SMILES, SMARTS

Code name: smiles, smarts=smiles:s

Marvin imports and exports SMILES strings with the following additional features:

• A subset of SMARTS extensions:
  • atom lists like [C,N,P] and 'NOT' lists like [!C!N!P]
  • any atom: *
  • any bond: ~
  • 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, ...
  • aromatic and aliphatic atoms: a, A
  • single_or_double, single_or_aromatic, double_or_aromatic bonds
  • aliphatic, aromatic, aliphatic_or_aromatic atom query properties
• 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]
• Query SMARTS.
  • Impicit H atoms are not written inside brackets. Eg: [C:1]
  • Query H atoms are written inside brackets using the low precedence "and" operator ';'. Eg: [C;H3]
  • Every bond type is written explicitly except single_or_aromatic bonds.
• Unique SMILES.

  The initial ranks of atoms for the canonization are calculated using the following graph 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].
• Stereochemistry
  • Parity is a general type of chirality specification based on the local chirality.
    The most common tetrahedral class is implemented. An atom can have parity (odd, even) if the following conditions are met:
    • number of ligands + implicit H > 3
    • implicit + explicit H < 2
    • number of ligands is < 5
    • if the atom is not in ring then the graph invariants of the ligands must differ
    Parity value 0 is used for atoms which cannot have parity.
  • Cis-trans isomerism
    The default stereoisomers in rings are cis, which are not written explicitly.
• Reactions (Reaction SMILES and Reaction SMARTS)
  • syntax: reactant(s)>agent(s)>product(s), where
         reactants = reactant1 . reactant2.....
         agents = agent1.agent2 . ....
         products = product1.product2 . ...
    

    Agents are molecule structures that do not take part in the chemical reaction, but are added to the reaction equation for informative purpose only.

    All of the above sections are optional. For example:

    • a reaction with no agents: reactant(s)>>product(s)
    • a reaction with no agents and no products (mainly used in reaction search): reactant(s)>>
    • a reaction with no agents and no reactants (mainly used in reaction search): >>product(s)
  • atom maps

f {fFIELD1,fFIELD2,...}

Import data fields from a multi-column file. The first column contains the SMILES 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.

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	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. Note: Use this option if you want unique smiles export. 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]).
h	Convert explicit H atoms to query hydrogen count.

References