[Rdkit-discuss] Writing a Tripos MOL2 file with charges

2016-10-30 Thread James Johnson
Hello all, I've been trying to output my 3D mol object that has Gasteiger charges to mol2 file format. How would I go about that? I've only found it for mol and pdb. Here is the code I'be been using if that helps: ~~~ from rdkit

[Rdkit-discuss] Problems Installing RDKit for Python Under Ubuntu

2016-10-30 Thread Jonathan Saboury
Hello all, I've been having problems installing RDKit for python in Ubuntu. The installation guide simply states to run: "sudo apt-get install python-rdkit librdkit1 rdkit-data". I've done this but when I run a python with "from rdkit import Chem" it says that "ImportError: No module named

Re: [Rdkit-discuss] reading multiple conformers from file

2016-10-30 Thread Brian Kelley
Rdkit already has a way to serialize conformers, the binary pickle format! Perhaps we should make a file extension for multiple molecules. Say ".rdk" and call it a day. Like inchi the source code is the reference :) Brian Kelley > On Oct 27, 2016, at 2:05 AM, Greg Landrum