On 06/05/2013 03:50 PM, Maciek Wójcikowski wrote:
... although I believe that 'b' : None should be 'b' : '' if you
> wish to pass empty value, since None is reserved for options without value.
Hehe. I wanted "b" : "none", actually (Geoff was right) and I didn't
even notice myself until the pictur
On 06/05/2013 03:50 PM, Maciek Wójcikowski wrote:
> There is an undocumented option in molecule.write() and .readfile() which
> allows of passing options to reading/writing. You must pass opt with
> dictionary of options. For line you gave: opt = {'b' : None, 'i' : None,
> 'a' : None} although I be
> All I can see in TFM is pybel.Molecule.addh() for "-h" -- is there way
> to get to the rest? Specifically, "-xa" and "-xi", as I can
> post-process the SVG to change the size and the background.
These are output options in the Python openbabel module (not accessible from
pybel, IIRC)
conv = ob
There is an undocumented option in molecule.write() and .readfile() which
allows of passing options to reading/writing. You must pass opt with
dictionary of options. For line you gave: opt = {'b' : None, 'i' : None,
'a' : None} although I believe that 'b' : None should be 'b' : '' if you
wish to pa
On 06/05/2013 03:01 PM, Noel O'Boyle wrote:
> Sorry - I misunderstood. atom.isotope is already there; just the
> ability to set it is not...
I'm setting it to get the weight of C13 and/or N15-labelled molecule.
I'm not sure why we record those in our DB -- they're easy to calculate
if anyone needs
Sorry - I misunderstood. atom.isotope is already there; just the
ability to set it is not...
On 5 June 2013 20:48, Noel O'Boyle wrote:
> Sounds good Geoff.
>
> Regarding atom.isotope and others, just to note that Pybel is not
> intended to wrap all of Open Babel's functionality but just the most
Hi everyone,
one more python question: I'm trying to do
obabel -h --canonical -xb none -xi -xa -xP1000 -osvg ...
All I can see in TFM is pybel.Molecule.addh() for "-h" -- is there way
to get to the rest? Specifically, "-xa" and "-xi", as I can
post-process the SVG to change the size and the back
Sounds good Geoff.
Regarding atom.isotope and others, just to note that Pybel is not
intended to wrap all of Open Babel's functionality but just the most
common (although it also wraps stuff that is awkward to use otherwise,
e.g. unitcell). A small API makes it easy to use. Where to draw the
line
> While you're at it & if you feel like it, things like
> atom.isotope = property( OBAtom.GetIsotope(), OBAtom.SetIsotope() )
> (not to be taken literally, obviously ;) would be more "pythonic", too.
Well, if you or others have suggestions, I can try hacking those too. If you're
willing to rebuil
On 06/05/2013 10:48 AM, Geoffrey Hutchison wrote:
>> etab = ob.OBElementTable()
>> etab.GetSymbol(6)
>
> Although I can see some benefit for Pybel to have a wrapper to
> handle
something like atom.element and hide all this in something more "Pythonic".
>
> (Noel, would you let me try doing this?)
> etab = ob.OBElementTable()
> etab.GetSymbol(6)
Although I can see some benefit for Pybel to have a wrapper to handle something
like atom.element and hide all this in something more "Pythonic".
(Noel, would you let me try doing this?)
-Geoff
--
Yes.
etab = ob.OBElementTable()
etab.GetSymbol(6)
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2013/6/5 Dimitri Maziuk
> On 2013-06-05 02:54, Maciek Wójcikowski wrote:
> > If you realy need symbol of an element in automated fassion, then there
> > is OBElementTab
On 2013-06-05 02:54, Maciek Wójcikowski wrote:
> If you realy need symbol of an element in automated fassion, then there
> is OBElementTable.GetSymbol( atomicnum ) that you can use.
>
> http://openbabel.org/dev-api/classOpenBabel_1_1OBElementTable.shtml#a18907ad1590deb926b43c4f08cac9405
So it's ex
Welcome to path-based fingerprints. It is supposed to approximate
graph-edit distance, but here a single substitution leads to a large
change.
Anyhoo, just use -xs to see what each bit corresponds to and all
becomes clear (see the docs for more info):
C:\Users\noel>obabel -:Clc1c1 -:Fc1c1
Hello everybody,
recently I computed the Tanimoto between Clc1c1 and Fc1c1 with
openbabel by -ofpt and I was very surprised to see 0.3 as result.
Do you know if what I got is correct or what should I exactly do in
order to get the correct tanimoto between these two fragments?
Thank you t
If you realy need symbol of an element in automated fassion, then there is
OBElementTable.GetSymbol( atomicnum ) that you can use.
http://openbabel.org/dev-api/classOpenBabel_1_1OBElementTable.shtml#a18907ad1590deb926b43c4f08cac9405
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@woj
Hello,
Sure - try atom.atomicnum (pybel) or OBAtom.GetAtomicNum() (openbabel). It
returns atomic number of element (fe. C - 6).
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2013/6/5 Dimitri Maziuk
> Hi all,
>
> I'm after the atom (element) type letter. What I ge
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