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. Author manuscript; available in PMC: 2013 Dec 21.
Published in final edited form as: J Chem Inf Model. 2012 Nov 28;52(12):3144–3154. doi: 10.1021/ci300363c

Table 1.

Overview of all the condition keywords supported by the atom typer. The type of condition can be “atom”: evaluate an atomic property, “topology”: related to the connectivity of the molecular graph, “bond”: evaluate a bond property, “logic”: logical operator or “action”: optional action (see text). Note that the latter are not conditions in the sense that they don’t test anything - performing an action instead - although they could be regarded as conditions that always evaluate true.

Condition Meaning Type
el <element> element atom
elha halogen atom
elos chalcogen atom
nb <#> valence atom
rings <#> # of rings atom
ring3 <size> all-sp3 ring atom
ring2 <size> all-sp2 ring atom
arom <size> aromatic ring atom
ring23 <size> mixed sp2/sp3 ring atom
ring <size> any ring atom
self parent atom atom/topology
ne ( <cond> ) ( <cond> ) … neighbor topology
bo <order> bond order bond
inring bond in ring bond
! ( <cond> ) not operator logic
or ( <cond> ) ( <cond> ) … or operator logic
charge <#> formal charge action
impr improper dihedral action
warn “<message>” (non-fatal) warning action
err “<message>” (fatal) error action
altnum alternate numbering action
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