Re: [Rdkit-discuss] 2D drawing with atoms labeled by index

2016-10-24 Thread Peter S. Shenkin 
Consider the following excerpt:

svg = drawer.GetDrawingText()
svg2 = svg.replace('svg:','')
svg3 = SVG(svg2)
print 'displaying svg:'
display(svg)
print 'displaying svg2:'
display(svg2)
print 'displaying svg3:'
display(svg3)

svg and svg2 display as xml text. svg3 displays as the image, in a Jupyter
notebook in Chrome.

On Mon, Oct 24, 2016 at 6:44 PM, Dimitri Maziuk 
wrote:

> On 10/24/2016 04:39 PM, Peter S. Shenkin wrote:
>
> > Or is it
> > rather because chemists in your target audience will be thinking of the
> > first atom in, say, a structure from an sd file as atom #1?
>
> That
>
> > 2. Regarding the last line, most of the RDKit code I've seen in past
> > examples displays the molecule using code like the following. When is it
> > necessary/not necessary to remove the "svg" string from the results of
> > GetDrawingText()?
>
> Not sure: it's a namespace, I'm assuming ipython can't deal with xml
> namespaces. Properly written programs should show it either way,
> unfortunately my target viewer is firefox (it's a web application and
> the user's default browser is firefox) and firefox isn't one of them.
> Without svg:'s it'll show the file as xml text instead of the image.
>
> HTH
> --
> Dimitri Maziuk
> Programmer/sysadmin
> BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu
>
>
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Re: [Rdkit-discuss] 2D drawing with atoms labeled by index

2016-10-24 Thread Dimitri Maziuk 
On 10/24/2016 04:39 PM, Peter S. Shenkin wrote:

> Or is it
> rather because chemists in your target audience will be thinking of the
> first atom in, say, a structure from an sd file as atom #1?

That

> 2. Regarding the last line, most of the RDKit code I've seen in past
> examples displays the molecule using code like the following. When is it
> necessary/not necessary to remove the "svg" string from the results of
> GetDrawingText()?

Not sure: it's a namespace, I'm assuming ipython can't deal with xml
namespaces. Properly written programs should show it either way,
unfortunately my target viewer is firefox (it's a web application and
the user's default browser is firefox) and firefox isn't one of them.
Without svg:'s it'll show the file as xml text instead of the image.

HTH
-- 
Dimitri Maziuk
Programmer/sysadmin
BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu



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Re: [Rdkit-discuss] 2D drawing with atoms labeled by index

2016-10-24 Thread Peter S. Shenkin 
Hi, Dimitri,

I have two questions about your code.

1. Why are you incrementing the atom index by 1? Are there functions in
RDKit, for example, that use atom indices using index-origin 1? Or is it
rather because chemists in your target audience will be thinking of the
first atom in, say, a structure from an sd file as atom #1?

2. Regarding the last line, most of the RDKit code I've seen in past
examples displays the molecule using code like the following. When is it
necessary/not necessary to remove the "svg" string from the results of
GetDrawingText()?

svg = drawer.GetDrawingText().replace('svg:','')
SVG(svg)

Thanks,
-P.

On Mon, Oct 24, 2016 at 2:31 PM, Dimitri Maziuk 
wrote:

> Since you already got your answer I'll just post this for posterity:
>
>
> import sys
> import rdkit
> import rdkit.Chem
> import rdkit.Chem.AllChem
> import rdkit.Chem.Draw
> import rdkit.Chem.Draw.rdMolDraw2D
>
> mol=rdkit.Chem.SupplierFromFilename(sys.argv[1],removeHs=False).next()
> dr=rdkit.Chem.Draw.rdMolDraw2D.MolDraw2DSVG(800,800)
> dr.SetFontSize(0.3)
> op = dr.drawOptions()
> for i in range(mol.GetNumAtoms()) :
> op.atomLabels[i]=mol.GetAtomWithIdx(i).GetSymbol() + str((i+1))
> rdkit.Chem.AllChem.Compute2DCoords(mol)
> dr.DrawMolecule(mol)
> dr.FinishDrawing()
> svg=dr.GetDrawingText()
>
>
> --
> Dimitri Maziuk
> Programmer/sysadmin
> BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu
>
>
> 
> --
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Re: [Rdkit-discuss] 2D drawing with atoms labeled by index

2016-10-24 Thread Dimitri Maziuk 
Since you already got your answer I'll just post this for posterity:


import sys
import rdkit
import rdkit.Chem
import rdkit.Chem.AllChem
import rdkit.Chem.Draw
import rdkit.Chem.Draw.rdMolDraw2D

mol=rdkit.Chem.SupplierFromFilename(sys.argv[1],removeHs=False).next()
dr=rdkit.Chem.Draw.rdMolDraw2D.MolDraw2DSVG(800,800)
dr.SetFontSize(0.3)
op = dr.drawOptions()
for i in range(mol.GetNumAtoms()) :
op.atomLabels[i]=mol.GetAtomWithIdx(i).GetSymbol() + str((i+1))
rdkit.Chem.AllChem.Compute2DCoords(mol)
dr.DrawMolecule(mol)
dr.FinishDrawing()
svg=dr.GetDrawingText()


-- 
Dimitri Maziuk
Programmer/sysadmin
BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu



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Re: [Rdkit-discuss] 2D drawing with atoms labeled by index

2016-10-23 Thread Peter S. Shenkin 
Hi, Hongbin,

Thank you very much for your help. That worked! That blog entry is a great
tutorial, in general.

So it turned out that in the following test code, I had correctly figured
out how to set atomLabels, but instead of the last two lines in my .ipynb I
had just asserted "m". (How quickly we forget.. :-} )

Best,
-P.

rdDepictor.Compute2DCoords(m)
drawer = rdMolDraw2D.MolDraw2DSVG(400, 200)
drawer.drawOptions().atomLabels[0] = '0'
drawer.DrawMolecule(m)
drawer.FinishDrawing()
svg = drawer.GetDrawingText().replace('svg:','')
SVG(svg)



On Sun, Oct 23, 2016 at 11:38 PM, 杨弘宾  wrote:

> Hi，Peter S. Shenkin,
> I think this blog may help you draw molecule with labels and it told
> more about drawing with rdMolDraw2D.
> http://rdkit.blogspot.com/2015/02/new-drawing-code.html
>
> --
> Hongbin Yang
>
> *From:* Peter S. Shenkin 
> *Date:* 2016-10-24 10:18
> *To:* Dimitri Maziuk ; RDKit Discuss
> 
> *Subject:* [Rdkit-discuss] 2D drawing with atoms labeled by index
> Hi,
>
> How do you get RDKit to label the atoms in a 2D drawing with their indices?
>
> There was some discussion of this that included Dimitri Maziuk in
> September, but it wasn't clear to me whether he actually had to modify the
> underlying drawing code to get this behavior.
>
> -P.
>
>
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Re: [Rdkit-discuss] 2D drawing with atoms labeled by index

2016-10-23 Thread 杨弘宾 






Hi，Peter S. Shenkin,    I think this blog may help you draw molecule with 
labels and it told more about drawing with rdMolDraw2D.    
http://rdkit.blogspot.com/2015/02/new-drawing-code.html


Hongbin Yang From: Peter S. ShenkinDate: 2016-10-24 10:18To: Dimitri Maziuk; 
RDKit DiscussSubject: [Rdkit-discuss] 2D drawing with atoms labeled by indexHi,

How do you get RDKit to label the atoms in a 2D drawing with their indices?
There was some discussion of this that included Dimitri Maziuk in September, 
but it wasn't clear to me whether he actually had to modify the underlying 
drawing code to get this behavior.
-P.

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