On 12/28/18 4:43 PM, Spencer Trinh wrote:
> I still don't understand. If I use mol.write, I can only do one at a time
> right?Do I just loop mol.write and return the result at end or something ?
Yes. Collect them into an array of SVG strings.
I'd probably try to render them in a template as or s
I still don't understand. If I use mol.write, I can only do one at a time
right?Do I just loop mol.write and return the result at end or something ?
On Sat, Dec 29, 2018, 03:12 Dimitri Maziuk On 12/28/18 6:03 AM, Spencer Trinh wrote:
>
> > ... The xml file generated was thru Outputfile() and thus
On 12/28/18 6:03 AM, Spencer Trinh wrote:
> ... The xml file generated was thru Outputfile() and thus a file path
> is required. How to generate as a string?
For the 3rd time: pybel.Molecule.write()
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s
I was only able to do it for one molecule at a time, not a couple or
multiple. The xml file generated was thru Outputfile() and thus a file path
is required. How to generate as a string? I'm guessing Outputfile is not
the way to go because to output multiple files it just overlaps the
structures an
On Thu, 27 Dec 2018 07:55:08 -0500
Spencer Trinh wrote:
> I tried using opt={ ’u’:None, ’C’:None, ’x’:None},
>
> however the XML file still encounters a parsing error:
So you see, the issue is not how to generate an SVG dynamically ;)
Did you try generating them as strings with Molecule.write(
I tried using opt={ ’u’:None, ’C’:None, ’x’:None},
however the XML file still encounters a parsing error:
XML Parsing Error: junk after document element
Location: file:///C:/svg.svg
Line Number 62, Column 1: đã viết:
> i played around with the xml file and indeed, if you remove the repeated
> de
i played around with the xml file and indeed, if you remove the repeated
declarations and shift the x-axis of the other structures around relative
to the first, then the added structures can be seen, otherwise they overlap
each other and only one structure is viewable.
Vào Th 4, 26 thg 12, 2018 va
PS I haven't looked at SVG specs too closely: anyone knows what is does
with multiple "..." elements in the same file?
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On 12/26/18 4:23 PM, Fredrik Wallner wrote:
> The svg-format has an option to omit the XML declaration, namely ’x’. So try
> with opt={’u’:None, ’C’:None, ’x’:None}
> I haven’t had time to test though...
Outputfile shouldn't need an extra option for writing out valid files. A
valid XML file shoul
The svg-format has an option to omit the XML declaration, namely ’x’. So try
with opt={’u’:None, ’C’:None, ’x’:None}
I haven’t had time to test though...
> 26 dec. 2018 kl. 21:14 skrev Dimitri Maziuk via OpenBabel-discuss
> :
>
> (Repost with a catchy Subject)
>
> Noel, Geoff,
>
> this sounds
(Repost with a catchy Subject)
Noel, Geoff,
this sounds like a bug:
On 12/23/18 2:52 PM, Spencer Trinh wrote:
>
> output=pybel.Outputfile('svg',filename='testsvg.svg',opt={'u':None,'C':None})
> for name,mol in mols.items():
> mol.removeh()
> mol.title=name
> output.write(mol)
> output.close()
Geoff,
I will complies a list of SMILES and will post it to the issue tracker.
Thanks,
Sam
On Sat, Sep 17, 2016 at 12:33 PM, Geoffrey Hutchison <
geoff.hutchi...@gmail.com> wrote:
> There's currently no code to test for chiral nitrogens - the
> stereochemical analysis assumes all nitrogens can
There's currently no code to test for chiral nitrogens - the stereochemical
analysis assumes all nitrogens can invert and are therefore non-chiral.
Would you be willing to upload this example as a SMILES or Mol to the issue
tracker for 2.4.1?
http://github.com/openbabel/openbabel/issues
Thanks!
Hello everyone,
I was trying to filter through the SMILES with missing stereochemistry
information. So I am using the below script to loop over the atoms and
check if the atom is a chiral center and if so, is the stereochemistry
information there or not.
mol = pybel.readstring('smi', smi)
>
Hi,
As posted some weeks ago, I'm wondering if there is a bug in
mol2format.cpp, in the patch from Paolo Tosco, related to 5-membered cycle
in mol2 format.
E.g.
obabel imidazole.mol2 -O imidazole.smi (mol2 attached)
with version 2.3.2, give a segmentation fault... (see my previous message
(C++ /
> I am new here and I found a bug, where can i report it?
A lot of people post thorough discussions on the mailing list. That's fine,
although the best place for bug reports is the tracker:
https://sourceforge.net/p/openbabel/bugs/
Please try to give as much information as possible, like the ve
Hi guys,
I am new here and I found a bug, where can i report it?
Regards
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On Wed, Nov 6, 2013 at 11:13 PM, Francois Berenger wrote:
> obabel test.mol2 -Oref.smi
> and
> obabel test.mol2 -Otest.sdf
> obabel test.sdf -Ocurr.smi
>
> will create some different SMILES string in the .smi files.
> Not all different, bu some will differ
>
> for example these 2 simles are suppos
Dear Francois,
If you neglect the stereochemical information, these SMILES are the
same. I am not sure if stereochemistry is read properly from all input
formats, see http://openbabel.org/wiki/Stereochemistry
Best wishes,
Michal
On 7 November 2013 07:13, Francois Berenger wrote:
> obabel test.mo
obabel test.mol2 -Oref.smi
and
obabel test.mol2 -Otest.sdf
obabel test.sdf -Ocurr.smi
will create some different SMILES string in the .smi files.
Not all different, bu some will differ
for example these 2 simles are supposed to be about the same
molecule:
c1ccc(cc1)C(=O)c1ccc(cc1)C(C(=O)O)C
c1ccc
I'll take a look asap...
On 9 May 2013 22:14, Craig James wrote:
> Hi Noel,
>
> On Thu, May 9, 2013 at 1:33 PM, Noel O'Boyle wrote:
>>
>> I'm going to edit DeleteAtom so that any Stereo object containing the
>> deleted atom is invalidated but all other stereos remain unchanged.
>
>
> While you'r
Hi Noel,
On Thu, May 9, 2013 at 1:33 PM, Noel O'Boyle wrote:
> I'm going to edit DeleteAtom so that any Stereo object containing the
> deleted atom is invalidated but all other stereos remain unchanged.
>
While you're in there, if you spot a simple way to fix this problem (e.g.
invalidating the
I'm going to edit DeleteAtom so that any Stereo object containing the
deleted atom is invalidated but all other stereos remain unchanged.
For the record, deleting all of the stereo objects is the wrong
solution as the stereo cannot be lazily reperceived (in the general
case). It was known at the p
Using Chris's op, and a shorter testcase ("C=CC1=CN=CC1"), the problem
is that when you delete an Atom, the perceived stereo is invalid
(well, may be invalid). To work around this, you should remove the
perceived stereo. We should probably sort it out at our end.
In C++, I have:
while (pmol->Delet
On 24/04/2013 16:01, Pascal Muller wrote:
Hi,
I have a little pybel script for generating Murcko scaffolds, which
works well with 2.3.1, but fails on a few molecules ("Segmentation
fault") with 2.3.2.
Depending on code modifications, the fault raises at different points,
but I have no clue on w
Hi,
> Can you give us an example file or two? This would help us debug by
> reproducing the problem.
Yes, 2 smiles are included in the code:
mol1 = pybel.readstring("smi", "C1(=Cc2cn(nc2)CC(=O)N)C(=O)NC(=O)S1")
mol2 = pybel.readstring("smi", "C1(=CC2=C(N=C(C2)C(=O)N)C)C(=O)NC(=O)S1")
I may sea
Can you give us an example file or two? This would help us debug by reproducing
the problem.
Thanks very much,
-Geoff
On Apr 24, 2013, at 11:01 AM, Pascal Muller wrote:
> Hi,
>
> I have a little pybel script for generating Murcko scaffolds, which
> works well with 2.3.1, but fails on a few m
Hi,
I have a little pybel script for generating Murcko scaffolds, which
works well with 2.3.1, but fails on a few molecules ("Segmentation
fault") with 2.3.2.
Depending on code modifications, the fault raises at different points,
but I have no clue on why the bug is happening.
Below is my code s
On 01/16/2011 07:54 PM, Geoffrey Hutchison wrote:
>> The following informations could be useful:
>> 1) I exported the file directly from Material Studio
>> 2) The problem seemsto be size dependent, i.e. conversion works if I cut
>> down the structure to 150 atoms
>>
> I suspect this isn't a specifi
> The following informations could be useful:
> 1) I exported the file directly from Material Studio
> 2) The problem seemsto be size dependent, i.e. conversion works if I cut
> down the structure to 150 atoms
I suspect this isn't a specific problem with "car" format, rather with
bond/aromaticit
Hello anybody,
I'm an openbabel user, the following is to be intended as a bug report.
I've recently updated my system and I'm having problems in converting
this "car" file to "xyz" format
http://dl.dropbox.com/u/9206107/10_10_capped_long.car
It looks like the code is stuck in some inifinte loo
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