add protein transforms

torchdrug/transforms/__init__.py

@@ -1,6 +1,7 @@
-from .transform import TargetNormalize, RemapAtomType, RandomBFSOrder, Shuffle, VirtualNode, VirtualAtom, Compose
+from .transform import NormalizeTarget, RemapAtomType, RandomBFSOrder, Shuffle, VirtualNode, \
+        VirtualAtom, TruncateProtein, ProteinView, Compose
 
 __all__ = [
-    "TargetNormalize", "RemapAtomType", "RandomBFSOrder", "Shuffle",
-    "VirtualNode", "VirtualAtom", "Compose",
+    "NormalizeTarget", "RemapAtomType", "RandomBFSOrder", "Shuffle",
+    "VirtualNode", "VirtualAtom", "TruncateProtein", "ProteinView", "Compose",
 ]

torchdrug/transforms/transform.py

@@ -1,14 +1,19 @@
 import copy
 import logging
 from collections import deque
+from random import randint
 
 import torch
 
+from torchdrug import core
+from torchdrug.core import Registry as R
+
 
 logger = logging.getLogger(__name__)
 
 
-class TargetNormalize(object):
+@R.register("transforms.NormalizeTarget")
+class NormalizeTarget(core.Configurable):
     """
     Normalize the target values in a sample.
 
@@ -30,9 +35,11 @@ def __call__(self, item):
         return item
 
 
-class RemapAtomType(object):
+@R.register("transforms.RemapAtomType")
+class RemapAtomType(core.Configurable):
     """
     Map atom types to their index in a vocabulary. Atom types that don't present in the vocabulary are mapped to -1.
+
     Parameters:
         atom_types (array_like): vocabulary of atom types
     """
@@ -51,7 +58,8 @@ def __call__(self, item):
         return item
 
 
-class RandomBFSOrder(object):
+@R.register("transforms.RandomBFSOrder")
+class RandomBFSOrder(core.Configurable):
     """
     Order the nodes in a graph according to a random BFS order.
     """
@@ -81,9 +89,11 @@ def __call__(self, item):
         return item
 
 
-class Shuffle(object):
+@R.register("transforms.Shuffle")
+class Shuffle(core.Configurable):
     """
     Shuffle the order of nodes and edges in a graph.
+
     Parameters:
         shuffle_node (bool, optional): shuffle node order or not
         shuffle_edge (bool, optional): shuffle edge order or not
@@ -125,7 +135,8 @@ def transform_data(self, data, meta):
         return new_data
 
 
-class VirtualNode(object):
+@R.register("transforms.VirtualNode")
+class VirtualNode(core.Configurable):
     """
     Add a virtual node and connect it with every node in the graph.
 
@@ -199,9 +210,11 @@ def __call__(self, item):
         return item
 
 
-class VirtualAtom(VirtualNode):
+@R.register("transforms.VirtualAtom")
+class VirtualAtom(VirtualNode, core.Configurable):
     """
     Add a virtual atom and connect it with every atom in the molecule.
+
     Parameters:
         atom_type (int, optional): type of the virtual atom
         bond_type (int, optional): type of the virtual bonds
@@ -215,9 +228,73 @@ def __init__(self, atom_type=None, bond_type=None, node_feature=None, edge_featu
                                           edge_feature=edge_feature, atom_type=atom_type, **kwargs)
 
 
-class Compose(object):
+@R.register("transforms.TruncateProtein")
+class TruncateProtein(core.Configurable):
+    """
+    Truncate over long protein sequences into a fixed length.
+
+    Parameters:
+        max_length (int, optional): maximal length of the sequence. Truncate the sequence if it exceeds this limit.
+        random (bool, optional): truncate the sequence at a random position.
+            If not, truncate the suffix of the sequence.
+        keys (str or list of str, optional): keys for the items that require truncation in a sample
+    """
+
+    def __init__(self, max_length=None, random=False, keys="graph"):
+        self.truncate_length = max_length
+        self.random = random
+        if isinstance(keys, str):
+            keys = [keys]
+        self.keys = keys
+
+    def __call__(self, item):
+        new_item = item.copy()
+        for key in self.keys:
+            graph = item[key]
+            if graph.num_residue > self.truncate_length:
+                if self.random:
+                    start = randint(0, graph.num_residue - self.truncate_length)
+                else:
+                    start = 0
+                end = start + self.truncate_length
+                mask = torch.zeros(graph.num_residue, dtype=torch.bool, device=graph.device)
+                mask[start:end] = True
+                graph = graph.subresidue(mask)
+
+            new_item[key] = graph
+        return new_item
+
+
+@R.register("transforms.ProteinView")
+class ProteinView(core.Configurable):
+    """
+    Convert proteins to a specific view.
+
+    Parameters:
+        view (str): protein view. Can be ``atom`` or ``residue``.
+        keys (str or list of str, optional): keys for the items that require view change in a sample
+    """
+
+    def __init__(self, view, keys="graph"):
+        self.view = view
+        if isinstance(keys, str):
+            keys = [keys]
+        self.keys = keys
+
+    def __call__(self, item):
+        item = item.copy()
+        for key in self.keys:
+            graph = copy.copy(item[key])
+            graph.view = self.view
+            item[key] = graph
+        return item
+
+
+@R.register("transforms.Compose")
+class Compose(core.Configurable):
     """
     Compose a list of transforms into one.
+
     Parameters:
         transforms (list of callable): list of transforms
     """