Re: [Rdkit-discuss] rotate a conformer around an axis?
Hi Mchal, TransformConformer can rotate molecule with given rotation matrix I think. I rotate mol by using the method. Following code rotates molecule around x, y, z axis. https://nbviewer.jupyter.org/github/iwatobipen/playground/blob/master/rotation_mol.ipynb Unfortunately molecule will not render on github but you can view molecule if you run the code on your PC. I hope this would be some of help. Best regards, Taka 2019年2月26日(火) 17:55 Michal Krompiec : > Hello, > I'd like to check if a particular axis is a C2 symmetry axis of a > conformer. How do I rotate my conformer around an axis? (apart from > extracting the coordinates into numpy, multiplying by a rotation matrix and > updating the coordinates) > Can TransformConformer function be used for this? > Thanks, > Michal > > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Atom coordinates from PDB-file
Hi Illimar, if you are familiar with pandas DataFrames, then I would also recommend BioPandas for this: https://github.com/rasbt/biopandas Cheers, Jose Manuel On 26.02.19 00:05, Stéphane Téletchéa wrote: Hi all, Le 25/02/2019 à 12:38, Lukas Pravda a écrit : Hi Illimar, If you need to access coordinates without creating conformer object do you really need to use rdkit I the first place? PDB file is column based format, so extracting coordinates for atoms for example with python is very straightforward. Lukas To pick certains atoms on a PDB file, I'd go for biopython's Bio.PDB -> https://biopython.org/wiki/The_Biopython_Structural_Bioinformatics_FAQ HTH, Stéphane ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] rotate a conformer around an axis?
Hello, I'd like to check if a particular axis is a C2 symmetry axis of a conformer. How do I rotate my conformer around an axis? (apart from extracting the coordinates into numpy, multiplying by a rotation matrix and updating the coordinates) Can TransformConformer function be used for this? Thanks, Michal ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
