Skip to content

Fixed bug that made --print output inconsitent #112

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
charnley merged 6 commits into from
Nov 23, 2024
Merged

Fixed bug that made --print output inconsitent #112

Changes from 1 commit
Commits
Show all changes
6 commits
Select commit Hold shift + click to select a range
612552e
Added tests for --no-hydrogen --print is consistent
charnley Nov 19, 2024
826ca3e
fix the printed structure with selected atoms (#111)
takafumi-shiraogawa Nov 23, 2024
7f5101d
Updated test coverage to cover bad --print order, Restructured main t…
charnley Nov 23, 2024
098a480
Deleted duplicate test files
charnley Nov 23, 2024
04dc65c
Removed unused protocol
charnley Nov 23, 2024
9424f25
Removed out-commented code and added clarification comment
charnley Nov 23, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
Prev Previous commit
Removed out-commented code and added clarification comment
  • Loading branch information
@charnley
charnley committed Nov 23, 2024
commit 9424f25a6f54380fe99b5c9f7f32f6d45cb7e099
10 changes: 2 additions & 8 deletions rmsd/calculate_rmsd.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2054,24 +2054,18 @@ def main(args: Optional[List[str]] = None) -> str:
if q_reflection is not None:
q_coord_sub = np.dot(q_coord_sub, np.diag(q_reflection))

# q_coord -= q_coord

# Rotate q coordinates
# TODO Should actually follow rotation method
# q_coord = kabsch_rotate(q_coord, p_coord)
# rotation_matrix = kabsch(q_coord, p_coord)
U = kabsch(q_coord_sub, p_coord_sub)

# done and done
if settings.print_only_rmsd_atoms or not use_view:
q_coord_sub = np.dot(q_coord_sub, U)
q_coord_sub += p_cent_sub
return set_coordinates(
q_atoms_sub,
q_coord_sub,
title=f"Rotated {settings.structure_b} to match {settings.structure_a}, with RMSD of {result_rmsd:.8f}",
title=f"Rotated '{settings.structure_b}' to match '{settings.structure_a}', with a RMSD of {result_rmsd:.8f}",
)

# Swap, reflect, rotate and re-center on the full atom and coordinate set
q_coord -= q_cent_sub

if q_swap is not None:
Expand Down