Rotatable Bonds

Is there a function to calculate Rotatable Bonds?

combipure wrote:

Is there a function to calculate Rotatable Bounds?

Unfortunately, there is no such API function. However, you can use the following smarts query to match rotatable bonds:





[!$([NH]!@C(=O))&!D1&!$(*#*)]-&!@[!$([NH]!@C(=O))&!D1&!$(*#*)]





I recommend to use MolSearch and its findAll() method. It will match the two ends of rotatable bonds.





For an example of the usage of MolSearch, see





http://www.jchem.com/doc/api/chemaxon/sss/search/MolSearch.html





Please note that the above smarts query uses smarts features not available in our latest release (2.2.1.) yet. You have to use our pre-release, which is available from here:





http://www.chemaxon.com/restricted/jtest/





Use your usual username/password.





Best regards,


Szabolcs

combipure wrote:

Is there a function to calculate Rotatable Bonds?

How about the following code to figure it out?

Code:

static int getRotors(Molecule mol) {     int numrotors = 0;     for (int i = 0; i<mol.getBondCount(); i++) {       MolBond bond = mol.getBond(i);       if (bond.getType() == 1 && !mol.isRingBond(i)) {         MolAtom atom1 = bond.getAtom1();         MolAtom atom2 = bond.getAtom2();         if (!atom1.isTerminalAtom() && !atom2.isTerminalAtom()) {           numrotors ++;         }       }     }     return numrotors;   }

We built a new plugin called TopologyAnalyser (currently free), which has a function calculating the number of rotatable bonds.


http://www.chemaxon.com/marvin/chemaxon/marvin/help/calculator-plugins.html#topolanal





API usage example (as an alternative, you can also use the TopologyAnalyser class directly):

Code:

// read input molecule     MolImporter mi = new MolImporter("test.mol");     Molecule mol = mi.read();     mi.close();     // create plugin     TopologyAnalyserPlugin plugin = new TopologyAnalyserPlugin();     // set target molecule     plugin.setMolecule(mol);     // run the calculation     plugin.run();     // get result     int rotatableBondCount = plugin.getRotatableBondCount();     // do something with the results ...