[Pybel, make3d, .mol] Why is there no "make2D()", and why can't I just "flatten()" a mol file?
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Hi,
In Pybel, it seems like every InChi or SMILES string I convert into a molecule object (after "pybel.readstring") file using the method ".write(format="mol")" generates mol files where the atoms are all at the center. The coordinates are all 0's and it's really frustrating because I know there is in fact a mol.make3d() that will add those 3d coordinates in space for even the most complex molecules, so it's possible that they could be given the correct coordinates. All I really need is a way to render my mol files with the first two columns so that I have 2d representation as you would typically expect when you save a mol file. I'm using kekule to render those mol files into pngs, and just look horribly warped in 3D. Additionally, I know openbabel is capable of generating 2d images because mol.write(format="png") is possible and will generate a perfect 2d image despite having all its coordinates be 0. Additionlly the obabel command option of "-Opng" seems to be able to make images from inchi, smiles, or mol into 2d plots regardless of the fact that I never provided the 2d coordinates. So why can't I just simply get the mol file with those same coordinates? -- Thanh
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Re: [Pybel, make3d, .mol] Why is there no "make2D()", and why can't I just "flatten()" a mol file?
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Take a look at the draw method. On 20 Oct 2016 2:08 p.m., "T V" <[hidden email]> wrote:
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Draw doesn't have a means of flattening the molecule. And basically does the same thing as write. I don't need a picture, I need the mol file, with JUST 2d coordinates. On Thu, Oct 20, 2016 at 6:35 AM, Noel O'Boyle <[hidden email]> wrote:
-- Thanh
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Re: [Pybel, make3d, .mol] Why is there no "make2D()", and why can't I just "flatten()" a mol file?
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Administrator
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If you read the output of help(pybel.Molecule.draw) you will see that
it does what you want: >>> mol = pybel.readstring("smi", "CC(=O)Cl") >>> mol.draw(show=False, update=True) >>> print mol.write("mol") OpenBabel10221609022D 4 3 0 0 0 0 0 0 0 0999 V2000 1.7321 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -0.0000 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 2 4 1 0 0 0 0 M END On 21 October 2016 at 22:17, T V <[hidden email]> wrote: > Draw doesn't have a means of flattening the molecule. And basically does the > same thing as write. I don't need a picture, I need the mol file, with JUST > 2d coordinates. > > On Thu, Oct 20, 2016 at 6:35 AM, Noel O'Boyle <[hidden email]> wrote: >> >> Take a look at the draw method. >> >> >> On 20 Oct 2016 2:08 p.m., "T V" <[hidden email]> wrote: >>> >>> Hi, >>> >>> In Pybel, it seems like every InChi or SMILES string I convert into a >>> molecule object (after "pybel.readstring") file using the method >>> ".write(format="mol")" generates mol files where the atoms are all at the >>> center. The coordinates are all 0's and it's really frustrating because I >>> know there is in fact a mol.make3d() that will add those 3d coordinates in >>> space for even the most complex molecules, so it's possible that they could >>> be given the correct coordinates. All I really need is a way to render my >>> mol files with the first two columns so that I have 2d representation as you >>> would typically expect when you save a mol file. I'm using kekule to render >>> those mol files into pngs, and just look horribly warped in 3D. >>> >>> >>> Additionally, I know openbabel is capable of generating 2d images because >>> mol.write(format="png") is possible and will generate a perfect 2d image >>> despite having all its coordinates be 0. Additionlly the obabel command >>> option of "-Opng" seems to be able to make images from inchi, smiles, or mol >>> into 2d plots regardless of the fact that I never provided the 2d >>> coordinates. >>> So why can't I just simply get the mol file with those same coordinates? >>> >>> -- >>> Thanh >>> >>> >>> ------------------------------------------------------------------------------ >>> Check out the vibrant tech community on one of the world's most >>> engaging tech sites, SlashDot.org! http://sdm.link/slashdot >>> _______________________________________________ >>> OpenBabel-discuss mailing list >>> [hidden email] >>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss >>> > > > > -- > Thanh ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot _______________________________________________ OpenBabel-discuss mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/openbabel-discuss |
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