Is there any way to save a set of the possible ionized molecules to a specific PH as a result of a pKa calculation?
Input would be an SD file. Output would contain the list of the ionized molecules and pKa values.
I am also interested in an API solution, if possible.
Microspecies (protonation form at a specified pH) list with distributions at given pH can be calculated with cxcalc
. You have to use microspeciesdistribution
|cxcalc -o result.sdf microspeciesdistribution -H 4.5 test.sdf |
The example calculates the microspecies distribution at pH 4.5. The input file (test.sdf) and the output file (result.sdf) is attached; the default ouput format is SDF, with distribution values in SDF fields. See also the attached image, it shows the four microspecies with largest distribution at pH 4.5.
For API usage example see the API header of the pKaPlugin class.
Marvin GUI: pKa Plugin can display microspecies distribution chart.
I hope this helps,
Thank you for the prompt answer. This is very nice. Your command line worked very well.
Is there any soultion to narrow the output SD file in order to get results listed only with a DISTR number is higher than zero?