Thanks Noel
When do you think this fix will get into the public version? I found a
not-soelegant workaround using the Cactus server, so no great hurry.
Sorry about the title :) I hit send before I was done typing
Best regards, Jan
> On 22 Mar 2017, at 21:24, Noel O'Boyle wrote:
>
> This i
I can't say anything regarding releases dates. But at some point, it
will reach sufficient quality that it will be merged into the
development codebase and you can download and compile it from there.
I'll try to remember to ping you at that point, but we're talking
timescales of a few months.
At t
This is already fixed in my development code, where I have changed the
handling of implicit hydrogens throughout the library:
>obabel -:"CCOC(=O)c1ccc([NH3+])cc1" -oinchi -xF | obabel -iinchi -osmi
==
*** Open Babel Warning in InChI code
#1 :Proton(s) added/removed
1
On Mar 18, 2017, at 16:00, Jan Halborg Jensen wrote:
> babel -:"CCOC(=O)c1ccc([NH3+])cc1" -oinchi -xF
>
> gives
>
> InChI=1/C9H11NO2/c1-2-12-9(11)7-3-5-8(10)6-4-7/h3-6H,2,10H2,1H3/p+1/fC9H12NO2/h10H/q+1
>
>
> but converting this InChI back to smiles gives CCOC(=O)c1ccc(cc1)[NH2+]
>
> I use
Hi all
babel -:"CCOC(=O)c1ccc([NH3+])cc1" -oinchi -xF
gives
InChI=1/C9H11NO2/c1-2-12-9(11)7-3-5-8(10)6-4-7/h3-6H,2,10H2,1H3/p+1/fC9H12NO2/h10H/q+1
but converting this InChI back to smiles gives CCOC(=O)c1ccc(cc1)[NH2+]
I use obabel -oinchi temp3.inchi -osmi
Any help appreciated
Best regards,
Dear Noel,
thanks again, this is of great help.
I think the new code is somehow faulty and for some reason it returns
1.79769313486e+308 for any molecule. The updated code is posted at the
end of the message.
The old code worked for what I thought it was molecules with different
labelling.
Hi Giulio,
Problem 1: check out vectorVector3. Initialized with a list of vector3,
e.g. my_vv = ob.vectorVector3([a, b])
Problem 3: What I meant is that the RMSD only takes into account the
aligned coordinates. If you want to include the RMSD of the other
coordinates, you need to work it out your
Dear Noel,
just a few problems I am stuck with, using this procedure:
- SetRef() and SetTarget() need a vector of vector3 objects as argument.
While vector3 is an OpenBabel class, vector is not (I assume it is the
C++ vector?). How do I feed them a vector? Is a python list going to be
fine?
Try using SetRef() and SetTarget() instead with just the coordinates for
the atoms you want to align (in the same order for both, as given by the
match to the Smarts). Afterwards, if you want the RMSD for the whole
molecule, you can manually calculate the whole molecule RMSD by translating
one of t
Hi there,
I am building a script in python that removes a certain moiety from two
molecules and calculates the RMSD between the remaining structure.
I am doing this by asking for one or more SMARTS strings to find in the
molecules, labelling these atoms and deleting them using
OBMol.DeleteAtom
To make it clear, the current implementation of RMSD with symmetry does
not support objects that consist of several molecules such as dimers or
multimers.
Thank you Noel for your advice. I may try it.
Igor
On 1/9/2014 1:33 AM, Noel O'Boyle wrote:
> Sorry - my suggestion was dumb. That's not go
Sorry - my suggestion was dumb. That's not going to work.
The only workaround I can think of is to do the alignment (using
OBAlign) using the coordinates (rather than the molecule), and juggle
around the coordinates of the Target yourself based on the 12 * 12
automorphisms. In other words, get the
Looks like something's up. I'll look into it. In the meanwhile, as a
workaround, try adding a bond between the two dimers.
- Noel
On 6 January 2014 08:51, Igor Leontyev wrote:
> Dear OB community,
>
> I'm faced with a problem of computing RMSD with symmetry correction. My
> code (given bellow) u
Dear Geoffrey,
Thank you for being willing to fix the issue. It will be really helpful
for projects like mine.
Igor
On 11/8/2013 9:54 AM, Geoffrey Hutchison wrote:
>
> On Nov 8, 2013, at 2:50 AM, David van der Spoel wrote:
>
>> However even for good geometries OB has problems with bond orders
>>
On 2013-11-08 18:54, Geoffrey Hutchison wrote:
>
> On Nov 8, 2013, at 2:50 AM, David van der Spoel wrote:
>
>> However even for good geometries OB has problems with bond orders
>> sometimes as I pointed out the other day. Is there anything that can be
>> done about that? Changing smiles?
>
> Bond o
On Nov 8, 2013, at 2:50 AM, David van der Spoel wrote:
> However even for good geometries OB has problems with bond orders
> sometimes as I pointed out the other day. Is there anything that can be
> done about that? Changing smiles?
Bond order perception is never going to be bullet-proof, part
On 2013-11-08 04:05, Igor Leontyev wrote:
> Dear Geoffrey,
> Thanks for your response.
> The structure was optimized at MP2/aTZ level. I use XYZ-format because it
> is the main format in MolPro QM program. The problem with C=N bond was met
> in several compounds listed bellow.
Is aTZ an abbreviatio
Dear Geoffrey,
Thanks for your response.
The structure was optimized at MP2/aTZ level. I use XYZ-format because it
is the main format in MolPro QM program. The problem with C=N bond was met
in several compounds listed bellow.
Methanimine
EthanImine
VinylImine
Benzenemethanimine
and Imidazoline
The
> I came across a problem of converting XYZ to HIN format for imine
> compounds. In more detail, the double C=N bond in imine series is
> determined as a single bond. (As a result, atom typification for Merck
> force field is completely screwed up.)
The problem here is that the H-N-C bond angle is
Dear OB users,
I came across a problem of converting XYZ to HIN format for imine
compounds. In more detail, the double C=N bond in imine series is
determined as a single bond. (As a result, atom typification for Merck
force field is completely screwed up.)
See the output hin-file bellow, the C=N b
Dear all,
I use OpenBabel to determine chemical informations like bond orders and
formal charges. Therefore I convert a molecule in xyz-format, in which
only topology and atom positions are known, into cml-format. From
cml-format I can extract the needed informations: bond orders, formal
charg
I know radicals are not fully supported (correct valence is available
only in the developer version), and I don't really know if I should
fill a bug report or add a request for future release.
My question: shouldn't the connectivity (in SMARTS X) be, by
definition, lower than or equal to the valen
Hi all.
I'm trying to convert a pdb (PDB ID 1A94). In the beginning there are
2 ligangs with residue number 100 (named 0Q4) and chains A and E
accordingly. But after conversion by babel there is no more chain E
for residue 100, but there are 2 residues with id 100 and chain A.
In the HET section of
Hi guys,
I've a problem using the last Open Babel 2.3.1 in an GNU/Linux ubuntu OS.
When I convert an sdf file to a mol2 (or whatever other format) using the
"--partialcharge gasteiger" option, I obtain molecules with wrong partial
charges.
case A) obabel -isdf mols_charged.sdf -omol2 --partialcha
El vie, 01-07-2011 a las 14:13 +0100, Noel O'Boyle escribió:
> 2011/7/1 Miguel Quirós Olozábal :
> > El vie, 01-07-2011 a las 10:08 +0200, Pascal Muller escribió:
> >> Dear Miguel,
> >>
> >>
> >> Hello. I posted the attached long message a couple of weeks
> >> ago and I
> >>
2011/7/1 Miguel Quirós Olozábal :
> El vie, 01-07-2011 a las 10:08 +0200, Pascal Muller escribió:
>> Dear Miguel,
>>
>>
>> Hello. I posted the attached long message a couple of weeks
>> ago and I
>> have had no reply at all, not even a comment. Fully
>> uninteresting
El vie, 01-07-2011 a las 10:08 +0200, Pascal Muller escribió:
> Dear Miguel,
>
>
> Hello. I posted the attached long message a couple of weeks
> ago and I
> have had no reply at all, not even a comment. Fully
> uninteresting
> subject?
>
>
> Of c
Dear Miguel,
> Hello. I posted the attached long message a couple of weeks ago and I
> have had no reply at all, not even a comment. Fully uninteresting
> subject?
>
>
Of course not - the COD is of great interest, I think. But I never worked
with metal-containing molecules, and don't have progra
Hello. I posted the attached long message a couple of weeks ago and I
have had no reply at all, not even a comment. Fully uninteresting
subject?
El vie, 17-06-2011 a las 09:58 +0200, Miguel Quirós Olozábal escribió:
> Hello.
>
> I am working in the Crystallography Open Database
> (www.crystallog
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