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MolAtom Class Reference

class/struct which holds data for one atom. More...

#include <Atom.h>

List of all members.

Public Methods

void init (int n, int theresid, const char *insertion)

int add_bond (int a, int type)

add a bond into the atom. Note that each bond will be stored twice, so make sure when using bonds to define whether the 'official' bond is from low # atom -> high #, or vice versa. More...

int bonded (int a)

return TRUE if this atom is bonded to the specified atom. Returns FALSE otherwise. More...

Public Attributes

short nameindex

atom name string index. More...

short typeindex

atom type string index. More...

unique resid, since there can be dups. More...

int bondTo [MAXATOMBONDS]

list of atoms to which this atom is bonded. More...

signed char bonds

how many bonds this atom has. More...

signed char atomicnumber

element atomic number. More...

signed char altlocindex

alternate location identifier index. More...

char insertionstr [2]

for insertion codes (padded to 2 chars). More...

short chainindex

chain identifier. More...

short segnameindex

atom segment name string index. More...

int resid

resid from original file. More...

short resnameindex

atom residue name string index. More...

signed char atomType

is this atom part of the backbone? More...

signed char residueType

is this part of a larger component? for instance, is this CG atom in an amino acid of some sort? More...

Detailed Description

class/struct which holds data for one atom.

Definition at line 61 of file Atom.h.

Member Function Documentation

int MolAtom::add_bond ( int a,

int type

) [inline]

add a bond into the atom. Note that each bond will be stored twice, so make sure when using bonds to define whether the 'official' bond is from low # atom -> high #, or vice versa.

Definition at line 113 of file Atom.h.

References ATOMNUCLEICBACK, ATOMPROTEINBACK, atomType, bonds, bondTo, and MAXATOMBONDS.

Referenced by BaseMolecule::add_bond.

int MolAtom::bonded ( int a ) [inline]

return TRUE if this atom is bonded to the specified atom. Returns FALSE otherwise.

Definition at line 126 of file Atom.h.

References bonds, and bondTo.

Referenced by contacts, measure_hbonds, PickModeAddBond::pick_molecule_end, and vmd_measure_contacts.

void MolAtom::init ( int n,

int theresid,

const char * insertion

) [inline]

Definition at line 95 of file Atom.h.

References altlocindex, atomicnumber, ATOMNORMAL, atomType, bonds, bondTo, insertionstr, MAXATOMBONDS, n, nameindex, resid, residueType, resnameindex, RESNOTHING, segnameindex, typeindex, and uniq_resid.

Referenced by BaseMolecule::add_atoms.

Member Data Documentation

signed char MolAtom::altlocindex

alternate location identifier index.

Definition at line 74 of file Atom.h.

Referenced by BaseMolecule::add_atoms, GeometryMol::atom_formatted_name, init, VMDApp::molecule_from_selection_list, vmd_bond_search, and MolFilePlugin::write_structure.

signed char MolAtom::atomicnumber

element atomic number.

Definition at line 73 of file Atom.h.

Referenced by BaseMolecule::add_atoms, assign_atoms, GeometryMol::atom_formatted_name, QMData::create_unique_basis, AtomColor::find, init, QMData::init_electrons, VMDApp::molecule_from_selection_list, MolFilePlugin::read_optional_structure, write_ss_input_pdb, and MolFilePlugin::write_structure.

signed char MolAtom::atomType

is this atom part of the backbone?

Definition at line 86 of file Atom.h.

Referenced by add_bond, BaseMolecule::analyze, atomsel_backbonetype, AtomColor::find, init, measure_hbonds, and vmd_bond_search.

signed char MolAtom::bonds

how many bonds this atom has.

Definition at line 72 of file Atom.h.

Referenced by access_tcl_atomsel, BaseMolecule::add_bond, add_bond, BaseMolecule::add_bond_dupcheck, assign_atoms, bonded, BaseMolecule::clear_bonds, BaseMolecule::count_bonds, AtomColor::find, getbonds, init, measure_hbonds, VMDApp::molecule_from_selection_list, PickModeAddBond::pick_molecule_end, MolFilePlugin::read_optional_structure, setbonds, topo_del_bond, topo_get_bond, and MolFilePlugin::write_structure.

int MolAtom::bondTo[MAXATOMBONDS]

list of atoms to which this atom is bonded.

Definition at line 71 of file Atom.h.

Referenced by access_tcl_atomsel, add_bond, BaseMolecule::add_bond_dupcheck, assign_atoms, bonded, BaseMolecule::count_bonds, AtomColor::find, getbonds, init, measure_hbonds, VMDApp::molecule_from_selection_list, PickModeAddBond::pick_molecule_end, setbonds, topo_del_bond, topo_get_bond, and MolFilePlugin::write_structure.

short MolAtom::chainindex

chain identifier.

Definition at line 79 of file Atom.h.

Referenced by BaseMolecule::add_atoms, GeometryMol::atom_formatted_name, VMDApp::molecule_from_selection_list, print_atom_info, write_ss_input_pdb, and MolFilePlugin::write_structure.

char MolAtom::insertionstr[2]

for insertion codes (padded to 2 chars).

Definition at line 75 of file Atom.h.

Referenced by init, VMDApp::molecule_from_selection_list, and MolFilePlugin::write_structure.

short MolAtom::nameindex

atom name string index.

Definition at line 68 of file Atom.h.

Referenced by BaseMolecule::add_atoms, BaseMolecule::analyze, GeometryMol::atom_formatted_name, GeometryMol::atom_short_name, atomsel_name, colvarproxy_vmd::check_atom_id, BaseMolecule::find_atom_in_residue, init, VMDApp::molecule_from_selection_list, print_atom_info, vmd_bond_search, write_ss_input_pdb, and MolFilePlugin::write_structure.

int MolAtom::resid

resid from original file.

Definition at line 81 of file Atom.h.

Referenced by GeometryMol::atom_formatted_name, GeometryMol::atom_short_name, init, VMDApp::molecule_from_selection_list, print_atom_info, and MolFilePlugin::write_structure.

signed char MolAtom::residueType

is this part of a larger component? for instance, is this CG atom in an amino acid of some sort?

Definition at line 91 of file Atom.h.

Referenced by BaseMolecule::analyze, atomsel_residuetype, init, and write_ss_input_pdb.

short MolAtom::resnameindex

atom residue name string index.

Definition at line 82 of file Atom.h.

Referenced by BaseMolecule::add_atoms, GeometryMol::atom_formatted_name, GeometryMol::atom_short_name, AtomColor::find, init, VMDApp::molecule_from_selection_list, print_atom_info, write_ss_input_pdb, and MolFilePlugin::write_structure.

short MolAtom::segnameindex

atom segment name string index.

Definition at line 80 of file Atom.h.

Referenced by BaseMolecule::add_atoms, GeometryMol::atom_formatted_name, colvarproxy_vmd::check_atom_id, init, VMDApp::molecule_from_selection_list, print_atom_info, and MolFilePlugin::write_structure.

short MolAtom::typeindex

atom type string index.

Definition at line 69 of file Atom.h.

Referenced by BaseMolecule::add_atoms, GeometryMol::atom_formatted_name, atomsel_type, init, VMDApp::molecule_from_selection_list, print_atom_info, and MolFilePlugin::write_structure.

int MolAtom::uniq_resid

unique resid, since there can be dups.

Definition at line 70 of file Atom.h.

Referenced by BaseMolecule::atom_fragment, BaseMolecule::atom_residue, AtomColor::find, init, measure_avpos_perresidue, measure_center_perresidue, measure_rmsd_perresidue, measure_sasa_perresidue, print_atom_info, and write_ss_input_pdb.

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

Atom.h

Generated on Tue Nov 18 02:49:42 2025 for VMD (current) by doxygen1.2.14 written by Dimitri van Heesch, © 1997-2002