Fix Protoss pathing: source PDB from project root, bypass Protoss dir#3
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amengland9 wants to merge 2 commits into
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Fix Protoss pathing: source PDB from project root, bypass Protoss dir#3amengland9 wants to merge 2 commits into
amengland9 wants to merge 2 commits into
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Added a function to find Protoss-processed PDB files with case-insensitive lookup and fallback to source PDB.
Benzoin96485
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July 15, 2026 19:24
| Full path to the matched Protoss PDB, or ``None`` if the | ||
| Protoss folder or a matching file inside it doesn't exist. | ||
| """ | ||
| protoss_dir = os.path.join(project_root, "out", pdb_name, "Protoss") |
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Why does this always hold? Where does the out directory come from?
Benzoin96485
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Benzoin96485
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Left some comments because I don't think there is a standard output directory prefix like "out" and we shouldn't assume any. Regarding your question, user may confirm the protonation themselves
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| if "out" in cwd_parts: | ||
| project_root = os.sep.join(cwd_parts[:cwd_parts.index("out")]) |
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The same question: why "out"?
Benzoin96485
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Description
Fixes the Protoss pathing bug in
get_charges()(qp/manager/charge_embedding.py). Before, the function always sourced the structure PDB for charge embedding fromout/<pdb>/Protoss/<pdb>_protoss.pdb, with no way to point it elsewhere. This PR changes it to look for the source.pdbin the project root (the directory containingout/) using a case-insensitive filename match if it cannot find a Protoss folder, so charge embedding can be run against a structure that bypasses Protoss entirely if desired.Todos
find_source_pdb()helper with case-insensitive glob match and clear errors on zero/multiple matches"out"in the cwd path'/'splitting toos.sepfor Windows compatibility (I usually use the package on my local machine so this was moreso for me)Questions
rename_and_clean_resnames()runs immediately after this and assigns HIP/HIE/HID based onHD1/HE2hydrogens being present which means it assumes a protonated structure. Should there be an explicit check/warning if the bypassed structure isn't already protonated, rather than relying on the user to confirm this themselves?Status