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.