* Sketch of a solution to preserve bond direction in fragmentOnBonds
* A bit of cleanup work based on Andrew's original commit for #1039
Add a couple of tests too
* forgot to save a file before the commit
* Fix core labelling and multi-core hydrogen removals
* Add comment that explains confusing bit about indexlabels for multicores
* Multi core fixes: hydrogens properly removed, fixed labelling
* clang-format
* update version of japanese docs
* Remove external labels from cores
* Fix syntax errors
* Add better autodetection of labels, add dummyatom label, don't fall back to indexes when onlyMatchAtRgroups are set
* Add better autodetection of labels, add dummyatom label, don't fall back to indexes when onlyMatchAtRgroups are set
* Move autodetection before alignment, fix final core labelling
* Fix stupid bit twiddling mistake
* None of the original mol's should actually match the cores with onlyMatchAtRgroups
* Convert PRECONDITION to CHECK_INVARIANT
* Run clang-format
* use nullptr instead of 0 for pointers
* Handle cases where molecules don't have anything for an R-group properly.
Here's the python demo of the bug:
```
In [14]: scaffold2 = Chem.MolFromSmiles('c1c([*:1])cncn1')
In [15]: scaffold = Chem.MolFromSmiles('c1c([*:1])cccn1')
In [19]: mols2 = [Chem.MolFromSmiles(smi) for smi in 'c1c(F)cc(O)cn1 c1c(F)cncn1 c1c(Cl)cc(O)cn1'.split()]
In [20]: print(rdRGroupDecomposition.RGroupDecompose([scaffold,scaffold2],mols2,asSmiles=True,asRows=False))
({'Core': ['c1ncc([*:2])cc1[*:1]', 'c1ncc([*:1])cn1', 'c1ncc([*:2])cc1[*:1]'], 'R1': ['F[*:1]', 'F[*:1]', 'Cl[*:1]'], 'R2': ['[H]O[*:2]', '[H]O[*:2]', '']}, [])
```
* Fixes#2471
* updated atomic radii to follow the Blue Obelisk Data Repository
Ubuntu package bodr version 10-1; radii are from file
/usr/share/bodr/elements.xml
* typo
* use 2.0 as default VDW radius instead of 1.7
for elements missing from the Blue Obelisk Data Repository
* Document the atomic_data
* update expected test results
* update java tests
* allow a bit more slop when comparing confs
For cross-platform stability
* Fixes#2450
adds `hasOwningMol()` to the public API for Bond and Atom
* add to other classes;
add to python wrappers
* get the smiles generation partially working
* changes in response to review
* - added two convenience functions to allow miniming all molecule confs with a pre-generated force-field (e.g., to use constraints)
- removed a lot of code duplication between Code/GraphMol/ForceFieldHelpers/MMFF/MMFF.h Code/GraphMol/ForceFieldHelpers/UFF/UFF.h
- homogenized the nonBondedThreshold to 100.0 across all MMFF functions
* - avoided code duplication
- added tests
- added PRECONDITION clauses
* Fixes#2437
getting the canonical atom ranking no longer results in molecules have a
RingInfo structure that's been initialized but contains nothing.
* update expected results for the MMPA tests
Fixes#2420
Tests updated to reflect changes.
The existing CompleteRingsOnly code wasn't actually guaranteeing CompleteRingsOnly at all, it was just causing #2420.
The updated code actually makes sure that bonds that were ring bonds in one of the queries are ring bonds in the final MCS.
This is done via a relatively simple DFS.
* Issue #2403: Speed up SSSR symmetrization
For my horrible example molecule (a highly symmetric
nanotube with 2400 atoms and > 1000 rings), this speeds up
symmetrizeSSSR() from 5s to about 0.002s. findSSSR() takes
another .4s or so.
* Refactor after Ricardo's suggestions
* Greg's review comments. use std::vector
This removes some redundancy from some of the test code in order to bring
the runtime down. This does not affect test coverage and shouldn't do
anything bad to the overall test quality.
* Potential implementation of copying enhanced stereo groups
Copies the enhanced stereo if all atoms in the reactant
end up in the same molecule of the product with valid
ChiralTags.
Current implementation: Only copy StereoGroup if all atoms are "valid" in the product.
Possible implementation: Copy StereoGroup for all atoms that are "valid" in the product.
Details:
Uses ChiralTag invalidation to decide whether StereoGroup should be copied. If
the product atoms have valid ChiralTag, then the reaction was able to
meaningfully propogate chirality from the reactant to the product. This means
that it is also meaningful to propogate the StereoGroup from the reactant to
the product.
The only exception to this is if the product template defines a specific
absolute configuration for an atom. This means that the reaction defines the
stereochemistry for the atom, so the stereochemistry of that atom is no longer
relative.
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.
Still developing test cases.
from rdkit import Chem
from rdkit.Chem import AllChem
# Duplicate a molecule example:
mol1 = Chem.MolFromSmiles('Cl[C@@H](Br)C[C@H](Br)CCO |&1:1,4|')
mol2 = Chem.MolFromSmiles('CC(=O)C')
rxn = AllChem.ReactionFromSmarts('[O:1].[C:2]=O>>[O:1][C:2][O:1]')
for prods in rxn.RunReactants([mol1, mol2]):
for p in prods:
for a in p.GetAtoms():
for k in a.GetPropsAsDict():
a.ClearProp(k)
print(Chem.MolToCXSmiles(p))
Output:
[21:26:08] product atom-mapping number 1 found multiple times.
CC(C)(OCC[C@@H](Br)C[C@@H](Cl)Br)OCC[C@@H](Br)C[C@@H](Cl)Br |&1:6,9,15,18
* Issue 2366: Documentation and fix stereo group invalidation
Adds some documentation to EnhancedStereo.md
Also invalidates StereoGroup if a reaction specifies the
stereochemistry of a center. This destroys the relative
relationship of the center to other centers.
* Demo python file examples for Enhanced Stereochemistry in reactions
This is not intended to be pushed. These probably will become test
cases. For the output looks like this:
0a. Reaction preserves stereo:
[C@:1]>>[C@:1]
F[C@H](Cl)Br |o1:1|
>>
F[C@H](Cl)Br |o1:1|
0b. Reaction preserves stereo:
[C@:1]>>[C@:1]
F[C@@H](Cl)Br |&1:1|
>>
F[C@@H](Cl)Br |&1:1|
0c. Reaction preserves stereo:
[C@:1]>>[C@:1]
FC(Cl)Br
>>
FC(Cl)Br
1a. Reaction ignores stereo:
[C:1]>>[C:1]
F[C@H](Cl)Br |a:1|
>>
F[C@H](Cl)Br |a:1|
1b. Reaction ignores stereo:
[C:1]>>[C:1]
F[C@@H](Cl)Br |&1:1|
>>
F[C@@H](Cl)Br |&1:1|
1c. Reaction ignores stereo:
[C:1]>>[C:1]
FC(Cl)Br
>>
FC(Cl)Br
2a. Reaction inverts stereo:
[C@:1]>>[C@@:1]
F[C@H](Cl)Br |o1:1|
>>
F[C@@H](Cl)Br |o1:1|
2b. Reaction inverts stereo:
[C@:1]>>[C@@:1]
F[C@@H](Cl)Br |&1:1|
>>
F[C@H](Cl)Br |&1:1|
2c. Reaction inverts stereo:
[C@:1]>>[C@@:1]
FC(Cl)Br
>>
FC(Cl)Br
3a. Reaction destroys stereo:
[C@:1]>>[C:1]
F[C@H](Cl)Br |o1:1|
>>
FC(Cl)Br
3b. Reaction destroys stereo:
[C@:1]>>[C:1]
F[C@@H](Cl)Br |&1:1|
>>
FC(Cl)Br
3c. Reaction destroys stereo:
[C@:1]>>[C:1]
FC(Cl)Br
>>
FC(Cl)Br
3d. Reaction destroys stereo (but preserves unaffected group):
[C@:1]F>>[C:1]F
F[C@H](Cl)[C@@H](Cl)Br |o1:1,&2:3|
>>
FC(Cl)[C@@H](Cl)Br |&1:3|
3e. Reaction destroys stereo:
[C@:1]F>>[C:1]F
F[C@H](Cl)[C@@H](Cl)Br |&1:1,3|
>>
FC(Cl)[C@@H](Cl)Br
4a. Reaction creates stereo:
[C:1]>>[C@@:1]
F[C@H](Cl)Br |o1:1|
>>
F[C@@H](Cl)Br
4b. Reaction creates stereo:
[C:1]>>[C@@:1]
F[C@@H](Cl)Br |&1:1|
>>
F[C@@H](Cl)Br
4c. Reaction creates stereo:
[C:1]>>[C@@:1]
FC(Cl)Br
>>
F[C@@H](Cl)Br
4d. Reaction creates stereo (preserve unaffected group):
[C:1]F>>[C@@:1]F
F[C@H](Cl)[C@@H](Cl)Br |o1:1,&2:3|
>>
F[C@@H](Cl)[C@@H](Cl)Br |&1:3|
4e. Reaction creates stereo:
[C:1]F>>[C@@:1]F
F[C@H](Cl)[C@@H](Cl)Br |o1:1,3|
>>
F[C@@H](Cl)[C@@H](Cl)Br
5a. Reaction preserves unrelated stereo:
[C@:1]F>>[C@:1]F
F[C@H](Cl)[C@@H](Cl)Br |o1:3|
>>
F[C@H](Cl)[C@@H](Cl)Br |o1:3|
5b. Reaction ignores unrelated stereo:
[C:1]F>>[C:1]F
F[C@H](Cl)[C@@H](Cl)Br |o1:3|
>>
F[C@H](Cl)[C@@H](Cl)Br |o1:3|
5c. Reaction inverts unrelated stereo:
[C@:1]F>>[C@@:1]F
F[C@H](Cl)[C@@H](Cl)Br |o1:3|
>>
F[C@@H](Cl)[C@@H](Cl)Br |o1:3|
5d. Reaction destroys unrelated stereo:
[C@:1]F>>[C:1]F
F[C@H](Cl)[C@@H](Cl)Br |o1:3|
>>
FC(Cl)[C@@H](Cl)Br |o1:3|
5e. Reaction creates unrelated stereo:
[C:1]F>>[C@@:1]F
F[C@H](Cl)[C@@H](Cl)Br |o1:3|
>>
F[C@@H](Cl)[C@@H](Cl)Br |o1:3|
6e. Reaction splits StereoGroup atoms into two Mols:
[C:1]OO[C:2]>>[C:2]O.O[C:1]
F[C@H](Cl)OO[C@@H](Cl)Br |o1:1,5|
>>
O[C@@H](Cl)Br + O[C@H](F)Cl
>>
O[C@H](F)Cl + O[C@@H](Cl)Br
7. Add two copies:
[O:1].[C:2]=O>>[O:1][C:2][O:1]
Cl[C@@H](Br)C[C@H](Br)CCO |&1:1,4| + CC(=O)C
[17:15:38] product atom-mapping number 1 found multiple times.
>>
CC(C)(OCC[C@@H](Br)C[C@@H](Cl)Br)OCC[C@@H](Br)C[C@@H](Cl)Br |&1:6,9,15,18|
8. Add two copies:
[O:1].[C:2]=O>>[O:1][C:2][O:1]
Cl[C@@H](Br)C[C@H](Br)CCO |&1:1,4| + CC(=O)C
[17:15:38] product atom-mapping number 1 found multiple times.
>>
CC(C)(OCC[C@@H](Br)C[C@@H](Cl)Br)OCC[C@@H](Br)C[C@@H](Cl)Br |&1:6,9,15,18|
* Updates StereoGroup strategy in reactions to copy all possible atoms.
Copy all atoms for which the stereochemistry was not created or destroyed
in the reaction. Any StereoGroup which has at least one atom will appear
in the product.
Also updates the documentation to match this description, and adds C++
and Python tests which fail before this PR and pass after. The Python
tests are more extensive.
Test output was validated by hand (especially the stereo groups
generated. I'm less confident in the reaction processing in my head,
but I truested the existing validation there.)
For future diagnosis: Python unittest failures will look like:
AssertionError: 'F[C@H](Cl)Br' != 'F[C@H](Cl)Br |&1:1|'
- F[C@H](Cl)Br
+ F[C@H](Cl)Br |&1:1|
? +++++++
For future diagnosis: C++ Catch2 failures will look like:
CHECK( MolToCXSmiles(*p) == "F[C@H](Cl)Br |o1:1|" )
with expansion:
"FC(Cl)[C@@H](Cl)Br |&1:3|"
==
"F[C@H](Cl)Br |o1:1|"
* Add a couple of new tests.
* rename "relative" to "enhanced"
some reformatting
* Factor out test helper function.
* Actually, enhanced stereo groups are exposed ot Python
* Added discussion of enhanced stereochemistry in reactions to docs
* Fix new test
* Fixes#2311
at least I hope it does
* Stop using deprecated boost functionality
* allow the Murtagh module to import even if the code isn't built
update the associated tests
* update release notes
* typo
* fix integer division
* Fixes#2383 (tests coming in the next commit)
Minor typo fix
Fixes a "bug" in one of the default transforms
* Adds support for directly providing normalization parameter data
instead of requiring the use of a text file.
* allow fragment removers to be initialized with string data
* remove unicode
* allow the reionizer to be initialized from a stream
* modify the uncharger to be use a canonical atom ordering
* add doCanonical cleanup parameter
make canonical ordering the default
document the change
* Add neutralization of additonal negative groups (not just acids).
This may not be the right thing to do.
* expose the new parameter to python
* changes in response to review
* Move DetectAtomStereoChemistry to Molops::assignChiralTypesFromBondDirs
DetectAtomStereoChemistry in MolFileStereochem is more broadly
useful. Additionally, it was not named very clearly for what
it was actually doing.
* Wraps assignChiralTypesFromBondDirs for use in Python
Makes assignChiralTypesFromBondDirs available in Python
and adds a test demonstrating that availability.
