Re: [Rdkit-discuss] Align SDF to user-supplied template coordinates (2D)
On Mon, Aug 16, 2010 at 7:12 AM, James Davidson j.david...@vernalis.com wrote: You're doing it correctly; no worries there. The problem is that most pieces of chemical drawing software generate 2D coordinates for molecules such that a C-C single bond is 1.0A long. The RDKit, on the other hand, sets the C-C single bond to be 1.5A long. The consequence is a depiction with a core that's smaller than it should be. I was using ISISDraw for sketching the core motif. It seems that the single-bond length (from the Origdraw settings) is ~ 0.825 A (!) that's seems peculiar, but I guess there's some rationale behind it. So I modified the scalar to 1.818 (1.5/0.825) in your code and it works beautifully! Glad to hear it. It should be possible to specify the scale used in the RDKit depictions so that these contortions are not necessary. I will put a feature request in for this and get it in the next version. Thanks for this - I certainly think this would be a worthwhile feature. What I may implement in the meantime is running through all the bonds of type SINGLE in the core molecule, taking the average, then using 1.5/(average) as the scalar to protect against differing user settings! I checked the changes in this weekend. From python you can now provide a bondLength argument to set the value that's used while generating depictions. The default value for this is -1, which means don't mess with the default. -greg -- This SF.net email is sponsored by Make an app they can't live without Enter the BlackBerry Developer Challenge http://p.sf.net/sfu/RIM-dev2dev ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] Align SDF to user-supplied template coordinates (2D)
Dear All, I am currently struggling with something that I expect is very easy to solve (I have just got back from holiday, so I think my brain isn't quite in the zone!) I am trying to read in an SDF and align each molecule to a template scaffold provided in molfile format. I want to supply a tool that allows a user to sketch in a template and view their SDF entries in 2D all aligned (where there is a match) to the supplied template. I have essentially followed this entry in the Chemistry Toolkit Rosetta - http://ctr.wikia.com/wiki/Align_the_depiction_using_a_fixed_substructure http://ctr.wikia.com/wiki/Align_the_depiction_using_a_fixed_substructur e , which in essence is pretty-much the same as the info in the RDKit documentation. However, when I am using pre-supplied 2D coordinates for the template, rather than generating them from the first substructure match (as in the CTR example), I find that the alignment proceeds as required, but there is a mis-match between the scaling of the bond-lengths in the aligned substructure compared with the rest of the molecule... Is there a way to 'scale' the molecules according to the template mol (or alternatively scale the template according to the RDKit default)? Or is it that I am tackling this in the wrong way? Kind regards James __ PLEASE READ: This email is confidential and may be privileged. It is intended for the named addressee(s) only and access to it by anyone else is unauthorised. If you are not an addressee, any disclosure or copying of the contents of this email or any action taken (or not taken) in reliance on it is unauthorised and may be unlawful. If you have received this email in error, please notify the sender or postmas...@vernalis.com. Email is not a secure method of communication and the Company cannot accept responsibility for the accuracy or completeness of this message or any attachment(s). Please check this email for virus infection for which the Company accepts no responsibility. If verification of this email is sought then please request a hard copy. Unless otherwise stated, any views or opinions presented are solely those of the author and do not represent those of the Company. The Vernalis Group of Companies Oakdene Court 613 Reading Road Winnersh, Berkshire RG41 5UA. Tel: +44 118 977 3133 To access trading company registration and address details, please go to the Vernalis website at www.vernalis.com and click on the Company address and registration details link at the bottom of the page.. __-- This SF.net email is sponsored by Make an app they can't live without Enter the BlackBerry Developer Challenge http://p.sf.net/sfu/RIM-dev2dev ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Align SDF to user-supplied template coordinates (2D)
Hi James,
On Mon, Aug 16, 2010 at 1:09 PM, James Davidson j.david...@vernalis.com wrote:
I am currently struggling with something that I expect is very easy to solve
(I have just got back from holiday, so I think my brain isn't quite in the
zone!)
yes, I know that feeling well.
I am trying to read in an SDF and align each molecule to a template scaffold
provided in molfile format. I want to supply a tool that allows a user to
sketch in a template and view their SDF entries in 2D all aligned (where
there is a match) to the supplied template.
I have essentially followed this entry in the Chemistry Toolkit Rosetta -
http://ctr.wikia.com/wiki/Align_the_depiction_using_a_fixed_substructure,
which in essence is pretty-much the same as the info in the RDKit
documentation.
However, when I am using pre-supplied 2D coordinates for the template,
rather than generating them from the first substructure match (as in the CTR
example), I find that the alignment proceeds as required, but there is a
mis-match between the scaling of the bond-lengths in the aligned
substructure compared with the rest of the molecule...
Ah yes, the depictions that you get look rather silly, no?
Is there a way to 'scale' the molecules according to the template mol (or
alternatively scale the template according to the RDKit default)? Or is it
that I am tackling this in the wrong way?
You're doing it correctly; no worries there. The problem is that most
pieces of chemical drawing software generate 2D coordinates for
molecules such that a C-C single bond is 1.0A long. The RDKit, on the
other hand, sets the C-C single bond to be 1.5A long. The consequence
is a depiction with a core that's smaller than it should be.
It's straightforward to solve the problem:
#---
from rdkit import Chem
from rdkit.Chem import AllChem
core = Chem.MolFromMolFile('core.mol')
# first scale the core so that a single bond is 1.5A:
center = AllChem.ComputeCentroid(core.GetConformer())
import numpy
tf = numpy.identity(4,numpy.float)
tf[0][3] -= center[0]
tf[1][3] -= center[1]
tf[0][0] = tf[1][1] = tf[2][2] = 1.5
AllChem.TransformMol(core,tf)
m = Chem.MolFromSmiles('c12c1nc(CC)cc2C(=O)O')
from rdkit import Geometry
coords = [core.GetConformer().GetAtomPosition(x) for x in
range(core.GetNumAtoms())]
coords2D = [Geometry.Point2D(pt.x,pt.y) for pt in coords]
cd = {}
match = m.GetSubstructMatch(core)
for i,coord in enumerate(coords2D): cd[match[i]] = coord
AllChem.Compute2DCoords(m,coordMap=cd)
#---
It should be possible to specify the scale used in the RDKit
depictions so that these contortions are not necessary. I will put a
feature request in for this and get it in the next version.
-greg
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Re: [Rdkit-discuss] Align SDF to user-supplied template coordinates (2D)
Thanks Greg, Greg wrote: Ah yes, the depictions that you get look rather silly, no? Yes they do! You're doing it correctly; no worries there. The problem is that most pieces of chemical drawing software generate 2D coordinates for molecules such that a C-C single bond is 1.0A long. The RDKit, on the other hand, sets the C-C single bond to be 1.5A long. The consequence is a depiction with a core that's smaller than it should be. I was using ISISDraw for sketching the core motif. It seems that the single-bond length (from the Origdraw settings) is ~ 0.825 A (!) So I modified the scalar to 1.818 (1.5/0.825) in your code and it works beautifully! It should be possible to specify the scale used in the RDKit depictions so that these contortions are not necessary. I will put a feature request in for this and get it in the next version. Thanks for this - I certainly think this would be a worthwhile feature. What I may implement in the meantime is running through all the bonds of type SINGLE in the core molecule, taking the average, then using 1.5/(average) as the scalar to protect against differing user settings! Kind regards James __ PLEASE READ: This email is confidential and may be privileged. It is intended for the named addressee(s) only and access to it by anyone else is unauthorised. If you are not an addressee, any disclosure or copying of the contents of this email or any action taken (or not taken) in reliance on it is unauthorised and may be unlawful. If you have received this email in error, please notify the sender or postmas...@vernalis.com. Email is not a secure method of communication and the Company cannot accept responsibility for the accuracy or completeness of this message or any attachment(s). Please check this email for virus infection for which the Company accepts no responsibility. If verification of this email is sought then please request a hard copy. Unless otherwise stated, any views or opinions presented are solely those of the author and do not represent those of the Company. The Vernalis Group of Companies Oakdene Court 613 Reading Road Winnersh, Berkshire RG41 5UA. Tel: +44 118 977 3133 To access trading company registration and address details, please go to the Vernalis website at www.vernalis.com and click on the Company address and registration details link at the bottom of the page.. __ -- This SF.net email is sponsored by Make an app they can't live without Enter the BlackBerry Developer Challenge http://p.sf.net/sfu/RIM-dev2dev ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
