TUPÃ v1.7.0

TUPÃ update (May 5 2025):

• PBC correction for solvent molecules is done by entire residues now

• Self contribution removal is done by residues now

• Fixed bug for empty environment checking (issue #8 )

• Fixed bug for residue contribution for multiple chains/segments

• Streamlined parts of utils.py

• Formatting of probe position when writing output

• Fix small typos

TUPÃ v1.6.0

TUPÃ update (Aug 27 2023):

• Implementation of multiprocessing, allowing electric field calculation across multiple cores
  

• Minor bug fix for residue contribution to electric field.
  

• Minor bug fix to allow 1 frame trajectories (either PDB or DCD files).
  

TUPÃ v1.5.0

TUPÃ update (Mar 31 2023):

• Analysis results are now stored in Results object. 
  

• Configuration parameters are now stored in Configuration object as attributes (see config_parser.py)
  

• Subroutines were transformed into functions (see lib/utils.py)
  

• Setup run info is saved in a file (run_info.dat) inside the results folder.
  

TUPÃ v1.4.0

TUPÃ update (Aug 03 2022):

• Empty environment selection now issues an error.
  

• Empty probe selection now issues an error.
  

• Improved Help/Usage 
  

• Configuration file examples are based on common syntax
  

TUPÃ v1.3.0

TUPÃ update (Jun 21 2022):

• -dumptime now accepts multiple entries
• Add average and standard deviation values at the end of ElecField_proj_onto_bond.dat and ElecField_alignment.dat
• Add Angle column in ElecField_alignment.dat with the average angle between Efield(t) and bond axis.
• Fix documentation issues/typos.

TUPÃ v1.2.0

TUPÃ update (Apr 18 2022):

• Make -dump now writes the entire system instead of just the environment selection.
• Add field average and standard deviation values at the end of ElecField.dat
• Fix documentation issues/typos.
• Update paper metadata

TUPÃ v1.1.0

TUPÃ update (Mar 22 2022):

• Inclusion of LIST mode: TUPÃ reads a file containing XYZ coordinates that will be used as the probe position. Useful for binding sites or other pockets.
• Fix documentation issues/typos.

pyTUPÃ update (Mar 22 2022):

• Support for a 3D representation of electric field standard deviation as a truncated cone that involves the electric field arrow.

TUPÃ v1.0.0

TUPÃ first release (Feb 13 2022):

• Calculation modes available: ATOM, BOND, COORDINATE
• Support for triclinic simulation boxes only.
• PBC support is limited to triclinic boxes. Future versions are expected to handle PBC corrections.
• Removal of "self-contributions" are available to the COORDINATE mode only.
• Users can dump a specific frame as a .pdb file. Futures versions are expected to allow the extraction of the environment set coordinates.
• Residue contributions are calculated.

pyTUPÃ first release (Feb 13 2022):

• Support for draw_bond, efield_bond and efield_point.
• EField vectors can be scaled up/down