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core: replace RedBlackMap and RedBlackSet implementation with standard containers #520

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mkviatkovskii opened this issue Nov 11, 2021 · 0 comments
Open

core: replace RedBlackMap and RedBlackSet implementation with standard containers #520

mkviatkovskii opened this issue Nov 11, 2021 · 0 comments
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@AMazhyrau
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Motivation
Currently Indigo uses own-written implementation of ordered associative containers and ordered sets using red-black trees. The implementation could be found in core/indigo-core/common/base_cpp/red_black.h.
In many cases order of elements is not important and int is a key type, so it could be easily replaced with hash maps and also lead to performance improvement. Same for unordered sets.

ToDo

  1. Find all places in code that use RedBlackMap<K, V>, check if K is trivially hashable and order of elements is required, and replace it with std::map<K, V> or std::unordered_map<K, V> depending on the situation.
  2. Find all places in code that use RedBlackSet<K>, check if K is trivially hashable and order of elements is required, and replace it with std::set<K> or std::unordered_set<K> depending on the situation.
  3. Check if core/indigo-core/common/base_cpp/red_black.h and eliminate it if it's not required anymore.
@mkviatkovskii mkviatkovskii added this to the indigo-1.6 milestone Nov 11, 2021
@mkviatkovskii mkviatkovskii changed the title core: replace own maps and sets implementation with std core: replace RedBlackMap and RedBlackSet implementation with standard containers Nov 11, 2021
@khyurri khyurri self-assigned this Nov 12, 2021
@khyurri khyurri removed their assignment Nov 22, 2021
@AMazhyrau AMazhyrau self-assigned this Feb 21, 2022
AStepaniuk pushed a commit that referenced this issue Aug 1, 2022
Issue #520: core: replace RedBlackMap and RedBlackSet implementation …
a23e3ba 
…with standard containers

IndigoDeconvolution class is updated.
@AStepaniuk AStepaniuk mentioned this issue Aug 1, 2022
Merged
AStepaniuk pushed a commit that referenced this issue Aug 1, 2022
Issue #520: core: replace RedBlackMap and RedBlackSet implementation …
b1f9e2b 
…with standard containers

Fix clang-formatter issue
AStepaniuk pushed a commit that referenced this issue Aug 2, 2022
Issue #520: core: replace RedBlackMap and RedBlackSet implementation …
3ff4596 
…with standard containers

Partial implementation: BingoContext and MoleculeMass are updated
AStepaniuk pushed a commit that referenced this issue Aug 2, 2022
Issue #520: core: replace RedBlackMap and RedBlackSet implementation …
838cf2e 
…with standard containers

Fix clang_format
@AStepaniuk AStepaniuk mentioned this issue Aug 2, 2022
Merged
AStepaniuk pushed a commit that referenced this issue Aug 2, 2022
Issue #520: core: replace RedBlackMap and RedBlackSet implementation
a0e88b6 
Partial implementation: GraphEmbeddingsStorage class update
@AStepaniuk AStepaniuk mentioned this issue Aug 2, 2022
Merged
AStepaniuk pushed a commit that referenced this issue Aug 2, 2022
Issue #520: core: replace RedBlackMap and RedBlackSet implementation …
f9f4ba8 
…with standard containers

Removed internal usage of RedBlackMap from IndigoDeconvolution.
AStepaniuk pushed a commit that referenced this issue Aug 2, 2022
Issue #520: core: replace RedBlackMap and RedBlackSet implementation
6c4c27c 
Partial implementation: Removed RedBlackMap from SimpleCycleBasis
@AStepaniuk AStepaniuk mentioned this issue Aug 2, 2022
Merged
@loimu loimu mentioned this issue Aug 3, 2022
Closed
AStepaniuk pushed a commit that referenced this issue Aug 3, 2022
Issue #520: core: replace RedBlackMap and RedBlackSet implementation
2f63e37 
Partial implementation: MangoPg is updated
@AStepaniuk AStepaniuk mentioned this issue Aug 3, 2022
Merged
@loimu loimu mentioned this issue Aug 3, 2022
Merged
loimu pushed a commit that referenced this issue Aug 3, 2022
Issue #520: core: replace RedBlackMap and RedBlackSet implementation
e9fa994 
Change formatting (clang-formatter)
loimu pushed a commit that referenced this issue Aug 4, 2022
Issue #520: core: replace RedBlackMap and RedBlackSet implementation
2e952b6 
Partial implementation: replace RedBlackMap in BaseMolecule class
loimu pushed a commit that referenced this issue Aug 4, 2022
Issue #520: core: replace RedBlackMap and RedBlackSet implementation
bddafcf 
Partial implementation: replace RedBlackMap in MoleculeRGroupsComposition class
loimu pushed a commit that referenced this issue Aug 4, 2022
Issue #520: core: replace RedBlackMap and RedBlackSet implementation
a878af6 
Partial implementation: replace RedBlackMap in MoleculeGrossFormula class
@loimu loimu mentioned this issue Aug 4, 2022
Merged
loimu pushed a commit that referenced this issue Aug 4, 2022
Issue #520: core: replace RedBlackMap and RedBlackSet implementation
6e2f689 
Partial implementation: replace RedBlackMap in MoleculeGrossFormula class
loimu pushed a commit that referenced this issue Aug 4, 2022
Issue #520: core: replace RedBlackMap and RedBlackSet implementation
fdf279a 
Partial implementation: replace RedBlackMap in MoleculeGrossFormula class
loimu pushed a commit that referenced this issue Aug 4, 2022
Issue #520: core: replace RedBlackMap and RedBlackSet implementation
70666a0 
Partial implementation: replace RedBlackMap in MoleculeCdxLoader class
@loimu loimu mentioned this issue Aug 4, 2022
Merged
AStepaniuk pushed a commit that referenced this issue Aug 4, 2022
Issue #520: core: replace RedBlackMap and RedBlackSet implementation …
0b5c735 
…with standard containers

Partial implementation: fix for MoleculeAlleneStereo
@AStepaniuk AStepaniuk mentioned this issue Aug 4, 2022
Open
loimu pushed a commit that referenced this issue Aug 5, 2022
Issue #520: core: replace RedBlackMap and RedBlackSet implementation
f87732c 
Partial implementation: replace RedBlackMap in MolfileSaver class
@loimu loimu mentioned this issue Aug 5, 2022
Merged
loimu pushed a commit that referenced this issue Aug 5, 2022
Issue #520: core: replace RedBlackMap and RedBlackSet implementation
e8fc8fd 
Partial implementation: replace RedBlackMap in BaseReactionSubstructureMatcher class
@loimu loimu mentioned this issue Aug 5, 2022
Merged
mkviatkovskii pushed a commit that referenced this issue Aug 7, 2022
@AStepaniuk
Issue #520: api: replace RedBlackMap in IndigoDeconvolution (#803)
14d7805 
* Issue #520: core: replace RedBlackMap and RedBlackSet implementation with standard containers
IndigoDeconvolution class is updated.

* Issue #520: core: replace RedBlackMap and RedBlackSet implementation with standard containers
Fix clang-formatter issue

* Issue #520: core: replace RedBlackMap and RedBlackSet implementation with standard containers
Removed internal usage of RedBlackMap from IndigoDeconvolution.

Co-authored-by: Alexander Stepaniuk <AStepanjuk@gmail.com>
Co-authored-by: Aliaksander Stsepaniuk <Aliaksander_Stsepaniuk@epam.com>
AStepaniuk pushed a commit that referenced this issue Sep 25, 2022
Issue #520 Replace RedBlackMap in MoleculeStereocenters
876a4de
MysterionRise added a commit that referenced this issue Oct 13, 2022
@MysterionRise
Merge pull request #804 from epam/feature/520_std_map_bingo_context
c96b1a1 
Issue #520: core: replace RedBlackMap and RedBlackSet implementation
MysterionRise added a commit that referenced this issue Oct 13, 2022
@MysterionRise
Merge pull request #805 from epam/feature/520_std_map_embedding_storage
bb5a66c 
Issue #520: core: replace RedBlackMap for GraphEmbeddingsStorage
MysterionRise added a commit that referenced this issue Oct 13, 2022
@MysterionRise
Merge pull request #806 from epam/feature/520_std_map_simple_cycle_basis
c4179fb 
Issue #520: core: replace RedBlackMap in SimpleCycleBasis
MysterionRise added a commit that referenced this issue Oct 13, 2022
@MysterionRise
Merge pull request #809 from epam/feature/520_std_map_postgres
834d1e3 
Issue #520: core: replace RedBlackMap for MangoPg
MysterionRise added a commit that referenced this issue Oct 13, 2022
@MysterionRise
Merge pull request #810 from epam/feature/520_std_map_molecule_rgroup…
9549d2b 
…s_composition

Issue #520: core: replace RedBlackMap in MoleculeRGroupsComposition class
MysterionRise added a commit that referenced this issue Oct 13, 2022
@MysterionRise
Merge pull request #811 from epam/feature/520_std_map_canonical_smile…
8ea11d2 
…s_saver

Issue #520: core: replace RedBlackMap in CanonicalSmilesSaver
MysterionRise added a commit that referenced this issue Oct 13, 2022
@MysterionRise
Merge pull request #812 from epam/feature/520_std_map_base_molecule
d0cfc76 
Issue #520: core: replace RedBlackMap in BaseMolecule class
MysterionRise added a commit that referenced this issue Oct 13, 2022
@MysterionRise
Merge pull request #813 from epam/feature/520_std_map_molecule_3d_con…
30b81a0 
…straints

Issue #520: core: replace RedBlackMap for Molecule3dConstraints
MysterionRise added a commit that referenced this issue Oct 13, 2022
@MysterionRise
Merge pull request #814 from epam/feature/520_std_map_molecule_gross_…
92eb206 
…formula

Issue #520: core: replace RedBlackMap in MoleculeGrossFormula class
MysterionRise added a commit that referenced this issue Oct 13, 2022
@MysterionRise
Merge pull request #816 from epam/feature/520_std_map_molecule_cdx_lo…
171cbf2 
…ader

Issue #520: core: replace RedBlackMap in MultipleCdxLoader class
MysterionRise added a commit that referenced this issue Oct 13, 2022
@MysterionRise
Merge pull request #819 from epam/feature/520_std_map_molfile_saver
6a9e42a 
Issue #520: core: replace RedBlackMap  in MolfileSaver class
MysterionRise added a commit that referenced this issue Oct 13, 2022
@MysterionRise
Merge pull request #820 from epam/feature/520_std_map_base_reaction_s…
6d46e0e 
…ubstructure_matcher

Issue #520: core: replace RedBlackMap in BaseReactionSubstructureMatcher class
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@mkviatkovskii @AMazhyrau @khyurri @AlexanderSavelyev