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internal go contact map#643

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csbrasnett wants to merge 20 commits intomastermarrink-lab/vermouth-martinize:masterfrom Go-contact-mapmarrink-lab/vermouth-martinize:Go-contact-mapCopy head branch name to clipboard

+1,265-58

Commits

Commits on Nov 21, 2024

• basis of implementation

  csbrasnett

  committed
  8591a5a

Commits on Nov 26, 2024

• basic implementation of go model

  csbrasnett

  committed
  56d319d

Commits on Dec 6, 2024

• implementation of working go model with flexible CLI

  Show description for 5ca464f
  csbrasnett

  committed
  5ca464f

Commits on Dec 7, 2024

• change to using _res_serial attribute, so we can deal with > 1 chain

  csbrasnett

  committed
  ba02c22

Commits on Dec 12, 2024

• fix contact map calculation

  Show description for 4ecfe5a
  csbrasnett

  committed
  4ecfe5a

• Merge branch 'master' into Go-contact-map

  csbrasnett

  authored
  cf7cc8b

Commits on Dec 16, 2024

• change implementation to using KDTree.

  csbrasnett

  committed
  a1a217f

• tidy up for readability and testing, added comments and docstrings

  csbrasnett

  committed
  3468c0e

Commits on Dec 18, 2024

• addressed smaller comments. atom2res now significantly faster with prearranged dictionary

  csbrasnett

  committed
  3678176

Commits on Dec 20, 2024

• changed to run the processor on molecule not system.

  Show description for 2d1da84
  csbrasnett

  committed
  2d1da84

• fixed deferred file writing and corrected associated cli

  csbrasnett

  committed
  6c6f935

• made small corrections.

  Show description for 7880986
  csbrasnett

  committed
  7880986

Commits on Jan 3, 2025

• fix test_read_go_map.py

  csbrasnett

  committed
  af2eff2

• fix test_go_structure_bias.py

  csbrasnett

  committed
  4777f21

• fixed the reading/generation check for go map

  csbrasnett

  committed
  4053b66

• changed make_surface to _make_surface, shouldn't need function externally

  csbrasnett

  committed
  8c9585e

• first tests for contact map generation. Improved PROTEIN map handling to ensure test coverage

  csbrasnett

  committed
  cae3923

• more tests for contact map generation. refactored some contact_map functions. added more information to test_molecule.

  Show description for ba24c49
  csbrasnett

  committed
  ba24c49

• more contact map generation tests for main contact finding functions.

  Show description for b7c8da7
  csbrasnett

  committed
  b7c8da7

• sorted out written contact map checking

  csbrasnett

  committed
  4a36a8e