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implement coarse-grain #1152

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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 October 2, 2024 16:32
@rversin
function to add a line in pdb file
1545790
@rversin
successfull creation of a temporary pdb file with a cryst line to be …
42c8901 
…used my DSSP
@rversin
absence of secondary structure predicted is coil (C)
a9de70e
@rversin
secondary structure correctly assigned to each residues of the struct…
9fd4b1f 
…ures
@rversin
DSSP from Bio.PDB removed
5e4ac3f
@rversin
adapted create_file_with_cryst function to open file using with
b141dbb
@rversin
changed position of p.communicate
d455ca2
@rversin
use of python tooling for removal of temporary files
b8e2c74
@rversin
type signatures added
3e2f958
@rversin
os.linestep added
a25b188
@rversin
superfluous 1st line of dssp output removed
559bdfd
@rversin
removal of temporary file placed in the finally clause
c9d95e2
@rversin
create_file_with_cryst function modified
8715599
@rversin
temporary file name changed
ce6b33f
@rversin
output_path argument removed from determine_ss
7623a10
@rversin
creation of temporary file placed in the try
2600bd3
@rversin
dssp dictionary creation reworked
c7047a3
@rversin
Merge pull request #1090 from haddocking/CG-topocg-DSSP
859e974 
Correction of the usage of DSSP in the topocg module
@rversin
Merge branch 'main' into CG-HADDOCK to keep the CG branch up to date …
17419de 
…with the main branch.
@rversin
formating issues and unused variable
9a1049b
@rversin
unecessary else removed
7ef1522
@rversin
subprocess shell=true removed
c796027
@rversin
docstrings added to the martinize function
3125ef3
@rversin
subprocess call removed
3886b51
@rversin @VGPReys
Update src/haddock/modules/topology/topocg/aa2cg.py
e2e2768 
Co-authored-by: Victor Reys <132575181+VGPReys@users.noreply.github.com>
@rversin @VGPReys
Update src/haddock/modules/topology/topocg/aa2cg.py
43480c1 
Co-authored-by: Victor Reys <132575181+VGPReys@users.noreply.github.com>
@rversin
unused module removed
c2158ec
@rvhonorato
Merge branch 'main' into CG-HADDOCK
8ef3ff2
@rvhonorato
Merge branch 'CG-HADDOCK' into CG-HADDOCK-aa2cg-fix
8f75d87
@rversin
Merge pull request #1125 from haddocking/CG-HADDOCK-aa2cg-fix
7dc7866 
Minor fix of aa2cg script
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3 participants
@rvhonorato @rversin @amjjbonvin