moldb-extract-confs.md

Job: moldb-extract-confs

This describes how to run the moldb-extract-confs job from the ligand preparation category in the moldb collection.

What the job does

The extracts low energy 3D conformers from the MolDB database and saves them to a file suitable for virtual screening. Files can be saved in CXSMILES or SDF formats.

NOTE: Before running this job ensure you have run the moldb-gen-confs jobs to completion to generate a full set of molecules otherwise you will not get a complete set.

Implementation details

• Job implementation: filter.nf
• Job definition: jobs.moldb-extract-confs in moldb.yaml

How to run the job

For general information on using this job and interpreting the output look at the Extracting 3D conformers section here.

Inputs

• Filter specification file: file containing the specification of molecular property filters

Options

• Output file name: output file name (.sdf)
• Max number of molecules to extract: the maximum number of molecules to extract
• Include tautomers include tautomers in the output (1)
• Include microstates include microstates (charge forms) in the output (1)
• Include stereoisomers include stereoisomers in the output (1)

(1) The base molecule (non enumerated) is always output

Related topics

• About MOlDB
• moldb-enumerate-mols job