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Move structural analysis methods to child classes in SepTop Protocol #8742

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Run time

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Job	Run time
💻-ubuntu-latest 🐍-3.12 oechem: no	48m 55s
💻-ubuntu-latest 🐍-3.13 oechem: yes	48m 46s
💻-macos-latest 🐍-3.14 oechem: no	31m 5s
💻-ubuntu-latest 🐍-3.14 oechem: no	43m 4s
💻-ubuntu-latest 🐍-3.13 oechem: no	47m 30s
	3h 39m 20s