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Introduce SMILES property #4

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Introduce SMILES property #4

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67b3776
Initial scaffold for SMILES property definition.
merkys Nov 14, 2024
c47acb8
Extend the title.
merkys Nov 14, 2024
0b2722d
Transfer the description from https://github.com/Materials-Consortia/…
merkys Nov 15, 2024
69abb8d
Add a SMILES example for caffeine.
merkys Nov 15, 2024
1b1f4c9
OpenSMILES is RECOMMENDED (as discussed in today's meeting).
merkys Nov 15, 2024
d66c9ae
Add _cheminfo_standard property metadata to allow specifying SMILES s…
merkys Nov 15, 2024
4de1abd
Minor rewording.
merkys Nov 18, 2024
5933169
Fix property definition validation errors.
merkys Nov 18, 2024
ab1a585
Rename `_cheminfo_standard` to `_cheminfo_standard_name`, redefine it…
merkys Nov 18, 2024
741ccb4
Add `_cheminfo_standard_version`.
merkys Nov 18, 2024
5f90d7c
Add `_cheminfo_standard_name_other`.
merkys Nov 18, 2024
c376199
Update src/v0.1.0/properties/structures/_cheminfo_smiles.yaml
merkys Nov 18, 2024
4d7f610
Update src/v0.1.0/properties/structures/_cheminfo_smiles.yaml
merkys Nov 18, 2024
1b24d6f
Remove the restriction of `_cheminfo_standard_version` to not start w…
merkys Nov 18, 2024
fff49d2
Replace "standard" with "specification" after discussing it with @vai…
merkys Nov 18, 2024
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7 changes: 7 additions & 0 deletions src/v0.1.0/entrytypes/structures.yaml
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Expand Up @@ -23,6 +23,13 @@ properties:
sortable: false
query-support: "none"
response-level: "yes"
_cheminfo_smiles:
$$inherit: "/properties/structures/_cheminfo_smiles"
x-optimade-implementation:
support: "may"
sortable: false
query-support: "none"
response-level: "yes"
_cheminfo_stdinchikey:
$$inherit: "/properties/structures/_cheminfo_stdinchikey"
x-optimade-implementation:
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23 changes: 23 additions & 0 deletions src/v0.1.0/properties/structures/_cheminfo_smiles.yaml
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Original file line number Diff line number Diff line change
@@ -0,0 +1,23 @@
$$schema: "https://schemas.optimade.org/meta/v1.2/optimade/property_definition"
$id: "https://schemas.optimade.org/namespaces/cheminformatics/v0.1/properties/structures/_cheminfo_smiles"
title: "SMILES (Simplified Molecular Input Line Entry Specification) representation of the structure"
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x-optimade-type: "string"
x-optimade-definition:
kind: "property"
version: "0.1.0"
format: "1.2"
name: "_cheminfo_smiles"
label: "_cheminfo_smiles_structures"
type:
- "string"
- "null"
description: |-
SMILES (Simplified Molecular Input Line Entry System) representation of the structure.
Values MUST adhere to the OpenSMILES specification v1.0 (http://opensmiles.org/opensmiles.html).
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Consensus is that we should recommend our favourite specifications, rather than necessarily enforcing it.

We can also recommend that implementations announce which flavour of SMILES they are using as human-readable metadata

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We can also recommend that implementations announce which flavour of SMILES they are using as human-readable metadata

There was a suggestion of having an enumerator for most-widely-used values and value other with another field defined for free-form text.

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Also just remembered this point that either this field should be multivalued, or we have a proper recommendation for how to deal with multiple disconnected chemical subcomponents, or the case where the SMILES does not include all atoms in the "unit cell"

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Also just remembered this point that either this field should be multivalued, or we have a proper recommendation for how to deal with multiple disconnected chemical subcomponents, or the case where the SMILES does not include all atoms in the "unit cell"

I have mentioned this issue in the initial PR message, but please correct me if you meant a different thing.

The issue of not representing all atoms in the structure (sort of "unit cell") is a good catch, though.

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 the stable order of atoms) the produced SMILES representations, but this is not mandatory and no particular set of rules is recommended.
Generally, providers SHOULD NOT change the representation more frequently than the structure itself is modified.
examples:
- "c1ccccc1"
- "CN1C=NC2=C1C(=O)N(C(=O)N2C)C"
x-optimade-unit: "inapplicable"