[Open Babel] Questionable behavior in obrotate (or babel)

raightforward if the atom numbers could be taken from the XYZ file and not determined from the SMART pattern. If the atom numbers must be determined from the SMART pattern, then it should be done in a manner consistent with the numbering scheme in 'babel'. Thanks! Lee-Ping Wang Simb

Re: [Open Babel] Questionable behavior in obrotate (or babel)

hanks, - Lee-Ping - Original Message - From: "Geoffrey Hutchison" To: "Lee-Ping Wang" Cc: openbabel-discuss@lists.sourceforge.net Sent: Friday, April 27, 2012 6:15:22 PM Subject: Re: [Open Babel] Questionable behavior in obrotate (or babel) > I believe that '

[Open Babel] Type error when using Python API to OBReaction

Hi there, I'm using OpenBabel in a Python script, and I created several OBMol objects that I would like to organize into an OBReaction object. However, I am getting the following TypeError: obm = ob.OBMol() obcsvg = ob.OBConversion() obcsvg.SetInAndOutFormats("xyz","svg") obcsvg.ReadFile(obm,

[Open Babel] Two-Dimensional Alignment in Script

-Ping Wang -- Introducing Performance Central, a new site from SourceForge and AppDynamics. Performance Central is your source for news, insights, analysis and resources for efficient Application Performance Management

Re: [Open Babel] Type error when using Python API to OBReaction

nbabel-python.i file might simply sort > out the problem. I'll take a look asap. > > - Noel > > On 20 August 2013 19:13, Lee-Ping Wang wrote: >> Hi there, >> >> I'm using OpenBabel in a Python script, and I created several OBMol >> objects that

Re: [Open Babel] Type error when using Python API to OBReaction

M, Noel O'Boyle wrote: > Looks like a SWIG wrapping issue. > > If you are compiling the bindings yourself, adding: > %include > ...close to the start of the openbabel-python.i file might simply sort > out the problem. I'll take a look asap. > > - Noel > > On

[Open Babel] Multimolecule canonical SMILES

Hi there, I have a number of multimolecular complexes that I'm converting into canonical SMILES. Some of these molecules are carbon monoxide, and I am noticing that sometimes they are written as [C]=O, and sometimes as O=[C]. Is the expected behavior of canonical SMILES - or should it instea

Re: [Open Babel] [OpenBabel-Devel] Multimolecule canonical SMILES

Hi there, Thanks for including me in the developer discussion, the bug report must have come from somebody else because I didn't submit one. I'm actually looking at a bunch of chemical reactions, but I'm not using the OpenBabel functionality for reactions because I had issues with it - just t

Re: [Open Babel] [OpenBabel-Devel] Multimolecule canonical SMILES

3/newsmiles.txt If they are correct then I would support adding this patch to the next OpenBabel release. Thanks, - Lee-Ping From: Lee-Ping Wang [mailto:leep...@stanford.edu] Sent: Tuesday, February 18, 2014 7:25 PM To: Tim Vandermeersch Cc: Geoffrey Hutchison; Craig James;

[Open Babel] File conversion adds unwanted hydrogens

Hi there,I'm converting some molecules to 2D format, and some of them are extremely small and/or uncommon in normal chemistry (e.g. nitrogen atoms).  I'm running into an issue where sometimes it automatically adds hydrogen atoms.  For example, I have a reaction where NH is split into N and H atoms,

[Open Babel] Bond order in canonical SMILES

Hi there, It would be nice if I had the ability to write (canonical) SMILES strings without any bond order information, as a "round trip" to another format (say, .xyz with gen3D) may cause this information to be lost and I end up with different strings for the same molecule. For example, [NH3]

[Open Babel] SVG draws unwanted extra hydrogens

Hi there, I'm using the Python interface to OpenBabel to create 2D representations of my molecules. I'm having a great time except when it decides to draw extra hydrogens. I'm quite sure these hydrogens are not supposed to be drawn. In the attached image, the "CH" on carbon monoxide is not n

Re: [Open Babel] SVG draws unwanted extra hydrogens

Sorry for the extra email; I'm attaching the original .xyz file that I am trying to represent in the 2D image. - Original Message - From: "Lee-Ping Wang" To: openbabel-discuss@lists.sourceforge.net Sent: Thursday, September 25, 2014 8:34:41 PM Subject: SVG draws unwanted

Re: [Open Babel] SVG draws unwanted extra hydrogens

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 st

[Open Babel] Occasional incorrect 2D depiction from 3D structure

Hi there,When I use the following one-liner to convert in.xyz to out.svg, the CO2 molecule is incorrectly represented as three overlapping letters (so it looks like a single atom).  In the svg file, the coordinates are exactly the same.  I wonder what could be causing this?  I have tried to set all

Re: [Open Babel] SVG draws unwanted extra hydrogens

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 wrote:

Re: [Open Babel] 2d SVG Label positions

Hi Christian, My approach to addressing this issue was to parse the SVG file using Python (it is an editable XML document) and move the atoms slightly. I realize this is outside of OpenBabel but it could be helpful. Thanks, - Lee-Ping From: Christian Meisenbichler [mailt