Fix/cap.pdb file lookup when colbuilder is launched outside the working directory - #27
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Fix/cap.pdb file lookup when colbuilder is launched outside the working directory#27ingcoder wants to merge 2 commits into
ingcoder wants to merge 2 commits into
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Remap TER-extracted files to sparse system IDs and defer MODELLER-dependent imports for non-sequence runs.
Topology now reads caps from the configured working directory instead of the shell cwd, which removes the need for TER-extraction ID remapping.
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How the bug was discovered
The bug appeared during a combined geometry and topology build of the 67 nm rat glucosepane fibril.
Geometry correctly wrote its cap files under the configured working directory:
rat_glucosepane_67nm_build/.tmp/geometry_gen/D/
However, Colbuilder was launched from /private/tmp. Topology step then searched for .tmp/geometry_gen relative to that shell directory instead:
/private/tmp/.tmp/geometry_gen
It found no caps and incorrectly used the existing fallback that re-extracts models from the fibril PDB. This changed the model numbering and caused topology generation to fail.
Why the fix is necessary
Temporary files should be found using config.working_directory, regardless of where the user launches Colbuilder. Fibril re-extraction should happen only when geometry caps are truly unavailable.
Fix
Use file_manager.geometry_dir and file_manager.mixing_dir to locate caps.
This allows the existing search to set cap_files_found = True and prevents unnecessary fibril re-extraction.
Import MODELLER-dependent sequence code only when sequence generation runs.
Test
Confirmed from a separate temporary launch directory that topology finds and copies the configured geometry caps without calling the fibril-extraction fallback.