pxmeter 0.1.2__tar.gz → 0.1.3__tar.gz

{pxmeter-0.1.2/pxmeter.egg-info → pxmeter-0.1.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pxmeter
-Version: 0.1.2
+Version: 0.1.3
 Summary: PXMeter is a comprehensive toolkit for evaluating the quality of         structures generated by biomolecular structure prediction models.
 Author: Bytedance Inc.
 Author-email: ai4s-bio@bytedance.com

{pxmeter-0.1.2 → pxmeter-0.1.3}/pxmeter/calc_metric.py

@@ -34,6 +34,7 @@ from pxmeter.configs.run_config import RUN_CONFIG
 from pxmeter.constants import IONS, LIGAND
 from pxmeter.data.ccd import get_ccd_mol_from_chain_atom_array
 from pxmeter.data.struct import Structure
+from pxmeter.metrics.clashes import check_clashes_by_vdw
 from pxmeter.metrics.lddt_metrics import LDDT
 from pxmeter.metrics.rmsd_metrics import RMSDMetrics
 
@@ -554,6 +555,16 @@ class MetricResult:
         meta_info_dict["ref_to_model_chain_mapping"] = chain_map
         meta_info_dict["ref_chain_info"] = cls._get_chain_info(ref_struct)
 
+        # Calculate clashes
+        if metric_config.calc_clashes:
+            clashes = check_clashes_by_vdw(
+                model_struct.atom_array,
+                vdw_scale_factor=metric_config.clashes.vdw_scale_factor,
+            )
+            complex_result_dict["clashes"] = len(
+                {x for a, b in clashes for x in (a, b)}
+            )
+
         # Calculate RMSD (if ligand and pocket specified in ref_features)
         if metric_config.calc_rmsd and interested_lig_label_asym_id:
             rmsd_metrics = RMSDMetrics(

{pxmeter-0.1.2 → pxmeter-0.1.3}/pxmeter/configs/run_config.py

@@ -23,6 +23,7 @@ RUN_CONFIG = ConfigDict(
             "enumerate_all_anchors": True,
         },
         "metric": {
+            "calc_clashes": True,
             "calc_lddt": True,
             "calc_dockq": True,
             "calc_rmsd": True,
@@ -32,6 +33,9 @@ RUN_CONFIG = ConfigDict(
                 "nucleotide_threshold": 30.0,
                 "non_nucleotide_threshold": 15.0,
             },
+            "clashes": {
+                "vdw_scale_factor": 0.5,
+            },
         },
     }
 )

{pxmeter-0.1.2 → pxmeter-0.1.3}/pxmeter/mapping.py

@@ -924,15 +924,28 @@ class MappingCIF:
         # This step will be change the res_id, res_name, atom_name in self.model_struct.atom_array
         self._align_model_lig_atom_to_ref(self.model_struct, model_to_ref_atom_mapping)
 
+        # Re-order model struct by res_id for each chain
+        order = []
+        for chain_id in np.unique(self.model_struct.uni_chain_id):
+            chain_mask = np.where(self.model_struct.uni_chain_id == chain_id)[0]
+            # Remove unmapped ligands
+            valid_chain_mask = chain_mask[
+                ~(
+                    (
+                        (self.model_struct.atom_array.res_name[chain_mask] == ".")
+                        & (self.model_struct.atom_array.atom_name[chain_mask] == ".")
+                    )
+                    | (
+                        self.model_struct.atom_array.res_id[chain_mask] < 0
+                    )  # -1 for unmapped residues
+                )
+            ]
+            res_ids = self.model_struct.atom_array.res_id[valid_chain_mask]
+            order.extend(valid_chain_mask[np.argsort(res_ids)])
+
         # Remove unmapped ligand of model and reset unique atom id
         self.model_struct = self.model_struct.select_substructure(
-            ~(
-                (
-                    (self.model_struct.atom_array.res_name == ".")
-                    & (self.model_struct.atom_array.atom_name == ".")
-                )
-                | (self.model_struct.atom_array.res_id < 0)  # -1 for unmapped residues
-            ),
+            order,
             reset_uni_id=True,
         )
 

pxmeter-0.1.3/pxmeter/metrics/clashes.py

@@ -0,0 +1,88 @@
+# Copyright 2025 ByteDance and/or its affiliates.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+from typing import Sequence
+
+import numpy as np
+from biotite.structure import AtomArray
+from biotite.structure.info.radii import vdw_radius_single
+from scipy.spatial import KDTree
+
+
+def check_clashes_by_vdw(
+    atom_array: AtomArray,
+    query_mask: Sequence[bool] = None,
+    vdw_scale_factor: float = 0.5,
+) -> list[tuple[int, int]]:
+    """
+    Check clashes between atoms in the given atom array.
+
+    Args:
+        atom_array (AtomArray): The atom array to check for clashes.
+        query_mask (bool, optional): A boolean mask to select atoms to check for clashes.
+                   If None, all atoms are checked.
+        vdw_scale_factor (float, optional): The scale factor to apply to the Van der Waals radii.
+                         Defaults to 0.5.
+
+    Returns:
+        list[tuple[int, int]]: A list of tuples representing the indices of atoms that are in clash.
+    """
+    if query_mask is None:
+        # query all atoms
+        query_mask = np.ones(len(atom_array), dtype=bool)
+    elif not np.any(query_mask):
+        # no query atoms, return empty list
+        return []
+
+    if query_mask is None:
+        query_mask = np.ones(len(atom_array), dtype=bool)
+
+    query_idx_in_ref = np.where(query_mask)[0]
+
+    vdw_radii = np.array([vdw_radius_single(e) for e in atom_array.element])
+    query_vdw_radii = vdw_radii[query_mask]
+
+    clashes = []
+    query_tree = KDTree(atom_array.coord)
+    for query_idx, nbs_idx in enumerate(
+        query_tree.query_ball_point(atom_array.coord[query_mask], r=3.0)
+    ):
+        query_bonds, _query_bond_types = atom_array.bonds.get_bonds(
+            query_idx_in_ref[query_idx]
+        )
+        query_vdw = query_vdw_radii[query_idx]
+        if query_vdw is None:
+            # undefined vdw for elem, use 1.7 as "C"
+            query_vdw = vdw_radius_single("C")
+
+        for nb_idx in nbs_idx:
+            if query_idx_in_ref[query_idx] == nb_idx:
+                # clash with self
+                continue
+
+            if nb_idx in query_bonds:
+                # clash with bonded atoms
+                continue
+
+            nb_vdw = vdw_radii[nb_idx]
+            if nb_vdw is None:
+                # undefined vdw for elem, use 1.7 as "C"
+                nb_vdw = vdw_radius_single("C")
+
+            dist = np.linalg.norm(
+                atom_array.coord[query_mask][query_idx] - atom_array.coord[nb_idx]
+            )
+            if dist < vdw_scale_factor * (query_vdw + nb_vdw):
+                clashes.append((query_idx_in_ref[query_idx], nb_idx))
+    return clashes

{pxmeter-0.1.2 → pxmeter-0.1.3/pxmeter.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pxmeter
-Version: 0.1.2
+Version: 0.1.3
 Summary: PXMeter is a comprehensive toolkit for evaluating the quality of         structures generated by biomolecular structure prediction models.
 Author: Bytedance Inc.
 Author-email: ai4s-bio@bytedance.com

{pxmeter-0.1.2 → pxmeter-0.1.3}/pxmeter.egg-info/SOURCES.txt

@@ -26,6 +26,7 @@ pxmeter/data/struct.py
 pxmeter/data/utils.py
 pxmeter/data/writer.py
 pxmeter/metrics/__init__.py
+pxmeter/metrics/clashes.py
 pxmeter/metrics/lddt_metrics.py
 pxmeter/metrics/rmsd.py
 pxmeter/metrics/rmsd_metrics.py

{pxmeter-0.1.2 → pxmeter-0.1.3}/setup.py

@@ -20,7 +20,7 @@ with open("requirements.txt") as f:
 setup(
     name="pxmeter",
     python_requires=">=3.11",
-    version="0.1.2",
+    version="0.1.3",
     description="PXMeter is a comprehensive toolkit for evaluating the quality of \
         structures generated by biomolecular structure prediction models.",
     author="Bytedance Inc.",