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Atoms bonded to metal atoms should always have their H counts explicit in SMILES (#8318)

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* refactor the code to determine whether or not an atom is in brackets

* move the definition of isMetal to QueryOps

* atoms bound to metals in SMILES should always be in square brackets

Implementation and some test updates

needs confirmation that all of tests run

* basic tests pass

* java tests pass

* update js tests

* doc updates

* Update Code/GraphMol/catch_graphmol.cpp

Co-authored-by: Ricardo Rodriguez <ricrogz@users.noreply.github.com>

* Update Code/GraphMol/SmilesParse/test.cpp

Co-authored-by: Ricardo Rodriguez <ricrogz@users.noreply.github.com>

* finish fixing tests

* bump yaehmop version to allow compilation to work

---------

Co-authored-by: Ricardo Rodriguez <ricrogz@users.noreply.github.com>
This commit is contained in:
Greg Landrum
2025-03-29 07:26:03 +01:00
committed by GitHub
parent 643b13cba4
commit 32608ae0b4
23 changed files with 157 additions and 104 deletions
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4
External/YAeHMOP/CMakeLists.txt vendored
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@@ -9,8 +9,8 @@ if(NOT DEFINED YAEHMOP_DIR)
endif()
if(NOT EXISTS "${YAEHMOP_DIR}/tightbind/bind.h")
set(RELEASE_NO "2024.03.1")
set(MD5 "ebbddca4f79ab71544cb1fef9a7eca8a")
set(RELEASE_NO "2025.03.1")
set(MD5 "93b7c8d9419b4899b44699cba3e23404")
downloadAndCheckMD5("https://github.com/greglandrum/yaehmop/archive/refs/tags/v${RELEASE_NO}.tar.gz"
"${CMAKE_CURRENT_SOURCE_DIR}/yaehmop-${RELEASE_NO}.tar.gz" ${MD5})
execute_process(COMMAND ${CMAKE_COMMAND} -E tar zxf