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score_docking_geometry function issue #88

@LuppovDaniil

Description

@LuppovDaniil

Hello,
I'm trying to use stcrpy inside a conda environment (Python 3.12) to score TCR docking geometry.
While calculate_docking_geometry() works without issues, calling score_docking_geometry() fails with the following traceback:


---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
Cell In[14], line 1
----> 1 tcr.score_docking_geometry()

File ~/.conda/envs/stcrpy_env/lib/python3.12/site-packages/stcrpy/tcr_processing/TCR.py:361, in TCR.score_docking_geometry(self, **kwargs)
    358 if not hasattr(self, "geometry"):
    359     self.calculate_docking_geometry(mode="com")
    360 return geom_filter.score_docking_geometry(
--> 361     self.geometry.get_scanning_angle(mode="com"),
    362     self.geometry.get_pitch_angle(mode="com"),
    363     self.geometry.tcr_com[-1],  # z component of TCR centre of mass
    364 )

TypeError: TCRGeom.get_scanning_angle() got an unexpected keyword argument 'mode'

tcr object was created and geometry was calculated as follows:

tcr = stcrpy.load_TCR("/projects/structures/clusters/HLA_A_align/ALSKGVHFV/aligned_9e7adc6b9c8348bbf11a5221e9f19d6166457015171612340c3f4a58998c662b.pdb")
geometry = tcr.calculate_docking_geometry(mode='rudolph')

It seems there is an inconsistency in the library:

  • tcr.get_scanning_angle(mode='com') works as expected.
  • However, tcr.geometry.get_scanning_angle(mode='com') raises the error above.

Could you please confirm whether this is a bug? Or am I missing something in how I should call these functions?

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