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Add delete_atoms method and use bonding info for add_hatoms SO107 #278

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Run time

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Job	Run time
lint	40s
build-docs	50s
unit-test (ubuntu-latest, 3.8)	1m 17s
unit-test (ubuntu-latest, 3.9)	1m 17s
unit-test (ubuntu-latest, 3.10)	1m 14s
unit-test (ubuntu-latest, 3.11)	1m 24s
unit-test (ubuntu-latest, 3.12)	1m 33s
unit-test (macos-latest, 3.8)	1m 33s
unit-test (macos-latest, 3.9)	1m 25s
unit-test (macos-latest, 3.10)	1m 26s
unit-test (macos-latest, 3.11)	1m 14s
unit-test (macos-latest, 3.12)	1m 20s
unit-test (windows-latest, 3.8)	2m 37s
unit-test (windows-latest, 3.9)	2m 56s
unit-test (windows-latest, 3.10)	3m 5s
unit-test (windows-latest, 3.11)	4m 28s
unit-test (windows-latest, 3.12)	3m 26s
	31m 45s