Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

SMILES property #392

Open
wants to merge 16 commits into
base: develop
Choose a base branch
from
Open

SMILES property #392

Changes from 4 commits
Commits
Show all changes
16 commits
Select commit Hold shift + click to select a range
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
8072ca8
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
408ce29
Merge branch 'develop' into SMILES-property
merkys May 31, 2022
5d6b82c
Merge branch 'develop' into SMILES-property
merkys Jun 20, 2022
f998720
Remove "descriptor" from SMILES property description.
merkys Jun 20, 2022
79958c6
Update optimade.rst
merkys Jun 27, 2022
2da23b5
Update optimade.rst
merkys Jun 27, 2022
03f4144
Update optimade.rst
merkys Jun 27, 2022
ed5f2b4
Merge branch 'develop' into SMILES-property
merkys Jul 5, 2022
88b6303
Merge branch 'develop' into SMILES-property
merkys Aug 19, 2022
066a861
Update optimade.rst
merkys Sep 23, 2022
f4c7526
Merge branch 'develop' into SMILES-property
merkys Jun 7, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
16 changes: 16 additions & 0 deletions optimade.rst
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -1988,6 +1988,22 @@ chemical\_formula\_anonymous

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

smiles
merkys marked this conversation as resolved.
Show resolved Hide resolved
~~~~~~

- **Description**: The SMILES (Simplified Molecular Input Line Entry Specification) descriptor for the structure.
merkys marked this conversation as resolved.
Show resolved Hide resolved
- **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
Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

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.

Copy link
Member Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

I have responded to these concerns already.

Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

@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).

- MUST adhere to the `OpenSMILES specification v1.0 <http://opensmiles.org/opensmiles.html>`__.
merkys marked this conversation as resolved.
Show resolved Hide resolved
- When structures or their parts cannot be unambiguously depicted in SMILES according to OpenSMILES recommendations, using the guidelines from `Quirós et al. 2018 <https://jcheminf.biomedcentral.com/articles/10.1186/s13321-018-0279-6>`__ is RECOMMENDED.
- Providers MAY canonicalize produced SMILES descriptors, but this is not mandatory.
ml-evs marked this conversation as resolved.
Show resolved Hide resolved
Generally, providers SHOULD NOT change the descriptor more frequently than the structure itself is modified.

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

Expand Down