Move Sgroups functionality off of ROMol#1
Merged
ricrogz merged 7 commits intoricrogz:sgroups_prfrom Nov 28, 2018
Merged
Conversation
d-b-w
approved these changes
Nov 26, 2018
Collaborator
d-b-w
left a comment
d-b-w
left a comment
There was a problem hiding this comment.
I generally like this reorganization. I particularly like that it removes the expansion of the Mol interface.
When I read your comment in the rdkit repo PR, I thought you were considering some type of even more general data structure like a map of:
std::map<std::vector<Atom>, RDProps> d_atom_groups;
which could hold SGroups, stereo groups, PDB Residue information, etc. I guess that seems like excessive complexity/flexibility.
Owner
|
Ok, after commenting with @d-b-w, we have decided to make the following changes to this, and update the PR to rdkit/rdkit:
|
ricrogz
pushed a commit
that referenced
this pull request
Mar 20, 2023
…it#5991) * Add CHEMBL filters to the filter catalog * Add catalogs to the top level, add basic tests * Remove explicit hydrogens in queries Changes: acyclic imine: C-!@[NX2]=[C!R,#1]-C -> C-!@[NX2]=[C!R]-C hypervalent hydrogen dropped Filter5_azo: [!#7,#1]~[NX2R0]=[NX2R0]~[!#7,#1] => [!#7]~[NX2R0]=[NX2R0]~[!#7] X is explicit connections, don't need explicit hydrogen Filter18_oxime_ester: [!#7,#1]C=NO[C,S,P](=O)* -> [!#7][CX3]=NO[C,S,P](=O)* Adding explicit connections takes care of #1 Filter30_beta_halo_carbonyl: [#6,#1]C(=O)CC[Br,I] -> [$(C(-C)(-C)(=O)),$([CH](=O)-C)](=O)CC[Br,I] Make explicit recursive smarts for the #6,#1 * Remove std::cout * Add a basic test that we can get the CHEMBL filters * Add CHEMBL filters to wrappers * Fix a dropped paren * Fix capitalization * Fix more hydrogen or queries * Finish removing hydrogens in ors, add tests * Separate the filter files for readability * Add missing zinc.in * Remove Filters.cpp.in --------- Co-authored-by: Brian Kelley <bkelley@relaytx.com>
ricrogz
pushed a commit
that referenced
this pull request
Feb 1, 2024
…rocycles (rdkit#7032) * Fix macrocycle bounds calculation, and make it accessible from Python * Previously, C=C([#1])-C([#1])=C groups in a macrocycle were always cis. Although the bounds within the group allowed cis or trans, the 1-4 bounds of the H atoms were always set to trans, which forces the carbons into the cis position. This change fixes this behavior to allow cis or trans conformations * Previously, the useMacrocycle14config flag could only be used from Python by creating an ETKDGv3 object, and defaulted to False otherwise. This change adds the flag to EmbedMolecule, EmbedMultipleConfs, and the EmbedParameters Python interface. * The new default for useMacrocycle14config is True to be consistent with the default for useMacrocycleTorsions. Since the old default was False, this could change the output of existing scripts. * Add test case for updated macrocycle distance bounds * Remove 2 unused variables * Fix a python test that set .seed instead of .randomSeed on an ETKDGv3 --------- Co-authored-by: Franz Waibl <waiblfranz@gmail.com>
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
3 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
This moves the public interface off of ROMol and into free functions.