stcrpy 1.0.5__tar.gz → 1.0.6__tar.gz

{stcrpy-1.0.5 → stcrpy-1.0.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: stcrpy
-Version: 1.0.5
+Version: 1.0.6
 Summary: Set of methods to parse, annotate, and calculate features of TCR structures
 Maintainer-email: Nele Quast <quast@stats.ox.ac.uk>
 Requires-Python: >=3.10
@@ -12,6 +12,7 @@ Requires-Dist: numpy==1.26.4
 Requires-Dist: lxml
 Requires-Dist: openbabel-wheel==3.1.1.21
 Requires-Dist: rdkit
+Requires-Dist: pyhmmer==0.11.4
 Requires-Dist: anarci-mhc
 Requires-Dist: pandas
 Requires-Dist: matplotlib
@@ -42,7 +43,7 @@ Please feel free to reach out with any comments or feedback.
 
 Under review, please cite: 
 
-**Quast, N. , Deane, C., & Raybould, M. (2025). STCRpy: a software suite for TCR:pMHC structure parsing, interaction profiling, and machine learning dataset preparation. BioRxiv. https://doi.org/10.1101/2025.04.25.650667**
+**Quast, N. , Deane, C., & Raybould, M. (2025). STCRpy: a software suite for TCR:pMHC structure parsing, interaction profiling, and machine learning dataset preparation. Bioinformatics. [https://doi.org/10.1093/bioinformatics/btaf566](https://doi.org/10.1093/bioinformatics/btaf566)**
 
 <img src="./stcrpy_main_fig.png" alt="drawing" width="1500"/>
 

{stcrpy-1.0.5 → stcrpy-1.0.6}/README.md

@@ -15,7 +15,7 @@ Please feel free to reach out with any comments or feedback.
 
 Under review, please cite: 
 
-**Quast, N. , Deane, C., & Raybould, M. (2025). STCRpy: a software suite for TCR:pMHC structure parsing, interaction profiling, and machine learning dataset preparation. BioRxiv. https://doi.org/10.1101/2025.04.25.650667**
+**Quast, N. , Deane, C., & Raybould, M. (2025). STCRpy: a software suite for TCR:pMHC structure parsing, interaction profiling, and machine learning dataset preparation. Bioinformatics. [https://doi.org/10.1093/bioinformatics/btaf566](https://doi.org/10.1093/bioinformatics/btaf566)**
 
 <img src="./stcrpy_main_fig.png" alt="drawing" width="1500"/>
 

{stcrpy-1.0.5 → stcrpy-1.0.6}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "stcrpy"
-version = "1.0.5"
+version = "1.0.6"
 description = "Set of methods to parse, annotate, and calculate features of TCR structures"
 readme = "README.md"
 license-files = [
@@ -17,10 +17,11 @@ maintainers = [
 requires-python = ">=3.10"
 dependencies = [
   "biopython",
-  "numpy==1.26.4",
+  "numpy==1.26.4",      # required by DockQ
   "lxml",
   "openbabel-wheel==3.1.1.21",
   "rdkit",
+  "pyhmmer==0.11.4",        # fix pyhmmer version to prevent string encoding bu. TODO:fix this within anarci-mhc directly and redeploy
   "anarci-mhc",
   "pandas",
   "matplotlib",

{stcrpy-1.0.5 → stcrpy-1.0.6}/stcrpy/tcr_interactions/TCRInteractionProfiler.py

@@ -8,6 +8,7 @@ from ..tcr_processing.TCRParser import TCRParser
 try:
     import plip
     from plip.basic.remote import VisualizerData
+    from plip.visualization.visualize import visualize_in_pymol
 
 except ModuleNotFoundError as e:
     if "pymol" in str(e):
@@ -413,7 +414,8 @@ class TCRInteractionProfiler:
             heatmap_b[pair[0][1], ligand_number_mapping[int(pair[1][1])]] = (
                 heatmap_b[pair[0][1], ligand_number_mapping[int(pair[1][1])]] + 1
             )
-        ax_beta.imshow(heatmap_b.T, cmap="PuRd")
+
+        im_beta = ax_beta.imshow(heatmap_b.T, cmap="PuRd")
         for i in plot_index:
             ax_beta.axhline(y=i - 0.5, color="blue", linewidth=1)
             ax_beta.axhline(y=i + 0.5, color="blue", linewidth=1)
@@ -427,6 +429,11 @@ class TCRInteractionProfiler:
             ax_beta.set_xticks([], [], rotation=90)
             ax_beta.set_yticks([], [])
 
+        cbar = fig.colorbar(
+            im_beta, ax=[ax_alpha, ax_beta], orientation="vertical", shrink=0.8
+        )
+        cbar.set_label("Interaction count", rotation=270, labelpad=15)
+
         if save_as is not None:
             fig.savefig(save_as, bbox_inches="tight", dpi=200)
 

{stcrpy-1.0.5 → stcrpy-1.0.6}/stcrpy/tcr_processing/TCRParser.py

@@ -1130,9 +1130,11 @@ class TCRParser(PDBParser, MMCIFParser):
             and len(mhc_complexes) > 0
         ):  # check if all TCRs have been paired if MHC is present.
             # try searching for symmetry mates
-            symmetry_mates = self._generate_symmetry_mates()
-            mhc_complexes.extend([m for t in symmetry_mates for m in t.get_MHCs()])
-
+            try:
+                symmetry_mates = self._generate_symmetry_mates()
+                mhc_complexes.extend([m for t in symmetry_mates for m in t.get_MHCs()])
+            except Exception as e:
+                warnings.warn(f"Symmetry mate generation failed with: {str(e)}")
             (
                 model,
                 tcell_receptors,

{stcrpy-1.0.5 → stcrpy-1.0.6}/stcrpy/tcr_processing/utils/symmetry_mates.py

@@ -35,33 +35,39 @@ def get_symmetry_mates(filename):
     tcp = TCRParser()
     pdp = PDBParser(QUIET=True)
     pdbio = PDBIO()
-    with tempfile.TemporaryDirectory() as tmpdir:
-        for i, obj in enumerate(cmd.get_object_list()):
-            fn = os.path.join(tmpdir, f"{obj_name}_symmetry_mate_{i}.pdb")
-            cmd.save(fn, obj)
-            symmetry_mate = pdp.get_structure("tmp", fn)
-            if i == 0:
-                chain_ids = generate_chain_id_list(
-                    len(list(symmetry_mate.get_chains()) * len(cmd.get_object_list()))
-                )
-                for c in symmetry_mate.get_chains():
-                    chain_ids.remove(
-                        c.id
-                    )  # remove all chain ids of the original structure
-            if i > 0:  # Skip the original structure
-                # rename chain ids, this cannot be done directly to TCR structure without breaking the TCR and MHC chain assignments.
-                for chain in reversed(list(symmetry_mate.get_chains())):
-                    symmetry_mate[0].detach_child(chain.id)
-                    new_id = chain_ids.pop(0)
-                    chain.id = new_id
-                    symmetry_mate[0].add(chain)
-                pdbio.set_structure(symmetry_mate)
-                pdbio.save(fn)
+    try:
+        with tempfile.TemporaryDirectory() as tmpdir:
+            for i, obj in enumerate(cmd.get_object_list()):
+                fn = os.path.join(tmpdir, f"{obj_name}_symmetry_mate_{i}.pdb")
+                cmd.save(fn, obj)
+                symmetry_mate = pdp.get_structure("tmp", fn)
+                if i == 0:
+                    chain_ids = generate_chain_id_list(
+                        len(
+                            list(symmetry_mate.get_chains())
+                            * len(cmd.get_object_list())
+                        )
+                    )
+                    for c in symmetry_mate.get_chains():
+                        chain_ids.remove(
+                            c.id
+                        )  # remove all chain ids of the original structure
+                if i > 0:  # Skip the original structure
+                    # rename chain ids, this cannot be done directly to TCR structure without breaking the TCR and MHC chain assignments.
+                    for chain in reversed(list(symmetry_mate.get_chains())):
+                        symmetry_mate[0].detach_child(chain.id)
+                        new_id = chain_ids.pop(0)
+                        chain.id = new_id
+                        symmetry_mate[0].add(chain)
+                    pdbio.set_structure(symmetry_mate)
+                    pdbio.save(fn)
 
-                symmetry_mate = tcp.get_tcr_structure(
-                    f"{obj_name}_symmetry_{i}", fn, include_symmetry_mates=False
-                )
-                tcr_symmetry_mates.append(symmetry_mate)
+                    symmetry_mate = tcp.get_tcr_structure(
+                        f"{obj_name}_symmetry_{i}", fn, include_symmetry_mates=False
+                    )
+                    tcr_symmetry_mates.append(symmetry_mate)
+    except Exception as e:
+        warnings.warn(f"Symmetry mate generation failed with: {str(e)}")
 
     # clean up the pymol cmd space
     for obj in cmd.get_object_list():

{stcrpy-1.0.5 → stcrpy-1.0.6}/stcrpy.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: stcrpy
-Version: 1.0.5
+Version: 1.0.6
 Summary: Set of methods to parse, annotate, and calculate features of TCR structures
 Maintainer-email: Nele Quast <quast@stats.ox.ac.uk>
 Requires-Python: >=3.10
@@ -12,6 +12,7 @@ Requires-Dist: numpy==1.26.4
 Requires-Dist: lxml
 Requires-Dist: openbabel-wheel==3.1.1.21
 Requires-Dist: rdkit
+Requires-Dist: pyhmmer==0.11.4
 Requires-Dist: anarci-mhc
 Requires-Dist: pandas
 Requires-Dist: matplotlib
@@ -42,7 +43,7 @@ Please feel free to reach out with any comments or feedback.
 
 Under review, please cite: 
 
-**Quast, N. , Deane, C., & Raybould, M. (2025). STCRpy: a software suite for TCR:pMHC structure parsing, interaction profiling, and machine learning dataset preparation. BioRxiv. https://doi.org/10.1101/2025.04.25.650667**
+**Quast, N. , Deane, C., & Raybould, M. (2025). STCRpy: a software suite for TCR:pMHC structure parsing, interaction profiling, and machine learning dataset preparation. Bioinformatics. [https://doi.org/10.1093/bioinformatics/btaf566](https://doi.org/10.1093/bioinformatics/btaf566)**
 
 <img src="./stcrpy_main_fig.png" alt="drawing" width="1500"/>
 

{stcrpy-1.0.5 → stcrpy-1.0.6}/stcrpy.egg-info/SOURCES.txt

@@ -80,7 +80,6 @@ stcrpy/tcr_processing/utils/symmetry_mates.py
 stcrpy/utils/__init__.py
 stcrpy/utils/error_stream.py
 test/test_annotations.py
-test/test_symmetry_mates.py
 test/test_tcr_datasets.py
 test/test_tcr_formats.py
 test/test_tcr_geometry.py

{stcrpy-1.0.5 → stcrpy-1.0.6}/stcrpy.egg-info/requires.txt

@@ -3,6 +3,7 @@ numpy==1.26.4
 lxml
 openbabel-wheel==3.1.1.21
 rdkit
+pyhmmer==0.11.4
 anarci-mhc
 pandas
 matplotlib

{stcrpy-1.0.5 → stcrpy-1.0.6}/test/test_tcr_datasets.py

@@ -22,13 +22,13 @@ class TestTCRDatasets(unittest.TestCase):
         tcr = stcrpy.fetch_TCRs("8gvb")[0]
         graph_constructor.build_graph(tcr)
 
-    def test_TCRGraphDataset(self):
-        dataset = TCRGraphDataset(
-            root="./test_files/TCRGraphDataset_test_files",
-            data_paths="./test_files/TCRGraphDataset_test_files/raw_files",
-            force_reload=True,
-        )
-        print(dataset)
-        for i in range(len(dataset)):
-            datapoint = dataset[i]
-            print(datapoint)
+    # def test_TCRGraphDataset(self):
+    #     dataset = TCRGraphDataset(
+    #         root="./test_files/TCRGraphDataset_test_files",
+    #         data_paths="./test_files/TCRGraphDataset_test_files/raw_files",
+    #         force_reload=True,
+    #     )
+    #     print(dataset)
+    #     for i in range(len(dataset)):
+    #         datapoint = dataset[i]
+    #         print(datapoint)

stcrpy-1.0.6/test/test_tcr_formats.py

@@ -0,0 +1,79 @@
+import unittest
+import glob
+import os
+
+import stcrpy.tcr_processing
+
+
+class TestTCRFormats(unittest.TestCase):
+    def test_tcr_to_haddock(self):
+        import stcrpy
+
+        tcrs = stcrpy.load_TCRs(
+            glob.glob("./test_files/TCRParser_test_files/*.pdb")
+        ) + stcrpy.load_TCRs(glob.glob("./test_files/TCRParser_test_files/*.cif"))
+
+        from stcrpy.tcr_formats import tcr_haddock
+
+        haddock_formatter = tcr_haddock.HADDOCKFormatter("./test_files/out/haddock/")
+        for tcr in tcrs:
+            if tcr is not None:
+                haddock_formatter.tcr_to_haddock(tcr)
+
+    def test_pMHC_to_haddock(self):
+        import stcrpy
+
+        tcrs = stcrpy.load_TCRs(
+            glob.glob("./test_files/TCRParser_test_files/*.pdb")
+        ) + stcrpy.load_TCRs(glob.glob("./test_files/TCRParser_test_files/*.cif"))
+
+        from stcrpy.tcr_formats import tcr_haddock
+
+        haddock_formatter = tcr_haddock.HADDOCKFormatter(
+            save_dir="./test_files/out/haddock/"
+        )
+        for tcr in tcrs:
+            if (
+                tcr is not None
+                and len(tcr.get_MHC()) > 0
+                and len(tcr.antigen) > 0
+                and isinstance(tcr.antigen[0], stcrpy.tcr_processing.AGchain.AGchain)
+            ):
+                haddock_formatter.pMHC_to_haddock(tcr.get_MHC()[0], tcr.antigen)
+
+    # def test_from_haddock_to_TCR_pMHC(self):
+    #     import stcrpy
+    #     from stcrpy.tcr_formats import tcr_haddock
+
+    #     haddock_results_parser = tcr_haddock.HADDOCKResultsParser(
+    #         haddock_results_dir="./test_files/TCRHaddock_test_files/387937-tcr_6eqa_mel5_bulged",
+    #         tcr_renumbering_file="./test_files/TCRHaddock_test_files/6eqa_TCR_haddock_renumbering.txt",
+    #         pmhc_renumbering_file="./test_files/TCRHaddock_test_files/6eqa_pMHC_haddock_renumbering.txt",
+    #     )
+
+    #     for renumbered_file_path in glob.glob(
+    #         "./test_files/TCRHaddock_test_files/haddock_output/renumbered_complex*.pdb"
+    #     ):
+    #         os.remove(renumbered_file_path)
+
+    #     haddock_results_parser.renumber_all_haddock_predictions()
+    #     for file_path in glob.glob(
+    #         "./test_files/TCRHaddock_test_files/haddock_output/complex*.pdb"
+    #     ):
+    #         renumbered_file_path = (
+    #             file_path.split("complex")[0]
+    #             + "renumbered_complex"
+    #             + file_path.split("complex")[1]
+    #         )
+    #         assert os.path.exists(renumbered_file_path)
+
+    # def test_get_haddock_scores(self):
+    #     import stcrpy
+    #     from stcrpy.tcr_formats import tcr_haddock
+
+    #     haddock_results_parser = tcr_haddock.HADDOCKResultsParser(
+    #         haddock_results_dir="./test_files/TCRHaddock_test_files/387937-tcr_6eqa_mel5_bulged",
+    #     )
+
+    #     scores = haddock_results_parser.get_haddock_scores()
+    #     assert len(scores) == 200

stcrpy-1.0.6/test/test_tcr_geometry.py

@@ -0,0 +1,260 @@
+import unittest
+import glob
+import numpy as np
+
+import stcrpy
+from stcrpy.tcr_processing import TCRParser
+from stcrpy.tcr_geometry import TCRDock, TCRCoM, TCRGeom
+
+
+class TestTCRGeometry(unittest.TestCase):
+    def test_TCRDock_init(self):
+        tcr = stcrpy.fetch_TCRs("5hyj")
+        [TCRDock.TCRDock(x) for x in tcr]
+
+    def test_calculate_docking_angle_5hyj(self):
+        tcr = stcrpy.fetch_TCRs("5hyj")
+
+        tcr_docks = [TCRDock.TCRDock(x) for x in tcr]
+        assert all(
+            [
+                x.calculate_docking_angle() < 50.0
+                and x.calculate_docking_angle() > 40.0
+                for x in tcr_docks
+            ]
+        )
+
+    # def test_calculate_docking_angle_7l1d(self):
+    #     parser = TCRParser.TCRParser()
+    #     pdb_file = "./test_files/7l1d.pdb"
+    #     tcr = parser.get_tcr_structure("test", pdb_file)
+    #     tcr = stcrpy.fetch_TCRs("7l1d")
+
+    #     tcr_docks = [TCRDock.TCRDock(x) for x in tcr.get_TCRs()]
+    #     assert all(
+    #         [
+    #             x.calculate_docking_angle() < 50.0
+    #             and x.calculate_docking_angle() > 40.0
+    #             for x in tcr_docks
+    #         ]
+    #     )
+
+    # def test_calculate_docking_angle_7rrg(self):
+    #     # parser = TCRParser.TCRParser()
+    #     # pdb_file = "./test_files/7rrg.pdb"
+    #     # tcr = parser.get_tcr_structure("test", pdb_file)
+    #     tcr = stcrpy.fetch_TCRs("7rrg")
+
+    #     tcr_docks = [TCRDock.TCRDock(x) for x in tcr]
+    #     angles = [x.calculate_docking_angle() for x in tcr_docks]
+    #     print(angles)
+    #     assert all(
+    #         [
+    #             x.calculate_docking_angle() < 80.0
+    #             and x.calculate_docking_angle() > 70.0
+    #             for x in tcr_docks
+    #         ]
+    #     )
+
+    def test_calculate_docking_angle_of_docks(self):
+        parser = TCRParser.TCRParser()
+        dock_pdb_files = glob.glob(
+            "./test_files/TCRHaddock_test_files/predictions/renumbered_complex*.pdb"
+        )
+        dock_pdb_files.sort()
+        for pdb_file in dock_pdb_files:
+            tcr = parser.get_tcr_structure("test", pdb_file)
+            [TCRDock.TCRDock(x) for x in tcr.get_TCRs()]
+
+    # def test_docking_angle_reverse_docks(self):
+    #     parser = TCRParser.TCRParser()
+    #     reverse_dock_108 = "./test_files/aligned_complex_108.pdb"
+    #     dock_63 = "./test_files/aligned_complex_63.pdb"
+    #     dock_pdb_files = [dock_63, reverse_dock_108]
+    #     docking_angles = []
+    #     for pdb_file in dock_pdb_files:
+    #         tcr = parser.get_tcr_structure("test", pdb_file)
+
+    #         tcr_docks = [TCRDock.TCRDock(x) for x in tcr.get_TCRs()]
+    #         docking_angles.append(tcr_docks[0].calculate_docking_angle())
+
+    #     print(docking_angles)
+
+    # def test_MH1_TCRCoM(self):
+    #     parser = TCRParser.TCRParser()
+    #     pdb_file = "./test_files/4nhu.pdb"
+    #     tcr_structure = parser.get_tcr_structure("test", pdb_file)
+    #     tcr_com = TCRCoM.MHCI_TCRCoM()
+    #     # TEST DEPRECATED
+    #     # for tcr in tcr_structure.get_TCRs():
+    #     #     r, theta, phi = tcr_com.calculate_geometry(
+    #     #         tcr,
+    #     #         save_aligned_as=f"./test_files/out/aligned_test_{tcr.id}.pdb",
+    #     #     )
+    #     #     print(r, theta, phi)
+    #     # pdb_file = "./stcrpy/stcrpy/tcr_geometry/reference_data/dock_reference_1_imgt_numbered.pdb"
+    #     # tcr_structure = parser.get_tcr_structure("test", pdb_file)
+    #     # tcr_com = TCRCoM.MHCI_TCRCoM()
+    #     # for tcr in tcr_structure.get_TCRs():
+    #     #     r, theta, phi = tcr_com.calculate_geometry(
+    #     #         tcr,
+    #     #         save_aligned_as=f"./test_files/out/aligned_test_dock_ref_mhcI_{tcr.id}.pdb",
+    #     #     )
+    #     #     print(r, theta, phi)
+
+    # def test_MH2_TCRCoM(self):
+    #     parser = TCRParser.TCRParser()
+    #     pdb_file = "./test_files/6r0e.cif"
+    #     tcr_structure = parser.get_tcr_structure("test", pdb_file)
+    #     tcr_com = TCRCoM.MHCII_TCRCoM()
+    #     # TEST DEPRECATED
+    #     # for tcr in tcr_structure.get_TCRs():
+    #     #     r, theta, phi = tcr_com.calculate_geometry(
+    #     #         tcr,
+    #     #         save_aligned_as=f"./test_files/out/aligned_test_{tcr.id}.pdb",
+    #     #     )
+
+    #     # pdb_file = (
+    #     #     "./stcrpy/stcrpy/tcr_geometry/include/dock_reference_2_imgt_numbered.pdb"
+    #     # )
+    #     # tcr_structure = parser.get_tcr_structure("test", pdb_file)
+    #     # tcr_com = TCRCoM.MHCII_TCRCoM()
+    #     # for tcr in tcr_structure.get_TCRs():
+    #     #     r, theta, phi = tcr_com.calculate_geometry(
+    #     #         tcr,
+    #     #         save_aligned_as=f"./test_files/out/aligned_test_dock_ref_mhcII_{tcr.id}.pdb",
+    #     #     )
+    #     #     print(r, theta, phi)
+
+    def testTCRGeom(self):
+        parser = TCRParser.TCRParser()
+        pdb_files = glob.glob("./test_files/TCRCoM_test_files/*.cif")
+        # 'TCRpy/test/test_files/TCRCoM_test_files/7sg0.cif')
+        for file in pdb_files:
+            file_id = file.split("/")[-1].split(".")[0]
+            print(file_id)
+            tcr = parser.get_tcr_structure(file_id, file)
+            for x in tcr.get_TCRs():
+                try:
+                    x.geometry = TCRGeom.TCRGeom(
+                        x,
+                        save_aligned_as=f"./test_files/out/{file_id}_aligned.pdb",
+                    )
+                    print(x.geometry)
+                except Exception as e:
+                    print(e)
+
+    # def test_TCR_geom_methods(self):
+    #     parser = TCRParser.TCRParser()
+    #     test_file = "./test_files/8gvb.cif"
+    #     tcr = list(parser.get_tcr_structure("8gvb", test_file).get_TCRs())[0]
+    #     geometry = tcr.calculate_docking_geometry()
+    #     assert "scanning_angle" in geometry
+
+    # def test_calculate_docking_angle_cys_method(self):
+    #     import stcrpy
+
+    #     pdb_files = [
+    #         "./test_files/5hyj.pdb",
+    #         "./test_files/7l1d.pdb",
+    #         "./test_files/7rrg.pdb",
+    #     ]
+    #     tcrs = stcrpy.load_TCRs(pdb_files)
+
+    #     true_scanning_angles = [
+    #         42.9581,
+    #         47.4101,
+    #         47.4101,
+    #         73.7909,
+    #     ]  # [5hyj, 7l1d, 7rrg] - repeat value is for TCR repeats in PDB file parsed as independent TCR structures
+    #     true_pitch_angles = [12.3062, 3.46555, 3.46555, 12.0141]
+
+    #     cys_crossing_angles = []
+    #     com_crossing_angles = []
+    #     for i, tcr in enumerate(tcrs):
+    #         cys_crossing_angles.append(tcr.get_scanning_angle(mode="cys"))
+    #         com_crossing_angles.append(tcr.get_scanning_angle(mode="com"))
+
+    #     self.assertTrue(
+    #         np.sum(
+    #             np.abs(
+    #                 np.asarray(cys_crossing_angles) - np.asarray(true_scanning_angles)
+    #             )
+    #         )
+    #         / len(cys_crossing_angles)
+    #         < 1.5
+    #     )
+
+    #     # pitch = tcr.get_pitch_angle()
+    #     # self.assertAlmostEqual(pitch, true_pitch_angles[i])
+
+    # def test_calculate_docking_angle_com_method(self):
+    #     import stcrpy
+
+    #     pdb_files = [
+    #         "./test_files/5hyj.pdb",
+    #         "./test_files/7l1d.pdb",
+    #         "./test_files/7rrg.pdb",
+    #     ]
+    #     tcrs = stcrpy.load_TCRs(pdb_files)
+
+    #     true_scanning_angles = [42.9581, 47.4101, 73.7909]  # [5hyj, 7l1d, 7rrg]
+    #     true_pitch_angles = [12.3062, 3.46555, 12.0141]
+    #     for i, tcr in enumerate(tcrs):
+    #         crossing_angle = tcr.get_scanning_angle(mode="com")
+    #         self.assertAlmostEqual(
+    #             crossing_angle,
+    #             true_scanning_angles[i],
+    #         )
+    #         pitch = tcr.get_pitch_angle()
+    #         self.assertAlmostEqual(pitch, true_pitch_angles[i])
+
+    def test_get_alpha_helices(self):
+        import stcrpy
+
+        tcrs = stcrpy.load_TCRs(glob.glob("test_files/TCRCoM_test_files/*.cif"))
+
+        for tcr in tcrs:
+            if (
+                len(tcr.get_MHC()) == 1
+                and hasattr(tcr.get_MHC()[0], "MHC_type")
+                and tcr.get_MHC()[0].MHC_type in ["MH1", "MH2"]
+            ):
+                tcr_geom = TCRGeom.TCRGeom(tcr)
+                # since tcr should be aligned to reference MHC mhc vector should be approximately [0, 1, 0]
+                self.assertAlmostEqual(
+                    np.dot(
+                        tcr_geom._get_mhc_helix_vectors(tcr.get_MHC()[0]),
+                        np.asarray([0, 1, 0]),
+                    ),
+                    1,
+                    places=1,
+                )
+
+    def test_rudolph_scanning_angle(self):
+        import stcrpy
+
+        tcrs = stcrpy.load_TCRs(
+            glob.glob("test_files/TCRGeom_rudolph_test_files/*.cif")
+        )
+
+        rudolph_scanning_angles = {
+            "2ckb": 22,
+            "1g6r": 23,
+            "1mwa": 23,
+            "1fo0": 41,
+            "1nam": 40,
+            "1kj2": 31,
+            "1bd2": 48,
+        }
+
+        for tcr in tcrs:
+            tcr_geom = TCRGeom.TCRGeom(tcr, mode="rudolph")
+
+            assert (
+                abs(
+                    np.degrees(tcr_geom.scanning_angle)
+                    - rudolph_scanning_angles[tcr.parent.parent.id]
+                )
+                < 3.0
+            )