Retrieve Drug Molecules in MOL Format from the PubChem Database
Source:R/101-getDrugPubChem.R
getMolFromPubChem.RdRetrieve Drug Molecules in MOL Format from the PubChem Database
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 than20.
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] "7847562\n -OEChem-04252420502D\n\n 9 8 0 1 0 0 0 0 0999 V2000\n 14.1653 -22.6051 0.0000 S 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 9.3576 -22.6100 0.0000 O 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 12.9779 -21.9196 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 10.5700 -21.9100 0.0000 C 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 5 1 0 0 0 0\n 2 7 2 0 0 0 0\n 3 7 1 0 0 0 0\n 6 4 1 1 0 0 0\n 5 6 1 0 0 0 0\n 5 8 1 0 0 0 0\n 5 9 1 0 0 0 0\n 6 7 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>\n52-67-5\nCuprimine (TN)\nD00496\nDepen (TN)\nPenicillamine (JAN/USP/INN)\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>\n6 4 5\n\n$$$$\n"
#> [2] "7847563\n -OEChem-04252420502D\n\n 26 27 0 1 0 0 0 0 0999 V2000\n 34.3547 -18.4020 0.0000 K 0 3 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 27.0539 -17.3222 0.0000 O 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 25.8603 -16.6202 0.0000 O 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 29.6517 -16.6202 0.0000 N 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 29.6517 -15.2160 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0\n 28.2474 -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 28.2474 -16.6202 0.0000 C 0 0 0 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 31.4771 -18.3753 0.0000 C 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 25.8603 -15.2160 0.0000 C 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 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 21.0247 -15.2132 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 19.8127 -14.5138 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 29.6517 -13.8117 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0\n 2 10 1 0 0 0 0\n 2 14 1 0 0 0 0\n 3 13 2 0 0 0 0\n 4 15 1 0 0 0 0\n 5 15 2 0 0 0 0\n 6 18 2 0 0 0 0\n 7 19 1 0 0 0 0\n 7 20 1 0 0 0 0\n 8 10 1 0 0 0 0\n 8 12 1 0 0 0 0\n 8 13 1 0 0 0 0\n 11 9 1 1 0 0 0\n 9 18 1 0 0 0 0\n 10 11 1 0 0 0 0\n 10 26 1 6 0 0 0\n 11 13 1 0 0 0 0\n 12 14 1 0 0 0 0\n 12 15 1 6 0 0 0\n 14 16 1 0 0 0 0\n 14 17 1 0 0 0 0\n 18 19 1 0 0 0 0\n 20 21 2 0 0 0 0\n 20 22 1 0 0 0 0\n 21 23 1 0 0 0 0\n 22 24 2 0 0 0 0\n 23 25 2 0 0 0 0\n 24 25 1 0 0 0 0\nM CHG 2 1 1 4 -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>\n9\n\n> <PUBCHEM_EXT_DATASOURCE_NAME>\nKEGG\n\n> <PUBCHEM_EXT_DATASOURCE_REGID>\nD00497\n\n> <PUBCHEM_SUBSTANCE_COMMENT>\nTarget: penicillin binding protein\nActivity: Antibacterial, Cell wall biosynthesis inhibitor\nATC code: J01CE02\n\n> <PUBCHEM_SUBSTANCE_SYNONYM>\n132-98-9\nD00497\nPenicillin V potassium (USP)\nPhenoxymethylpenicillin potassium (JAN)\nVeetids (TN)\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>\n10 26 6\n12 15 6\n11 9 5\n\n$$$$\n"