Hi Mathias,
Thanks for the tip. Your solution is cleaner than mine; I didn't know it
was possible to do something like gen2D = ob.OBOp.FindType("gen2D") . :)
- Lee-Ping
From: Mathias Laurin [mailto:mathias.lau...@gmail.com]
Sent: Wednesday, October 01, 2014 2:42 AM
To: Lee-Ping Wang
Cc: openbabel-discuss@lists.sourceforge.net
Subject: Re: [Open Babel] SVG draws unwanted extra hydrogens
Dear Lee-Ping,
I do my 2D structure diagram generation [1] from 3D coordinates like this:
import openbabel as ob
molecule = ob.OBMol()
# load your file into `molecule` with ob.OBConversion()
molecule2D = ob.OBMol(molecule)
gen2D = ob.OBOp.FindType("gen2D")
if not gen2D: raise NameError("name 'gen2D' is not defined")
gen2D.Do(molecule2D)
assert(not molecule2D.Has3D())
assert(molecule.NumAtoms() == molecule2D.NumAtoms())
This is copy-edited-pasted from my code [2], I hope I did not forget
anything crucial and that it helps...
[1] Helson Rev. Comput. Chem. 1999 pp. 313-398
[2] http://vibeplot.sf.net
Best regards
Mathias Laurin
On 26 Sep 2014, at 14:53, Lee-Ping Wang <leep...@stanford.edu> wrote:
Hi everyone,
Thanks for the suggestions - I realize that by starting with the SMILES
string and not the 3D structure I might have caused some confusion.
My main goal is actually to draw the 2D representation from the 3D
structure, attached again here (I'm a quantum chemist); the SMILES string is
derived from the 3D structure and I think it's correct, though I could be
wrong about that.
This is a more general problem - often I want to draw carbenes, radicals,
and isolated atoms from the 3D structure where the hydrogens are there
(though the octet rule may not be satisfied) - thus I don't want the program
to interpret the molecules chemically and fill in hydrogens that it thinks
is missing. I don't think the OBMol object is adding any extra atoms
because it corresponds to the 3D structure, but when I draw the SVG the
extra hydrogens show up.
Note that the added unnumbered hydrogens appear as "CH" rather than "C-H",
so they are different from the hydrogens that I explicitly added when
creating the OBMol object from the 3D structure.
Noel: I do want explicit hydrogens to be displayed, but only the hydrogens
that I explicitly have. I don't want carbon monoxide to be shown as O#CH
since my starting point is the CO in the 3D structure.
If you could point me to the correct file, I could write the code myself.
I'm a bit new to the code base so I might have some questions along the way.
Thanks,
- Lee-Ping
From: Pascal Muller [ <mailto:pascal.jm.mul...@gmail.com>
mailto:pascal.jm.mul...@gmail.com]
Sent: Friday, September 26, 2014 3:03 AM
Cc: <mailto:openbabel-discuss@lists.sourceforge.net>
openbabel-discuss@lists.sourceforge.net
Subject: Re: [Open Babel] SVG draws unwanted extra hydrogens
Hi,
For carbon monoxyde, try this smile: [C-]#[O+]
Regards,
Pascal
<coords.xyz><can.svg>-------------------------------------------------------
-----------------------
Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer
Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports
Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper
Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer
<http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktr
k_______________________________________________>
http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk
_______________________________________________
OpenBabel-discuss mailing list
<mailto:OpenBabel-discuss@lists.sourceforge.net>
OpenBabel-discuss@lists.sourceforge.net
<https://lists.sourceforge.net/lists/listinfo/openbabel-discuss>
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
------------------------------------------------------------------------------
Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer
Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports
Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper
Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer
http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk
_______________________________________________
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
