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

In 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')

BioMedR documentation built on Nov. 17, 2017, 10:08 a.m.