int BaseMolecule::nSegments

number of segments.

Definition at line 65 of file BaseMolecule.h.
Referenced by analyze.

int BaseMolecule::nWaters

number of waters.

Definition at line 64 of file BaseMolecule.h.
Referenced by analyze.

ResizeArray<int> BaseMolecule::pfragCyclic

flag indicating cyclic fragment.

Definition at line 82 of file BaseMolecule.h.
Referenced by analyze.

ResizeArray<Fragment *> BaseMolecule::pfragList

list of connected protein residues this is a single chain from N to C.

Definition at line 80 of file BaseMolecule.h.
Referenced by analyze, BaseMolecule, and ~BaseMolecule.

ResizeArray<Residue *> BaseMolecule::residueList

residue connectivity list.

Definition at line 77 of file BaseMolecule.h.
Referenced by analyze, read_stride_record, residue, and ~BaseMolecule.

NameList<int> BaseMolecule::resNames

list of unique residue names.

Definition at line 72 of file BaseMolecule.h.
Referenced by add_atom, MoleculeList::add_color_names, GeometryMol::atom_formatted_name, GeometryMol::atom_short_name, atomsel_resname, AtomColor::find, print_atom_info, write_stride_record, and MolFilePlugin::write_structure.

NameList<int> BaseMolecule::segNames

list of unique segment names.

Definition at line 74 of file BaseMolecule.h.
Referenced by add_atom, MoleculeList::add_color_names, AtomColor::find, print_atom_info, and MolFilePlugin::write_structure.

ResizeArray<VolumetricData *> BaseMolecule::volumeList [protected]

array of volume data sets.

Definition at line 346 of file BaseMolecule.h.
Referenced by add_volume_data, DrawMolecule::cov, get_volume_data, num_volume_data, DrawMolecule::scale_factor, and ~BaseMolecule.

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

Generated on Thu Jul 24 01:27:58 2008 for VMD (current) by

BaseMolecule Class Reference

Public Methods

Public Attributes

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation