Multimer WIP

openfold/model/structure_module.py

@@ -184,7 +184,7 @@ class PointProjection(nn.Module):
 
         return points_global 
 
-
+# WEIGHTS CHANGED
 class InvariantPointAttention(nn.Module):
     """
     Implements Algorithm 22.
@@ -578,7 +578,7 @@ class StructureModule(nn.Module):
             self.dropout_rate,
         )
 
-        self.bb_update = BackboneUpdate(self.c_s)
+        self.bb_update = QuatRigid(self.c_s, full_quat=False)
 
         self.angle_resnet = AngleResnet(
             self.c_s,

openfold/utils/argparse.py

-from argparse import HelpFormatter
-from operator import attrgetter
-
-class ArgparseAlphabetizer(HelpFormatter):
-    """
-        Sorts the optional arguments of an argparse parser alphabetically
-    """
-
-    @staticmethod
-    def sort_actions(actions):
-        return sorted(actions, key=attrgetter("option_strings"))
-
-    # Formats the help message
-    def add_arguments(self, actions):
-        actions = ArgparseAlphabetizer.sort_actions(actions)
-        super(ArgparseAlphabetizer, self).add_arguments(actions)
-
-    # Formats the usage message
-    def add_usage(self, usage, actions, groups, prefix=None):
-        actions = ArgparseAlphabetizer.sort_actions(actions)
-        args = usage, actions, groups, prefix
-        super(ArgparseAlphabetizer, self).add_usage(*args)
-
-
-def remove_arguments(parser, args):
-    for arg in args:
-        for action in parser._actions:
-            opts = vars(action)["option_strings"]
-            if(arg in opts):
-                parser._handle_conflict_resolve(None, [(arg, action)])

train_openfold.py

@@ -31,7 +31,7 @@ from openfold.utils.callbacks import (
     EarlyStoppingVerbose,
 )
 from openfold.utils.exponential_moving_average import ExponentialMovingAverage
-from openfold.utils.argparse import remove_arguments
+from openfold.utils.argparse_utils import remove_arguments
 from openfold.utils.loss import AlphaFoldLoss, lddt_ca, compute_drmsd
 from openfold.utils.seed import seed_everything
 from openfold.utils.superimposition import superimpose