As an example, below will follow a small script that takes a PubChem compound identifier (CID) and downloads the corresponding ASN.1 XML file, parses it and counts the number of atoms:
Script code/PubChemDownload.py
cid = 5282253
reader = PCCompoundXMLReader(
URL(
"https://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=" + str(cid) +
"&disopt=SaveXML"
).openStream()
)
mol = reader.read(SilentChemObjectBuilder.getInstance().newAtomContainer())
print("CID: {}".format(mol.getProperty("PubChem CID")))
print(f"Atom count: {mol.getAtomCount()}")
It reports:
CID: 5282253
Atom count: 43
PubChem ASN.1 files come with an extensive list of molecular properties. These
are stored as properties on the molecule object and can be retrieved using the
getProperties() method, or, using the Groovy bean formalism:
Script code/PubChemDownloadProperties.py
cid = 5282253
reader = PCCompoundXMLReader(
URL(
"https://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=" + str(cid) +
"&disopt=SaveXML"
).openStream()
)
mol = reader.read(SilentChemObjectBuilder.getInstance().newAtomContainer())
for key, value in mol.getProperties().items():
print(f"{key}={value}")
which lists the properties for the earlier downloaded domoic acid:
PubChem CID=5282253
Compound Complexity=510
Fingerprint (SubStructure Keys)=00000371E0723800000000000000000000000000000160...
000000000000000000000000000000001E00100800000D28C18004020802C00200880220D208...
000000002000000808818800080A001200812004400004D000988003BC7F020E800000000000...
00000000000000000000000000000000
IUPAC Name (Allowed)=(2S,3S,4S)-3-(carboxymethyl)-4-[(1Z,3E,5R)-5-carboxy-1-me...
thyl-hexa-1,3-dienyl]pyrrolidine-2-carboxylic acid
IUPAC Name (CAS-like Style)=(2S,3S,4S)-4-[(2Z,4E,6R)-6-carboxyhepta-2,4-dien-2...
-yl]-3-(carboxymethyl)-2-pyrrolidinecarboxylic acid
IUPAC Name (Markup)=(2<I>S</I>,3<I>S</I>,4<I>S</I>)-4-[(2<I>Z</I>,4<I>E</I>,6<...
I>R</I>)-6-carboxyhepta-2,4-dien-2-yl]-3-(carboxymethyl)pyrrolidine-2-carbox...
ylic acid
IUPAC Name (Preferred)=(2S,3S,4S)-4-[(2Z,4E,6R)-6-carboxyhepta-2,4-dien-2-yl]-...
3-(carboxymethyl)pyrrolidine-2-carboxylic acid
IUPAC Name (Systematic)=(2S,3S,4S)-3-(2-hydroxy-2-oxoethyl)-4-[(2Z,4E,6R)-6-me...
thyl-7-oxidanyl-7-oxidanylidene-hepta-2,4-dien-2-yl]pyrrolidine-2-carboxylic...
acid
IUPAC Name (Traditional)=(2S,3S,4S)-3-(carboxymethyl)-4-[(1Z,3E,5R)-5-carboxy-...
1-methyl-hexa-1,3-dienyl]proline
InChI (Standard)=InChI=1S/C15H21NO6/c1-8(4-3-5-9(2)14(19)20)11-7-16-13(15(21)2...
2)10(11)6-12(17)18/h3-5,9-11,13,16H,6-7H2,1-2H3,(H,17,18)(H,19,20)(H,21,22)/...
b5-3+,8-4-/t9-,10+,11-,13+/m1/s1
InChIKey (Standard)=VZFRNCSOCOPNDB-AOKDLOFSSA-N
Log P (XLogP3-AA)=-1.3
Mass (Exact)=311.13688739
Molecular Formula=C15H21NO6
Molecular Weight=311.33
SMILES (Canonical)=CC(C=CC=C(C)C1CNC(C1CC(=O)O)C(=O)O)C(=O)O
SMILES (Isomeric)=C[C@H](/C=C/C=C(/C)\[C@H]1CN[C@@H]([C@H]1CC(=O)O)C(=O)O)C(=O)O
Topological (Polar Surface Area)=124
Weight (MonoIsotopic)=311.13688739
Another common input mechanism in cheminformatics is the line notation. Several line notations have been proposed, including the Wiswesser Line Notation (WLN) [1] and the Sybyl Line Notation (SLN) [2], but the most popular is SMILES [3]. There is a Open Standard around this format called OpenSMILES, available at http://www.opensmiles.org/.
The CDK can both read and write SMILES, or at least a significant subset of the
line notation. You can parse a SMILES into a IAtomContainer with the
SmilesParser. The constructor of the parser takes an IChemObjectBuilder (see Section ??)
because it needs to know what CDK interface implementation it must use to create
classes. This example uses the DefaultChemObjectBuilder:
Script code/ReadSMILES.py
sp = SmilesParser(Builder.getInstance())
mol = sp.parseSmiles("CC(=O)OC1=CC=CC=C1C(=O)O")
print(f"Aspirin has {mol.getAtomCount()} atoms.")
This outputs:
Aspirin has 13 atoms.