Martini3-IDP #647
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Martini3-IDP #647
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- enforce that the cgsecstruct is "C" to make sure we don't overapply a folded domain in the links later - adapt the secondary structure header to get the header from the cg not atomistic graph
- in FFs where we have -go but not -water-bias, cross disordered-folded go bonds won't be removed because this is buried in the water_bias processor. - so call it anyway with an empty list of water biases, which will remove them
- reverting dssp sequence_from_residues behaviour so doesn't default to something with cg - move the ss_cg conversion into martinize2 using a global variable
pckroon
requested changes
Jan 27, 2025
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| 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?
Comment on lines
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| if "cgsecstruct" in molecule.nodes[key]: | ||
| molecule.nodes[key]["cgsecstruct"] = "C" | ||
| else: | ||
| molecule.nodes[key][annotation] = False |
There was a problem hiding this comment.
Suggested change
| if "cgsecstruct" in molecule.nodes[key]: | |
| molecule.nodes[key]["cgsecstruct"] = "C" | |
| else: | |
| molecule.nodes[key][annotation] = False | |
| if "cgsecstruct" in molecule.nodes[key]: | |
| molecule.nodes[key]["cgsecstruct"] = "C" | |
| molecule.nodes[key][annotation] = True # ??? | |
| else: | |
| molecule.nodes[key][annotation] = False |
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This PR:
Note that the martini3-IDP/aminoacids.ff file is slightly different here to ensure that it works properly with martinize.
Will need to update citations.bib once the paper is accepted