Re: [Rdkit-discuss] About Building The Cartrige

Dear Greg. Thank you for your quick reply. Your advice is helpful for me. I tried rebuilding the .o files, then all tests were passed ! I'm very grateful to you. takayuki 2013/1/26 Greg Landrum > Dear Takayuki, > > On Sat, Jan 26, 2013 at 5:37 AM, Taka Seri wrote: > > Dear all. > > > > I trie

Re: [Rdkit-discuss] PyMol

Nick, On Fri, Jan 25, 2013 at 11:42 AM, Nicholas Firth wrote: > Hi RDKitters, > > I've been looking at using RDKit to view molecules in PyMol as Greg showed > at the UGM. I found the test file in the source and started firstly to > replicate this, which threw and error so I then tried to run the

Re: [Rdkit-discuss] About Building The Cartrige

Dear Takayuki, On Sat, Jan 26, 2013 at 5:37 AM, Taka Seri wrote: > Dear all. > > I tried to build the postgresql cartridge. > (=>http://code.google.com/p/rdkit/wiki/BuildingTheCartridge) > Os X 10.7.5, RDKit ver 2012_12_1, and PostgreSQL ver 9.1.3 > I could not build the cartridge. > I got follow

[Rdkit-discuss] About Building The Cartrige

Dear all. I tried to build the postgresql cartridge. (=> http://code.google.com/p/rdkit/wiki/BuildingTheCartridge) Os X 10.7.5, RDKit ver 2012_12_1, and PostgreSQL ver 9.1.3 I could not build the cartridge. I got following error messages. > cd $RDBASE/Code/PgSQL/rdkit Then, > make g++ -I/opt/loc

Re: [Rdkit-discuss] SMILES Depiction

Yeah apologies I just found this answer in another thread: http://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg02495.html Thanks very much that did the trick. On 25 January 2013 04:40, Greg Landrum wrote: > Huw, > > > On Wed, Jan 23, 2013 at 1:54 PM, Huw Jones wrote: > >> Hi t

Re: [Rdkit-discuss] Fwd: Problem with InChI generation

Francis, On Jan 25, 2013, at 6:21 PM, Francis Atkinson wrote: > Hello, > >I have noticed an issue with InChI generation, in a rather specific > situation... > > There are cases where the following generates different InChIs, whereas they > ought to be identical > James Davidson has

[Rdkit-discuss] Fwd: Problem with InChI generation

Hello, I have noticed an issue with InChI generation, in a rather specific situation... There are cases where the following generates different InChIs, whereas they ought to be identical new_mol = reduce(Chem.CombineMols, Chem.GetMolFrags(old_mol, asMols=True)) old_inchi = Chem.Mol

[Rdkit-discuss] Problem with InChI generation

Hello, I have noticed an issue with InChI generation, in a rather specific situation. I have found cases where the following generates different InChIs, whereas they ought to be identical new_mol = reduce(Chem.CombineMols, Chem.GetMolFrags(old_mol, asMols=True)) old_inchi =

Re: [Rdkit-discuss] Detecting R groups using RDKit and the MCS code (R group decomposition).

On Fri, Jan 25, 2013 at 12:47 PM, JP wrote: > > Out of pedantry, why do some labels *not* have a numeric label (using > 2012_12_1)? All atoms have a numeric id; so the label should all be > attached to a numeric label e.g. > > mols = [ Chem.MolFromSmiles('CC(=O)CN(C)C'), > Chem.MolFromSmiles('c1c

Re: [Rdkit-discuss] Detecting R groups using RDKit and the MCS code (R group decomposition).

Hi Greg, On 25 January 2013 04:36, Greg Landrum wrote: > > That's pretty much what I would do. Fortunately, you don't have to > code it, because it's already there:[1] > [1] Incidentally, I love being given that answer :) > > In [6]: [Chem.MolToSmiles(x,True) for x in pieces] > Out[6]: ['[1*

[Rdkit-discuss] PyMol

Hi RDKitters, I've been looking at using RDKit to view molecules in PyMol as Greg showed at the UGM. I found the test file in the source and started firstly to replicate this, which threw and error so I then tried to run the test "python Code/RDKit/RDKit_2012_06_1/rdkit/Chem/Subshape/testCombin