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SMILES property #392

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SMILES property #392

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55be0a4
Initial proposal for SMILES property (#368).
merkys Dec 3, 2021
6f03d44
Describing canonicalization.
merkys Dec 3, 2021
75d1bba
Update optimade.rst
merkys Dec 4, 2021
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Update optimade.rst
merkys Dec 4, 2021
72a5409
Explaining what "canonicalize" means.
merkys Dec 6, 2021
8485be4
Merge branch 'develop' into SMILES-property
merkys Apr 1, 2022
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Merge branch 'develop' into SMILES-property
merkys May 31, 2022
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Merge branch 'develop' into SMILES-property
merkys Jun 20, 2022
f998720
Remove "descriptor" from SMILES property description.
merkys Jun 20, 2022
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Update optimade.rst
merkys Jun 27, 2022
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Update optimade.rst
merkys Jun 27, 2022
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Merge branch 'develop' into SMILES-property
merkys Jul 5, 2022
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Merge branch 'develop' into SMILES-property
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Update optimade.rst
merkys Sep 23, 2022
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Merge branch 'develop' into SMILES-property
merkys Jun 7, 2023
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Expand Up @@ -2500,6 +2500,25 @@ chemical\_formula\_anonymous

- A filter that matches an exactly given formula is :filter:`chemical_formula_anonymous="A2B"`.

smiles
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~~~~~~

- **Description**: The SMILES (Simplified Molecular Input Line Entry System) representation of the structure.
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I think we need a bit more clarification of the expected use.

How "much" of the structure should be described by the SMILES string for it to be valid here (e.g., that it should appear in the results when someone searches for it?) Do we need to require that every "site" in the OPTIMADE structure is present in the SMILES string? Obviously for nperiodic_dimensions=0 and a single molecule this makes sense, same for an nperiodic_dimensions=3 molecular crystal, but what about:

  • co-crystal with two distinct molecules (does SMILES do something fancy for this already?)
  • an inorganic surface with adsorbed molecule
  • a hybrid perovskite structure with molecular unit as a cation

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How "much" of the structure should be described by the SMILES string for it to be valid here (e.g., that it should appear in the results when someone searches for it?) Do we need to require that every "site" in the OPTIMADE structure is present in the SMILES string?

This is a good point. I would say that every "site" has to be represented in SMILES. There surely will be situations where this is not attainable (i.e., OpenSMILES cannot express polymers and there will be difficulties in depicting mixture sites). Maybe at this point it would be easier to say that only the structures that are "expressible" using OpenSMILES should have smiles, that is, no nonstandard approximations should be done.

Obviously for nperiodic_dimensions=0 and a single molecule this makes sense, same for an nperiodic_dimensions=3 molecular crystal, but what about:

  • co-crystal with two distinct molecules (does SMILES do something fancy for this already?)

SMILES can contain many distinct molecules, disconnected components are joined with . (if I get the question right)

  • an inorganic surface with adsorbed molecule
  • a hybrid perovskite structure with molecular unit as a cation

I would say these two fall under class "polymer", thus inexpressible.

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co-crystal with two distinct molecules (does SMILES do something fancy for this already?
This can be described using a "dot bond", e.g. CuSO4.O.O

- **Type**: string
- **Requirements/Conventions**:

- **Support**: OPTIONAL support in implementations, i.e., MAY be :val:`null`.
- **Query**: Support for queries on this property is OPTIONAL.
Queries MUST treat the value of this property as a raw string, without SMILES-specific semantics.
That is, providers MUST NOT perform substructure search, just regular string comparison.
Comment on lines +2512 to +2513
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Suggested change
Queries MUST treat the value of this property as a raw string, without SMILES-specific semantics.
That is, providers MUST NOT perform substructure search, just regular string comparison.

A molecule can have hundreds of valid SMILES descriptors. A client would have to include all of them in a query, to determine whether a particular molecule is present in the database.
I can imagine that such a query would be slow to execute.
A more efficient way, would be to convert the SMILES string of the query into a structure and then back into a SMILES string using the same method that was used to generate the SMILES strings in the database.
These lines however explicitly forbid databases from implementing this method.

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I have responded to these concerns already.

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@JPBergsma, are you OK with leaving these two lines intact and marking the conversation as resolved?

From what I understand from the discussions in #392, it was agreed to implement the complex structure search functionality in a different way (e.g. by using SMARTS).

- Value MUST adhere to the `OpenSMILES specification v1.0 <http://opensmiles.org/opensmiles.html>`__.
- When structures or their parts cannot be unambiguously represented in SMILES according to OpenSMILES recommendations, using the guidelines from `Quirós et al. 2018 <https://doi.org/10.1186/s13321-018-0279-6>`__ is RECOMMENDED.
- Providers MAY canonicalize (i.e., use rules to establish stable order of atoms) produced SMILES representations, but this is not mandatory.
Generally, providers SHOULD NOT change the representation more frequently than the structure itself is modified.
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- **Examples**:
- caffeine: `CN1C=NC2=C1C(=O)N(C(=O)N2C)C`

dimension\_types
~~~~~~~~~~~~~~~~

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