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| @@ -138,17 +137,16 @@ | |||
| "metadata": {}, | |||
| "outputs": [], | |||
| "source": [ | |||
| "from openfe.setup import LigandAtomMapper\n", | |||
| "from openfe.setup.atom_mapping import LigandAtomMapper\n", | |||
| "\n", | |||
| "class CustomMapper(LigandAtomMapper):\n", | |||
| " def __init__(self, remove_middle):\n", | |||
| " super().__init__()\n", | |||
| " self.remove_middle = remove_middle\n", | |||
| " \n", | |||
| " def _mappings_generator(self, molA, molB):\n", | |||
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Do we want to rename things to componentA/B or is it suitably clear if we keep molA/B?
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I think it's probably better of two evils to use componentA/B consistently and explain why.
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Done! please revisit. I didn't completely excise the word "molecule," but I used component where I thought it made sense, and added a bit about components.
| @@ -646,11 +644,11 @@ | |||
| " # This score is the highest indices of mapped atoms plus the length of the molecule names\n", | |||
| " # It shows you how to access this information from the mapping. I wouldn't recommend\n", | |||
| " # it for production work.\n", | |||
| " molA_to_molB = mapping.molA_to_molB\n", | |||
| " molA_to_molB = mapping.componentA_to_componentB\n", | |||
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One option might just be to explain why it's called component somewhere?
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wait.. my push didn't take |
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ok, there it is... Working from a outside my home, looks like WiFi here blocked SSH activity. Just used my phone as a hotspot. |
This brings this notebook in line with openfe 0.4 and gufe 0.4. Also adds it to testing.