createMolfile: Create MOL file for a chemical structure

In sneumann/RMassBank: Workflow to process tandem MS files and build MassBank records

Description

Creates a MOL file (in memory or on disk) for a compound specified by the compound ID or by a SMILES code.

Usage

createMolfile(id_or_smiles, fileName = FALSE)

Arguments

id_or_smiles	The compound ID or a SMILES code.
fileName	If the filename is set, the file is written directly to disk using the specified filename. Otherwise, it is returned as a text array.

Details

The function invokes OpenBabel (and therefore needs a correctly set OpenBabel path in the RMassBank settings), using the SMILES code retrieved with findSmiles or using the SMILES code directly. The current implementation of the workflow uses the latter version, reading the SMILES code directly from the MassBank record itself.

Value

A character array containing the MOL/SDF format file, ready to be written to disk.

Author(s)

Michael Stravs

References

OpenBabel: http://openbabel.org

See Also

findSmiles

Examples

# Benzene:
## Not run: 
createMolfile("C1=CC=CC=C1")

## End(Not run)

sneumann/RMassBank documentation built on Oct. 20, 2020, 3:19 p.m.