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[Pybel, make3d, .mol] Why is there no "make2D()", and why can't I just "flatten()" a mol file?

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T V

[Pybel, make3d, .mol] Why is there no "make2D()", and why can't I just "flatten()" a mol file?

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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Noel O'Boyle

Re: [Pybel, make3d, .mol] Why is there no "make2D()", and why can't I just "flatten()" a mol file?

Administrator

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

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T V

Re: [Pybel, make3d, .mol] Why is there no "make2D()", and why can't I just "flatten()" a mol file?

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

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Thanh

Noel O'Boyle

Re: [Pybel, make3d, .mol] Why is there no "make2D()", and why can't I just "flatten()" a mol file?

Administrator

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