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

```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 <axelp...@gmx.de <mailto:axelp...@gmx.de>> 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

------------------------------------------------------------------------------
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
<mailto:Rdkit-discuss@lists.sourceforge.net>
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
<https://lists.sourceforge.net/lists/listinfo/rdkit-discuss>

```
```
```
```------------------------------------------------------------------------------
```
```_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
```