public methods: int areEqual -- checks a SMILES string against a reference (-1 for error; 0 for no finds; >0 for number of finds) BitSet[] find -- finds one or more occurances of a SMILES or SMARTS string within a SMILES string int[][] getCorrelationMaps -- returns correlated arrays of atoms String getLastError -- returns any error that was last encountered. String getMolecularFormula -- returns the MF of a SMILES or SMARTS string String getSmiles -- returns a standard SMILES string or a Jmol BIOSMILES string with comment header. BitSet getSubstructureSet -- returns a single BitSet with all found atoms included in Jmol script: string2.find("SMILES", string1) string2.find("SMARTS", string1) e.g. print "CCCC".find("SMILES", "C[C]") select search("smartsString") All bioSMARTS strings begin with ~ (tilde). | |