[Rdkit-discuss] Is there someone who manages to compile rdkit Release_2020_03_4 from sources on a Mac?

2020-07-07 Thread Francois Berenger
Dear rdkiters, I am trying to repair the brew formula. Currently, I get this when I try to compile Release_2020_03_4: $ cd build $ cmake -DPYTHON_EXECUTABLE=/usr/local/bin/python-3.7 -DRDK_INSTALL_INTREE=OFF -DRDK_BUILD_INCHI_SUPPORT=ON -DRDK_BUILD_AVALON_SUPPORT=ON

Re: [Rdkit-discuss] ConstrainedEmbed issue

2020-07-07 Thread Pavel Polishchuk
Thank you, Sereina. I understand importance of addition of hydrogens to get a reasonable 3D coordinates. But the situation may be not that simple. 1. Addition of hydrogen is only required for custom coordinates supplied from an external file. If coordinates of a template is generated with

Re: [Rdkit-discuss] ConstrainedEmbed issue

2020-07-07 Thread Sunhwan Jo
Makes sense :) > On Jul 7, 2020, at 12:35 PM, Sereina Riniker > wrote: > > Dear Pavel and Sunhwan, > > Please note that hydrogens should always be added for the embedding algorithm > to work properly (i.e. it’s not a walk around but what should be done). > See also Section “Working with 3D

Re: [Rdkit-discuss] ConstrainedEmbed issue

2020-07-07 Thread Sereina Riniker
Dear Pavel and Sunhwan, Please note that hydrogens should always be added for the embedding algorithm to work properly (i.e. it’s not a walk around but what should be done). See also Section “Working with 3D Molecules” in https://www.rdkit.org/docs/GettingStartedInPython.html Best regards,

[Rdkit-discuss] ConstrainedEmbed issue

2020-07-07 Thread Pavel Polishchuk
Hi all,   I have an issue with ConstrainedEmbed and I cannot figure out what exactly causes this.   I have a molecule C[C@@H]1C1=O with 3D coordinates in 1.mol file (attached). And I want to generate coordinates for another structure with this core - C[C@@H]1CC[C@H](O)CC1=O.   This is