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implement coarse-grain #1152

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rversin and others added 30 commits August 1, 2024 12:47
@rversin
copy files from topoaa
cecec48
@rversin
adapted the code to be used as a secondary module
3da47ab
@rversin
AA to CG mapping retrieved
77a7a93
@rversin
helper of aa2cg.py
87e0ee9
@rversin
path to helper corrected
1b391f7
@rversin
pdb output path corrected
606ad87
@rversin
topology file created
4048363
@rversin
correct file names
193c1a1
@rversin
files renamed
eb88399
@rversin
force-field parameter added to the module
6006b95
@rversin
name change of the variable ffversion to cgffversion
42997cf
@rversin
adaptation of the cns file for the generation of topology
50c4e6a
@rversin
cgffversion parameter is changed from string to integer
85054c9
@rversin
topology files named as a function of the MARTINI version
5e6b852
@rversin
nucleic acid topology file as function of the MARTINI version
0b07eda
@rversin
cgffversion modified from integer to string
605a887
@rversin
pipeline removed: addition of a covalent bond between acetylated Nter…
53b5380 
… and a cysteine sulphur
@rversin
pipeline removed: addition of a covalent bond between a hemeC and a c…
b08ab61 
…ysteine
@rversin
martini3 option removed
78c1a50
@rversin
pipeline removed: build missing atoms (build-missing.cns)
8af1d3e
@rversin
files corrected
7a6b29d
@rversin
test files added
7084271
@rversin
parameter files recreated
eb354ff
@rversin
secondary structures analyzed by aa2cg.py
98f1a3f
@rversin
parameter files corrected
1c817c3
@amjjbonvin
Merge branch 'main' of https://github.com/haddocking/haddock3 into to…
a276094 
…pocg
@amjjbonvin
Updated dna-rna params to match the 2.5 HADDOCK version
d3804de
@rvhonorato
Merge branch 'main' into dna-CG-params
a6a793b
@rvhonorato
Merge pull request #1051 from haddocking/dna-CG-params
69ab9f3 
Updated DNA/RNA CG parameters
@amjjbonvin
Updated the topocg module - mainly the CNS scripts
343a524
rversin and others added 30 commits April 30, 2025 16:14
@rversin
CG protprot complex
c04a901
@rversin
protprot_input_list_cg fixture added
96e50cd
@rversin
all protprot tests adapted
a54b6ff
@rversin
CG protprot 1bkd complex
b59e135
@rversin
protprot_1bkd_input_list_cg fixture added
5c61855
@rversin
all protprot 1bkd tests adapted
8d5a997
@rversin
protdna_input_list_cg fixture added
00df53b
@rversin
CG protdna complex
f61b781
@rversin
all protdna tests adapted
4713495
@rversin
name of the protdna_input_list_cg fixture corrected
af1f5a6
@rversin
missing histidine added
5673382
@rversin
cg capri test added to test_module_caprieval.py and test_module_capri…
d8d0572 
…eval_cg.py removed
@rversin
unecessary lines removed
e4a0702
@rversin
code of martinization of the reference simplified
6b4f863
@rversin
cg parameter changed to ff
d0a8c9a
@rversin
debugging lines removed
842ba32
@rversin
update quotes
321da5b
@rversin
prints removed
bc58241
@rversin
update quotes
2b03007
@rversin
update quotes
09721e3
@rversin @VGPReys
Update src/haddock/modules/analysis/caprieval/__init__.py
54365ad 
Co-authored-by: Victor Reys <[email protected]>
@rversin
cgffversion variable removed
472868f
@rversin
docstring corrected
18d4cf8
@rversin
find_ff function created
a79269d
@rversin @VGPReys
find_ff corrected
7c06726 
Co-authored-by: Victor Reys <[email protected]>
@rversin
find_ff outputs aa when all-atom
1a69d44
@rversin
missing docstring added
dd72621
@VGPReys
Update src/haddock/modules/analysis/caprieval/__init__.py
252712b
@rversin
Merge pull request #1223 from haddocking/CG-HADDOCK-cgcapri into CG-H…
50425c8 
…ADDOCK

update `caprieval` to handle coarse-grained structures
@rversin
Merge branch 'main' into CG-HADDOCK
c6803a0
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CNS Improvements in the CNS engine feature Adding something new to the codebase m|cgtoaa m|emref emref module m|flexref flexref module m|rigidbody rigidbody sampling m|topocg topocg module
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@rvhonorato @rversin @amjjbonvin @VGPReys