SMARTS

    Chemaxon products import and export SMARTS strings with the following features:

    Full-functional (editable) query features

    SMARTS features interpreted during import/export as full-functional (editable) query features:

    • atom lists like [C,N,P] and 'NOT' lists like [!#6!#7!#15]

    • any bond: ~

    • ring bond: C@C

    • hydrogen count: H0, H1, H2, H3, H4

    • valence: v0, v1, ..., v8

    • connectivity: X0, X1, X2, X3, X4

    • in ring: R

      ring count: R0, R1, ..., R6

    • size of smallest ring: r3, r4, r5, r..

    • number of ring bonds: x2, x3, x4

      at least one ring bond: x

    • aromatic and aliphatic atoms: a, A

    • aliphatic, aromatic atom query properties

    • single_or_double, single_or_aromatic, double_or_aromatic bonds (used in Marvin)

    • directional or unspecified bonds: C\C=C/?C

    • chiral or unspecified atoms: CC@?HBr

    • component level grouping: (C).(O) (C.O)

      Code : smarts, smiles:s

      See also:

    • SMILES

    • SMILES and SMARTS import and export options

    • Chemaxon Extended SMILES and SMARTS - CXSMILES and CXSMARTS

    Features with limited editing support

    A subset of SMARTS features are imported as SMARTS atoms/bonds. These atoms/bonds have limited editing support in the Marvin GUI, but can be exported and evaluated (e.g. JChem structure searching handles them correctly):

    • implicit hydrogen count: h2, h3, h..

    • degree: D2, D3, D..

    • more difficult logical expressions in atom or bond expressions: &,;!

      (Simpler cases, like atom lists, not lists, "and"-expressions are handled by the above features.)

    • recursive SMARTS: [$(CCC)]

    Features exported as SMARTS atoms/bonds

    A subset of features are exported as SMARTS atoms/bonds.

    • MDL Substitution Count query atom property s<n> is converted to degree Dn . In case of *s* the non-H neighbours are counted and exported as degree D<number>* .

    • MDL Unsaturated Atom query atom property u is converted to recursive SMARTS: $([,#1]=,#,:[,#1]) is appended after the SMARTS atom.

    Implicit and Query Hydrogen Atoms

    • Impicit Hydrogen atoms are not written inside brackets. Eg: [C:1]

    • Query Hydrogen atoms are written inside brackets without using the low precedence "and" operator ';'. Eg: [CH3]

    Implicit bond types

    The default bond types for import and export strongly depend on the atoms connected by the bond.

    • Aromatic bonds are not written explicitly if neither atoms are aliphatic and they are in a ring.

      e.g .: c1ccccc1 But: c:c, c:[c;a], [#6]:c

    • Single bonds are not written explicitly if at least one atom is not aromatic.

      e.g. : CC, C[c;a], Cc, C[C;A], [#6]C But: [#6]-[c;a], c1ccc(cc1)-c2ccccc2

    • Single_or_aromatic bonds are not written explicitly if both atoms of the bond are aromatic and any of them is not in the same ring.

      e.g. : [#6]cc, [#6][c;a], [#6][#6]

    ™: SMILES, SMARTS, and SMIRKS are trademarks of Daylight Chemical Information Systems.