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rdkit/Code
Ichiru Take 9822e9439c [ENH]: Support greater use of findAtomEnvironmentOfRadiusN() (#4970)
* [WIP-ENH]: Support greater use of `findAtomEnvironmentOfRadiusN()`

This PR is the feature support for PR 4262. I am not so confident when coding the C++ as it is my first time hands-on experience

There are still many thing that should be done but I still need several support

* Update MolOps.cpp

* Fix build error

Fix according to this? https://www.boost.org/doc/libs/1_42_0/libs/python/doc/v2/object.html#object-spec-ctors

* Fix build error

* Fix test2.cpp

* Fix `include` issue

* Fixed as requested

* Update Subgraphs.cpp

* Update Subgraphs.cpp

* Update Subgraphs.cpp

* Fix reported error, correct doc

* Update MolOps.cpp

* Update test and fix error

* Fix default argument

* Fix duplication

* Update Subgraphs.cpp

* Fix test bug

* Updated a test and fix reported error

* Update Subgraphs.cpp

* Fix reported error

* Update test2.cpp

* Fix reported error of memleak and introduce new function

* Fix incorrect variable

* Update test2.cpp

* Update test2.cpp

* Update MolOps.cpp

* Update MolOps.cpp

* Fix algorithm & Add test docs

* Update test2.cpp

* Update Subgraphs.cpp

* New argument `bondDist` - Optimize the `FindAtomEnvFromMToN`

Documentation is syncronized the meaning between C++ and Python

- New argument `bondDist`
- `findAtomEnvironmentOfRadiusMToN()` now called once instead of twice due to the introduction of `bondDist`

* Update Subgraphs.cpp

* Update test2.cpp

* Fix casting

* Correct the test

* Update Subgraphs.cpp

* Remove buggy function and replace argument position

* Update Subgraphs.h

* Fix build failed

* Optimization

Reduce graph expansion if it is the last radius

* Adjust codebase based on review

- Update Copyright
- Add doc to prove optimization

* suggested changes

Co-authored-by: greg landrum <greg.landrum@gmail.com>
2022-03-09 14:01:24 +01:00
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