Daylight v4.9
Release Date: 1 February 2008

Object Synopsis

atom -- object representing an atom in a molecule


An atom object represents a single atom in a molecule. Atom objects are always a constituent part of a molecule object, and never exist in isolation. Atoms have a number of properties: atomic number, atomic weight, atomic symbol, charge, chirality, aromaticity, implicit hydrogen count, total hydrogen count, symmetry order and class, canonical order in the molecule, and a user-set arbitrary order in the molecule. Atoms can only be allocated or deallocated when a molecule is in the "modify on" state (see dt_mod_on(3) and dt_mod_off(3)).

A hydrogen pseudo-atom object is available for use in chirality specifications; see dt_isohydro(3) for details.

Related Topics

bond(3ob) molecule(3ob) cycle(3ob) depiction(3ob) conformation(3ob)

dt_aromatic(3) dt_setinteger(3) dt_typename(3) dt_remove(3) dt_symclass(3) dt_sethandle(3) dt_isohydro(3) dt_cansmiles(3) dt_integer(3) dt_add(3) dt_setarborder(3) dt_getmap(3) dt_weight(3) dt_xatom(3) dt_label2(3) dt_fp_partfp(3) dt_setga(3) dt_real(3) dt_setcoord(3) dt_handle(3) dt_label2ga(3) dt_count(3) dt_symbol(3) dt_setlabel2(3) dt_setweight(3) dt_ischiral(3) dt_string(3) dt_fp_generatefp(3) dt_setstring(3) dt_setadjunct(3) dt_setbondstyle(3) dt_stream(3) dt_bond(3) dt_setmap(3) dt_getcoord(3) dt_xsmiles(3) dt_boolean(3) dt_mapped(3) dt_setchival(3) dt_setlabel1ga(3) dt_setreal(3) dt_symorder(3) dt_proptype(3) dt_dealloc(3) dt_setlabel1(3) dt_label1ga(3) dt_arborder(3) dt_chiseq(3) dt_chival(3) dt_fp_differencefp(3) dt_copy(3) dt_hcount(3) dt_imp_hcount(3) dt_setimp_hcount(3) dt_number(3) dt_setboolean(3) dt_suppressh(3) dt_addbond(3) dt_label1(3) dt_parent(3) dt_adjunct(3) dt_uid(3) dt_charge(3) dt_addatom(3) dt_bondstyle(3) dt_member(3) dt_chiperm(3) dt_setnumber(3) dt_ga(3) dt_origstream(3) dt_setaromatic(3) dt_getrole(3) dt_molgraph(3) dt_setcharge(3) dt_type(3) dt_addh(3) dt_propnames(3) dt_appendstring(3)