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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:

DrawMolecule Molecule List of all members.

Public Types

enum  dataset_flag {
  NODATA = 0x0000, INSERTION = 0x0001, OCCUPANCY = 0x0002, BFACTOR = 0x0004,
  MASS = 0x0008, CHARGE = 0x0010, RADIUS = 0x0020, ALTLOC = 0x0040,
  ATOMICNUMBER = 0x0080, BONDS = 0x0100, BONDORDERS = 0x0200, ANGLES = 0x0400,
  CTERMS = 0x0800, BONDTYPES = 0x1000, ANGLETYPES = 0x2000
}
 flags indicating what data was loaded or user-specified vs. guessed. More...


Public Methods

void set_dataset_flag (int flag)
void unset_dataset_flag (int flag)
int test_dataset_flag (int flag)
float * radius ()
 various standard per-atom fields. More...

float * mass ()
float * charge ()
float * beta ()
float * occupancy ()
void set_radii_changed ()
void get_radii_minmax (float &min, float &max)
float * bondorders ()
 number of electron pairs, also fractional. More...

void setbondorder (int atom, int bond, float order)
float getbondorder (int atom, int bond)
int * bondtypes ()
 per atom/bond bond type list. More...

void setbondtype (int atom, int bond, int type)
 set new bond type. More...

int getbondtype (int atom, int bond)
 quest bond type. More...

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, 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, int)
 add a bond after checking for duplicates. More...

void clear_angles (void)
 clear list of angles and types. More...

int num_angles ()
 count angle list entries. More...

int add_angle (int a, int b, int c, int type=-1)
 add an angle definition to existing list with optional angletype. checks for duplicates and returns angle index number. More...

int set_angletype (int a, int type)
 set new angle type. More...

int get_angletype (int a)
 query angle type. More...

void clear_dihedrals (void)
 clear list of dihedrals and types. More...

int num_dihedrals ()
 count dihedral list entries. More...

int add_dihedral (int a, int b, int c, int d, int type=-1)
 append a dihedral definition to existing list with optional dihedraltype. checks for duplicates. return dihedral index number. More...

int set_dihedraltype (int d, int type)
 set new dihedral type. return type index number. More...

int get_dihedraltype (int d)
 query dihedral type for number. More...

void clear_impropers (void)
 clear list of impropers and types. More...

int num_impropers ()
 count improper list entries. More...

int add_improper (int a, int b, int c, int d, int type=-1)
 append a improper definition to existing list with optional impropertype. checks for duplicates. return improper index number. More...

int set_impropertype (int i, int type)
 set new improper type. returns type index number. More...

int get_impropertype (int i)
 query improper type for number;. More...

void clear_cterms ()
 clear list of improper definitions. More...

int num_cterms ()
 count number of crossterm list entries. More...

void add_cterm (int a, int b, int c, int d, int e, int f, int g, int h)
 add cross term definition. 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...

ResizeArray< int > angles
 list of angles. More...

ResizeArray< int > dihedrals
 list of dihedrals. More...

ResizeArray< int > impropers
 list of impropers. More...

ResizeArray< int > cterms
 list of cross-terms. More...

NameList< float * > extraflt
 optional floating point data. More...

NameList< int * > extraint
 optional integer data. More...

ResizeArray< int > angleTypes
 type of angle. More...

ResizeArray< int > dihedralTypes
 type of dihedral. More...

ResizeArray< int > improperTypes
 type of improper. More...

NameList< int > bondTypeNames
 list of unique bond type names. More...

NameList< int > angleTypeNames
 list of unique angle type names. More...

NameList< int > dihedralTypeNames
 list of unique dihedral type names. More...

NameList< int > improperTypeNames
 list of unique improper type names. More...

QMData * qm_data
int datasetflags
int radii_minmax_need_update
 methods for querying the min/max atom radii, used by the the QuickSurf representation. More...

float radii_min
float radii_max

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

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.

Definition at line 57 of file BaseMolecule.h.

Member Enumeration Documentation

enum BaseMolecule::dataset_flag
 

flags indicating what data was loaded or user-specified vs. guessed.

Enumeration values:
NODATA 
INSERTION 
OCCUPANCY 
BFACTOR 
MASS 
CHARGE 
RADIUS 
ALTLOC 
ATOMICNUMBER 
BONDS 
BONDORDERS 
ANGLES 
CTERMS 
BONDTYPES 
ANGLETYPES 

Definition at line 132 of file BaseMolecule.h.

Constructor & Destructor Documentation

BaseMolecule::BaseMolecule (  int    ) 
 

constructor takes molecule ID.

Definition at line 48 of file BaseMolecule.C.

References datasetflags, moleculename, nAtoms, nfragList, NODATA, NULL, pfragList, qm_data, radii_max, radii_min, and radii_minmax_need_update.

BaseMolecule::~BaseMolecule (  void    )  [virtual]
 

destructor.

Definition at line 72 of file BaseMolecule.C.

References NameList< int * >::data, NameList< float * >::data, extraflt, extraint, fragList, nfragList, NameList< int * >::num, NameList< float * >::num, ResizeArray< VolumetricData * >::num, ResizeArray< Fragment * >::num, ResizeArray< Residue * >::num, pfragList, qm_data, residueList, and volumeList.

Member Function Documentation

int BaseMolecule::add_angle (  int    a,
int    b,
int    c,
int    type = -1
) 
 

add an angle definition to existing list with optional angletype. checks for duplicates and returns angle index number.

Definition at line 319 of file BaseMolecule.C.

References angles, ResizeArray< int >::append, num_angles, and set_angletype.

Referenced by molinfo_set, MolFilePlugin::read_optional_structure, and MolFilePlugin::read_structure.

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 176 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 VMDApp::molecule_new, and MolFilePlugin::read_structure.

int BaseMolecule::add_bond (  int   ,
int   ,
float   ,
int   ,
int    = ATOMNORMAL
) 
 

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

Definition at line 240 of file BaseMolecule.C.

References MolAtom::add_bond, atom, MolAtom::bonds, MAXBONDERRORS, nAtoms, setbondorder, and setbondtype.

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   ,
int   
) 
 

add a bond after checking for duplicates.

Definition at line 298 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_cterm (  int    a,
int    b,
int    c,
int    d,
int    e,
int    f,
int    g,
int    h
)  [inline]
 

add cross term definition.

Definition at line 437 of file BaseMolecule.h.

References ResizeArray::append.

Referenced by MolFilePlugin::read_optional_structure, and MolFilePlugin::read_structure.

int BaseMolecule::add_dihedral (  int    a,
int    b,
int    c,
int    d,
int    type = -1
) 
 

append a dihedral definition to existing list with optional dihedraltype. checks for duplicates. return dihedral index number.

Definition at line 363 of file BaseMolecule.C.

References ResizeArray< int >::append, dihedrals, num_dihedrals, and set_dihedraltype.

Referenced by molinfo_set, MolFilePlugin::read_optional_structure, and MolFilePlugin::read_structure.

int BaseMolecule::add_improper (  int    a,
int    b,
int    c,
int    d,
int    type = -1
) 
 

append a improper definition to existing list with optional impropertype. checks for duplicates. return improper index number.

Definition at line 407 of file BaseMolecule.C.

References ResizeArray< int >::append, impropers, num_impropers, and set_impropertype.

Referenced by molinfo_set, MolFilePlugin::read_optional_structure, and MolFilePlugin::read_structure.

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 2209 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 638 of file BaseMolecule.C.

References angleTypeNames, atom, ATOMHYDROGEN, atomNames, ATOMNORMAL, MolAtom::atomType, bondTypeNames, ResizeArray< int >::clear, ResizeArray< Fragment * >::clear, ResizeArray< Residue * >::clear, count_bonds, dihedralTypeNames, fragList, improperTypeNames, IS_HYDROGEN, NameList< int >::name, MolAtom::nameindex, nAtoms, need_find_bonds, nfragCyclic, nfragList, nFragments, nNucleicFragments, nProteinFragments, nResidues, nSegments, NULL, ResizeArray< Fragment * >::num, NameList< int >::num, num_angles, num_cterms, num_dihedrals, num_impropers, 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 455 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_backbonetype, atomsel_name, atomsel_residuetype, atomsel_type, contacts, QMData::create_unique_basis, AtomColor::find, find_atom_in_residue, getbondorder, getbonds, getbondtype, QMData::init_electrons, PickModeAddBond::pick_molecule_end, print_atom_info, MolFilePlugin::read_optional_structure, setbondorder, setbonds, setbondtype, 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 542 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 531 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 164 of file BaseMolecule.h.

References NameList::data.

Referenced by GeometryMol::atom_formatted_name, AtomColor::find, VMDApp::molecule_new, MolFilePlugin::read_optional_structure, MolFilePlugin::read_structure, and MolFilePlugin::write_structure.

float* BaseMolecule::bondorders (    )  [inline]
 

number of electron pairs, also fractional.

Definition at line 199 of file BaseMolecule.h.

References NameList::data.

int* BaseMolecule::bondtypes (    )  [inline]
 

per atom/bond bond type list.

Definition at line 204 of file BaseMolecule.h.

References NameList::data.

float* BaseMolecule::charge (    )  [inline]
 

Definition at line 163 of file BaseMolecule.h.

References NameList::data.

Referenced by GeometryMol::atom_formatted_name, compute_elect_energy, AtomColor::find, measure_dipole, VMDApp::molecule_new, MolFilePlugin::read_optional_structure, MolFilePlugin::read_structure, and MolFilePlugin::write_structure.

void BaseMolecule::clear_angles (  void    )  [inline]
 

clear list of angles and types.

Definition at line 384 of file BaseMolecule.h.

References ResizeArray::clear.

Referenced by molinfo_set, MolFilePlugin::read_optional_structure, and MolFilePlugin::read_structure.

void BaseMolecule::clear_bonds (  void    ) 
 

clear the entire bond list for all atoms.

Definition at line 626 of file BaseMolecule.C.

References MolAtom::bonds, and nAtoms.

Referenced by DrawMolecule::recalc_bonds.

void BaseMolecule::clear_cterms (    )  [inline]
 

clear list of improper definitions.

Definition at line 431 of file BaseMolecule.h.

References ResizeArray::clear.

void BaseMolecule::clear_dihedrals (  void    )  [inline]
 

clear list of dihedrals and types.

Definition at line 400 of file BaseMolecule.h.

References ResizeArray::clear.

Referenced by molinfo_set, MolFilePlugin::read_optional_structure, and MolFilePlugin::read_structure.

void BaseMolecule::clear_impropers (  void    )  [inline]
 

clear list of impropers and types.

Definition at line 416 of file BaseMolecule.h.

References ResizeArray::clear.

Referenced by molinfo_set, MolFilePlugin::read_optional_structure, and MolFilePlugin::read_structure.

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 608 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 483 of file BaseMolecule.h.

Referenced by VMDApp::molecule_new, and MolFilePlugin::read_structure.

float BaseMolecule::default_charge (  char *    ) 
 

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

Definition at line 599 of file BaseMolecule.C.

Referenced by VMDApp::molecule_new, and MolFilePlugin::read_structure.

float BaseMolecule::default_mass (  char *    ) 
 

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

Definition at line 575 of file BaseMolecule.C.

Referenced by VMDApp::molecule_new, and MolFilePlugin::read_structure.

float BaseMolecule::default_occup (  void    )  [inline]
 

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

Definition at line 482 of file BaseMolecule.h.

Referenced by VMDApp::molecule_new, and MolFilePlugin::read_structure.

float BaseMolecule::default_radius (  char *    ) 
 

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

Definition at line 552 of file BaseMolecule.C.

Referenced by VMDApp::molecule_new, and 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 1179 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 465 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 368 of file BaseMolecule.h.

References need_find_bonds.

Referenced by MolFilePlugin::read_structure.

void BaseMolecule::find_unique_bonds_from_timestep (    )  [inline]
 

Definition at line 369 of file BaseMolecule.h.

References need_find_bonds.

Referenced by MolFilePlugin::read_structure.

Fragment * BaseMolecule::fragment (  int    ) 
 

return Nth fragment.

Definition at line 524 of file BaseMolecule.C.

References fragList.

Referenced by atom_fragment.

int BaseMolecule::get_angletype (  int    a ) 
 

query angle type.

Definition at line 354 of file BaseMolecule.C.

References angleTypes, and ResizeArray< int >::num.

Referenced by molinfo_get, and MolFilePlugin::write_structure.

int BaseMolecule::get_dihedraltype (  int    d ) 
 

query dihedral type for number.

Definition at line 399 of file BaseMolecule.C.

References dihedralTypes, and ResizeArray< int >::num.

Referenced by molinfo_get, and MolFilePlugin::write_structure.

int BaseMolecule::get_impropertype (  int    i ) 
 

query improper type for number;.

Definition at line 443 of file BaseMolecule.C.

References improperTypes, and ResizeArray< int >::num.

Referenced by molinfo_get, and MolFilePlugin::write_structure.

void BaseMolecule::get_radii_minmax (  float &    min,
float &    max
)  [inline]
 

Definition at line 174 of file BaseMolecule.h.

References NameList::data, minmax_1fv_aligned, nAtoms, NULL, radii_max, radii_min, and radii_minmax_need_update.

Referenced by QuickSurf::calc_surf.

const VolumetricData * BaseMolecule::get_volume_data (  int    ) 
 

return requested data set.

Definition at line 2242 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, vmd_volmap_compare, and GraphicsFltkMenu::volindex_update.

float BaseMolecule::getbondorder (  int    atom,
int    bond
) 
 

Definition at line 473 of file BaseMolecule.C.

References atom, NameList< float * >::data, extraflt, MAXATOMBONDS, and NULL.

Referenced by access_tcl_atomsel, assign_atoms, and MolFilePlugin::write_structure.

int BaseMolecule::getbondtype (  int    atom,
int    bond
) 
 

quest bond type.

Definition at line 505 of file BaseMolecule.C.

References atom, NameList< int * >::data, extraint, MAXATOMBONDS, and NULL.

Referenced by access_tcl_atomsel, and MolFilePlugin::write_structure.

int BaseMolecule::has_structure (    )  const [inline]
 

has structure information already been loaded for this molecule?

Definition at line 213 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 450 of file BaseMolecule.h.

Referenced by GraphicsFltkMenu::act_on_command, MoleculeList::add_color_names, MoleculeList::add_molecule, MoleculeList::add_rep, GeometryMol::atom_formatted_name, GeometryMol::atom_full_name, atomsel_new, atomsel_set, atomselect, DrawMolecule::change_ts, IMDMgr::check_event, Molecule::close_coor_file, create, MoleculeList::del_molecule, Tool::dograb, 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, 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, Tool::ungrab, 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 123 of file BaseMolecule.C.

References NameList< int * >::add_name, NameList< float * >::add_name, NameList< int * >::data, NameList< float * >::data, data, extraflt, extraint, nAtoms, NULL, NameList< int * >::num, and NameList< float * >::num.

Referenced by VMDApp::molecule_load, VMDApp::molecule_new, and MolFilePlugin::read_structure.

float* BaseMolecule::mass (    )  [inline]
 

Definition at line 162 of file BaseMolecule.h.

References NameList::data.

Referenced by Tool::assign_rep, GeometryMol::atom_formatted_name, center_of_mass, AtomColor::find, measure_dipole, measure_inertia, VMDApp::molecule_new, 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 451 of file BaseMolecule.h.

References moleculename.

Referenced by GeometryMol::atom_formatted_name, VMDApp::molecule_name, molinfo_get, and MolBrowser::update.

int BaseMolecule::num_angles (    )  [inline]
 

count angle list entries.

Definition at line 387 of file BaseMolecule.h.

References ResizeArray::num.

Referenced by add_angle, analyze, molinfo_get, set_angletype, and MolFilePlugin::write_structure.

int BaseMolecule::num_cterms (    )  [inline]
 

count number of crossterm list entries.

Definition at line 434 of file BaseMolecule.h.

References ResizeArray::num.

Referenced by analyze, and MolFilePlugin::write_structure.

int BaseMolecule::num_dihedrals (    )  [inline]
 

count dihedral list entries.

Definition at line 403 of file BaseMolecule.h.

References ResizeArray::num.

Referenced by add_dihedral, analyze, molinfo_get, set_dihedraltype, and MolFilePlugin::write_structure.

int BaseMolecule::num_impropers (    )  [inline]
 

count improper list entries.

Definition at line 419 of file BaseMolecule.h.

References ResizeArray::num.

Referenced by add_improper, analyze, molinfo_get, set_impropertype, and MolFilePlugin::write_structure.

int BaseMolecule::num_volume_data (    ) 
 

return number of volume data sets in molecule.

Definition at line 2238 of file BaseMolecule.C.

References ResizeArray< VolumetricData * >::num, and volumeList.

Referenced by VolMapCreateILS::add_map_to_molecule, AtomColor::find, SaveTrajectoryFltkMenu::molchooser_activate_selection, VMDApp::molecule_load, VMDApp::molecule_savetrajectory, molinfo_get, MolBrowser::update, GraphicsFltkMenu::update_molchooser, vmd_volmap_compare, GraphicsFltkMenu::volindex_update, and VolMapCreateILS::write_map.

float* BaseMolecule::occupancy (    )  [inline]
 

Definition at line 165 of file BaseMolecule.h.

References NameList::data.

Referenced by GeometryMol::atom_formatted_name, AtomColor::find, VMDApp::molecule_new, MolFilePlugin::read_optional_structure, MolFilePlugin::read_structure, and MolFilePlugin::write_structure.

float* BaseMolecule::radius (    )  [inline]
 

various standard per-atom fields.

Definition at line 161 of file BaseMolecule.h.

References NameList::data.

Referenced by VMDApp::molecule_new, MolFilePlugin::read_optional_structure, MolFilePlugin::read_structure, vmd_bond_search, and MolFilePlugin::write_structure.

Residue * BaseMolecule::residue (  int    ) 
 

return Nth residue.

Definition at line 518 of file BaseMolecule.C.

References residueList.

Referenced by atom_fragment, atom_residue, AtomColor::find, find_atom_in_residue, PickModeForceFragment::pick_molecule_move, PickModeForceFragment::pick_molecule_start, PickModeMoveFragment::rotate, and PickModeMoveFragment::translate.

int BaseMolecule::set_angletype (  int    a,
int    type
) 
 

set new angle type.

Definition at line 334 of file BaseMolecule.C.

References ANGLETYPES, angleTypes, ResizeArray< int >::append, ResizeArray< int >::num, num_angles, and set_dataset_flag.

Referenced by add_angle.

void BaseMolecule::set_dataset_flag (  int    flag )  [inline]
 

Definition at line 150 of file BaseMolecule.h.

References datasetflags.

Referenced by access_tcl_atomsel, VMDApp::molecule_set_dataset_flag, molinfo_set, PickModeAddBond::pick_molecule_end, MolFilePlugin::read_optional_structure, MolFilePlugin::read_structure, set_angletype, set_dihedraltype, and set_impropertype.

int BaseMolecule::set_dihedraltype (  int    d,
int    type
) 
 

set new dihedral type. return type index number.

Definition at line 379 of file BaseMolecule.C.

References ANGLETYPES, ResizeArray< int >::append, dihedralTypes, ResizeArray< int >::num, num_dihedrals, and set_dataset_flag.

Referenced by add_dihedral.

int BaseMolecule::set_impropertype (  int    i,
int    type
) 
 

set new improper type. returns type index number.

Definition at line 423 of file BaseMolecule.C.

References ANGLETYPES, ResizeArray< int >::append, improperTypes, ResizeArray< int >::num, num_impropers, and set_dataset_flag.

Referenced by add_improper.

void BaseMolecule::set_radii_changed (    )  [inline]
 

Definition at line 172 of file BaseMolecule.h.

References radii_minmax_need_update.

Referenced by MolFilePlugin::read_optional_structure, and MolFilePlugin::read_structure.

void BaseMolecule::setbondorder (  int    atom,
int    bond,
float    order
) 
 

Definition at line 453 of file BaseMolecule.C.

References NameList< float * >::add_name, atom, NameList< float * >::data, extraflt, MAXATOMBONDS, nAtoms, and NULL.

Referenced by access_tcl_atomsel, and add_bond.

void BaseMolecule::setbondtype (  int    atom,
int    bond,
int    type
) 
 

set new bond type.

Definition at line 485 of file BaseMolecule.C.

References NameList< int * >::add_name, atom, NameList< int * >::data, extraint, MAXATOMBONDS, nAtoms, and NULL.

Referenced by access_tcl_atomsel, and add_bond.

int BaseMolecule::test_dataset_flag (  int    flag )  [inline]
 

Definition at line 156 of file BaseMolecule.h.

References datasetflags.

Referenced by MolFilePlugin::write_structure.

void BaseMolecule::unset_dataset_flag (  int    flag )  [inline]
 

Definition at line 153 of file BaseMolecule.h.

References datasetflags.

Referenced by VMDApp::molecule_set_dataset_flag.

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, GeometryMol::atom_formatted_name, AtomColor::find, vmd_bond_search, and MolFilePlugin::write_structure.

ResizeArray<int> BaseMolecule::angles
 

list of angles.

Definition at line 106 of file BaseMolecule.h.

Referenced by add_angle, molinfo_get, and MolFilePlugin::write_structure.

NameList<int> BaseMolecule::angleTypeNames
 

list of unique angle type names.

Definition at line 121 of file BaseMolecule.h.

Referenced by analyze, molinfo_get, molinfo_set, MolFilePlugin::read_optional_structure, MolFilePlugin::read_structure, and MolFilePlugin::write_structure.

ResizeArray<int> BaseMolecule::angleTypes
 

type of angle.

Definition at line 117 of file BaseMolecule.h.

Referenced by get_angletype, molinfo_get, and set_angletype.

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, GeometryMol::atom_formatted_name, atomsel_type, AtomColor::find, print_atom_info, and MolFilePlugin::write_structure.

NameList<int> BaseMolecule::bondTypeNames
 

list of unique bond type names.

Definition at line 120 of file BaseMolecule.h.

Referenced by access_tcl_atomsel, analyze, MolFilePlugin::read_optional_structure, MolFilePlugin::read_structure, 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, GeometryMol::atom_formatted_name, AtomColor::find, print_atom_info, and MolFilePlugin::write_structure.

ResizeArray<int> BaseMolecule::cterms
 

list of cross-terms.

Definition at line 109 of file BaseMolecule.h.

Referenced by MolFilePlugin::write_structure.

int BaseMolecule::datasetflags
 

Definition at line 149 of file BaseMolecule.h.

Referenced by BaseMolecule, set_dataset_flag, test_dataset_flag, and unset_dataset_flag.

ResizeArray<int> BaseMolecule::dihedrals
 

list of dihedrals.

Definition at line 107 of file BaseMolecule.h.

Referenced by add_dihedral, molinfo_get, and MolFilePlugin::write_structure.

NameList<int> BaseMolecule::dihedralTypeNames
 

list of unique dihedral type names.

Definition at line 122 of file BaseMolecule.h.

Referenced by analyze, molinfo_get, molinfo_set, MolFilePlugin::read_optional_structure, MolFilePlugin::read_structure, and MolFilePlugin::write_structure.

ResizeArray<int> BaseMolecule::dihedralTypes
 

type of dihedral.

Definition at line 118 of file BaseMolecule.h.

Referenced by get_dihedraltype, molinfo_get, and set_dihedraltype.

NameList<float *> BaseMolecule::extraflt
 

optional floating point data.

Definition at line 113 of file BaseMolecule.h.

Referenced by VolMapCreate::calculate_max_radius, VolMapCreateCoulombPotentialMSM::compute_frame, VolMapCreateCoulombPotential::compute_frame, VolMapCreateDistance::compute_frame, VolMapCreateOccupancy::compute_frame, VolMapCreateDensity::compute_frame, getbondorder, init_atoms, minmax, sasa, setbondorder, vmd_measure_minmax, vmd_measure_sasa, vmd_volmap_ils, and ~BaseMolecule.

NameList<int *> BaseMolecule::extraint
 

optional integer data.

Definition at line 114 of file BaseMolecule.h.

Referenced by getbondtype, init_atoms, setbondtype, and ~BaseMolecule.

ResizeArray<Fragment *> BaseMolecule::fragList
 

list of connected residues.

Definition at line 78 of file BaseMolecule.h.

Referenced by analyze, fragment, and ~BaseMolecule.

ResizeArray<int> BaseMolecule::impropers
 

list of impropers.

Definition at line 108 of file BaseMolecule.h.

Referenced by add_improper, molinfo_get, and MolFilePlugin::write_structure.

NameList<int> BaseMolecule::improperTypeNames
 

list of unique improper type names.

Definition at line 123 of file BaseMolecule.h.

Referenced by analyze, molinfo_get, molinfo_set, MolFilePlugin::read_optional_structure, MolFilePlugin::read_structure, and MolFilePlugin::write_structure.

ResizeArray<int> BaseMolecule::improperTypes
 

type of improper.

Definition at line 119 of file BaseMolecule.h.

Referenced by get_impropertype, molinfo_get, and set_impropertype.

char* BaseMolecule::moleculename [protected]
 

name of the molcule.

Definition at line 345 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, get_radii_minmax, 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, setbondtype, 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 346 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, and AtomColor::find.

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.

QMData* BaseMolecule::qm_data
 

Definition at line 126 of file BaseMolecule.h.

Referenced by BaseMolecule, VMDApp::molecule_orblocalize, molinfo_get, GraphicsFltkRepOrbital::regen_excitationlist, GraphicsFltkRepOrbital::regen_orbitallist, GraphicsFltkRepOrbital::regen_wavefunctypes, and ~BaseMolecule.

float BaseMolecule::radii_max
 

Definition at line 171 of file BaseMolecule.h.

Referenced by BaseMolecule, and get_radii_minmax.

float BaseMolecule::radii_min
 

Definition at line 170 of file BaseMolecule.h.

Referenced by BaseMolecule, and get_radii_minmax.

int BaseMolecule::radii_minmax_need_update
 

methods for querying the min/max atom radii, used by the the QuickSurf representation.

Definition at line 169 of file BaseMolecule.h.

Referenced by BaseMolecule, get_radii_minmax, and set_radii_changed.

ResizeArray<Residue *> BaseMolecule::residueList
 

residue connectivity list.

Definition at line 77 of file BaseMolecule.h.

Referenced by analyze, QuickSurf::calc_surf, 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, 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, GeometryMol::atom_formatted_name, AtomColor::find, print_atom_info, and MolFilePlugin::write_structure.

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

array of volume data sets.

Definition at line 496 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 Sat May 25 01:49:37 2013 for VMD (current) by doxygen1.2.14 written by Dimitri van Heesch, © 1997-2002