[Rdkit-discuss] UpdatePropertyCache() after RunReactants

2017-01-11 Thread Curt Fischer
Hi all, I recently wanted to use RDKit to model the famous copper-catalyzed cycloaddition of alkynes and azides. I eventually got things working, kind of, but had two questions. First, I was surprised to find that the products of RunReactants don't have update property caches. Is this

[Rdkit-discuss] Operations dependent on Kekulization

2017-01-11 Thread Juuso Lehtivarjo
Dear RDKit users, Interpreting the default sanitization order (in http://www.rdkit.org/docs/RDKit_Book.html), I assume that SetAromaticity must be preceded with Kekulization (otherwise, why to Kekulize at all if atoms and bonds are to be marked as aromatic anyway). However, I wonder if any of the

Re: [Rdkit-discuss] SD file read error

2017-01-11 Thread Steve O'Hagan
OK, error messages where hidden by IPython for me too. I used "Knime" to look at the sdf file, and it seems that the errors are "real" - polymers, organometallic compounds or completely daft, two examples: The structure in the first column is the input sdf. Simple workflow was: "RDKit

[Rdkit-discuss] SD file read error

2017-01-11 Thread Milinda Samaraweera
Dear Experts, I was trying to read in the attached SD file (downloaded from HMDB) and trying to calculate the exact mass of each entry: ​ structures.sdf ​ from rdkit import Chem from rdkit.Chem import Descriptors

Re: [Rdkit-discuss] RDKit conformer handling possible bug?

2017-01-11 Thread Stephen Roughley
Thanks Greg. I think I understand! Let me just check this to be certain. If the molecule came from SMILES, it has no conformers, so all appears to work as expected. If the molecule came from MOL/SDF etc, then it has coordinates in the input, and thus a conformer. When I then add a conformer,

Re: [Rdkit-discuss] RDKit conformer handling possible bug?

2017-01-11 Thread Greg Landrum
On Wed, Jan 11, 2017 at 10:47 AM, Stephen Roughley wrote: > Thanks Greg. I think I understand! > > > > Let me just check this to be certain. > > > > If the molecule came from SMILES, it has no conformers, so all appears to > work as expected. > correct > If the

Re: [Rdkit-discuss] RDKit conformer handling possible bug?

2017-01-11 Thread Stephen Roughley
Thanks Greg. For completeness, for anyone trying this from the Java wrappers, the relevant methods are mol.clearConformers(); and mol.addConformer(conf, true); Steve From: Greg Landrum [mailto:greg.land...@gmail.com] Sent: 11 January 2017 11:01 To: Stephen Roughley Cc: RDKit Discuss

Re: [Rdkit-discuss] Operations dependent on Kekulization

2017-01-11 Thread Greg Landrum
Hi Juuso, Reading aromatic bonds from a mol file is problematic (the mol file spec is clear that aromatic bond orders are only for use in queries), but ignoring that for a moment... There's an RDKit blog post on this very topic:

Re: [Rdkit-discuss] SD file read error

2017-01-11 Thread Steve O'Hagan
With same code and fresh file download, works fine for me without error. ms contains 35177 molecules. Perhaps your download was corrupt? On 11/01/2017 18:26, Milinda Samaraweera wrote: Dear Experts, I was trying to read in the attached SD file (downloaded from HMDB) and trying to calculate

Re: [Rdkit-discuss] SD file read error

2017-01-11 Thread Jan Holst Jensen
On 2017-01-11 19:26, Milinda Samaraweera wrote: Dear Experts, I was trying to read in the attached SD file (downloaded from HMDB) and trying to calculate the exact mass of each entry: ​[...] By running the script, I got a barrage of errors as: [13:15:14] ERROR: Could not sanitize molecule

Re: [Rdkit-discuss] SD file read error

2017-01-11 Thread Curt Fischer
I also got this to run with no problem in a Jupyter notebook. BUT...I did see the error messages Milinda mentioned in the terminal that was running the jupyter notebook server. If I do *from rdkit.Chem.Draw import IPythonConsole *before running the code, I see all the errors/warnings in Jupyter.