Table 6 Jmol SMARTS atom selection primitives

S-

*

Any atom

*1**1

Any three-membered ring

S-

a

Any aromatic atom

a1aaaa1

A five-membered aromatic ring

S-

A

Any non-aromatic atom

AAAA

A chain of at least four nonaromatic atoms

+-

H

Hydrogen

OH

All OH groups; SMARTS only

a+

#-<n>

Negative of atom number

[#-36]

Atom number 36, as defined by the application. (In Jmol, this corresponds to “@36” or “atomno=36”.)

+

<n>?

Mass number or unspecified mass number

[12?#6]

Carbon that isn’t explicitly C13 or C14

[0?]

Atom with unspecified mass

[!0?]

Any atom with mass specified

S

X<n>

Total number of connections

[X2]

This includes all implicit hydrogens, whether in a molecule or SMILES string

+

d<n>

Number of non-hydrogen connections

[n;d3]

Aromatic trivalent nitrogen with no attached H atom. Note that [nd3] would be read as an aromatic neodymium with an atomic mass improperly positioned after it

S

D<n>

Number of explicit connections

[#6D3]

Carbon atoms with exactly three connections (either in a molecule with bonds to three atoms or in a SMILES string with three explicit atoms connected to it

S

h<n>

Number of implicit hydrogens

[C;h2]

A methylene group written as “C” or [CH2] in a SMILES string; a methylene carbon atom from a PDB file or other file that does not contain hydrogen atoms. (In Jmol, for example, a non-NMR PDB file loaded before issuing SET pdbAddHydrogens TRUE.)

S

H<n>

Total hydrogen count (sum of attached [H] and implicit)

[CH3]

A methyl group

[H0]

No attached hydrogens

[!H0]

At least one attached hydrogen

a*

x<n>

Total number of bonds that terminate on ring atoms

[x1]

A non-ring atom that is connected to a ring

[x0]

No ring connections

[!x0] or [x]

At least one ring connection

a*

R<n>

Ring membership

[R]

A ring atom

[!R]

A non-ring atom

[R2]

An atom in exactly two rings

a*

r<n>

Ring size

[O;r3]

An oxygen in a three-membered ring

[O;!r3]

An oxygen that is not in a three-membered ring

*+

r500

Five-membered aromatic ring

[n;r500]

Aromatic nitrogen in a 5-membered aromatic ring (not an aromatic nitrogen in a 500-membered ring)

*+

r600

Six-membered aromatic ring

[n;r600]

Aromatic nitrogen a 6-membered aromatic ring (not an aromatic nitrogen in a 600-membered ring)

S

v<n>

Total bond order (valence)

[C;v3]

Total bond count (note that ill-defined resonance structures such as proteins without hydrogen atoms will overestimate valence for arginine sidechains

+

Xxx#nn^c.yyyy#mm

PDB residue name#number^insertionCode. atom name#atomic number

For PDB data:

[ALA.C]

 Carbonyl carbon of all alanines

[ILE#35.*]

 All atoms in ILE35

[#35.*]

 Residue 35

[*.CA&!CA.CA]

 Alpha carbons (not calcium ions)

[*.CA#6]

 Just alpha carbons (atomic number specified)

Note that all matches are by name only, not by analyzing substructure; atom name may include “.” or “*”; residue name may contain “*”

+

=<n>

Atom index

[=22]

Atom with atom index 22, however that is defined by the application

+

“xxx”

Atom type

[“7”]

However that is defined by the application; for example, in Jmol, [“7”] is a carbonyl carbon atom after assignment by MMFF94

$(…)

Nesting

[$(aaN)$(aaaC)]

An aromatic atom that is both ortho to an amino group and meta to a methyl group

+

$(select ….)

Processor-specific selection phrase

[$(select atomno=x)]

Selects the atom with atom number equal to the value of the Jmol variable x

+

$<n>(pattern)

A specific number of occurrences of pattern

C[$3(C=C)]C

Nonterminal conjugated triene

+

$min-max(pattern)

A variable number of occurrences of pattern

C[$2-3(C=C)]C

Nonterminal conjugated diene or triene

+

$<varName>

A predefined variable

[$a1]

Replaces “[$a1]” with whatever $a1 is defined to be (see below)