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Retrieve Drug Molecules in MOL Format from the PubChem Database

Source: R/101-getDrugPubChem.R
getMolFromPubChem.Rd

Retrieve Drug Molecules in MOL Format from the PubChem Database

Usage

getMolFromPubChem(id, parallel = 5)

Arguments

id

A character vector, as the PubChem drug ID.

parallel

An integer, the parallel parameter, indicates how many processes 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.

Value

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

Details

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

See also

See getSmiFromPubChem for retrieving drug molecules in SMILES format from the PubChem database.

Examples

id = c('7847562', '7847563')  # Penicillamine
# \donttest{
getMolFromPubChem(id)# }
#> [[1]]
#> [1] "7847562\n  -OEChem-09182409172D\n\n  9  8  0     1  0  0  0  0  0999 V2000\n   10.5700  -21.9100    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   11.7824  -22.6100    0.0000 C   0  0  3  0  0  0  0  0  0  0  0  0\n    9.3576  -22.6100    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n   10.5700  -20.5100    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n   12.9779  -21.9196    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   14.1653  -22.6051    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0\n   11.7825  -24.0098    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n   12.9780  -20.5103    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   14.1904  -21.2196    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  1  2  1  0  0  0  0\n  1  3  1  0  0  0  0\n  1  4  2  0  0  0  0\n  2  5  1  0  0  0  0\n  5  6  1  0  0  0  0\n  2  7  1  1  0  0  0\n  5  8  1  0  0  0  0\n  5  9  1  0  0  0  0\nM  END\n> <PUBCHEM_COMPOUND_ID_TYPE>\n0\n\n> <PUBCHEM_TOTAL_CHARGE>\n0\n\n> <PUBCHEM_SUBSTANCE_ID>\n7847562\n\n> <PUBCHEM_SUBSTANCE_VERSION>\n11\n\n> <PUBCHEM_EXT_DATASOURCE_NAME>\nKEGG\n\n> <PUBCHEM_EXT_DATASOURCE_REGID>\nD00496\n\n> <PUBCHEM_SUBSTANCE_COMMENT>\nSame as: <a href=\"http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?sid=9622\">C07418</a>\nATC code: M01CC01\n\n> <PUBCHEM_SUBSTANCE_SYNONYM>\nPenicillamine (JAN/USP/INN)\nCuprimine (TN)\nDepen (TN)\n52-67-5\nD00496\n\n> <PUBCHEM_GENERIC_REGISTRY_NAME>\n52-67-5\n\n> <PUBCHEM_XREF_EXT_ID>\nD00496\n\n> <PUBCHEM_EXT_DATASOURCE_URL>\nhttp://www.genome.jp/kegg/\n\n> <PUBCHEM_EXT_SUBSTANCE_URL>\nhttp://www.genome.jp/dbget-bin/www_bget?dr:D00496\n\n> <PUBCHEM_CID_ASSOCIATIONS>\n5852  1\n\n> <PUBCHEM_COORDINATE_TYPE>\n1\n3\n\n> <PUBCHEM_BONDANNOTATIONS>\n2  7  5\n\n$$$$\n"
#> 
#> [[2]]
#> [1] "7847563\n  -OEChem-09182409172D\n\n 26 27  0     1  0  0  0  0  0999 V2000\n   28.2474  -15.2160    0.0000 C   0  0  3  0  0  0  0  0  0  0  0  0\n   28.2474  -16.6202    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   29.6517  -16.6202    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n   29.6517  -15.2160    0.0000 C   0  0  3  0  0  0  0  0  0  0  0  0\n   30.9856  -17.0414    0.0000 C   0  0  3  0  0  0  0  0  0  0  0  0\n   31.8280  -15.9180    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   30.9856  -14.7946    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0\n   32.8111  -16.9009    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   32.8111  -14.9350    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   31.4771  -18.3753    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   32.8811  -18.3753    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0\n   30.6344  -19.4986    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n   29.6517  -13.8117    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0\n   27.0539  -14.5138    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n   25.8603  -15.2160    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   27.0539  -17.3222    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n   25.8603  -16.6202    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n   24.6414  -14.5187    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   23.4495  -15.2137    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n   22.2365  -14.5133    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   22.2362  -13.0845    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   21.0242  -12.3850    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   19.8125  -13.0849    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   19.8127  -14.5138    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   21.0247  -15.2132    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   34.3547  -18.4020    0.0000 K   0  3  0  0  0  0  0  0  0  0  0  0\n  1  2  1  0  0  0  0\n  2  3  1  0  0  0  0\n  3  4  1  0  0  0  0\n  1  4  1  0  0  0  0\n  3  5  1  0  0  0  0\n  5  6  1  0  0  0  0\n  6  7  1  0  0  0  0\n  4  7  1  0  0  0  0\n  6  8  1  0  0  0  0\n  6  9  1  0  0  0  0\n  5 10  1  6  0  0  0\n 10 11  1  0  0  0  0\n 10 12  2  0  0  0  0\n  4 13  1  6  0  0  0\n  1 14  1  1  0  0  0\n 14 15  1  0  0  0  0\n  2 16  2  0  0  0  0\n 15 17  2  0  0  0  0\n 15 18  1  0  0  0  0\n 18 19  1  0  0  0  0\n 19 20  1  0  0  0  0\n 20 21  2  0  0  0  0\n 21 22  1  0  0  0  0\n 22 23  2  0  0  0  0\n 23 24  1  0  0  0  0\n 24 25  2  0  0  0  0\n 20 25  1  0  0  0  0\nM  CHG  2  11  -1  26   1\nM  END\n> <PUBCHEM_COMPOUND_ID_TYPE>\n0\n\n> <PUBCHEM_TOTAL_CHARGE>\n0\n\n> <PUBCHEM_SUBSTANCE_ID>\n7847563\n\n> <PUBCHEM_SUBSTANCE_VERSION>\n10\n\n> <PUBCHEM_EXT_DATASOURCE_NAME>\nKEGG\n\n> <PUBCHEM_EXT_DATASOURCE_REGID>\nD00497\n\n> <PUBCHEM_SUBSTANCE_COMMENT>\nTarget: penicillin binding protein\nATC code: J01CE02\n\n> <PUBCHEM_SUBSTANCE_SYNONYM>\nPenicillin V potassium (USP)\nPhenoxymethylpenicillin potassium (JAN)\nVeetids (TN)\n132-98-9\nD00497\n\n> <PUBCHEM_GENERIC_REGISTRY_NAME>\n132-98-9\n\n> <PUBCHEM_XREF_EXT_ID>\nD00497\n\n> <PUBCHEM_EXT_DATASOURCE_URL>\nhttp://www.genome.jp/kegg/\n\n> <PUBCHEM_EXT_SUBSTANCE_URL>\nhttp://www.genome.jp/dbget-bin/www_bget?dr:D00497\n\n> <PUBCHEM_CID_ASSOCIATIONS>\n23676814  1\n6869  2\n5462222  2\n\n> <PUBCHEM_COORDINATE_TYPE>\n1\n3\n\n> <PUBCHEM_BONDANNOTATIONS>\n1  14  5\n4  13  6\n5  10  6\n\n$$$$\n"
#>