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Simplify output_name #476

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Simplify output_name #476

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19 changes: 16 additions & 3 deletions alphapulldown/objects.py
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Original file line number Diff line number Diff line change
Expand Up @@ -450,12 +450,13 @@ class MultimericObject:
multimeric_template_dir: a directory where all the multimeric templates mmcifs files are stored
"""

def __init__(self, interactors: list, pair_msa: bool = True,
def __init__(self, interactors: list, input: list, pair_msa: bool = True,
multimeric_template: bool = False,
multimeric_template_meta_data: str = None,
multimeric_template_dir:str = None) -> None:
self.description = ""
self.interactors = interactors
self.input = input
self.build_description_monomer_mapping()
self.pair_msa = pair_msa
self.multimeric_template = multimeric_template
Expand All @@ -479,11 +480,23 @@ def build_description_monomer_mapping(self):

def create_output_name(self):
"""a method to create output name"""
list_oligo = self.input[0].split("+")
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would this work if is the delimiter is other than '+'?

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Between differents proteins, delimiter is always "+", if there is no "+" in self.input[0] so list_oligo will look like [P13979] (monomer) or [P13979:2] (dimere)

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Sorry, I mean we can choose a delimiter when run structure predictions. The '+' symbol is the default one, but it can be set to any other character:
https://github.com/KosinskiLab/AlphaPulldown/blob/main/alphapulldown/scripts/run_structure_prediction.py#L153
Therefore we have to pass the delimiter flag as well, otherwise it will not work for any custom delimiters other than '+'.
Then the code would look like:
list_oligo = self.input[0].split(self.delimiter)
and we need to pass this delimiter beforehand e.g.
object_to_model = MultimericObject( interactors=interactors, delimiter=delimiter, ...
On the other hand, maybe it makes more sense to move all this logic from objects.py to modelling_setup.py and keep MultimericObject logic as simple as possible (given it's already far from being simple)

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Ok, sorry I don't know delimiter flag exist. Yes that make more sense to add this at modelling_setup.py.

oligo_count = 0
for i in range(len(self.interactors)):
if i == 0:
self.description += f"{self.interactors[i].description}"
if ":" in list_oligo[i] :
self.description += f"{self.interactors[i].description}_homo_{list_oligo[i].split(':')[1]}er"
else :
self.description += f"{self.interactors[i].description}"
else:
self.description += f"_and_{self.interactors[i].description}"
if self.interactors[i].description in self.description :
oligo_count += 1
pass
else :
if ":" in list_oligo[i-oligo_count] :
self.description += f"_and_{self.interactors[i].description}_homo_{list_oligo[i-oligo_count].split(':')[1]}er"
else :
self.description += f"_and_{self.interactors[i].description}"

def create_chain_id_map(self):
"""a method to create chain id"""
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