Merge branch 'master' into hetatm_parsing

Author: a-r-j

.requirements/base.in

@@ -2,13 +2,15 @@ pandas<2.0.0
 biopandas>=0.5.1
 biopython
 bioservices>=1.10.0
+cpdb-protein==0.2.0
+cython
 deepdiff
 loguru
 looseversion
 matplotlib>=3.4.3
 multipledispatch
 networkx
-numpy<1.24.0
+numpy
 pandas
 plotly
 pydantic

CHANGELOG.md

@@ -4,6 +4,8 @@
 * Fixes progress bar for `download_pdb_multiprocessing`. [#394](https://github.com/a-r-j/graphein/pull/394)
 * Add support for DSSP >4. Backwards compatibility is still supported. [#355](https://github.com/a-r-j/graphein/pull/355). Fixes [#353](https://github.com/a-r-j/graphein/issues/353).
 * Fixes bug where RSA features are missing from nodes with insertion codes. [#355](https://github.com/a-r-j/graphein/pull/355). Fixes [#354](https://github.com/a-r-j/graphein/issues/353).
+* Fix bug where the `deprotonate` argument is not wired up to `graphein.protein.graphs.construct_graphs`. [#375](https://github.com/a-r-j/graphein/pull/375)
+* Add missing modified residue `AYA` to constants [#390](https://github.com/a-r-j/graphein/pull/390)
 * Fix bug where the `deprotonate` argument is not wired up to `graphein.protein.graphs.construct_graphs` [#375](https://github.com/a-r-j/graphein/pull/375)
 * Fix cluster file loading bug in `pdb_data.py` [#396](https://github.com/a-r-j/graphein/pull/396)
 
@@ -80,6 +82,7 @@ https://github.com/a-r-j/graphein/pull/334
 
 #### Other Changes
 
+-   Uses [`cpdb`](https://github.com/a-r-j/CPDB) as default PDB file parser for improved performance. [#323](https://github.com/a-r-j/graphein/pull/323).
 -   Adds transform composition to FoldComp Dataset [#312](https://github.com/a-r-j/graphein/pull/312)
 -   Adds entry point for biopandas dataframes in `graphein.protein.tensor.io.protein_to_pyg`. [#310](https://github.com/a-r-j/graphein/pull/310)
 -   Adds support for `.ent` files to `graphein.protein.graphs.read_pdb_to_dataframe`. [#310](https://github.com/a-r-j/graphein/pull/310)

graphein/protein/graphs.py

@@ -15,6 +15,7 @@
 from pathlib import Path
 from typing import Any, Callable, Dict, List, Optional, Tuple, Union
 
+import cpdb
 import networkx as nx
 import numpy as np
 import pandas as pd
@@ -109,32 +110,41 @@ def read_pdb_to_dataframe(
             or path.endswith(".pdb.gz")
             or path.endswith(".ent")
         ):
-            atomic_df = PandasPdb().read_pdb(path)
+            atomic_df = cpdb.parse(path)
         elif path.endswith(".mmtf") or path.endswith(".mmtf.gz"):
             atomic_df = PandasMmtf().read_mmtf(path)
+            atomic_df = atomic_df.get_model(model_index)
+            atomic_df = pd.concat(
+                [atomic_df.df["ATOM"], atomic_df.df["HETATM"]]
+            )
         elif (
             path.endswith(".cif")
             or path.endswith(".cif.gz")
             or path.endswith(".mmcif")
             or path.endswith(".mmcif.gz")
         ):
             atomic_df = PandasMmcif().read_mmcif(path)
+            atomic_df = atomic_df.get_model(model_index)
+            atomic_df = atomic_df.convert_to_pandas_pdb()
+            atomic_df = pd.concat(
+                [atomic_df.df["ATOM"], atomic_df.df["HETATM"]]
+            )
         else:
             raise ValueError(
                 f"File {path} must be either .pdb(.gz), .mmtf(.gz), .(mm)cif(.gz) or .ent, not {path.split('.')[-1]}"
             )
     elif uniprot_id is not None:
-        atomic_df = PandasPdb().fetch_pdb(
-            uniprot_id=uniprot_id, source="alphafold2-v3"
-        )
+        atomic_df = cpdb.parse(uniprot_id=uniprot_id)
     else:
-        atomic_df = PandasPdb().fetch_pdb(pdb_code)
-    atomic_df = atomic_df.get_model(model_index)
-    if len(atomic_df.df["ATOM"]) == 0:
+        atomic_df = cpdb.parse(pdb_code=pdb_code)
+
+    if "model_idx" in atomic_df.columns:
+        atomic_df = atomic_df.loc[atomic_df["model_idx"] == model_index]
+
+    if len(atomic_df) == 0:
         raise ValueError(f"No model found for index: {model_index}")
-    if isinstance(atomic_df, PandasMmcif):
-        atomic_df = atomic_df.convert_to_pandas_pdb()
-    return pd.concat([atomic_df.df["ATOM"], atomic_df.df["HETATM"]])
+
+    return atomic_df
 
 
 def label_node_id(
@@ -285,7 +295,7 @@ def remove_alt_locs(
     # Unsort
     if keep in ["max_occupancy", "min_occupancy"]:
         df = df.sort_index()
-
+    df = df.reset_index(drop=True)
     return df
 
 

graphein/protein/resi_atoms.py

@@ -463,6 +463,7 @@
     "ABA",
     "ACE",
     "AIB",
+    "AYA",
     "BMT",
     "BOC",
     "CBX",
@@ -535,6 +536,7 @@
     "ABA",
     "ACE",
     "AIB",
+    "AYA",
     "ALA",
     "ARG",
     "ASN",
@@ -639,6 +641,7 @@
     "ASN": "N",
     "ASP": "D",
     "ASX": "B",
+    "AYA": "A",
     "BMT": "T",
     "BOC": "X",
     "CBX": "X",
@@ -795,6 +798,7 @@
     "ABA": "ALA",
     "ACE": "-",
     "AIB": "ALA",
+    "AYA": "ALA",
     "BMT": "THR",
     "BOC": "-",
     "CBX": "-",

graphein/protein/utils.py

@@ -16,6 +16,7 @@
 from urllib.request import urlopen
 
 import networkx as nx
+import numpy as np
 import pandas as pd
 import requests
 import wget
@@ -25,6 +26,30 @@
 
 from .resi_atoms import BACKBONE_ATOMS, RESI_THREE_TO_1
 
+pdb_df_columns = [
+    "record_name",
+    "atom_number",
+    "blank_1",
+    "atom_name",
+    "alt_loc",
+    "residue_name",
+    "blank_2",
+    "chain_id",
+    "residue_number",
+    "insertion",
+    "blank_3",
+    "x_coord",
+    "y_coord",
+    "z_coord",
+    "occupancy",
+    "b_factor",
+    "blank_4",
+    "segment_id",
+    "element_symbol",
+    "charge",
+    "line_idx",
+]
+
 
 class ProteinGraphConfigurationError(Exception):
     """
@@ -418,12 +443,27 @@ def save_graph_to_pdb(
     :type gz: bool
     """
     ppd = PandasPdb()
-    atom_df = filter_dataframe(
-        g.graph["pdb_df"], "record_name", ["ATOM"], boolean=True
-    )
-    hetatm_df = filter_dataframe(
-        g.graph["pdb_df"], "record_name", ["HETATM"], boolean=True
-    )
+
+    df = g.graph["pdb_df"].copy()
+    # format charge correctly
+    df.charge = pd.to_numeric(df.charge, errors="coerce")
+
+    # Add blank columns
+    blank_cols = [
+        "blank_1",
+        "blank_2",
+        "blank_3",
+        "blank_4",
+        "segment_id",
+    ]
+    for col in blank_cols:
+        if col not in df.columns:
+            df[col] = ""
+    df["line_idx"] = list(range(1, len(df) + 1))
+    df = df[pdb_df_columns]
+    atom_df = filter_dataframe(df, "record_name", ["ATOM"], boolean=True)
+    hetatm_df = filter_dataframe(df, "record_name", ["HETATM"], boolean=True)
+
     if atoms:
         ppd.df["ATOM"] = atom_df
     if hetatms:
@@ -448,9 +488,22 @@ def save_pdb_df_to_pdb(
     :param gz: Whether to gzip the file. Defaults to ``False``.
     :type gz: bool
     """
+    df = df.copy()
+    # format charge correctly
+    df.charge = pd.to_numeric(df.charge, errors="coerce")
+    df.alt_loc = df.alt_loc.fillna(" ")
+    blank_cols = ["blank_1", "blank_2", "blank_3", "blank_4", "segment_id"]
+    for col in blank_cols:
+        if col not in df.columns:
+            df[col] = ""
+    df["line_idx"] = list(range(1, len(df) + 1))
+    df = df[pdb_df_columns]
+
     atom_df = filter_dataframe(df, "record_name", ["ATOM"], boolean=True)
     hetatm_df = filter_dataframe(df, "record_name", ["HETATM"], boolean=True)
+
     ppd = PandasPdb()
+
     if atoms:
         ppd.df["ATOM"] = atom_df
     if hetatms:
@@ -481,12 +534,21 @@ def save_rgroup_df_to_pdb(
     :type gz: bool
     """
     ppd = PandasPdb()
-    atom_df = filter_dataframe(
-        g.graph["rgroup_df"], "record_name", ["ATOM"], boolean=True
-    )
-    hetatm_df = filter_dataframe(
-        g.graph["rgroup_df"], "record_name", ["HETATM"], boolean=True
-    )
+    df = g.graph["rgroup_df"].copy()
+
+    # format charge correctly
+    df.charge = pd.to_numeric(df.charge, errors="coerce")
+
+    blank_cols = ["blank_1", "blank_2", "blank_3", "blank_4", "segment_id"]
+    for col in blank_cols:
+        if col not in df.columns:
+            df[col] = [""] * len(df)
+    df["line_idx"] = list(range(1, len(df) + 1))
+    df = df[pdb_df_columns]
+
+    atom_df = filter_dataframe(df, "record_name", ["ATOM"], boolean=True)
+    hetatm_df = filter_dataframe(df, "record_name", ["HETATM"], boolean=True)
+
     if atoms:
         ppd.df["ATOM"] = atom_df
     if hetatms:

tests/protein/tensor/test_data.py

@@ -16,5 +16,5 @@
 def test_save_and_load_protein():
     a = Protein().from_pdb_code("4hhb")
     torch.save(a, "4hhb.pt")
-    b = torch.load("4hhb.pt")
+    b = torch.load("4hhb.pt", weights_only=False)
     assert a == b

tests/protein/tensor/test_reconstruction.py

@@ -30,4 +30,3 @@ def test_dist_mat_to_coords():
         assert torch.allclose(d, torch.cdist(X, X), atol=1e-4)
         X_aligned = kabsch(X, coords)
         assert torch.allclose(coords, X_aligned, atol=1e-4)
-        return coords, X, X_aligned

tests/protein/test_graphs.py

@@ -439,7 +439,10 @@ def test_alt_loc_exclusion():
     ):
         config.alt_locs = opt
         g = construct_graph(config=config, pdb_code="2VVI")
-        assert np.array_equal(g.nodes[node_id]["coords"], expected_coords)
+        assert np.array_equal(
+            g.nodes[node_id]["coords"],
+            np.array(expected_coords, dtype=np.float32),
+        )
 
 
 def test_alt_loc_inclusion():

tests/protein/test_utils.py

@@ -27,11 +27,24 @@ def test_save_graph_to_pdb():
     # Check file exists
     assert os.path.isfile("/tmp/test_graph.pdb")
 
-    # Check for equivalence between saved and existing DFs.
-    # We drop the line_idx columns as these will be renumbered
+    graph_df = (
+        g.graph["pdb_df"]
+        .drop(
+            [
+                "node_id",
+                "residue_id",
+            ],
+            axis=1,
+        )
+        .reset_index(drop=True)
+    )
+
+    a.reset_index(drop=True, inplace=True)
+    a = a[graph_df.columns]  # Reorder columns
+
     assert_frame_equal(
-        a.drop(["line_idx"], axis=1),
-        g.graph["pdb_df"].drop(["line_idx", "node_id", "residue_id"], axis=1),
+        a,
+        graph_df,
     )
     h = construct_graph(path="/tmp/test_graph.pdb")
 
@@ -48,10 +61,17 @@ def test_save_pdb_df_to_pdb():
     # Check file exists
     assert os.path.isfile("/tmp/test_graph.pdb")
 
-    # We drop the line_idx columns as these will be renumbered
     assert_frame_equal(
-        a.drop(["line_idx"], axis=1),
-        g.graph["pdb_df"].drop(["line_idx", "node_id", "residue_id"], axis=1),
+        a,
+        g.graph["pdb_df"]
+        .drop(
+            [
+                "node_id",
+                "residue_id",
+            ],
+            axis=1,
+        )
+        .reset_index(drop=True),
     )
 
     # Now check for raw, unprocessed DF
@@ -73,10 +93,10 @@ def test_save_rgroup_df_to_pdb():
 
     # We drop the line_idx columns as these will be renumbered
     assert_frame_equal(
-        a.drop(["line_idx"], axis=1),
+        a,
         filter_dataframe(
             g.graph["rgroup_df"], "record_name", ["HETATM"], False
-        ).drop(["line_idx", "node_id", "residue_id"], axis=1),
+        ).drop(["node_id", "residue_id"], axis=1),
     )