Enumerating chemical species and conformers questions.

[Andrew Orry]

Q How to enumerate all possible protonation species at pH 7.4 (*_1, *_2 and so on for each protomer

A.

ICM has a  function Table( <chem> <r_pH> <r_percCutoff> charge  )

t_charge = Table( t.mol[1] 7.4 0.05 charge )   # returns table with species at 7.4 (keeping only with concentration > %5)
Column with specie concentration will also be return.

So for a table you can iterate through rows

for i=1,Nof(t)
  add t_charge Table( t.mol[i] 7.4 0.05 charge )
endfor

That will accumulate protonation states for all rows into one table

Q. Enumerate all tautomers (*_1, *_2 and so on for each tautomer)

A.

enumerate tautomer keep filter predict t.mol name="t_tauto"    # will return table 't_tauto' with tautomers from original input table 't'

Tautomers will be ranked by pKa model

Q. Enumerate all stereoisomers (*_1, *_2 and so on for each conformer)

A

enumerate chiral t.mol name="t_stereo"  # t_stereo will contains stereo isomeres

Note that command will enumerate only racemic centers (with no defined chirality)