Re: [Rdkit-discuss] AddHs()

2016-09-13 Thread Dimitri Maziuk
On 09/10/2016 12:08 PM, David Cosgrove wrote: > On the subject of the documentation, I would encourage you to find the > GettingStartedWithRDKit.rst in the Docs directory, find somewhere where > this discussion fits, add it, and send the new version to Greg. If everyone > did this every time they

Re: [Rdkit-discuss] Has3D?

2016-09-13 Thread Dimitri Maziuk
On 09/13/2016 05:24 PM, Rich Lewis wrote: > Hi Dimitri, > > 3D geometry information for rdkit `Mol`s is stored as `Conformer`s. These can be accessed with the `GetConformer` method, which takes a confId as an argument. If you have loaded the molecule from a mol/sdf file, there should be a single

[Rdkit-discuss] Has3D?

2016-09-13 Thread Dimitri Maziuk
Hi all, a quick one hopefully: is there something like Mol.Has3D()? I'm looking at "2D" vs "3D" MOL files and the best I can tell in the 2D ones Z coord is always 0 whereas in 3D there may (should?) be a non-zero one. Is there a quick way find out after reading in a MOL if it's one or the other?

Re: [Rdkit-discuss] Has3D?

2016-09-13 Thread Rich Lewis
Hi Dimitri, 3D geometry information for rdkit `Mol`s is stored as `Conformer`s. These can be accessed with the `GetConformer` method, which takes a confId as an argument. If you have loaded the molecule from a mol/sdf file, there should be a single conformer with ID 0, with the coordinates

[Rdkit-discuss] Angstroms Hydrogen bonding

2016-09-13 Thread Guillaume GODIN
Dear RDKiters, I have two question: 1 Does 3D coordinates of a conformer is in Angstroms ? 2 How to enumerate all HBonding to determine the bond length ? Best regards, Guillaume ** DISCLAIMER This email and any files