Re: [Rdkit-discuss] rdMolDraw2D drawing code

2016-09-08 Thread Greg Landrum 
On Tue, Sep 6, 2016 at 10:00 PM, Dimitri Maziuk 
wrote:

> On 09/05/2016 03:47 AM, Greg Landrum wrote:
> > Dave's right about the font size: it's expressed in whatever coordinates
> > the molecule is being drawn in.
>
> I'd put Dave's explanation in the doc++ (?) comment on FontSize
> get/setter in MolDraw2D:
> http://www.rdkit.org/Python_Docs/rdkit.Chem.Draw.
> rdMolDraw2D.MolDraw2D-class.html
>
> Right now they just say "float". If you're dealing with SVG output, font
> sizes are px, em, and points, and you need a couple of tries to figure
> them out. It's a minor thing.
>
>
Pull requests with documentation tweaks/corrections are always welcome.


> > I suspect the other part of Dmitri's question is about the way bonds are
> > shortened so that they don't draw all the way through the atom labels.
>
> Yes, I think. It looks like there's more padding on the top and the
> right, and less padding on the left and bottom. E.g. H39 in the attached
> "all" version is the worst, but it is consistent in all 3.
>
> The other one on the "all" picture is that the bond to O21 isn't
> shortened enough and there isn't much room left between 021 and O24.
>
> OTOH all three labels: H38, O21, H39 could be drawn without even
> shortening the bonds if we could just move them up a little. (Well, H39
> could be just drawn without shortening the bond at all.)
>
> Last but not least, my starting point is a 3D MOL file and I call
> rdkit.Chem.AllChem.Compute2DCoords( mh ) -- last thing before
> DrawMolecule(). Attached CID112084.svg is the one generated without
> AddHs(), notice how layout is very different on that one.
>

Yes, the layout will always be different when you are using different
atoms. ;-)

2D depictions of non-trivial molecules that include H atoms have a tendency
to be pretty crowded. This makes them a challenge for the coordinate
generation algorithm. This is an example of that. I'm not sure that there's
a good general solution, or if it's worth investing the time in trying to
find one given that this is something of a special case.


>
> I've a suspicion that that layout might look better with all the Hs and
> numbers added, than the one I get (the other 3 pictures).
>
> --
> Dimitri Maziuk
> Programmer/sysadmin
> BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu
>
> 
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Re: [Rdkit-discuss] rdMolDraw2D drawing code

2016-09-06 Thread Dimitri Maziuk 
PS. looking at this, it may have come out a little confusing, so

I start with a 3D mol file and run it through
rdkit.Chem.AllChem.Compute2DCoords()

CID112084.svg is what comes out.

Running rdkit.Chem.AddHs() before Compute2DCoords() generates the layout
seen on other 3 pictures.

CID112084.allh.svg is what comes out after AddHs().

CID112084.nonum.svg is what comes out after
op = dr.drawOptions()
for i in range( mh.GetNumAtoms() ) :
op.atomLabels[i] = mh.GetAtomWithIdx( i ).GetSymbol()

CID112084.all.svg is with the above loop changed to
op.atomLabels[i] = mh.GetAtomWithIdx( i ).GetSymbol() + str ((i+1))

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



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Re: [Rdkit-discuss] rdMolDraw2D drawing code

2016-09-06 Thread Dimitri Maziuk 
On 09/05/2016 03:47 AM, Greg Landrum wrote:
> Dave's right about the font size: it's expressed in whatever coordinates
> the molecule is being drawn in.

I'd put Dave's explanation in the doc++ (?) comment on FontSize
get/setter in MolDraw2D:
http://www.rdkit.org/Python_Docs/rdkit.Chem.Draw.rdMolDraw2D.MolDraw2D-class.html

Right now they just say "float". If you're dealing with SVG output, font
sizes are px, em, and points, and you need a couple of tries to figure
them out. It's a minor thing.

> I suspect the other part of Dmitri's question is about the way bonds are
> shortened so that they don't draw all the way through the atom labels.

Yes, I think. It looks like there's more padding on the top and the
right, and less padding on the left and bottom. E.g. H39 in the attached
"all" version is the worst, but it is consistent in all 3.

The other one on the "all" picture is that the bond to O21 isn't
shortened enough and there isn't much room left between 021 and O24.

OTOH all three labels: H38, O21, H39 could be drawn without even
shortening the bonds if we could just move them up a little. (Well, H39
could be just drawn without shortening the bond at all.)

Last but not least, my starting point is a 3D MOL file and I call
rdkit.Chem.AllChem.Compute2DCoords( mh ) -- last thing before
DrawMolecule(). Attached CID112084.svg is the one generated without
AddHs(), notice how layout is very different on that one.

I've a suspicion that that layout might look better with all the Hs and
numbers added, than the one I get (the other 3 pictures).

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


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Re: [Rdkit-discuss] rdMolDraw2D drawing code

2016-09-05 Thread Greg Landrum 
Dave's right about the font size: it's expressed in whatever coordinates
the molecule is being drawn in.
Cross-platform font handling is tough. Cross-platform, cross-toolkit font
handling is even tougher. What's currently there seems to be an
quasi-workable solution.

I suspect the other part of Dmitri's question is about the way bonds are
shortened so that they don't draw all the way through the atom labels. This
is handled by a function in MolDraw2D that attempts to take into account
the font size. It doesn't always succeed (see the comments above about font
handling). It's easy enough to add an option that allows you to adjust the
amount of padding that's used in that code.
Here's the github issue:
https://github.com/rdkit/rdkit/issues/1056

-greg



On Mon, Sep 5, 2016 at 9:57 AM, David Cosgrove 
wrote:

> HI Dmitri,
>
> Sorry for the delay replying. I assume that by 'add padding' you mean that
> the code that generates the 2D drawing coordinates should take account of
> the size of the labels and would, from your example, maybe open out the
> C9-O23-C14 bond a bit so that O21 and O24 are further apart?  If so, then I
> can duck that one cheerfully as it's not part of the MolDraw2D code. The 2D
> coordinates are generated in RDDepictor - MolDraw2D just uses the results
> from that.  Having just had a peer at $RDBASE/GraphMol/Depictor/Depictor.h,
> it would seem as though adding a padding as you suggest might not be
> straightforward, but I guess it might be possible to alter the distance
> matrix that is being embedded in 2D to take account of atom label sizes.
> The joy of open source projects is of course that you have the opportunity
> to change things if you don't like how they're done at present.  Maybe
> something to think about at the UGM hackathon day?
>
> As you say, your best bet in the short term is probably to adjust the font
> size in the drawing.  MolDraw2D.h says that the font sizes are given "in
> molecule coordinate units. That's probably Angstrom for RDKit" which in
> reality means it's relative to a C-C bond in benzene of 1.5 units. This is
> then changed internally to a value appropriate for the drawing engine that
> is being used in a particular instance.  If you can see a sensible place to
> put this information in the documentation, feel free to send a changed
> version to Greg for inclusion in the next release.  I am struggling to find
> any such documentation myself, and maybe that was your point ;-).
>
> Cheers,
> Dave
>
>
> On Fri, Sep 2, 2016 at 9:07 PM, Dimitri Maziuk 
> wrote:
>
>> Hi all,
>>
>> I finally got a round tuit for playing with the drawing code and I like
>> it -- great job, thank you Greg and Dave and everyone who contributed.
>>
>> One question though: is it possible to add padding around atom labels?
>> Or use some other trick to make the attached look less crowded? (Yes, I
>> do want all Hs and all atom labels with numbers.)
>>
>> The best I can come up with is reduce the font size a little, that works
>> fine. I think it'd be nice if the fine manual for MolDraw2D said what
>> the units used by FontSize()/SetFontSize() are.
>>
>> So, any better ideas than just slightly smaller labels?
>>
>> TIA
>> --
>> Dimitri Maziuk
>> Programmer/sysadmin
>> BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu
>>
>> 
>> --
>>
>> ___
>> Rdkit-discuss mailing list
>> Rdkit-discuss@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>
>>
>
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Re: [Rdkit-discuss] rdMolDraw2D drawing code

2016-09-05 Thread David Cosgrove 
HI Dmitri,

Sorry for the delay replying. I assume that by 'add padding' you mean that
the code that generates the 2D drawing coordinates should take account of
the size of the labels and would, from your example, maybe open out the
C9-O23-C14 bond a bit so that O21 and O24 are further apart?  If so, then I
can duck that one cheerfully as it's not part of the MolDraw2D code. The 2D
coordinates are generated in RDDepictor - MolDraw2D just uses the results
from that.  Having just had a peer at $RDBASE/GraphMol/Depictor/Depictor.h,
it would seem as though adding a padding as you suggest might not be
straightforward, but I guess it might be possible to alter the distance
matrix that is being embedded in 2D to take account of atom label sizes.
The joy of open source projects is of course that you have the opportunity
to change things if you don't like how they're done at present.  Maybe
something to think about at the UGM hackathon day?

As you say, your best bet in the short term is probably to adjust the font
size in the drawing.  MolDraw2D.h says that the font sizes are given "in
molecule coordinate units. That's probably Angstrom for RDKit" which in
reality means it's relative to a C-C bond in benzene of 1.5 units. This is
then changed internally to a value appropriate for the drawing engine that
is being used in a particular instance.  If you can see a sensible place to
put this information in the documentation, feel free to send a changed
version to Greg for inclusion in the next release.  I am struggling to find
any such documentation myself, and maybe that was your point ;-).

Cheers,
Dave


On Fri, Sep 2, 2016 at 9:07 PM, Dimitri Maziuk 
wrote:

> Hi all,
>
> I finally got a round tuit for playing with the drawing code and I like
> it -- great job, thank you Greg and Dave and everyone who contributed.
>
> One question though: is it possible to add padding around atom labels?
> Or use some other trick to make the attached look less crowded? (Yes, I
> do want all Hs and all atom labels with numbers.)
>
> The best I can come up with is reduce the font size a little, that works
> fine. I think it'd be nice if the fine manual for MolDraw2D said what
> the units used by FontSize()/SetFontSize() are.
>
> So, any better ideas than just slightly smaller labels?
>
> TIA
> --
> Dimitri Maziuk
> Programmer/sysadmin
> BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu
>
> 
> --
>
> ___
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
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[Rdkit-discuss] rdMolDraw2D drawing code

2016-09-02 Thread Dimitri Maziuk 
Hi all,

I finally got a round tuit for playing with the drawing code and I like
it -- great job, thank you Greg and Dave and everyone who contributed.

One question though: is it possible to add padding around atom labels?
Or use some other trick to make the attached look less crowded? (Yes, I
do want all Hs and all atom labels with numbers.)

The best I can come up with is reduce the font size a little, that works
fine. I think it'd be nice if the fine manual for MolDraw2D said what
the units used by FontSize()/SetFontSize() are.

So, any better ideas than just slightly smaller labels?

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


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