Re: [Rdkit-discuss] bond length in 2D structure drawing

[Axel P. <axe...@gm...>]

Hi Greg,

thanks a lot.
That is exactly what I was looking for!

RDKit rules!

Kind regards,
Axel


On 19.09.2016 09:35, Greg Landrum wrote:
> Hi Axel,
>
> It's probably most straightforward to use the function 
> AllChem.TransformMol() to scale the coordinates.
> Here's an example of applying the function to scale all the 
> coordinates by a factor of 2:
>
> In [1]: from rdkit import Chem
>
> In [2]: from rdkit.Chem import rdMolTransforms
>
> In [5]: from rdkit.Chem import AllChem
>
> In [6]: import numpy
>
> In [7]: tm = numpy.zeros((4,4),numpy.double)
>
> In [8]: for i in range(3): tm[i,i] = 2.
>
> In [9]: tm[3,3] = 1.
>
> In [10]: m = Chem.MolFromSmiles('C1CCC1')
>
> In [11]: AllChem.Compute2DCoords(m)
> Out[11]: 0
>
> In [12]: print(Chem.MolToMolBlock(m))
>
>      RDKit          2D
>
>   4  4  0  0  0  0  0  0  0  0999 V2000
>     1.0607   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
>    -0.0000   -1.0607    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
>    -1.0607    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
>     0.0000    1.0607    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
>   1  2  1  0
>   2  3  1  0
>   3  4  1  0
>   4  1  1  0
> M  END
>
>
> In [13]: AllChem.TransformMol(m,tm)
>
> In [14]: print(Chem.MolToMolBlock(m))
>
>      RDKit          2D
>
>   4  4  0  0  0  0  0  0  0  0999 V2000
>     2.1213   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
>    -0.0000   -2.1213    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
>    -2.1213    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
>     0.0000    2.1213    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
>   1  2  1  0
>   2  3  1  0
>   3  4  1  0
>   4  1  1  0
> M  END
>
>
> In your case, assuming that the bond length in the drawings is 1.0A, 
> you would use a scale factor of 1.5 (that's on line [8] above).
>
> Best,
> -greg
>
>
> On Mon, Sep 19, 2016 at 8:41 AM, Axel Pahl <axe...@gm... 
> <mailto:axe...@gm...>> wrote:
>
>     Dear fellow RDKitters,
>
>     I have an SD file with 2D molecules generated by another
>     Cheminformatics
>     toolkit (yes, there are others! ;-) ).
>     When I depict them with RDKit (with Draw.MolToImage()) they look very
>     condensed with too short bonds and just appear not right.
>     When I re-generate the coordinates by using Compute2DCoord(), the
>     structure drawings do look great, but RDkit re-calculates all
>     coordinates and the orientation of the whole molecule is
>     completely changed.
>     Can I avoid this, keep the original orientation of the molecules and
>     just do something like "apply drawing settings" or "use standard bond
>     lengths" to a molecule?
>
>     Many thanks in advance.
>
>     Kind regards,
>     Axel
>
>
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