* use std::span for substruct match callbacks
This removes a copy from every evaluation of potential matches
* some cleanup/modernization
* some modernization
* deprecate chiralAtomCompat
* small optimization
* remove naked pointers
* improve new_timings.py script
* changes suggested in review
* response to review
* response to review
* fix aliasing bug in MultithreadedSDMolSupplier
* update GeneralFileReader to v2 API
* add backwards incompatibility note
* v1 of this
* The helper function needs to be inline
* forgot the tests
* allow non-threadsafe builds
* MultithreadedMolSuppliers can now be destroyed without being used.
This was previously not possible
* add callbacks to the multithreaded readers
* document the new functions
* switch to storing the queues in unique_ptrs
* does not work
* only do those tests when in MT mode
* more generalfilereader cleanup
* tests pass
* passes tests
* extremely basic python wrapper
* better wrapper
* does not work
* tests pass
* test data
* fix failing test on ARM macs
we need to followup on why the wedging is different here
* move some stuff to the cpp file
the idea is to have the windows DLL builds not break
* fix(?) win64 linkage problems
* remove a warning in non-multi-threaded builds
* fix non-multi-threaded work
* well, at least local windows builds work
* remove duplicated code
* refactoring
simplification?
* simplify mutext handling
* review suggestions
* remove all of the "from __future__" imports
* remove the first batch of rdkit.six imports/uses
* next step of rdkit.six removal
* removing xrange, range, and some maps
* next round of removals
* next round of cleanups
* fix inchi test
* last bits of "from rdkit.six" are gone
* and the last of the six stuff is gone
* strange importlib problem
* findSSSR performance improvements for fragments without rings
This makes Chem.SanitizeMol significantly faster when dealing with
molecules with lots of disconnected fragments (like a box of water).
The following is the runtime of Chem.SanitizeMol while adding 10,000
waters with explicit hydrogens when running Chem.SanitizeMol on every
1,000th water added.
Before:
0 add_water = 0.00007s
0 Chem.SanitizeMol = 0.01991s
1000 add_water = 0.00009s
1000 Chem.SanitizeMol = 0.99659s
2000 add_water = 0.00013s
2000 Chem.SanitizeMol = 3.94565s
3000 add_water = 0.00018s
3000 Chem.SanitizeMol = 8.94760s
4000 add_water = 0.00023s
4000 Chem.SanitizeMol = 15.75187s
5000 add_water = 0.00035s
5000 Chem.SanitizeMol = 24.59318s
6000 add_water = 0.00048s
6000 Chem.SanitizeMol = 37.23530s
7000 add_water = 0.00042s
7000 Chem.SanitizeMol = 47.70860s
8000 add_water = 0.00105s
8000 Chem.SanitizeMol = 62.21912s
9000 add_water = 0.00056s
9000 Chem.SanitizeMol = 80.08511s
After:
0 add_water = 0.00003s
0 Chem.SanitizeMol = 0.01219s
1000 add_water = 0.00004s
1000 Chem.SanitizeMol = 0.01004s
2000 add_water = 0.00012s
2000 Chem.SanitizeMol = 0.01058s
3000 add_water = 0.00018s
3000 Chem.SanitizeMol = 0.01158s
4000 add_water = 0.00018s
4000 Chem.SanitizeMol = 0.01530s
5000 add_water = 0.00022s
5000 Chem.SanitizeMol = 0.02010s
6000 add_water = 0.00036s
6000 Chem.SanitizeMol = 0.02397s
7000 add_water = 0.00033s
7000 Chem.SanitizeMol = 0.02978s
8000 add_water = 0.00037s
8000 Chem.SanitizeMol = 0.04446s
9000 add_water = 0.00040s
9000 Chem.SanitizeMol = 0.04419s
* Refactor new_timings.py script a bit to be able to run only the first (reading molecules) test.
* Removing O(N^2) behavior of finding the number of bonds in the fragment during SSSR.
This only improves the case when there are long chains and a small
number of rings in the fragment. Many ring systems are still dominated
by the rest of the SSSR algorithm, and fragments with no ring systems
don't reach this part of the code.
For a test case with a single cyclicpropane and adding carbons while
calling Chem.SanitizeMol every 10,000 carbons added yield the
following improvement in performance:
before:
0 add_carbon = 0.00001s
0 Chem.SanitizeMol = 0.01237s
10000 add_carbon = 0.00017s
10000 Chem.SanitizeMol = 0.04453s
20000 add_carbon = 0.00017s
20000 Chem.SanitizeMol = 0.13038s
30000 add_carbon = 0.00029s
30000 Chem.SanitizeMol = 0.27671s
40000 add_carbon = 0.00063s
40000 Chem.SanitizeMol = 0.44774s
50000 add_carbon = 0.00106s
50000 Chem.SanitizeMol = 0.69433s
60000 add_carbon = 0.00181s
60000 Chem.SanitizeMol = 1.00577s
after:
0 add_carbon = 0.00001s
0 Chem.SanitizeMol = 0.01264s
10000 add_carbon = 0.00013s
10000 Chem.SanitizeMol = 0.01349s
20000 add_carbon = 0.00022s
20000 Chem.SanitizeMol = 0.02724s
30000 add_carbon = 0.00040s
30000 Chem.SanitizeMol = 0.04292s
40000 add_carbon = 0.00076s
40000 Chem.SanitizeMol = 0.06172s
50000 add_carbon = 0.00193s
50000 Chem.SanitizeMol = 0.07658s
60000 add_carbon = 0.00147s
60000 Chem.SanitizeMol = 0.08625s
Note, couldn't actually test a higher number of carbons as it led to a
stack overflow due to recursion in findSSSR.
