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

In Rcpi: Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery

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

Details

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

Value

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

Author(s)

Nan Xiao <https://nanx.me>

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')

mol1 = readMolFromSmi(smi, type = 'mol')
mol2 = readMolFromSmi(smi, type = 'text')

Example output

OpenJDK 64-Bit Server VM warning: Can't detect initial thread stack location - find_vma failed
Warning message:
system call failed: Cannot allocate memory 

Rcpi documentation built on Nov. 8, 2020, 8:23 p.m.