API suggestions

MoleculeGraph.getAtomCount(int atno) gets the number of atoms with the given atomic number; when atno == 1, sum includes both implicit and explicit H atoms

MoleculeGraph.getAtomCount(String symbol) gets the number of atoms with the given symbol; when atno == 1, sum includes both implicit and explicit H atoms

Hi Bob,

We are considering your request.
Did you mean that MoleculeGraph.getAtomCount(String symbol) shoud return the number of atoms with the given symbol; when symbol == H, sum includes both implicit and explicit H atoms?

Regards,
Erika

Yes.  I should add that D and T atoms should be included in getAtomCount("H").

Hi Bob,

Please use ElementalAnalyserPlugin. ElementalAnalyserPlugin.getAtomCount(int z) returns the number of atoms with given atomic number
(including its isotopes):

http://www.chemaxon.com/marvin/help/developer/beans/api/chemaxon/marvin/calculations/ElementalAnalyserPlugin.html

Regards,

Erika.

That procedure seems awfully cumbersome for something as simple as counting the number of atoms of a certain element.  

Both Molecule and ElementalAnalyserPlugin have getFormula() methods; seems to me that they should both have getAtomCount() methods, as well.

Hi Bob,

The Molecule.getAtomCount() returns the atom count without the implicit hydrogens. If we add a method like Molecule.getAtomCount(int z) then we expect that the sum of the atom-counts of the individual atom-types equals the Molecule.getAtomCount(). This condition won't be satisfied because of the implicit hydrogens.

We are just before a major refactoring/modularization step therefore we dont want to overload the Molecule with methods which might cause inconsistency and possible deprecation later. I added your feature request to our issue-tracking system and we will investigate this problem again during the refactoring. We will notify you about the decision.

 

Regards,

Erika

Erika wrote:

The Molecule.getAtomCount() returns the atom count without the implicit hydrogens. If we add a method like Molecule.getAtomCount(int z) then we expect that the sum of the atom-counts of the individual atom-types equals the Molecule.getAtomCount(). This condition won't be satisfied because of the implicit hydrogens.

OK, you can return getExplicitHCount() when z == 1.  The important thing is to have a method that counts atoms other than H.  We already have methods that count H atoms (explicit or implicit).  

BTW, are D and T atoms included in getExplicitHCount()?

Hi Bob,

We are going to implement the MoleculeGraph.getAtomCount(int z) this way,
the method will return getExplicitHCount() when z == 1.

BTW, are D and T atoms included in getExplicitHCount()?

 

Yes, they are included.

Regards,
Erika

Dear Bob,

FYI, MoleculeGraph.getAtomCount(int atomicNumber) will be available in release 5.5 which is planned for the beginning of April 2011.

Zsuzsa