Merge pull request #4 from Materials-Consortia/smiles

Introduce SMILES property

Author: merkys

src/v0.1.0/entrytypes/structures.yaml

@@ -21,6 +21,12 @@ properties:
       sortable: false
       query-support: "none"
       response-default: true
+  _cheminfo_smiles:
+    $$inherit: "/properties/structures/_cheminfo_smiles"
+    x-optimade-implementation:
+      sortable: false
+      query-support: "equality only"
+      response-default: true
   _cheminfo_stdinchi:
     $$inherit: "/properties/structures/_cheminfo_stdinchi"
     x-optimade-implementation:

src/v0.1.0/properties/structures/_cheminfo_smiles.yaml

@@ -0,0 +1,86 @@
+$$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 System) representation of the structure"
+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.
+  Property is string-valued, thus comparison operators (only '=' and '!=' are allowed) MUST compare literal strings.
+  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.
+  No particular specification (also known as flavor) for the provided SMILES strings is enforced, but if known, MUST be provided in metadata property '_cheminfo_specification_name'.
+examples:
+  - "c1ccccc1"
+  - "CN1C=NC2=C1C(=O)N(C(=O)N2C)C"
+  - "[Na+].[Cl-]"
+x-optimade-metadata-definition:
+  title: "Metadata for the _cheminfo_smiles field"
+  description: "This dictionary contains the per-entry metadata for the _cheminfo_smiles field."
+  x-optimade-type: "dictionary"
+  type:
+    - "object"
+    - "null"
+  properties:
+    _cheminfo_specification_name:
+      description: |-
+        A name of the specification the given SMILES string conforms to.
+        Takes value from an enumeration set containing 'IUPAC SMILES+' (https://github.com/IUPAC/IUPAC_SMILES_plus), 'OpenSMILES' (http://opensmiles.org/opensmiles.html) and 'other' (none of the above).
+        If 'other' is chosen, the specification MUST be specified in metadata property '_cheminfo_specification_name_other'.
+        'null' value means that the specification of the given SMILES string is not known.
+      x-optimade-type: "string"
+      type:
+        - "string"
+        - "null"
+      enum:
+        - "IUPAC SMILES+"
+        - "OpenSMILES"
+        - "other"
+      examples:
+        - "IUPAC SMILES+"
+        - "OpenSMILES"
+      x-optimade-unit: "inapplicable"
+    _cheminfo_specification_name_other:
+      description: |-
+        A name of the specification the given SMILES string conforms to, if different from the enumerator values for metadata property '_cheminfo_specification_name'.
+        MUST be defined (non-NULL) if and only if the value for '_cheminfo_specification_name' is known and is equal to 'other'.
+      x-optimade-type: "string"
+      type:
+        - "string"
+        - "null"
+      examples:
+        - "Daylight"
+        - "OpenBabel"
+      x-optimade-unit: "inapplicable"
+    _cheminfo_specification_version:
+      description: |-
+        The version of the SMILES specification given in metadata property '_cheminfo_specification_name'.
+        If '_cheminfo_specification_name_other' contains the name of a software library used to generate SMILES, '_cheminfo_specification_version' MUST be the version of this software library.
+      x-optimade-type: "string"
+      type:
+        - "string"
+        - "null"
+      examples:
+        - "1.0"
+        - "a76e26b32e6f0d18f7dd0cadf1b23449baebb04e"
+      x-optimade-unit: "inapplicable"
+    _cheminfo_special_details:
+      description: |-
+        Other details related to SMILES treatment by the provider that might need relaying.
+        For example, a provider might want to express that stereochemistry is not represented in this SMILES string.
+      x-optimade-type: "string"
+      type:
+        - "string"
+        - "null"
+      examples:
+        - "Stereochemistry is not represented"
+      x-optimade-unit: "inapplicable"
+  x-optimade-unit: "inapplicable"
+x-optimade-unit: "inapplicable"