Molconvert using InChI strings

Is is possible to do InChI to mol file conversion using the InChI string (including AuxInfo) in the same way as SMILES strings? i.e. I want to do this but it does not work





molconvert mol -s "InChI=1/ClH/h1H\r\nAuxInfo=1/1/N:2/rA:2nH+Cl-/rB:;/rC:-2.5,1.375,0;-1.5937,1.375,0;" -o /Users/stu/Desktop/test2.mol





I put in \r\n for the carriage return that is in a .inchi file





Stuart Chalk

Hello, are you trying to do it in a UNIX terminal? Unfortunatelly there is no easy way to dig into the InChi implementation, but try this:





$ echo "InChI=1/ClH/h1H^MAuxInfo=1/1/N:2/rA:2nH+Cl-/rB:;/rC:-2.5,1.375,0;-1.5937,1.375,0;" |molconvert mol -o test.mol





Where ^M is ctrl-M (enter it as ^V^M on xterm).

stuchalk wrote:

Is is possible to do InChI to mol file conversion using the InChI string (including AuxInfo) in the same way as SMILES strings? i.e. I want to do this but it does not work molconvert mol -s "InChI=1/ClH/h1H\r\nAuxInfo=1/1/N:2/rA:2nH+Cl-/rB:;/rC:-2.5,1.375,0;-1.5937,1.375,0;" -o /Users/stu/Desktop/test2.mol I put in \r\n for the carriage return that is in a .inchi file Stuart Chalk

Hello!


In Linux (and Linux-like terminals: cygwin in Windows, e.t.c.), the following command works for me:





echo -e "InChI=1/ClH/h1H\nAuxInfo=1/1/N:2/rA:2nH+Cl-/rB:;/rC:-2.5,1.375,0;-1.5937,1.375,0;" | molconvert mol -o test.mol





As far as I know Windows without cygwin does not support 2 line input.


Peter Vadasz

I'm on a Mac (OSX 10.4) and the unix echo command does not have -e as an option. In fact I can't find any way to incoporate a new line into a string on OSX - kinda strange.





I guess the only way I can do what I want is to write a temp file with the inchi and inchiaux data and then process that file.

I would still go for Ctrl-V Ctrl-M instead of \r\n (you will not see ^V when typing in, only ^M).

Thanks. I got it to work...however I had tried it before and for some reason on the keyboard I have even though the 'm' key gives an 'm' the ctrl-M after the ctrl-V gave me ^J! So, this time I did ctrl-J and it gave me ^M. Go figure;)





So, for anyone else reading this later





echo "InChI=1/ClH/h1H^MAuxInfo=1/1/N:2/rA:2nH+Cl-/rB:;/rC:-2.5,1.375,0;-1.5937,1.375,0;" | molconvert mol -o test.mol





does produce a mol file of HCl that correctly shows up in msketch





This was done on Mac OSX 10.4.8 (Build 8L112 - and developer release)


using jchem 3.1.7.1 with marvin 4.1.0.

Cool, thanks, hoping it will work for others as well.