readMolFromSmi: Read Molecules from SMILES Files and Return Parsed Java...

In wind22zhu/BioMedR: Generating Various Molecular Representations for Chemicals, Proteins, DNAs, RNAs and Their Interactions

Description

Read Molecules from SMILES Files and Return Parsed Java Molecular Object or Plain Text List

Usage

readMolFromSmi(smifile, type = c("mol", "text"))

Arguments

smifile	Character vector, containing SMILES file location(s).
type	'mol' or 'text'. 'mol' returns parsed Java molecular object, used for 'text' returns (plain-text) character string list. For common molecular descriptors and fingerprints, use 'mol'. For descriptors and fingerprints calculated by OpenBabel, i.e. functions named extrDrugOB...() , use 'text'.

Details

This function reads molecules from SMILES strings and return parsed Java molecular object or plain text list needed by extrDrug...() functions.

Value

A list, containing parsed Java molecular object or character strings.

Author(s)

Min-feng Zhu <[e-mail]>, Nan Xiao <http://r2s.name>

See Also

See readMolFromSDF for reading molecules from SDF files and returning parsed Java molecular object.

Examples

smi = system.file('vignettedata/test.smi', package = 'BioMedR')
mol1 = readMolFromSmi(smi, type = 'mol')
mol2 = readMolFromSmi(smi, type = 'text')

wind22zhu/BioMedR documentation built on Oct. 21, 2019, 12:51 p.m.