4.2.3 The Atom Block

The atom block consists of one line per atom, where the number of atoms is specified in the preceding counts block. Each atom line has the following format.

This line has the format:

Template: xxxxx.xxxxyyyyy.yyyyzzzzz.zzzz aaaddcccssshhhbbbvvvHHHrrriiimmmnnneee
Example:      0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0

Where:

xxxxx.xxxx is the Cartesian X co-ordinate of this atom.

yyyyy.yyyy is the Cartesian Y co-ordinate of this atom.

zzzzz.zzzz is the Cartesian Z co-ordinate of this atom.

aaa is the left-justified atomic symbol. The first character of this symbol should be uppercase, and any second character should be lower case. Any string other than one of the IUPAC mandated atomic symbols is assumed to represent a pseudo or superatom.

dd is the mass difference.

ccc is the formal charge.

sss is the atom stereo parity.

hhh specifies the hydrogen count in a substructure query.

bbb is the stereo care box.

vvv is the valence.

HHH is the H0 designator.

rrr is the reaction component type. The value "1" indicates a reactant atom, the value "2" indicates a product atom and the value "3" indicates an intermediate atom.

iii is the reaction component number.

mmm is the atom-atom mapping number.

nnn is the inversion/retention flag.

eee is the exact change flag.

				SMACK Substructure Query Conversion Tools

				SMACK Substructure Query Conversion Tools