Query File (CQF Files)
Query files (*.cqf) are used to store one or more encoded query strings, and represent the principal means by which ADMET Predictor encodes query information. These files are used in a variety of applications, including:
Class generation.
Each query in the file contains instructions for forming a single class from the set of molecules contained in the open spreadsheet. For instance, a user might create a query file containing a list of ten important scaffolds or substructures. When the file is used for class generation, the result will be to construct ten new classes, each containing only the spreadsheet molecules that contain the relevant scaffold in their molecular structure. The scaffolds themselves are highlighted in the Classes tab. See the Custom Scaffolds section for additional information. Note that a similar functionality is available using an SD file.
Spreadsheet search.
The Query by Structure/Property dialog includes an option to import a single query from an external query file. This query is then used to search the current spreadsheet and highlight those molecules that match it. See the Searching The Spreadsheet section for additional information. Note that a similar functionality is available using a molfile.
A valid query file consists of one or more encoded queries separated by delimiters ($$$$). A query file can also contain comment lines, which start with a “#” character. Thus the following is an example of a query file containing two queries:
# Query 1
MolWeight < 500 && RotBond < 10
&& HAcc > 3
$$$$
# Query 2
SLQ c1ccccc1 U = 3
$$$$
Note that a single encoded query can occupy more than a single line, which is why a delimiter symbol is required to separate queries. If a file contains only a single query, however, the delimiter is optional.
Query files can be generated either manually by users or automatically within ADMET Predictor using the Query Wizard.
A few special keywords allowed in CQF files are not described in the section on encoded queries. QUERYNAME can be used to provide an optional name for a query. QUERYTIP can be used to provide an optional tooltip, which is utilized when using the feature to add compound attributes to the spreadsheet using the Data >> Add Compound Attributes menu item. See the ADMET predictor distribution file called AttributeExamples.cqf for illustrations of these keywords. Please note that tooltips are not currently saved to XTK/CTK files.