Re: [Open Babel] What is the time complexity of generating a canonical SMILES

a...@dalkescientific.com>> wrote: On Nov 2, 2018, at 01:33, Xianghai Sheng mailto:xsh...@ucmerced.edu>> wrote: > I am trying to figure out the time complexity (Big O) of converting from > OBMol to canonical smiles. I don't think that's a useful way to think about your

[Open Babel] What is the time complexity of generating a canonical SMILES

Hi, I am trying to figure out the time complexity (Big O) of converting from OBMol to canonical smiles. I tried to look at the code but it looks too complex. (I am assuming "class OBMol2Cansmi" is the right place to look at.) Is there relevant documentation/paper on this? Does anyone know the t

Re: [Open Babel] Fail to reproduce obabel --gen3d in pybel

It still generates structures with overlapping atoms. Can anybody help please? Best, Xianghai On Thu, Feb 15, 2018 at 3:23 PM, Xianghai Sheng wrote: > Hi, > > I am trying to convert a smiles string into 3D structure in my program, > but the 3D structure I get sometimes have over

[Open Babel] Fail to reproduce obabel --gen3d in pybel

Hi, I am trying to convert a smiles string into 3D structure in my program, but the 3D structure I get sometimes have overlapping atoms, especially when there are multiple fragments in the smiles string. An example is 'CC(=O)OCC.CC(=O)OCC.CC[O-]', and the code I wrote to generate 3D structure is:

Re: [Open Babel] Using OBPairData in python

e deduced from the atomic > number and the valence so we don't need to track the number of lone pairs. > > Regards, > - Noel > > On 25 January 2018 at 01:43, Xianghai Sheng wrote: > >> Dear developers, >> >> I was wondering what is the proper way to use

[Open Babel] Using OBPairData in python

Dear developers, I was wondering what is the proper way to use OBPairData in python. For example, I want to store an OBPairData with attribute 'nLonePair' in an OBAtom. I managed to do this with the following code but don't know if it is the best way. d = ob.OBPairData() d

Re: [Open Babel] Adding readability to gaussian input files

, David van der Spoel wrote: > On 06/10/17 23:26, Xianghai Sheng wrote: > >> Hi, >> >> I noticed that gaussian input file (.com, .gjf) is not a readable format >> by openbabel. I personally need this functionality quite a bit. Is this >> left out intentionally? If not

[Open Babel] Adding readability to gaussian input files

Hi, I noticed that gaussian input file (.com, .gjf) is not a readable format by openbabel. I personally need this functionality quite a bit. Is this left out intentionally? If not, I can add a new plugin for reading this format. Since there exists a gaussformat.cpp in src/formats which is WRITEONL

Re: [Open Babel] In python how should I get a double* from C++?

enough to figure out the usage of other similar methods. Xianghai On Fri, Aug 25, 2017 at 12:59 PM, Xianghai Sheng wrote: > Edit: I'm aware of that atom.coords can get me the coordinates but this is > just an example. Things like GetGradients doesn't have a easy binding in > pyt

Re: [Open Babel] modify molecules through internal coordinates

Exactly what I need. Thank you! Xianghai On Fri, Jul 21, 2017 at 12:49 PM, Geoffrey Hutchison < geoff.hutchi...@gmail.com> wrote: > Sure. The API call would operate on an OBBond: > > http://openbabel.org/api/2.3/classOpenBabel_1_1OBBond.shtml# > a62b38719673238813acc911788969922 > > > I'm trying

[Open Babel] modify molecules through internal coordinates

Hi, I'm trying to edit a molecule through internal coordinates like you would do in a graphic editor. For example, I would like to change the bond length between atom A and atom B, and moving the connecting groups accordingly. Is this possible in python? or possible at all? Thank you, Xianghai --

[Open Babel] Website down?

Hi everyone, I can't visit openbabel.org. It says site not found. Is it just me? Xianghai -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot_