1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
|
# Enhanced Stereochemistry in the RDKit
Greg Landrum (greg.landrum@t5informatics.com)
September 2018
*This is still a DRAFT*
## Overview
We are going to follow, at least for the initial implementation, the enhanced stereo representation used in V3k mol files: groups of atoms with specified stereochemistry with an `ABS`, `AND`, or `OR` marker indicating what is known. The general idea is that `AND` indicates mixtures and `OR` indicates unknown single substances.
Here are some illustrations of what the various combinations mean:
| What's drawn | Mixture? | What it means |
|-----------------|-----------------------------|:--------------|
| | mixture |  |
| | mixture |  |
| | mixture | |
| | single |  |
| | single |  |
| | single | |
| | mixture | |
| | single | |
## Use cases
The initial target is to not lose data on an V3k mol -> RDKit -> V3k mol round trip. Manipulation,
depiction, and searching is a secondary goal.
## Representation
Stored as a vector of `StereoGroup` objects.
A `StereoGroup` contains an enum with the type as well as pointers to the atoms involved. We will need to adjust this when atoms are removed or replaced.
## Enumeration
The Python-only function `rdkit.Chem.EnumerateStereoisomers.EnumerateStereoisomers` can be used to enumerate
all stereoisomers represented by the StereoGroups. It is possible to enumerate _only_ the Stereo Groups,
ignoring other unspecified centers.
## Reactions
The reaction runner is aware of stereo groups associated with a Mol. Atoms in a Stereo Group are copied to
all products in which they appear, unless the reaction created or destroyed stereochemistry at that atom.
If an atom from a reactant StereoGroup appears multiple times in the product, all copies of that atom are
put in the same product StereoGroup.
## Searching
This will be handled by searching in MolBundle objects produced by the enumeration code. Substructure searching and canonicalization do not yet support stereo groups.
## Depiction
Something needs to be added to the depiction code to allow the groups to be seen.
|
