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Calculate HBA HBD Count: the algorithm behind

Dear,

What is the algorithm to calculate HBA_Count, HBD_Count. The help file has only the information:
* HBA Count : Returns the count of the number of hydrogen bond accepting groups in the molecule
* HBD Count : Returns the count of the number of hydrogen bond donating groups in the molecule

best regards, Paul Nelis
sarah.archibaldsarah.archibald
Hi Paul,

Have a look at the help text on the component 'Num H Acceptor Donors'.
We had some discussions with users a few years ago about the 'correct' values for these.

Sarah
sarah.archibaldsarah.archibald
Hi Paul,

Have a look at the help text on the component 'Num H Acceptor Donors'.
We had some discussions with users a few years ago about the 'correct' values for these.

Sarah
moises.hassanmoises.hassan
The help text in the 'Num H Acceptor Donors' calculator component can help clarify this issue. Here it is:

Calculates and outputs the counts of hydrogen bond donors and acceptors in the input molecules. Four properties can be calculated:

Num_H_Acceptors: number of heteroatoms (Oxygen, Nitrogen, Sulfur, or Phosphorus) with one or more lone pairs, excluding atoms with positive formal charges, amide and pyrrole-type Nitrogens, and aromatic Oxygen and Sulfur atoms in heterocyclic rings.
Num_H_Donors: number of heteroatoms (Oxygen, Nitrogen, Sulfur, or Phosphorus) with one or more attached Hydrogen atoms.
Num_H_Acceptors_Lipinski: number of acceptors using Lipinski's simpler convention of counting all Oxygen and Nitrogen atoms as acceptors.
Num_H_Donors_Lipinski: the number of OH and NH bonds.  Note that primary amines count as two donors.

Note:
The calculable properties HBA_Count and HBD_Count, available for use in PilotScript expressions, are defined differently than the properties described above. They are calculated using substructure queries to count the number of times the queries match structural features in the molecule. The substructure queries used to calculate these properties are present in the data/Queries folder:

Acceptors: HBA-Nitrogen.mol, HBA-Carboxylate.mol, HBA-Ester.mol, HBA-Ether.mol, HBA-Carbonyl.mol, HBA-Phenol.mol
Donors: HBD-PrimaryAlcohol.mol, HBD-PrimaryAmine.mol, HBD-SecondaryAlcohol.mol, HBD-SecondaryAmine.mol, HBD-TertiaryAmine.mol

Users can change the way hydrogen bond donors and acceptors are counted by adding their own definitions. The only constraint is that the file names should start with the prefix HBA- or HBD-