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: C[C@?H](Cl)Br

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

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]

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