Auto-QChem stores molecular descriptors in a MongoDB type database. A small web-based user-interface has been created to
facilitate extractions of descriptors from the database into .xlsx files for further analysis.
Navigate to the autoqchem.org
Query form has 6 fields, first 4 are required, last 2 are optional:
- Dataset tag - select dataset filter, use 'ALL' for a whole DB query. Each molecule in the DB has an associated datasets tag (or a list of tags), they are used to mark specific collections of molecules dedicated to specific analyses
- Solvent - solvent filter, use 'ALL' to ignore filter
- Functional - functional filter, use 'ALL' to ignore filter
- Basis Set - basis set filter, use 'ALL' to ignore filter
- SMARTS substructure - filters the molecules for substructre using the SMARTS query. A quick reference to the SMARTS query language can be looked up here https://www.daylight.com/dayhtml_tutorials/languages/smarts/index.html
- SMILES - smiles filter. This can be used for searches for a specific molecule. Canonicalization is not required.
Upon successful query additional 2 tabs will appear, "Download Descriptors" and "Export Molecule List"
Download form has 2 fields, both are required:
- Descriptor Presets (multiple choice) - the following presets are available, choose as many as needed:
- Global - molecule level descriptors, e.g. homo energy, dipole moment, molecular weight, etc.
- Min Max Atomic - atomic level descriptors minimum and maximum over the atoms within the molecule, e.g. buried volume, Mulliken charge, NMR shift, etc.
- Substructure Atomic - only relevant if substructure was used for the query. The atoms matching the substructure are extracted in consistent order and their descriptors are obtained
- Common Core - atomic level descriptors for the common core of atoms within the dataset, the common core is determined using the MCS procedure from rdkit. If substructure has been used for filtering, the common core will include the substructure and potentially more atoms.
- Labeled Atomic - atomic level descriptors for labeled molecules. The labels must be consistent, i.e. each molecule must have exactly the same labels, for example 1,2,3,4, the labelled elements can be different, only the numbering scheme shall be consistent.
- Transitions - top 10 excited state transitions ordered by their oscillation strength
- Conformer option (single choice) - choose one of the following options:
- Boltzmann - Boltzmann average
- Max - lowest energy conformer (maximum weight conformer)
- Min - highest energy conformer (minimum weight conformer)
- Mean - arithmetic average
- Std - standard deviation over the conformers
- Any - randomily chosen conformer The result of the query is downloaded into an
.xlsxsheet.
Export button downloads the queried list of molecules into an .xlsx sheet.
Result of an example query on a specific tag containing primary sulfonamides, and with SMARTS query for anhydrides,
resulting in 75 matches.
For each entry in the table a link to a descriptors lookup is available in the rightmost column. It displays an interactive 3D visualization of the molecule conformers as well as the descriptors of the molecule. If the molecule contains multiple conformations, the descriptors are Boltzman averages over the conformer ensemble.
