Re: [Rdkit-discuss] How to find the idx of hydrogens bonded to a specific atom
Hello Dimitri, Yes, I do have explicit hydrogen throughout entire process. Thank you for the tip. I will check out the link. Bin Original Message Subject: Re: [Rdkit-discuss] How to find the idx of hydrogens bonded to a specific atom Local Time: October 14, 2016 2:26 AM UTC Time: October 13, 2016 6:26 PM From: dmaz...@bmrb.wisc.edu To: rdkit-discuss@lists.sourceforge.net On 10/13/2016 12:12 PM, Paul Emsley wrote: > Are you sure? I use HasSubstrMatch to match hydrogens. Perhaps this http://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg05897.html may be useful? If OP's looking at crystal structures, they're likely dealing with pdb data model where all hydrogens are explicitly present and indexed. I wonder if they stay that way throughout the steps leading to (and past) the smarts match. -- Dimitri Maziuk Programmer/sysadmin BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu -- Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss-- Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] How to find the idx of hydrogens bonded to a specific atom
Hello Paul, I will take a look at your code. Thank you. Original Message Subject: Re: [Rdkit-discuss] How to find the idx of hydrogens bonded to a specific atom Local Time: October 14, 2016 1:12 AM UTC Time: October 13, 2016 5:12 PM From: pems...@mrc-lmb.cam.ac.uk To: rdkit-discuss@lists.sourceforge.net On 13/10/2016 05:04, Bin Song wrote: > Hello everyone, > > A new user of Rdkit and new subscriber of the mailing list reporting here. > > I have a question to ask, as stated in the subject. I have googled and > consulted the > documentation of rdkit, but found no answer. Basically, I want to run a > search with a smarts > string on my molecule. I am interested in the hydrogen atoms bonded to an > atom that is part > of the match, as GetSubstructMatches does not return the idx of hydrogens. > Because I am > looking at crystal structures, I want the idx of hydrogen so that I get the > 3D coordinates > of the hydrogen to perform further computations. If anyone has any tips and > good ideas, > please let me know. Are you sure? I use HasSubstrMatch to match hydrogens. see set_atom_type() here: https://github.com/pemsley/coot/blob/master/pyrogen/atom_types.py I think that this is more or less what you want to do. (As you might be able to work out, I too have an interest in hydrogens on ligands in protein ligand crystal structures.) Paul. -- Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss-- Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] How to find the idx of hydrogens bonded to a specific atom
On 10/13/2016 12:12 PM, Paul Emsley wrote: > Are you sure? I use HasSubstrMatch to match hydrogens. Perhaps this http://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg05897.html may be useful? If OP's looking at crystal structures, they're likely dealing with pdb data model where all hydrogens are explicitly present and indexed. I wonder if they stay that way throughout the steps leading to (and past) the smarts match. -- Dimitri Maziuk Programmer/sysadmin BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu signature.asc Description: OpenPGP digital signature -- Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] How to find the idx of hydrogens bonded to a specific atom
On 13/10/2016 05:04, Bin Song wrote: > Hello everyone, > > A new user of Rdkit and new subscriber of the mailing list reporting here. > > I have a question to ask, as stated in the subject. I have googled and > consulted the > documentation of rdkit, but found no answer. Basically, I want to run a > search with a smarts > string on my molecule. I am interested in the hydrogen atoms bonded to an > atom that is part > of the match, as GetSubstructMatches does not return the idx of hydrogens. > Because I am > looking at crystal structures, I want the idx of hydrogen so that I get the > 3D coordinates > of the hydrogen to perform further computations. If anyone has any tips and > good ideas, > please let me know. Are you sure? I use HasSubstrMatch to match hydrogens. see set_atom_type() here: https://github.com/pemsley/coot/blob/master/pyrogen/atom_types.py I think that this is more or less what you want to do. (As you might be able to work out, I too have an interest in hydrogens on ligands in protein ligand crystal structures.) Paul. -- Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] How to find the idx of hydrogens bonded to a specific atom
Hello everyone, A new user of Rdkit and new subscriber of the mailing list reporting here. I have a question to ask, as stated in the subject. I have googled and consulted the documentation of rdkit, but found no answer. Basically, I want to run a search with a smarts string on my molecule. I am interested in the hydrogen atoms bonded to an atom that is part of the match, as GetSubstructMatches does not return the idx of hydrogens. Because I am looking at crystal structures, I want the idx of hydrogen so that I get the 3D coordinates of the hydrogen to perform further computations. If anyone has any tips and good ideas, please let me know. If the question has been raised and answered before, please excuse me. Best wishes, Bin-- Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
