getDrug: Retrieve Drug Molecules in MOL and SMILES Format from...

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

Description

Retrieve Drug Molecules in MOL and SMILES Format from Databases(BMgetDrug)

Retrieve Drug Molecules in MOL and Smi Format from the PubChem Database(BMgetDrug...PubChem)

Retrieve Drug Molecules in MOL and Smi Format from the ChEMBL Database(BMgetDrug...ChEMBL)

Retrieve Drug Molecules in InChI Format from the CAS Database(BMDrugMolCAS)

Retrieve Drug Molecules in MOL and Smi Format from the KEGG Database(BMgetDrug...KEGG)

Retrieve Drug Molecules in MOL and Smi Format from the DrugBank Database(BMgetDrug...DrugBank)

Usage

BMgetDrug(id, from = c("pubchem", "chembl", "cas", "kegg", "drugbank"),
  type = c("mol", "smile"), parallel = 5)

BMgetDrugMolPubChem(id, parallel = 5)

BMgetDrugSmiPubChem(id, parallel = 5)

BMgetDrugMolChEMBL(id, parallel = 5)

BMgetDrugSmiChEMBL(id, parallel = 5)

BMDrugMolCAS(id, parallel = 5)

BMgetDrugMolKEGG(id, parallel = 5)

BMgetDrugSmiKEGG(id, parallel = 5)

BMgetDrugMolDrugBank(id, parallel = 5)

BMgetDrugSmiDrugBank(id, parallel = 5)

Arguments

id	A character vector, as the drug ID(s).
from	The database, one of 'pubchem', 'chembl', 'cas', 'kegg', 'drugbank'.
type	The returned molecule format, mol or smile.
parallel	An integer, the parallel parameter, indicates how many process the user would like to use for retrieving the data (using RCurl), default is 5. For regular cases, we recommend a number less than 20.

Details

This function retrieves drug molecules in MOL and SMILES format from five databases.

This function retrieves drug molecules in MOL format from the PubChem database.

This function retrieves drug molecules in MOL format from the ChEMBL database.

This function retrieves drug molecules in InChI format from the CAS database. CAS database only provides InChI data, so here we return the molecule in InChI format, users could convert them to SMILES format using Open Babel (http://openbabel.org/) or other third-party tools.

This function retrieves drug molecules in MOL format from the KEGG database.

This function retrieves drug molecules in MOL format from the DrugBank database.

Value

A length of id character vector, each element containing the corresponding drug molecule.

Author(s)

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

See Also

See BMgetProt for retrieving protein sequences from three databases.

Examples

# BMgetDrug
id = c('DB00859', 'DB00860')
BMgetDrug(id, 'drugbank', 'smile')


# BMgetDrugMolPubChem
id = c('7847562', '7847563')  # Penicillamine
BMgetDrugMolPubChem(id)


# BMgetDrugsmiPubChem
id = c('7847562', '7847563')  # Penicillamine
BMgetDrugSmiPubChem(id)


# BMgetDrugMolChEMBL
id = 'CHEMBL1430'  # Penicillamine
BMgetDrugMolChEMBL(id)


# BMgetDrugSmiChEMBL
id = 'CHEMBL1430'  # Penicillamine
BMgetDrugSmiChEMBL(id)


# BMDrugMolCAS
id = '52-67-5'  # Penicillamine
BMDrugMolCAS(id)


# BMgetDrugMolKEGG
id = 'D00496'  # Penicillamine
BMgetDrugMolKEGG(id)


# BMgetDrugSmiKEGG
id = 'D00496'  # Penicillamine
BMgetDrugSmiKEGG(id)


# BMgetDrugMolDrugBank
id = 'DB00859'  # Penicillamine
BMgetDrugMolDrugBank(id)


# BMgetDrugSmiDrugBank
id = 'DB00859'  # Penicillamine
BMgetDrugSmiDrugBank(id)

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