stcrpy 1.0.5__py3-none-any.whl → 1.0.6__py3-none-any.whl

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/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/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.dist-info → stcrpy-1.0.6.dist-info}/METADATA

@@ -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.dist-info → stcrpy-1.0.6.dist-info}/RECORD

@@ -33,7 +33,7 @@ stcrpy/tcr_geometry/reference_data/reference_D.pdb,sha256=O9LHeh3bWxeEWwuTcp1Hwz
 stcrpy/tcr_geometry/reference_data/reference_G.pdb,sha256=Fs8e_UDb6dI1qqhNSttWaHrzkjgzjFpMpC38_W9OXTg,2434
 stcrpy/tcr_geometry/reference_data/reference_data.py,sha256=q3L-cQ1UQUfZxeIMKIiiase_6SEEuWlx7UsLndwNLAk,1658
 stcrpy/tcr_interactions/PLIPParser.py,sha256=zetY_LvH_8E-26xXc02c7_edoHWEwIWB9_XIu1szRcA,5785
-stcrpy/tcr_interactions/TCRInteractionProfiler.py,sha256=56NeZZVIAjEqbbsM_qepjJQjoaR-RFt5OhhtcebiunI,17772
+stcrpy/tcr_interactions/TCRInteractionProfiler.py,sha256=Bn2HAHG158nE3PhL1UoaZCaexm-gK9F9_exYtTCJXtQ,18038
 stcrpy/tcr_interactions/TCRpMHC_PLIP_Model_Parser.py,sha256=-fm_rtPJhU-h3WuX1U5Cv3vjO0eAlzwbm1HTreQIDCI,5464
 stcrpy/tcr_interactions/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 stcrpy/tcr_interactions/utils.py,sha256=KEGybd1ugZvFdj4Gqn9Xo4lnJbU1ivADmEDjkvuaNiw,5177
@@ -59,7 +59,7 @@ stcrpy/tcr_processing/Model.py,sha256=K8wTrSCECHyqJX9811wU9MxgdGDVyCXraQ4-rOOa08
 stcrpy/tcr_processing/Select.py,sha256=VuVSgmqHBPD1DGRumM44HDzcQ-aQOwg_6zQHM3Ulm0U,3543
 stcrpy/tcr_processing/TCR.py,sha256=dcMdw2WEGa-BUZUqAAe0Dw4U2Qyh1xYUaS4N7E7J2AQ,33220
 stcrpy/tcr_processing/TCRIO.py,sha256=tSJLVN6MG6gyT26PreVJOz5DqD1e-VsBjBpu3mBBPKg,1501
-stcrpy/tcr_processing/TCRParser.py,sha256=Raz2W9tygpK3knzjIVCfqUyCGSFA7yhh4UBT5wuWLM4,56134
+stcrpy/tcr_processing/TCRParser.py,sha256=4C7wmW6ENgNLAZsxoxzl3lk6UFQmYOPcMLvIzjmms8k,56274
 stcrpy/tcr_processing/TCRStructure.py,sha256=yFiUeo02KXIBBEljy0mebv5ol5uCQRTy-Sfs94Rt6Hc,3810
 stcrpy/tcr_processing/TCRchain.py,sha256=2CdP_JX5LG7nM8Lsuhcevf7SyRaQUZlizt3ntEYVPjg,4769
 stcrpy/tcr_processing/__init__.py,sha256=BefeJ0jefteeOzWrkOMvxLCvzd0aJDhXWrdTm7zlP94,94
@@ -68,12 +68,12 @@ stcrpy/tcr_processing/utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMp
 stcrpy/tcr_processing/utils/common.py,sha256=5e-dP6jPlaFZEErusakdQYpyj79E3WvEGF5-sG0LitI,1869
 stcrpy/tcr_processing/utils/constants.py,sha256=AHReE1QkeqTnhjvQI7nrPqLF4XdtzHV9C1w1uHTiVcM,8151
 stcrpy/tcr_processing/utils/region_definitions.py,sha256=t3HT6FHFlGqS_DdV2xWLdTxhIUEjWHsf_0_f-06w94E,19198
-stcrpy/tcr_processing/utils/symmetry_mates.py,sha256=9U29IHs63llBzV9xBNCmv4BKTIachwO7T3orHywDn48,3262
+stcrpy/tcr_processing/utils/symmetry_mates.py,sha256=dvyfEWovnjh9SZMqSTCsO_HgpyA2TqxIwHkmG_HxcK8,3557
 stcrpy/utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 stcrpy/utils/error_stream.py,sha256=BLHJnf-tWU41MXh6sHSZgkTFOMiWZsCgwM2qIKBnwr4,247
-stcrpy-1.0.5.dist-info/licenses/LICENCE,sha256=G1FnVDsfeYoveKTu9Xaqukcm-4xZ4mzakjLpFMnNfJ0,1507
-stcrpy-1.0.5.dist-info/licenses/stcrpy/tcr_geometry/TCRCoM_LICENCE,sha256=93k_qqF0rgpyWEmxpcl2sbZS3CK1dkGrIuvJtKsBlCA,7844
-stcrpy-1.0.5.dist-info/METADATA,sha256=6rbC0l_TnXd9UMykkNKAlQCsy4VuBBud4DPQEXh-FtY,10512
-stcrpy-1.0.5.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-stcrpy-1.0.5.dist-info/top_level.txt,sha256=kAkgyHyGW-_YswJpcuA3pSqzuQVbUggFUmZg2OTx_B8,16
-stcrpy-1.0.5.dist-info/RECORD,,
+stcrpy-1.0.6.dist-info/licenses/LICENCE,sha256=G1FnVDsfeYoveKTu9Xaqukcm-4xZ4mzakjLpFMnNfJ0,1507
+stcrpy-1.0.6.dist-info/licenses/stcrpy/tcr_geometry/TCRCoM_LICENCE,sha256=93k_qqF0rgpyWEmxpcl2sbZS3CK1dkGrIuvJtKsBlCA,7844
+stcrpy-1.0.6.dist-info/METADATA,sha256=jYS1OQgMW6ZtxxfsHlqbIuCcwIGfZ9ikRGg_9BN1TbI,10605
+stcrpy-1.0.6.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
+stcrpy-1.0.6.dist-info/top_level.txt,sha256=kAkgyHyGW-_YswJpcuA3pSqzuQVbUggFUmZg2OTx_B8,16
+stcrpy-1.0.6.dist-info/RECORD,,

{stcrpy-1.0.5.dist-info → stcrpy-1.0.6.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (80.9.0)
+Generator: setuptools (80.10.2)
 Root-Is-Purelib: true
 Tag: py3-none-any