Chemistry Cartridge CGI Examples

Chemistry Cartridge CGI Functions

Daylight 4.61, dayblob 46107, Oracle Server 8.13

A number of the functions in the prototype Chemistry Cartridge v46107 are described below,

LOOKFOR
The lookfor operator allows selection of rows containing exactly the same structure as a given SMILES. This is a fast search which is done by indexed (hashed) retrieval.
A related operator, lookup, is also available. It is even faster, but requires a canonical SMILES as input. smi2usmi() and id2usmi() are available in functional form to return a canonical SMILES, given a generic SMILES and binary row ID, respectively.
TAUTOMERS
The tautomers operator allows selection of rows containing possible tautomers of a given SMILES. For this purpose, structures are considered tautomers if they have same molecular graph, molecular formula (including hydrogen count) and net charge. I.e., they can be changed into one another by moving only electrons and hydrogen atoms. This is a fast search which is done by indexed (hashed) retrieval.
The functional form is available as smi_tautomers() which tests if two SMILES are tautomeric by the above definition.
CONTAINS
The contains operator is extended to allow selection of structures which contain a query substructure. The query substructure is given as a SMILES structure; results will include all hydrogen substitutions. This is the classic "open substructure search". WARNING: Searching for superstructures of common substructures like CCC is not advised: it may take a long time, produce a lot of output, and the results will not be very interesting.
The functional form is available as smi_contains() which tests if one SMILES structure is contained by another.
SIMILAR (score)
The similar operator allows selection of rows containing structures which are similar to a given structure. A fingerprint-based binary Tanimoto coefficient is used for similarity determination, where a value of 1.0 means "identical", 0.0 means "completely dissimliar". The level of similarity to be required is user-adjustable. This is a fast, robust search type. At high levels (~0.8 or more), this is a fast, robust search type. At low levels (~0.65 or less), the results are not meaningful and result in large answer sets.
Functional forms smi_similarity() and id_similarity() are available which return the similarity of two SMILES and two Row IDs, respectively. The operator score() is also provided as an ancillary operator to similar().
NEAREST
The nearest operator allows selection of rows containing the nearest neighbors of a given structure. The Tanimoto similarity coefficient is used for nearest neighbor determination. The number of nearest neighbors to be selected is user-adjustable. This is a fast, robust search type.
MATCHES
The matches operator allows selection of rows containing structures which match a given SMARTS pattern. This very powerful search is primarily useful for advanced users. Though this search is highly optimized, it can be slow if all query nodes contain variablity. Note that this search takes a SMARTS (pattern) as input rather than a SMILES (structure).
The functional form is available as smi_matches() which tests if a SMILES structure matches a given pattern.

Daylight Chemical Information Systems, Inc.
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Chemistry Cartridge CGI Functions

`LOOKFOR`

`TAUTOMERS`

`CONTAINS`

`SIMILAR` (score)

`NEAREST`

`MATCHES`

Chemistry Cartridge CGI Functions

LOOKFOR

TAUTOMERS

CONTAINS

SIMILAR (score)

NEAREST

MATCHES

`LOOKFOR`

`TAUTOMERS`

`CONTAINS`

`SIMILAR` (score)

`NEAREST`

`MATCHES`