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implement coarse-grain#1152

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rvhonorato wants to merge 116 commits intomainhaddocking/haddock3:mainfrom CG-HADDOCKhaddocking/haddock3:CG-HADDOCKCopy head branch name to clipboard

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Commits on Aug 1, 2024

• copy files from topoaa

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Commits on Aug 5, 2024

• adapted the code to be used as a secondary module

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• AA to CG mapping retrieved

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• helper of aa2cg.py

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• path to helper corrected

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Commits on Aug 7, 2024

• pdb output path corrected

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Commits on Aug 9, 2024

• topology file created

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Commits on Aug 16, 2024

• correct file names

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Commits on Aug 19, 2024

• files renamed

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Commits on Aug 20, 2024

• force-field parameter added to the module

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Commits on Aug 28, 2024

• name change of the variable ffversion to cgffversion

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• adaptation of the cns file for the generation of topology

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Commits on Sep 4, 2024

• cgffversion parameter is changed from string to integer

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• topology files named as a function of the MARTINI version

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Commits on Sep 5, 2024

• nucleic acid topology file as function of the MARTINI version

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• cgffversion modified from integer to string

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Commits on Sep 11, 2024

• pipeline removed: addition of a covalent bond between acetylated Nter and a cysteine sulphur

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• pipeline removed: addition of a covalent bond between a hemeC and a cysteine

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• martini3 option removed

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Commits on Sep 12, 2024

• pipeline removed: build missing atoms (build-missing.cns)

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Commits on Sep 20, 2024

• files corrected

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Commits on Sep 23, 2024

• test files added

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• parameter files recreated

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Commits on Sep 25, 2024

• secondary structures analyzed by aa2cg.py

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• parameter files corrected

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• Merge branch 'main' of https://github.com/haddocking/haddock3 into topocg

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• Updated dna-rna params to match the 2.5 HADDOCK version

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• Merge branch 'main' into dna-CG-params

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• Merge pull request #1051 from haddocking/dna-CG-params

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• Updated the topocg module - mainly the CNS scripts

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• Merge branch 'CG-HADDOCK' of https://github.com/haddocking/haddock3 into CG-topo

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• Added a CG docking example (for devel purposes)

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• Modified rigidbody CNS scripts for CG docking

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• Added rigidbody CG integration test

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Commits on Sep 26, 2024

• added call to a missing CG-related script

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• Cleaning of CG CNS scripts

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• Updated CNS scripts

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• remove old protein Martini version

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• codacy style edits

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• Added proper warning logging

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• Restored original log level

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• Added logging import

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Commits on Sep 27, 2024

• Adapted to use haddock logging mechanism

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• Merge pull request #1053 from haddocking/CG-topo

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• Merge pull request #1054 from haddocking/CG-rigidbody

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• Merge branch 'main' into CG-HADDOCK

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Commits on Sep 28, 2024

• Merge branch 'CG-HADDOCK' into CG-topo

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• Corrected param/interactions settings

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• Merge pull request #1059 from haddocking/CG-topo

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• Adapted rigidbody CG mode for proper handling of param/interactions

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• Merge pull request #1061 from haddocking/cg-rigidbody

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• CG-related changes:

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• Added missing epsilon_cg variable

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• Removed electrostatic from final EM to focus on covalent geometry

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• Merge pull request #1062 from haddocking/cg-flexref

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Commits on Sep 29, 2024

• Added CG support to the emref module

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Commits on Oct 1, 2024

• Merge pull request #1063 from haddocking/CG-emref

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Commits on Oct 2, 2024

• function to add a line in pdb file

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Commits on Oct 8, 2024

• successfull creation of a temporary pdb file with a cryst line to be used my DSSP

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Commits on Oct 9, 2024

• absence of secondary structure predicted is coil (C)

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• secondary structure correctly assigned to each residues of the structures

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• DSSP from Bio.PDB removed

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Commits on Oct 11, 2024

• adapted create_file_with_cryst function to open file using with

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• changed position of p.communicate

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• use of python tooling for removal of temporary files

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• type signatures added

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• os.linestep added

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Commits on Oct 16, 2024

• superfluous 1st line of dssp output removed

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• removal of temporary file placed in the finally clause

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Commits on Oct 17, 2024

• create_file_with_cryst function modified

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• temporary file name changed

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Commits on Oct 18, 2024

• output_path argument removed from determine_ss

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• creation of temporary file placed in the try

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• dssp dictionary creation reworked

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Commits on Oct 25, 2024

• Merge pull request #1090 from haddocking/CG-topocg-DSSP

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Commits on Oct 29, 2024

• Merge branch 'main' into CG-HADDOCK to keep the CG branch up to date with the main branch.

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• formating issues and unused variable

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Commits on Oct 30, 2024

• unecessary else removed

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• subprocess shell=true removed

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Commits on Oct 31, 2024

• docstrings added to the martinize function

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Commits on Nov 1, 2024

• subprocess call removed

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Commits on Nov 18, 2024

• Update src/haddock/modules/topology/topocg/aa2cg.py

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• Update src/haddock/modules/topology/topocg/aa2cg.py

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• unused module removed

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• Merge branch 'main' into CG-HADDOCK

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• Merge branch 'CG-HADDOCK' into CG-HADDOCK-aa2cg-fix

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• Merge pull request #1125 from haddocking/CG-HADDOCK-aa2cg-fix

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Commits on Nov 19, 2024

• copy emref as a starting point

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Commits on Nov 22, 2024

• cgtoaa cns pipeline

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Commits on Nov 28, 2024

• emref explanations removed from script

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• explanation of the script added

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Commits on Dec 8, 2024

• Merge pull request #1171 from haddocking/main

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• Fixed failing test (reverted force constant assigment to AA version)

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Commits on Dec 9, 2024

• Removed overlap in atom types with the protein force field

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Commits on Dec 11, 2024

• Merge pull request #1178 from haddocking/main

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Commits on Dec 12, 2024

• files switched

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Commits on Dec 13, 2024

• aa_topology added

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Commits on Jan 8, 2025

• aa_topology inherited between modules rigidbody and sampling

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• aatocg_tbl added

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Commits on Jan 16, 2025

• Updated CNS scripts for the cg-to-aa module

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Commits on Jan 20, 2025

• parameters added to the input file

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Commits on Jan 21, 2025

• removal of ambig_fname

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• aa-to-cg tbl file corrected

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• AA topology saved into the topology parameter

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• line removed

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Commits on Jan 23, 2025

• Updated CNS cgtoaa module and scripts - now working

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• Removed file

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Commits on Jan 24, 2025

• aa_topology object modified to match topology

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Commits on Jan 27, 2025

• Update src/haddock/libs/libcns.py

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• removed some unneeded parameters

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Commits on Jan 29, 2025

• All-Atom instead of AA and Coarse-Grain instead of CG

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• Update src/haddock/modules/refinement/cgtoaa/__init__.py

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• aatocg changed to cgtoaa

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• explanation added

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Commits on Feb 3, 2025

• Merge pull request #1193 from haddocking/CG-HADDOCK-cg2aa

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Commits on Feb 6, 2025

• Merge branch 'main' into CG-HADDOCK

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