InChI error messages using Protonation plugin

If I were to fix a mol file that is at a pH of 7 thus:

./cxcalc majorms -H 7 -f inchi C00194.mol

I get an warning that "Proton(s) added/removed".  My problem is that this is a standard InChI message, one that I get if I use InChI directly without adjusting for pH etc.

I therefore have no way of knowing, so it seems, whether cxcalc actually did the adjustment, or the inChI module did, or both.

Hi,

I do not fully understand the question about the adjustment, but I can tell what happens during this cxcalc code.

First cxcalc calulates the majorms for Your molecule and creates the result molecule. After that it exports the result into inchi. During the export Marvin creates the inchi representation, and makes the conversion with inchi API. This message is created when the conversion is called, it is the standard InChI warning - the same as You would get if You call:

./cxcalc majorms -H 7 -f mol C00194.mol

and give the result to the standard inchi executable.

Hope this helps.

Peter

Let me try to explain more:

 

The whole point of using the Protonation plugin is to add or remove protons to the molecule as deemed correct for the pH level.  Therefore, for this molecule, I'm using majorms with the option -H 7 because I'd like the molecule to have the correct number of protons.

 

However, once this has been done, and the molecule is passed into the inchi API for processing, the inchi API tells me that it has added/removed protons.

 

Typically, the inchi API does this because of incorrect valences, am I right?  However, I do *not* want protons to be added/removed if the MarvinBeans code has already fixed the correct number of protons for a pH of 7, am I making sense here?

 

I've used the option '-f inchi:DoNotAddH' but it still tells me it added/removed protons.

 

From what I can tell, even if I don't use -H 7, and get a large number of inchi strings, the formula stays the same, ie the number of protons stay the same, even though I get the message, but the value in the '/p' sublayer can change,  so I may get a '/p-2' or a '/p-1'.  If *this* is what is meant by "Proton(s) added/removed" then I'd be OK with it from a formula perspective, but I'm still not sure if the charge should be adjusted thus....

Hi,

As far as I know InChI can not calculate with pH, and I don't think that the DoNotAddH option helps this. So when I give a molecule to the InChI API, it makes the same standardization steps - these steps are written in detail in the public documentation of IUPAC -, and among these there are proton adding/removing steps.  These are automatic steps, we just call the conversion.

I have tried to make a new file with:

./cxcalc majorms -H 7 -f inchi C00194.mol

and give both file ot the standard windows inchi executable, and I got the same result, so I think we do this conversion correctly.

About the standardization steps, and the details of the conversion You can ask on the inchi-discuss mailing list, they always answer to inchi questions soon.

Best Regards,

Peter