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Martini3-IDP #647

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Martini3-IDP #647

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4b21391
Overwrite cgsecstruct assignment in IDRs
csbrasnett Nov 4, 2024
db6722e
remove cross go bonds
csbrasnett Nov 4, 2024
4591a61
fixing tests
csbrasnett Nov 4, 2024
3ebabba
removed superfluous variable from dssp
csbrasnett Nov 4, 2024
4bf7810
Merge branch 'marrink-lab:master' into idp-go-ss
csbrasnett Nov 22, 2024
c510ef3
add Martini3-IDP forcefield
csbrasnett Jan 9, 2025
92d21f6
change .gitignore back
csbrasnett Jan 9, 2025
f4f61ea
add test to make sure secondary structure gets changed in disordered …
csbrasnett Jan 9, 2025
cf44b5d
Merge branch 'master' into idp-go-ss
csbrasnett Jan 28, 2025
b5a4b6d
made requested changes
csbrasnett Jan 28, 2025
e5ef2c0
corrected condition in martinize2 to generate ss_sequence string
csbrasnett Jan 29, 2025
cddf4eb
correct test
csbrasnett Jan 29, 2025
c5df2ee
add test case if idr regions but no secstruct.
csbrasnett Jan 29, 2025
44941d6
Merge branch 'master' into idp-go-ss
csbrasnett Jan 31, 2025
d01a03d
write out cg_ss if assignment changed in any molecule.
csbrasnett Jan 31, 2025
e553fc3
correct detection of changed cgsecstruct in martinize
csbrasnett Jan 31, 2025
72e8ade
make sure meta attribute not given if idr cg_ss is already C, otherwi…
csbrasnett Jan 31, 2025
008a4f0
added test for checking if cgsecstruct is already correct
csbrasnett Jan 31, 2025
9a99cba
Merge branch 'master' into idp-go-ss
pckroon Feb 7, 2025
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30 changes: 20 additions & 10 deletions bin/martinize2
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Original file line number Diff line number Diff line change
Expand Up @@ -78,6 +78,9 @@ LOGGER = StyleAdapter(LOGGER)

VERSION = "martinize with vermouth {}".format(vermouth.__version__)

SS_CG = {'1': 'H', '2': 'H', '3': 'H', 'H': 'H', 'G': 'H', 'I': 'H',
'B': 'E', 'E': 'E', 'T': 'T', 'S': 'S', 'C': 'C'}


def read_system(path, ignore_resnames=(), ignh=None, modelidx=None):
"""
Expand Down Expand Up @@ -952,16 +955,6 @@ def entry():
'for this force field',
type="missing-feature")

ss_sequence = list(
itertools.chain(
*(
dssp.sequence_from_residues(molecule, "secstruct")
for molecule in system.molecules
if selectors.is_protein(molecule)
)
)
)

if args.cystein_bridge == "none":
vermouth.RemoveCysteinBridgeEdges().run_system(system)
elif args.cystein_bridge != "auto":
Expand All @@ -977,6 +970,17 @@ def entry():
disordered_regions=args.water_idrs
)

ss_sequence = list(
itertools.chain(
*(
SS_CG[i]
for i in dssp.sequence_from_residues(molecule, "cgsecstruct")
for molecule in system.molecules
if selectors.is_protein(molecule) if i is not None
)
)
)
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This translation to CG is too simplistic, no?

Suggested change
ss_sequence = list(
itertools.chain(
*(
SS_CG[i]
for i in dssp.sequence_from_residues(molecule, "cgsecstruct")
for molecule in system.molecules
if selectors.is_protein(molecule) if i is not None
)
)
)
ss_sequence = list(
itertools.chain(
*(
dssp.convert_dssp_to_martini(dssp.sequence_from_residues(molecule, "cgsecstruct"))
for molecule in system.molecules
if selectors.is_protein(molecule) if i is not None
)
)
)

Also, how does this interact with the "normal" dssp processing, and people providing a secondary structure on the cli?

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This won't affect the "normal" processing, the annotation is done for both ways before martinize() is called. The dssp/ss flags are dealt with at that point, and this is only to make sure that the cg secondary structure is determined correctly. The ss_sequence needs to be moved here to align with the overwriting that happens in the idr annotation, otherwise the 'uncorrected' string is written out

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My concern with this is that it becomes ambiguous what's atomistic SS and whats CG SS. The idea of printing the found SS structure is so that users can pass it to the -ss flag to reproduce the behaviour. However, if that only works if the SS flavour that's expected is the same as the one printed.

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Point taken. However, for the purposes of the current IDP models, ensuring the ss used when the links are applied doesn't intersect in a nasty way with the -idr flags is fairly important.

Perhaps the way around is if the string gets changed, print it in the itp twice? first what was found by dssp, second what was actually applied in the links?

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That sounds reasonable


# Apply position restraints if required.
if args.posres != "none":
LOGGER.info("Applying position restraints.", type="step")
Expand Down Expand Up @@ -1004,6 +1008,12 @@ def entry():
defines = ("GO_VIRT",)
itp_paths = {"atomtypes": "go_atomtypes.itp",
"nonbond_params": "go_nbparams.itp"}
if not args.water_bias:
# this ensures that disordered-folded go bonds get removed regardless of force field.
vermouth.processors.ComputeWaterBias(args.water_bias,
{s: float(eps) for s, eps in args.water_bias_eps},
[(int(start), int(stop)) for start, stop in args.water_idrs],
).run_system(system)
Comment on lines +1039 to +1044
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Do args.water_bias_eps and args.water_idrs have sane defaults?

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False and [] respectively.

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s: float(eps) for s, eps in args.water_bias_eps will cause an error then?

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ah wait, args.water_bias_eps and args.water_idrsboth default to [], it's args.water_bias that defaults to []. As the comment says, this is intended to run empty so that cross domain Go bonds are removed. It can be changed to be explicitly empty though

else:
# don't write non-bonded interactions
itp_paths = []
Expand Down
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