I want to collect a decoy set of compounds for pharmacophore search. In this case I need to extract the number of Hydrogen bond donor, Hydrogen bond acceptor and also counts of nonpolar atom for a molecule. I found out that cxcalc could be useful for counts of hydrogen bonds. But my problem is about counts of nonpolar atoms. How can I extract this parameter from a given molecule? What is your opinion about my problem?
There is no a direct "tool" for your purposes. The only what you can do at present is to calculate the partial charges of the atoms in a molecule.And next ,take the difference of the partial charges of the neighbouring atoms at the end of a chemical bod. If the partial charge difference reaches a certain threshold value for a bond than you can say that the atoms of the bond are polarized ones.
A suitable threshold value is for example =0.12.
In you investigation you can specify weak , medium , strong ,...etc. type of polar atoms depending on the choosen threshold value.
For example ,on the attached figures the partial charge difference between C(7) and O(6) = 0.04 - (-.38)=0.42
since 0.42 is larger than 0.12 this is why the C(7) O(6) bond is polar, therefore, these two atoms can be called as polar.
All other bond can be checked in this way.
If I understand correctly, carbon atoms could be polar and also nonpolar, related to the situation. isn't it?
E.g. C(1) in nonpolar and C(4) is polar.
Thank you for your response.
I found an article that explains a formula. This formula needs the count of nonpolar atoms. I send an e-mail to correspondence and ask about it. The answer was, nonpolar atoms in this formula mean the count of carbons and halogens. So if I want to use this formula for my project, I need to extract the number of carbons and halogens in one molecule with cxcalc. Could please guide me to do this?
Thank you for your response. it worked.
my university exam is begining, so after the exams I will try to write a script that extract decoy compounds.