PDBQT connectivity improvement#307
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…/maxima to increase robustness of pdbqt connectivity.
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This PR adds a bond length tolerance factor (set at 1.1) to increase robustness of our pdbqt connectivity detection.
Connectivity is used in AD4/AD-GPU to exclude intramolecular pairs with bond distances up to 1-4 interactions. While a misdetection is usually not fatal to docking, it can lead to extra intramolecular pairs which in turn may affect docking results.
We've seen such misdetection in one of our E50 test ligands (1sq5) - so a full E50 test will be needed to verify this PR.