SMILES, SMARTS

Code name: smiles, smarts=smiles:s

Contents:

• Smiles
• Smarts
• Import options
• Export options
• References

Marvin imports and exports SMILES strings with the following specification rules:

• Atoms:
  • Atoms are represented by their atomic symbols.
  • Isotopic specifications are indicated by preceeding the atomic symbol.
  • Any atom but not hydrogen is represented with '*'.
• Bonds:
  • Single, double, triple, and aromatic bonds are represented by the symbols -, =, #, and :, respectively.
  • Single and aromatic bonds may be omitted.
  • Branches are specified by enclosing them in parentheses. The implicit connection to a parenthesized expression (a branch) is to the left.
  • Cyclic structures are represented by breaking one single (or aromatic) bond in each ring and the missing bond is denoted by connection placeholder numbers
• Disconnected structures:
  • Disconnected compounds are written as individual structures separated by a period.
• Isomeric specification
  • Configuration around double bonds is specified by "directional bonds": / and \.
  • Configuration around tetrahedral centers may be indicated by a simplified chiral specification (parity) @ or @@.
• Unique SMILES.
  The "unique" name can be sometimes misleading when dealing with compounds with stereo centres. The SMILES specification (3.1. SMILES Specification Rules) defines generic, unique, isomeric and absolute SMILES as:
  1. generic SMILES: representing a molecule (there can be many different representations)
  2. unique SMILES: generated from generic SMILES by a certain algorithm [3]
  3. isomeric SMILES: string with information about isotopism, configuration around double bonds and chirality
  4. absolute SMILES: unique SMILES with isomeric information - in Marvin during graph canonicalization the isomeric information is also considered as an atom invariant
  The name canonical SMILES is used for absolute or unique SMILES depending wether the string contains isomeric information or not (both strings are "canonicalized" where the atom/bond order is unambigous). Marvin generates always canonical SMILES with isomerism info if it is possible to find out from the input file. The molecule graph is always canonicalized using the algorithm in article [3] but it is not guaranteed to give absolute SMILES for all isomeric structures. With option u currently we are using an approximation to make the SMILES string as absolute (unique for isomeric structures) as possible. For correct exact (perfect) structure searching MolSearch and JChemSearch classes of JChem Base or the jc_equals SQL operator of the JChem Cartridge are suggested.
  The initial ranks of atoms for the canonization are calculated using the following atom invariants:
  1. number of connections
  2. sum of non-H bond orders (single=1, double=2, triple=3, aromatic=1.5, any=0)
  3. atomic number (list=110, any atom=112)
  4. sign of charge: 0 for nonnegative, 1 for negative charge
  5. formal charge
  6. number of attached hydrogens
  7. isotope mass number
  See ref. [3] for details.
  With option u it is possible to include chirality into graph invariants. This option must be used with care since for molecules with numerous chirality centres the canonicalization can be very CPU demanding [4].

Marvin imports and exports SMARTS strings with the following 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..
  • aromatic and aliphatic atoms: a, A
  • aliphatic, aromatic, aliphatic_or_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)
• 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)]

In case of SMARTS:

• Impicit H atoms are not written inside brackets. Eg: [C:1]
• Query H 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.
  Eg: c1ccccc1 But: c:c, c:[c;a], [#6]:c
• Single bonds are not written explicitly if at least one atom is not aromatic.
  Eg: 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.
  Eg: [#6]cc, [#6][c;a], [#6][#6]

f {fFIELD1,fFIELD2,...}

Import data fields from a multi-column file. The first column contains the SMILES/SMARTS strings, the second contains the data field called FIELD1, the third contains FIELD2, etc. Example: molconvert sdf "foo.smi{fname,fID}" reads the smiles string, the name and the ID from the foo.smi file and converts it to sdf format.

d

Import with Daylight compatiblity for query H. In daylight smarts, H is only considered as H atom when the atom expression has the syntax [<mass>H<charge><map>] (mass, charge and map are optional). Otherwise it is considered as query H count. Examples: [!H!#6] without d option is imported as an atom which is not H and not C. However with d option it is imported as an atom which has not one H attached, and which is not C. Use "H1" or "#1" or "#1A" instead of "H" to avoid ambiguous meaning of H. "H1" always means query H count. "#1" always means H atom, "#1A" means aliphatic H atom.

Export options

Export options can be specified in the format string. The format descriptor and the options are separated by a colon.

a or +a	Aromatize. Example: "smiles:a"
a_... or +a_...	Aromatize using the specified algorithm. ChemAxon: a_cx or a_chemaxon (default), Daylight: a_day or a_daylight. Example: "smiles:a_day"
-a	Dearomatize. Example: "smiles:-a"
-H	Remove explicit Hydrogen atoms. Example: "smiles:-H"
0	Do not include parity and double bond stereo (cis/trans) information. Examples: "smiles:0" (not stereo), "smiles:a0" (aromatic, not stereo)
q	Check atom equivalences using graph invariants at double bonds. The graph invariant is used for symmetry description at each atom in the molecule. If one end of the double bond is symmetric (the ligands' graph invariants equal), then the / and \ signs are not used in the description of the double bond, if this option is set. Example: molconvert smiles:q -s "C/C=C(/C)C" results CC=C(C)C
s	Write query smarts. (See query Smarts for details.)
u	Write uniqe smiles (considering chirality info also [4]). Note: Use this option if you want unique smiles export.
h	Convert explicit H atoms to query hydrogen count.
Tf1:f2:...	Export f1, f2 ... SDF fields.
n	Export molecule name (the first line of an MDL molfile).

See also

• ChemAxon Extended SMILES and SMARTS

References