refactor: Detect molecules#2528
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trisyoungs
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trisyoungs
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This is excellent and a whole lot cleaner than the old one, but I think there are some looping / workflow errors to address!
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Does this still need a rebase? This was in #2530 ...
| // Inputs | ||
| addInput<Structure>("Structure", "Input structure", inputStructure_); | ||
| } | ||
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| /* | |
| * Definition | |
| */ | |
| std::string_view DetectMoleculesNode::type() const { return "DetectMolecules"; } | ||
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| std::string_view DetectMoleculesNode::summary() const { return "Detect molecular species within a structure"; } | ||
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| /* | |
| * Processing | |
| */ | |
| for (int i = 0; i < structure.nAtoms(); i++) | ||
| fragments.emplace_back(fragment(i)); |
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Shouldn't this function start from the next un-selected atom? Need something like a std::set to track which atoms have been detected within instances (a bug that doesn't show up for the atomic NaCl or MgO cases!)
| detectedStructures_.clear(); | ||
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| // Return all discovered molecular fragment index vectors | ||
| auto allFragmentIndices = findMolecularFragments(inputStructure_); |
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If you're pre-detecting all bound fragments here (which is a good idea)....
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| std::set<const StructureAtom *> atomMask; | ||
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| for (int i = 0; i < inputStructure_.nAtoms(); i++) |
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...why is this a loop over structure atoms and not fragments?
| // Set up the return value and bind its contents | ||
| NETADefinition bestNETA; | ||
| std::vector<StructureAtom *> rootAtoms; | ||
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| // Maintain a set of atoms matched by any NETA description we generate | ||
| std::set<StructureAtom *> alreadyMatched; | ||
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| // Skip this atom? | ||
| if (alreadyMatched.find(fragmentAtom) != alreadyMatched.end()) | ||
| continue; | ||
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| // Create a NETA definition with this atom as the root | ||
| NETADefinition neta; | ||
| neta.create(static_cast<AtomBase *>(fragmentAtom), std::nullopt, | ||
| Flags<NETADefinition::NETACreationFlags>(NETADefinition::NETACreationFlags::ExplicitHydrogens, | ||
| NETADefinition::NETACreationFlags::IncludeRootElement)); | ||
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| // Apply this match over the whole species | ||
| std::vector<StructureAtom *> currentRootAtoms; | ||
| for (auto fragAtomIndex : fragmentIndices) | ||
| { | ||
| const auto fragmentAtom = inputStructure_.atom(fragAtomIndex); | ||
| if (neta.matches(fragmentAtom)) | ||
| { | ||
| currentRootAtoms.push_back(fragmentAtom); | ||
| alreadyMatched.insert(fragmentAtom); | ||
| } | ||
| } | ||
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| // Is this a better description? | ||
| auto better = false; | ||
| if (rootAtoms.empty() || currentRootAtoms.size() < rootAtoms.size()) | ||
| better = true; | ||
| else if (currentRootAtoms.size() == rootAtoms.size()) | ||
| { | ||
| // Replace the current match if there are more bonds on the current atom. | ||
| if (fragmentAtom->nBonds() > rootAtoms.front()->nBonds()) | ||
| better = true; | ||
| } | ||
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| if (better) | ||
| { | ||
| bestNETA = neta; | ||
| rootAtoms = currentRootAtoms; | ||
| } |
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This whole NETA creation part needs to run on each atom within a fragment, reason being to find the best, most concrete way of describing uniquely the bonding / atoms within it. Then it can be applied to each fragment (of the same size) in turn to see if the NETA matches.
| // Unfold all detected structures | ||
| for (auto &structure : detectedStructures_) | ||
| structure.unFold(); |
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This step needs to happen before you store the coordinates of the instances at the end of the loop above. Could happen immediately after the fragment detection at the top of the routine.
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