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z-surface restraints scripts #839

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z-surface restraints scripts #839

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@VGPReys VGPReys commented Mar 27, 2024

You are about to submit a new Pull Request. Before continuing make sure you read the contributing guidelines and that you comply with the following criteria:

  • You have sticked to Python. Please talk to us before adding other programming languages to HADDOCK3
  • Your PR is about CNS
  • Your code is well documented: proper docstrings and explanatory comments for those tricky parts
  • You structured the code into small functions as much as possible. You can use classes if there is a (state) purpose
  • Your code follows our coding style
  • You wrote tests for the new code
  • tox tests pass. Run tox command inside the repository folder
  • -test.cfg examples execute without errors. Inside examples/ run python run_tests.py -b
  • PR does not add any dependencies, unless permission granted by the HADDOCK team
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  • Your PR is about writing tests for already existing code :godmode:

Closes #834 by adding a new subcommand z-surface-restraints to the haddock3-restraints CLI.

haddock3-restraints z-surface-restraints
  --pdb my_structure.pdb
  --residues 1,2,3 7,8,9
  --spacing 40
  --x-size 200
  --y-size 200
  --output my_Zrestraints

Selected residues sets (in the above example 1,2,3 and 7,8,9), will define two plans with x-dim --x-size and y-dim --y-size placing beads every --spacing angstroms.
Also, corresponding restraints are generated, resulting in the generation of both:

  • a beads.pdb file containing the coordinates of the shape beads
  • a restraints.tbl file containing specific restraints to each plans.

A series of examples are also provided, in examples/docking-protein-surface

TODO LIST

  • Generate bead plans
  • Generate restraints to plans
  • Have proper tests
  • Benchmark

@VGPReys VGPReys self-assigned this Mar 27, 2024
@VGPReys VGPReys added feature New feature request community contributions from people outside the haddock team labels Mar 27, 2024
@VGPReys VGPReys marked this pull request as ready for review April 12, 2024 06:46
@VGPReys VGPReys requested a review from mgiulini April 23, 2024 15:11
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Z-surface and restraints definition
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