deprot-carboxy.java

// Pattern interface should be used for matching rather than SMARTSQueryTool,
// more efficient and easier to use.
Pattern carboxy = SmartsPattern.compile("[Ov2X2H1+0]-[Cv4X3]=[Ov2X1H0]", bldr);

// Mappings object has several utils, we need basics only here 
for (int[] mapping : caboxy.matchAll(mol).uniqueAtoms()) {
  IAtom hydroxy = mol.getAtom(mapping[0]); 
  hydroxy.setImplicitHydrogenCount(0);
  hydroxy.setFormalCharge(-1);
}

// don't output Canonical SMILES
String smi = SmilesGenerator.isomeric().create(mol);