Initial salt bridge implementation #1021
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Signed-off-by: Aritz Erkiaga <aerkiaga3@gmail.com>
| for (const auto &a: r.residueAtoms()) { | ||
| if (molecule.formalCharge(a.index()) != 0) | ||
| continue; | ||
| bool gammaOxygen = false; |
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Before you do this, don't you want to check the atom name to ignore "N" "CA" "C" and "O" atoms?
(It might be worth having Residue::isBackboneAtom() and Residue::isSideChainAtom() methods.
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| // Add predicted charged atoms from residues | ||
| for (const auto &r: molecule.residues()) { | ||
| for (const auto &a: r.residueAtoms()) { |
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Do you want to filter by residue? For example, this isn't important for ALA or GLY right?
| bool alphaDoubleBond = false; | ||
| auto bonds = molecule.getAtomBonds(a.index()); | ||
| auto orders = molecule.getAtomOrders(a.index()); | ||
| for (Index i = 0; i < bonds.size(); i++) { |
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Please add some comments about what you're doing here. You're trying to find particular atoms, right?
Do you want to look at residue atom names? Residue::atomNameMap() for example.
Check out LigandExpo:
- http://ligand-expo.rcsb.org/ld-search.html
- e.g. http://ligand-expo.rcsb.org/reports/H/HIS/HIS_D3L3.gif
Now some files will come in with problematic labels, but definitely check atom names first, because they'll save a lot of time.
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I don't think any of this code is bad but I think you should check the atom names (and/or add some methods to |
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Here are the build results |
Signed-off-by: Aritz Erkiaga <aerkiaga3@gmail.com>
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I've replaced all the code with some that checks for atom names. |
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I think a few of those should be fractional charges, but for the salt bridge visualization, the magnitude doesn't matter as far as I can tell, just + / - vs. + / +… So for now, it looks good to me. We'll make sure it compiles cleanly and merge. |
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Here are the build results |
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Here are the build results |
This displays interactions between oppositely charged atoms, as well as same-charge ("bad contacts"). Charged residues with no real formal charge in the molecule are also interpreted as charged.
Signed-off-by: Aritz Erkiaga aerkiaga3@gmail.com
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