fix(refgeom): center reference geometries on metal position#87
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Root cause analysis revealed that cosymlib reference geometries store vertex coordinates with the central metal atom NOT at the origin. Q-Shape was incorrectly normalizing these raw coordinates, resulting in distorted reference shapes with ~15° angular errors for some geometries like SS-4 and vTBPY-4. Fixed affected geometries (CN 2-6): - vT-2, vOC-2 (CN=2) - vT-3, fvOC-3, mvOC-3 (CN=3) - SS-4, vTBPY-4 (CN=4) - vOC-5 (CN=5) - PPY-6, JPPY-6 (CN=6) The fix subtracts the metal center position from each vertex before normalization, ensuring correct geometric relationships. This resolves discrepancies between Q-Shape and SHAPE software results, particularly for SS-4 (Seesaw) which showed the largest errors in test cases. Note: 28 high-CN geometries (CN 7-12) still need similar fixes.
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Root cause analysis revealed that cosymlib reference geometries store vertex coordinates with the central metal atom NOT at the origin. Q-Shape was incorrectly normalizing these raw coordinates, resulting in distorted reference shapes with ~15° angular errors for some geometries like SS-4 and vTBPY-4.
Fixed affected geometries (CN 2-6):
The fix subtracts the metal center position from each vertex before normalization, ensuring correct geometric relationships.
This resolves discrepancies between Q-Shape and SHAPE software results, particularly for SS-4 (Seesaw) which showed the largest errors in test cases.
Note: 28 high-CN geometries (CN 7-12) still need similar fixes.