adding hydrogen

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adding hydrogen

hao wang
Hi,everyone,
Can you teach me how to add hydrogen for each molecule by babel?(I know how add this for only one molecule) I have many molecules. I want to know a batch way.thankyou!
How to write the command line for this problem?
--
Best wishes,
       Hao Wang


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Re: adding hydrogen

Geoffrey Hutchison
> Can you teach me how to add hydrogen for each molecule by babel?(I know how add this for only one molecule) I have many molecules. I want to know a batch way.thankyou!
> How to write the command line for this problem?

Well, if you're using the command-line and you have one file with multiple molecules, you do:

babel -h [file.sdf] file-added-h.sdf

If you have many files, you use the "*" pattern to match multiple files, e.g.

babel -h *.sdf file-added-h.sdf

Here the last filename is assumed to be the output file.

Best regards,
-Geoff


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Re: adding hydrogen

Chris Morley-3
In reply to this post by hao wang
On 20/09/2010 09:41, hao wang wrote:
 > Can you teach me how to add hydrogen for each molecule by babel?(I
 > know how add this for only one molecule) I have many molecules. I want
 > to know a batch way.thankyou!
 > How to write the command line for this problem?

Normally, OpenBabel processes all the molecules that are in its input
and puts the results in a single output file. The input molecules can
be all in one file or can be in multiple files. So to add hydrogens to
all the molecules in in1.smi, in2.smi and in3.smi and put the results
in out.sdf :

   babel  in1.smi  in2.smi  in3.smi  out.sdf  -h

or you could use wildcard characters to specify multiple input files :

   babel  *.smi  out.sdf  -h

To put the output into separate files :

   babel  *.mol  H.mol  -h  -m

So HA.mol HB.mol HC.mol would be produced if the input files were
A.mol B.mol C.mol

Do not try to over-write the input files.


Chris


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Re: adding hydrogen

green69
In reply to this post by Geoffrey Hutchison
I have the following problem on adding hydrogens with babel.
When only certain hydrogens are present on the input structures (let says the "polar hydrogens", e.g. those bounded to etheroatoms) and I want to add the rest, it seems that babel (v. 2.3.0) first eliminate those already present and then add all hydrogens. This results in the change of the position of those hydrogens already present in the structure. A think this can lead to serious problem. Is it a bug?
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Re: adding hydrogen

rosalbasawyer
In reply to this post by Geoffrey Hutchison
Hydrogen bonding between phenol and alcohol is most durable. Because the hydrogen in phenol is the most active and the O in alcohol is the most negative.
Hydrogen bonding between water and alcohol. This is the most stable type - due to its greatest electrostatic interaction (Hydrogen in water is the most flexible, O in alcohol has the largest negative charge - due to ethyl alcohol having the -C2H5 group that ejects electrons) friv
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Re: adding hydrogen

DamianDoherty
In reply to this post by hao wang
Thanks for your helpful sharing. I have read that knowledge very much, it gives me a lot of things.
ball lines
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Re: adding hydrogen

arianapham
In reply to this post by hao wang
The content you have shared is very helpful and amazing…so nice happy room
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Re: adding hydrogen

nguyenthaovan
In reply to this post by hao wang
I personally like your post, you have shared good article. It will help me in great deal.
I like your article very much, thanks for sharing the good information we have read.
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