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

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 extractDrugOB...() , use 'text'.

Value

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

Details

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

See also

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

Examples

smi = system.file('vignettedata/FDAMDD.smi', package = 'Rcpi')
# \donttest{
mol1 = readMolFromSmi(smi, type = 'mol')
#> Error in parseSmiles(smi): The package "rcdk" is required to parse SMILES
mol2 = readMolFromSmi(smi, type = 'text')# }