Dear Noel,
Thank you for the answer.
I was able to actually remove all hydrogens, merge the two molecules and
reintroduce all the hydrogens.
Nevertheless, what I am getting is not methylbenzene (C7H8) but just the same
two molecules as before.
I believe I also created a new bond but I am pretty sure it is not correct!
Here’s my code:
>> mol1 = next(pb.readfile('xyz', 'benzene.xyz')) #loading molecules
>> from file
>> mol2 = next(pb.readfile('xyz', 'methane.xyz'))
>> mol1.removeh()
>> #removing loading molecules from file
>> mol2.removeh()
>> m1 = mol1.OBMol
>> m2 = mol2.OBMol
>> m1 += m2
>> #merging the two molecules
>> m1.AddBond(1,2,1) ## how
>> do I give the right indices here?
>> new_mol = pb.Molecule(m1)
>> new_mol.addh()
>> print(len(new_mol.atoms))
17
#this should rather be 15
Moreover I would like to check whether the bond I have inserted is correct.
But I am not able to print something that is useful to understand
>> print(m1.GetBond(1))
<openbabel.OBBond; proxy of <…>>
Thank you
Marco
From: Noel O'Boyle <baoille...@gmail.com>
Sent: Thursday, April 9, 2020 2:53 PM
To: Marco Di Gennaro (TME) <marco.di.genn...@external.toyota-europe.com>
Cc: openbabel-discuss@lists.sourceforge.net
Subject: Re: [Open Babel] read molecules from xyz files and merge them
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Use the Python keyword "next" on an iterator to get the next item:
mol1 = next(pybel.readfile(....)
You can add an OBMol to an existing one:
m1 += m2
I'd recommend writing it out as SMILES at this point, just to check the
structure:
print(pybel.Molecule(m1).write("smi"))
If the hydrogens are explicit in the XYZ, then you can call DeleteAtom() on the
hydrogens to delete them. To create a bond, use AddBond(). See the Doxygen
documentation.
- Noel
On Wed, 8 Apr 2020 at 17:31, Marco Di Gennaro (TME)
<marco.di.genn...@external.toyota-europe.com<mailto:marco.di.genn...@external.toyota-europe.com>>
wrote:
Hello everyone,
I have two molecules (benzene and methane) in two separate xyz files.
I would like to create a methylbenzene molecule out of these and relax it with
a UFF.
I am new to pybel (and babel in general). I would like to:
* open the two files
* remove one hydrogen from the benzene and one from the methane
* create a bond among the two carbons
* perform UFF relaxation.
So far I have tried several things, mostly trying to follow this discussion
(which is a bit outdated actually):
http://forums.openbabel.org/OBGenericData-and-OBPairData-td4651441.html#a4651899<https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fforums.openbabel.org%2FOBGenericData-and-OBPairData-td4651441.html%23a4651899&data=02%7C01%7CMarco.Di.Gennaro%40external.toyota-europe.com%7C10b274805dc7452f8f4f08d7dc84fc3e%7C52b742d13dc247acbf03609c83d9df9f%7C0%7C0%7C637220336034857892&sdata=QAp9Sv6sV%2F3pVgSQKZw95CvY6PBMAjcS%2BwkcHCzGV4k%3D&reserved=0>
I could not get much out of it for the moment:
* I could read the files with readfile(), but why do I get an iterator?
* Is OBBuilder() what I am looking for? How to use it properly?
* Should I rather use OBPairData() ?
* I know I can use -d to remove (all) hydrogens in babel. How do I do it
for specific atoms in pybel?
Below you can find the little code I could write at the moment. I am attaching
the two xyz files.
Any help would be greatly appreciated.
Thank you.
Marco
import pybel as pb
mol1 = [ m for m in pb.readfile('xyz',
'benzene.xyz<https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fbenzene.xyz%2F&data=02%7C01%7CMarco.Di.Gennaro%40external.toyota-europe.com%7C10b274805dc7452f8f4f08d7dc84fc3e%7C52b742d13dc247acbf03609c83d9df9f%7C0%7C0%7C637220336034867879&sdata=Q9g%2BvSeWh8EX8pQJsQv%2BruRJyEGryZQNoh9DhGs2dnc%3D&reserved=0>')][0]
mol2 = [ m for m in pb.readfile('xyz',
'methane.xyz<https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fmethane.xyz%2F&data=02%7C01%7CMarco.Di.Gennaro%40external.toyota-europe.com%7C10b274805dc7452f8f4f08d7dc84fc3e%7C52b742d13dc247acbf03609c83d9df9f%7C0%7C0%7C637220336034867879&sdata=xN1CRrauPYnV53lgBO2jZBEg9qnYi4c4l7UTTFJO160%3D&reserved=0>')][0]
mol1 + mol2 # This gives a TypeError: unsupported operand type(s) for +:
‘Molecule’ and ‘Molecule’
m1 = mol1.OBMol
m2 = mol2.OBMol
m3 = m1 + m2 # This gives a TypeError: unsupported operand type(s) for +:
‘OBMol’ and ‘OBMol’
==
Marco Di Gennaro, Ph.D.
Toyota Motor Europe
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