stcrpy 1.0.0__py3-none-any.whl

stcrpy/tcr_geometry/reference_data/reference_A.pdb

@@ -0,0 +1,31 @@
+ATOM      1  CA  GLY A  16     -12.766  -6.146   4.154  0.00  0.00           C  
+ATOM      2  CA  GLU A  17     -12.984  -3.096   1.985  0.00  0.00           C  
+ATOM      3  CA  ASN A  18     -10.777  -2.216  -0.940  0.00  0.00           C  
+ATOM      4  CA  THR A  20      -6.622   2.515  -3.475  0.00  0.00           C  
+ATOM      5  CA  ASN A  22      -2.375   6.893  -5.615  0.00  0.00           C  
+ATOM      6  CA  ASN A  38      10.871   1.660 -12.510  0.00  0.00           C  
+ATOM      7  CA  LEU A  39       8.338   2.153  -9.768  0.00  0.00           C  
+ATOM      8  CA  GLN A  40       8.338   0.459  -6.382  0.00  0.00           C  
+ATOM      9  CA  TRP A  41       5.923   0.253  -3.477  0.00  0.00           C  
+ATOM     10  CA  TYR A  42       7.139  -0.195   0.076  0.00  0.00           C  
+ATOM     11  CA  ARG A  43       5.258  -0.682   3.297  0.00  0.00           C  
+ATOM     12  CA  GLN A  44       6.468   0.441   6.681  0.00  0.00           C  
+ATOM     13  CA  ASN A  45       4.955  -0.914   9.806  0.00  0.00           C  
+ATOM     14  CA  HIS A  52       9.234  -4.199  -0.523  0.00  0.00           C  
+ATOM     15  CA  LYS A  85       2.672   9.293 -15.022  0.00  0.00           C  
+ATOM     16  CA  SER A  86       0.797   7.515 -12.294  0.00  0.00           C  
+ATOM     17  CA  SER A  88      -1.761   3.077  -8.014  0.00  0.00           C  
+ATOM     18  CA  LEU A  89      -1.639   0.408  -5.358  0.00  0.00           C  
+ATOM     19  CA  LEU A  90      -4.860  -1.486  -4.764  0.00  0.00           C  
+ATOM     20  CA  SER A  94      -8.077  -5.060   3.718  0.00  0.00           C  
+ATOM     21  CA  ARG A  95      -7.018  -6.656   6.969  0.00  0.00           C  
+ATOM     22  CA  ALA A  96      -5.916  -5.018  10.209  0.00  0.00           C  
+ATOM     23  CA  ALA A  97      -2.373  -6.175   9.542  0.00  0.00           C  
+ATOM     24  CA  ASP A  98      -2.346  -3.975   6.457  0.00  0.00           C  
+ATOM     25  CA  THR A  99      -2.284  -0.874   8.638  0.00  0.00           C  
+ATOM     26  CA  ALA A 100       0.968   0.902   7.897  0.00  0.00           C  
+ATOM     27  CA  SER A 101       2.587   3.693   5.962  0.00  0.00           C  
+ATOM     28  CA  TYR A 102       2.875   3.032   2.230  0.00  0.00           C  
+ATOM     29  CA  PHE A 103       5.639   4.573   0.152  0.00  0.00           C  
+ATOM     30  CA  CYS A 104       5.899   4.893  -3.569  0.00  0.00           C  
+TER

stcrpy/tcr_geometry/reference_data/reference_B.pdb

@@ -0,0 +1,31 @@
+ATOM      1  CA  THR B   5       7.680   4.957   6.318  0.00  0.00           C  
+ATOM      2  CA  GLN B   6       4.157   4.013   5.323  0.00  0.00           C  
+ATOM      3  CA  PRO B   8      -1.597   4.163   7.655  0.00  0.00           C  
+ATOM      4  CA  LYS B   9      -0.563   0.753   8.980  0.00  0.00           C  
+ATOM      5  CA  PHE B  10      -4.125  -0.534   8.872  0.00  0.00           C  
+ATOM      6  CA  GLN B  11      -7.228   0.591   7.033  0.00  0.00           C  
+ATOM      7  CA  VAL B  12     -10.787  -0.634   6.761  0.00  0.00           C  
+ATOM      8  CA  LYS B  14     -16.366   0.265   2.522  0.00  0.00           C  
+ATOM      9  CA  THR B  15     -16.732  -0.673  -1.121  0.00  0.00           C  
+ATOM     10  CA  GLY B  16     -16.733   2.365  -3.364  0.00  0.00           C  
+ATOM     11  CA  GLN B  22       1.267   7.341   1.834  0.00  0.00           C  
+ATOM     12  CA  CYS B  23       4.911   6.380   1.563  0.00  0.00           C  
+ATOM     13  CA  ALA B  24       7.861   8.498   2.594  0.00  0.00           C  
+ATOM     14  CA  TYR B  38      13.247   5.051  -7.303  0.00  0.00           C  
+ATOM     15  CA  MET B  39      10.086   4.125  -5.461  0.00  0.00           C  
+ATOM     16  CA  SER B  40       7.830   1.118  -5.919  0.00  0.00           C  
+ATOM     17  CA  TRP B  41       4.421  -0.118  -4.828  0.00  0.00           C  
+ATOM     18  CA  TYR B  42       3.741  -3.827  -4.381  0.00  0.00           C  
+ATOM     19  CA  ARG B  43       0.720  -5.770  -3.219  0.00  0.00           C  
+ATOM     20  CA  GLN B  44       0.883  -9.078  -1.429  0.00  0.00           C  
+ATOM     21  CA  ARG B  51       3.180  -8.202  -7.285  0.00  0.00           C  
+ATOM     22  CA  LEU B  52       4.411  -4.907  -8.681  0.00  0.00           C  
+ATOM     23  CA  ILE B  53       1.744  -2.252  -9.110  0.00  0.00           C  
+ATOM     24  CA  ASP B  86       6.783  11.037  -1.067  0.00  0.00           C  
+ATOM     25  CA  THR B  99      -8.080  -6.335   0.175  0.00  0.00           C  
+ATOM     26  CA  SER B 100      -4.378  -6.994   0.577  0.00  0.00           C  
+ATOM     27  CA  VAL B 101      -1.115  -5.893   2.125  0.00  0.00           C  
+ATOM     28  CA  TYR B 102       0.511  -2.993   0.305  0.00  0.00           C  
+ATOM     29  CA  PHE B 103       4.257  -2.495   0.489  0.00  0.00           C  
+ATOM     30  CA  CYS B 104       6.223   0.500  -0.633  0.00  0.00           C  
+TER

stcrpy/tcr_geometry/reference_data/reference_D.pdb

@@ -0,0 +1,31 @@
+ATOM      1  CA  GLY D  16     -12.766  -6.146   4.154  0.00  0.00           C  
+ATOM      2  CA  GLU D  17     -12.984  -3.096   1.985  0.00  0.00           C  
+ATOM      3  CA  ASN D  18     -10.777  -2.216  -0.940  0.00  0.00           C  
+ATOM      4  CA  THR D  20      -6.622   2.515  -3.475  0.00  0.00           C  
+ATOM      5  CA  ASN D  22      -2.375   6.893  -5.615  0.00  0.00           C  
+ATOM      6  CA  ASN D  38      10.871   1.660 -12.510  0.00  0.00           C  
+ATOM      7  CA  LEU D  39       8.338   2.153  -9.768  0.00  0.00           C  
+ATOM      8  CA  GLN D  40       8.338   0.459  -6.382  0.00  0.00           C  
+ATOM      9  CA  TRP D  41       5.923   0.253  -3.477  0.00  0.00           C  
+ATOM     10  CA  TYR D  42       7.139  -0.195   0.076  0.00  0.00           C  
+ATOM     11  CA  ARG D  43       5.258  -0.682   3.297  0.00  0.00           C  
+ATOM     12  CA  GLN D  44       6.468   0.441   6.681  0.00  0.00           C  
+ATOM     13  CA  ASN D  45       4.955  -0.914   9.806  0.00  0.00           C  
+ATOM     14  CA  HIS D  52       9.234  -4.199  -0.523  0.00  0.00           C  
+ATOM     15  CA  LYS D  85       2.672   9.293 -15.022  0.00  0.00           C  
+ATOM     16  CA  SER D  86       0.797   7.515 -12.294  0.00  0.00           C  
+ATOM     17  CA  SER D  88      -1.761   3.077  -8.014  0.00  0.00           C  
+ATOM     18  CA  LEU D  89      -1.639   0.408  -5.358  0.00  0.00           C  
+ATOM     19  CA  LEU D  90      -4.860  -1.486  -4.764  0.00  0.00           C  
+ATOM     20  CA  SER D  94      -8.077  -5.060   3.718  0.00  0.00           C  
+ATOM     21  CA  ARG D  95      -7.018  -6.656   6.969  0.00  0.00           C  
+ATOM     22  CA  ALA D  96      -5.916  -5.018  10.209  0.00  0.00           C  
+ATOM     23  CA  ALA D  97      -2.373  -6.175   9.542  0.00  0.00           C  
+ATOM     24  CA  ASP D  98      -2.346  -3.975   6.457  0.00  0.00           C  
+ATOM     25  CA  THR D  99      -2.284  -0.874   8.638  0.00  0.00           C  
+ATOM     26  CA  ALA D 100       0.968   0.902   7.897  0.00  0.00           C  
+ATOM     27  CA  SER D 101       2.587   3.693   5.962  0.00  0.00           C  
+ATOM     28  CA  TYR D 102       2.875   3.032   2.230  0.00  0.00           C  
+ATOM     29  CA  PHE D 103       5.639   4.573   0.152  0.00  0.00           C  
+ATOM     30  CA  CYS D 104       5.899   4.893  -3.569  0.00  0.00           C  
+TER

stcrpy/tcr_geometry/reference_data/reference_G.pdb

@@ -0,0 +1,31 @@
+ATOM      1  CA  THR G   5       7.680   4.957   6.318  0.00  0.00           C  
+ATOM      2  CA  GLN G   6       4.157   4.013   5.323  0.00  0.00           C  
+ATOM      3  CA  PRO G   8      -1.597   4.163   7.655  0.00  0.00           C  
+ATOM      4  CA  LYS G   9      -0.563   0.753   8.980  0.00  0.00           C  
+ATOM      5  CA  PHE G  10      -4.125  -0.534   8.872  0.00  0.00           C  
+ATOM      6  CA  GLN G  11      -7.228   0.591   7.033  0.00  0.00           C  
+ATOM      7  CA  VAL G  12     -10.787  -0.634   6.761  0.00  0.00           C  
+ATOM      8  CA  LYS G  14     -16.366   0.265   2.522  0.00  0.00           C  
+ATOM      9  CA  THR G  15     -16.732  -0.673  -1.121  0.00  0.00           C  
+ATOM     10  CA  GLY G  16     -16.733   2.365  -3.364  0.00  0.00           C  
+ATOM     11  CA  GLN G  22       1.267   7.341   1.834  0.00  0.00           C  
+ATOM     12  CA  CYS G  23       4.911   6.380   1.563  0.00  0.00           C  
+ATOM     13  CA  ALA G  24       7.861   8.498   2.594  0.00  0.00           C  
+ATOM     14  CA  TYR G  38      13.247   5.051  -7.303  0.00  0.00           C  
+ATOM     15  CA  MET G  39      10.086   4.125  -5.461  0.00  0.00           C  
+ATOM     16  CA  SER G  40       7.830   1.118  -5.919  0.00  0.00           C  
+ATOM     17  CA  TRP G  41       4.421  -0.118  -4.828  0.00  0.00           C  
+ATOM     18  CA  TYR G  42       3.741  -3.827  -4.381  0.00  0.00           C  
+ATOM     19  CA  ARG G  43       0.720  -5.770  -3.219  0.00  0.00           C  
+ATOM     20  CA  GLN G  44       0.883  -9.078  -1.429  0.00  0.00           C  
+ATOM     21  CA  ARG G  51       3.180  -8.202  -7.285  0.00  0.00           C  
+ATOM     22  CA  LEU G  52       4.411  -4.907  -8.681  0.00  0.00           C  
+ATOM     23  CA  ILE G  53       1.744  -2.252  -9.110  0.00  0.00           C  
+ATOM     24  CA  ASP G  86       6.783  11.037  -1.067  0.00  0.00           C  
+ATOM     25  CA  THR G  99      -8.080  -6.335   0.175  0.00  0.00           C  
+ATOM     26  CA  SER G 100      -4.378  -6.994   0.577  0.00  0.00           C  
+ATOM     27  CA  VAL G 101      -1.115  -5.893   2.125  0.00  0.00           C  
+ATOM     28  CA  TYR G 102       0.511  -2.993   0.305  0.00  0.00           C  
+ATOM     29  CA  PHE G 103       4.257  -2.495   0.489  0.00  0.00           C  
+ATOM     30  CA  CYS G 104       6.223   0.500  -0.633  0.00  0.00           C  
+TER

stcrpy/tcr_geometry/reference_data/reference_data.py

@@ -0,0 +1,104 @@
+import os
+
+reference_positions = {
+    "A": [
+        [0.170468, 0.120233, -0.978000],
+        [-0.460937, 0.886969, 0.028699],
+        [5.223556, 2.001083, 1.418880],
+    ],
+    "B": [
+        [0.595917, 0.758482, -0.263794],
+        [-0.056280, 0.367130, 0.928465],
+        [2.455201, -3.709282, -1.446316],
+    ],
+    "G": [
+        [0.170468, 0.120233, -0.978000],
+        [-0.460937, 0.886969, 0.028699],
+        [5.223556, 2.001083, 1.418880],
+    ],
+    "D": [
+        [0.595917, 0.758482, -0.263794],
+        [-0.056280, 0.367130, 0.928465],
+        [2.455201, -3.709282, -1.446316],
+    ],
+}
+
+reference_pdb_paths = {
+    chain_id: os.path.join(
+        os.path.dirname(os.path.abspath(__file__)), f"reference_{chain_id}.pdb"
+    )
+    for chain_id in ["A", "B", "G", "D"]
+}
+
+
+reference_origin_scaling = {
+    "A": [3.0, -1.0, 1.0],
+    "B": [-5.0, 0.5, 1.0],
+}
+
+reference_residues = {
+    "A": [
+        16,
+        17,
+        18,
+        20,
+        22,
+        38,
+        39,
+        40,
+        41,
+        42,
+        43,
+        44,
+        45,
+        52,
+        85,
+        86,
+        88,
+        89,
+        90,
+        94,
+        95,
+        96,
+        97,
+        98,
+        99,
+        100,
+        101,
+        102,
+        103,
+        104,
+    ],
+    "B": [
+        5,
+        6,
+        8,
+        9,
+        10,
+        11,
+        12,
+        14,
+        15,
+        16,
+        22,
+        23,
+        24,
+        38,
+        39,
+        40,
+        41,
+        42,
+        43,
+        44,
+        51,
+        52,
+        53,
+        86,
+        99,
+        100,
+        101,
+        102,
+        103,
+        104,
+    ],
+}

stcrpy/tcr_interactions/PLIPParser.py

@@ -0,0 +1,147 @@
+import typing
+import warnings
+import os
+import pandas as pd
+
+
+from . import utils as plip_utils
+from .TCRpMHC_PLIP_Model_Parser import TCRpMHC_PLIP_Model_Parser
+
+class PLIPParser:
+    """This class is used to parse the interactions of a TCR-pMHC complex using PLIP."""
+    def parse_complex(
+        self,
+        complex: "plip.structure.preparation.PDBComplex",
+        tcr_pmhc_complex: typing.Union["abTCR", "gdTCR"] = None,
+        renumbering=None,
+        domain_assignment=None,
+    ) -> pd.DataFrame:
+        """
+        Parses PLIP profiled interactions and maps them back onto a syctpy TCR object.
+
+        Args:
+            complex (plip.structure.preparation.PDBComplex):
+            tcr_pmhc_complex (typing.Union["abTCR", "gdTCR"], optional): _description_. Defaults to None.
+            renumbering (_type_, optional): _description_. Defaults to None.
+            domain_assignment (_type_, optional): _description_. Defaults to None.
+
+        Returns:
+            pd.DataFrame: _description_
+        """
+        all_interactions = []
+        for _, interaction_set in complex.interaction_sets.items():
+            for interaction in interaction_set.all_itypes:
+                try:
+                    all_interactions.append(plip_utils.parse_interaction(interaction))
+                except NotImplementedError as e:
+                    print(e)
+                    continue
+        interactions_df = self._interactions_to_dataframe(all_interactions)
+        if renumbering is not None and len(interactions_df) > 0:
+            self._renumber_interactions(interactions_df, renumbering)
+        if tcr_pmhc_complex is not None:
+            self._map_amino_acids_to_ligands(interactions_df, tcr_pmhc_complex)
+        if domain_assignment is not None:
+            self._assign_domains_to_chains(interactions_df, domain_assignment)
+
+        return interactions_df
+
+    def _renumber_interactions(self, interactions_df, renumbering):
+        # def imgt_number_mapping(original_idx):
+        #     imgt_insertions_to_number_map = {
+        #                 "A": 1,
+        #                 "B": 2,
+        #                 "C": 3,
+        #                 "D": 4,
+        #                 "E": 5,
+        #                 "F": 6,
+        #                 "G": 7,
+        #                 "H": 8,
+        #                 "I": 9,
+        #             }
+
+        #     if original_idx[-1] == ' ':
+        #         return original_idx[1]
+        #     else:
+        #         return original_idx[1] + 0.1*imgt_insertions_to_number_map[original_idx]
+        interactions_df["original_numbering"] = interactions_df.apply(
+            lambda x: str(renumbering[x.protein_chain][(" ", x.protein_number, " ")][1])
+            + renumbering[x.protein_chain][(" ", x.protein_number, " ")][2].strip(),
+            axis=1,
+        )
+        return interactions_df
+
+        for chain_id, renumber in renumbering.items():
+
+            for plip_idx, original_idx in renumber.items():
+                mask = (interactions_df.protein_chain == chain_id) & (
+                    interactions_df.protein_number == plip_idx[1]
+                )
+                if sum(mask) > 0:
+                    interactions_df[mask].loc[:, "protein_number"] = (
+                        str(original_idx[1]) + str(original_idx[-1])
+                    ).strip()
+        return interactions_df
+
+    def _assign_domains_to_chains(self, interactions_df, domains):
+        chain_to_domain_mapping = {v: k for k, v in domains.items()}
+
+        def assign_domain(chain_id):
+            if chain_id in chain_to_domain_mapping:
+                return chain_to_domain_mapping[chain_id]
+            else:
+                return None
+
+        interactions_df["domain"] = interactions_df.protein_chain.apply(assign_domain)
+
+    def _interactions_to_dataframe(self, interaction_list: list) -> pd.DataFrame:
+        columns = [
+            "type",
+            "protein_atom",
+            "protein_chain",
+            "protein_residue",
+            "protein_number",
+            "ligand_atom",
+            "distance",
+            "angle",
+            "plip_id",
+        ]
+
+        interactions_as_tuples = [
+            interaction.to_tuple() for interaction in interaction_list
+        ]
+        interactions = list(zip(*interactions_as_tuples))
+        if len(interactions) > 0:
+            interactions_as_dict = {
+                columns[i]: interactions[i] for i in range(len(columns))
+            }
+            return pd.DataFrame(interactions_as_dict)
+        else:
+            return pd.DataFrame(columns=columns)
+
+    def _map_amino_acids_to_ligands(
+        self, interactions_df: pd.DataFrame, tcr_pmhc_complex: str
+    ):
+        parser = TCRpMHC_PLIP_Model_Parser()
+        _, tcr_mhc_pdb, ligand_pdb, ligand_sdf = parser.parse_tcr_pmhc_complex(
+            tcr_pmhc_complex, delete_tmp_files=False, renumber=False
+        )
+        coordinate_mapping = parser.map_amino_acids_to_ligands(ligand_pdb, ligand_sdf)
+        if len(interactions_df) > 0:
+            ligand_residues = interactions_df.apply(
+                lambda x: coordinate_mapping[x.ligand_atom[0][0]], axis=1
+            )
+            interactions_df["ligand_residue"], interactions_df["ligand_number"] = map(
+                list, zip(*ligand_residues)
+            )
+        else:  # return empty dataframe with appropriate columns
+            extended_columns = list(interactions_df.columns)
+            extended_columns.extend(["ligand_residue", "ligand_number"])
+            interactions_df = pd.DataFrame(columns=extended_columns)
+
+        # delete temp files needed for renumbering
+        os.remove(tcr_mhc_pdb)
+        os.remove(ligand_pdb)
+        os.remove(ligand_sdf)
+
+        return interactions_df