[Rdkit-discuss] Cleaning SD files

2010-09-16 Thread James Davidson
Dear All, Today I have spent some time processing a freely-available SDF that contains many compounds and melting-points / ranges ( http://www.mdpi.org/molmall/mdpi1-51sd.zip). The reason for doing this is that I wanted to implement a melting-point predictor following the work of Andreas Bender

Re: [Rdkit-discuss] Cleaning SD files

2010-09-16 Thread Greg Landrum
Dear James, On Thu, Sep 16, 2010 at 8:01 PM, James Davidson j.david...@vernalis.com wrote: I have attached the python-script that I have at the moment (a) in case it is of some use to anybody else, (b) in the hope that I can improve my python and rdkit abilities through any suggested

Re: [Rdkit-discuss] newbie help cleaning up sterochemistry in SMILES string

2010-09-16 Thread Greg Landrum
Dear Hari, On Thu, Sep 16, 2010 at 8:44 PM, hari jayaram hari...@gmail.com wrote: I am working with several ligands from a database stored in a SMILES format.  I am using the SMILES string to get three dimensional coordinates (pdb format file)  using a third-party program called libcheck.

Re: [Rdkit-discuss] cmake does not find my boost libraries

2010-09-16 Thread Greg Landrum
Dear Jef, On Thu, Sep 16, 2010 at 7:39 AM, Jef K althusser...@hotmail.fr wrote: I am using a Linux machine which has an old version of boost. I am trying to install RDKit following these instructions http://code.google.com/p/rdkit/wiki/BuildingWithCmake Everything went OK in the Building

[Rdkit-discuss] question about resizing PDF depictions

2010-09-16 Thread ramgopal mettu
Hi All, I've just started using RDKit and am finding it extremely useful, particularly for generating for depictions. I have a rather simple question about generating PDFs. Is it possible to generate a PDF that is sized according to the molecule depicted? For example, if I execute: from

Re: [Rdkit-discuss] question about resizing PDF depictions

2010-09-16 Thread Greg Landrum
Dear Ram, On Fri, Sep 17, 2010 at 6:29 AM, ramgopal mettu chocolate.cu...@gmail.com wrote: Hi All,  I've just started using RDKit and am finding it extremely useful, particularly for generating for depictions. I have a rather simple I'm glad to hear it. question about generating PDFs. Is it