stcrpy 1.0.0__py3-none-any.whl

stcrpy/tcr_processing/Entity.py

@@ -0,0 +1,301 @@
+"""
+Created on 9 May 2017
+@author: leem
+
+A modified Entity class based on SAbDab's ABDB.AbPDB and Bio.PDB's entity
+
+"""
+
+import sys
+import io
+from copy import copy
+from textwrap import wrap
+
+import Bio
+import Bio.PDB
+from Bio.Data.IUPACData import atom_weights
+from .Select import select_all
+
+_ATOM_FORMAT_STRING = (
+    "%s%5i %-4s%c%3s %c%4i%c   %8.3f%8.3f%8.3f%6.2f%6.2f      %4s%2s%2s\n"
+)
+
+
+class Entity(Bio.PDB.Entity.Entity):
+    """
+    A modified entity object allows for direct writing of coordinates.
+    """
+
+    def _get_atom_line(self, atom, atom_number=None, charge="  "):
+        """
+        Modified from TCRDB.Bio.PDB.PDBIO
+        """
+        hetfield, resseq, icode = atom.parent.get_id()
+        resname = atom.parent.get_resname()
+        segid = atom.parent.get_segid()
+
+        if atom_number is None:
+            atom_number = atom.serial_number
+
+        chain_id = atom.parent.parent.get_id()
+
+        if hetfield != " ":
+            record_type = "HETATM"
+        else:
+            record_type = "ATOM  "
+
+        if atom.element:
+            element = atom.element.strip().upper()
+            if element.capitalize() not in atom_weights:
+                raise ValueError("Unrecognised element %r" % atom.element)
+            element = element.rjust(2)
+        else:
+            element = "  "
+
+        name = atom.get_fullname()
+        altloc = atom.get_altloc()
+        x, y, z = atom.get_coord()
+        bfactor = atom.get_bfactor()
+        occupancy = atom.get_occupancy()
+
+        args = (
+            record_type,
+            atom_number,
+            name,
+            altloc,
+            resname,
+            chain_id,
+            resseq,
+            icode,
+            x,
+            y,
+            z,
+            occupancy,
+            bfactor,
+            segid,
+            element,
+            charge,
+        )
+        return _ATOM_FORMAT_STRING % args
+
+    def _get_output_string(self, selection, n):
+        """
+        Method to get the atom lines of the entity's children.
+        @param selection: Selector object from TcrPDB.Select or inherited class.
+        @param n: An integer value to number the current atom with.
+                  If this is False the original numbering is used from the pdb file.
+        """
+        output_string = ""
+
+        for child in self.get_list():
+            if selection.accept(child):
+                if child.level == "A":
+                    output_string += self._get_atom_line(child, atom_number=n)
+                    if n:
+                        n += 1
+                else:
+                    output_string_add, n = child._get_output_string(selection, n)
+                    output_string += output_string_add
+        return output_string, n
+
+        # TODO
+
+    def save(self, output=sys.stdout, renumber=True, selection=False, remarks=True):
+        """
+        Save the coordinates of the entity
+
+        @param output: Where to write coordinates to. Should be an an open file, string or sys.stdout.
+                       By default the output is written to stdout
+        @param renumber: Flag whether to renumber the atoms to IMGT scheme
+                         Default is to renumber the atoms so that the first is 1 etc.
+                         Use renumber = False to retain the original atom numbering from the pdb file
+
+        @param selection: Provide a selector object to select which children of the entity should be outputted.
+                          Selection should be a selector object from TcrPDB.Select.
+                          Some basic selector classes are provided in the module. More complex classes can be created by inheriting from these.
+                          If selection = False (default) all atoms in the entity are output
+
+        @param remarks: Flag to print out remarks generated by TcrPDB. Default TRUE
+        Example:
+        entity.save("path/to/file/filename.pdb")
+        residue.save( "residue1.pdb" )
+        """
+
+        def ag_chain_and_type(ags):
+
+            if ags:
+                chains, types = [], []
+                for ag in ags:
+                    if ag.level == "C":  # peptide/protein/nucleic acid.
+                        chains.append(ag.id)
+                        types.append(ag.type)
+                    elif ag.level == "R":  # hapten / single carb
+                        chains.append(ag.parent.id)
+                        types.append(ag.type)
+                    elif ag.level == "F":  # carbs
+                        try:
+                            chains.append(ag.child_list[0].parent.id)
+                            types.append(ag.type)
+                        except IndexError:
+                            chains.append("UNKNOWN")
+                            types.append("UNKNOWN")
+                    else:
+                        chains.append("UNKNOWN")
+                        types.append("UNKNOWN")
+                return ";".join(chains), ";".join(types)
+            else:
+                return None, None
+
+        if renumber:
+            n = 1
+        else:
+            n = None
+
+        if not selection:
+            selection = select_all()
+
+        if self.level != "TS" or (self.level == "TS" and len(self.child_list) == 1):
+            output_string, n_atoms = self._get_output_string(selection, n)
+
+        elif self.level == "TS":
+            # output method for NMR structures
+            output_string, n_atoms = "", 0
+            # sort models by model id
+            self.child_list = sorted(self.child_list, key=lambda z: z.id)
+
+            for mod in self.child_list:
+                number = ("%d" % mod.id).rjust(9)  # space by 9 for models
+                output_string += "MODEL%s\n" % number
+                string, n_atoms = mod._get_output_string(selection, n_atoms + 1)
+                output_string += string
+                output_string += "ENDMDL\n"
+                n_atoms -= 1
+
+        remark_string = ""
+
+        if remarks:
+            remark_string = (
+                "REMARK   5 IMGT RENUMBERED STRUCTURE %s GENERATED BY STCRDAB\n"
+                % str(self.id).upper()
+            )
+            remark_string += (
+                "REMARK   5 TCR CHAINS ARE RENUMBERED IN THE VARIABLE REGIONS ONLY\n"
+            )
+            remark_string += "REMARK   5 MHC CHAINS ARE RENUMBERED IN THE G DOMAINS OR FOR B2M-GLOBULIN\n"
+            remark_string += "REMARK   5 NON-TCR and NON-MHC CHAINS ARE LEFT WITH RESIDUE IDS AS IN PDB\n"
+            p = self
+            i = 0
+            while i < 6:  # only try and go up residue,chain, holder, model, structure
+                if hasattr(p, "warnings"):
+                    # the entity is the top structure
+                    for TCR in p.get_TCRs():
+                        antigen_chain, antigen_type = ag_chain_and_type(TCR.antigen)
+                        if TCR.MHC:
+                            mh_chains = TCR.MHC[0].get_id()
+                        else:
+                            mh_chains = ""
+                        ch0, ch1 = [(c.chain_type, c.id) for c in TCR.get_chains()]
+                        remark_string += (
+                            "REMARK   5 PAIRED_%s %sCHAIN=%s %sCHAIN=%s MHCCHAINS=%s AGCHAIN=%s AGTYPE=%s\n"
+                            % (
+                                TCR.get_TCR_type(),
+                                ch0[0],
+                                ch0[1],
+                                ch1[0],
+                                ch1[1],
+                                mh_chains,
+                                antigen_chain,
+                                antigen_type,
+                            )
+                        )
+
+                    for TR_chain in p.get_unpaired_TCRchains():
+                        antigen_chain, antigen_type = ag_chain_and_type(
+                            TR_chain.antigen
+                        )
+                        if TR_chain.get_MHC():
+                            mh_chains = TR_chain.get_MHC()[0].get_id()
+                        else:
+                            mh_chains = ""
+                        remark_string += (
+                            "REMARK   5 SINGLE %sCHAIN=%s MHCCHAINS=%s AGCHAIN=%s AGTYPE=%s\n"
+                            % (
+                                TR_chain.chain_type,
+                                TR_chain.id,
+                                mh_chains,
+                                antigen_chain,
+                                antigen_type,
+                            )
+                        )
+                    for warning in str(p.warnings).split("\n"):
+                        if warning:
+                            remark_string += (
+                                "\n".join(
+                                    [
+                                        "REMARK   5 " + w.upper()
+                                        for w in wrap(warning, width=60)
+                                    ]
+                                )
+                                + "\n"
+                            )
+                    break
+                if p:
+                    p = p.get_parent()
+                    i += 1
+                else:
+                    remark_string = ""
+                    break
+
+        output_string = remark_string.upper() + output_string
+
+        if output is sys.stdout:
+            output.write(output_string)
+        elif type(output) is str:
+            with open(output, "w") as out:
+                out.write(output_string)
+        elif isinstance(output, io.IOBase):
+            output.write(output_string)
+
+    def transform(self, rot, tran):
+        """
+        Apply rotation and translation to the atomic coordinates.
+
+        Example:
+                >>> rotation=rotmat(pi, Vector(1,0,0))
+                >>> translation=array((0,0,1), 'f')
+                >>> entity.transform(rotation, translation)
+
+        @param rot: A right multiplying rotation matrix
+        @type rot: 3x3 Numeric array
+
+        @param tran: the translation vector
+        @type tran: size 3 Numeric array
+        """
+
+        for o in self.get_list():
+            o.transform(rot, tran)
+
+    def copy(self):
+        """
+        Copy has been played with a bit. For my purposes the version in 1.61 did not work as explicit copying of the child list
+        meant that the child objects became referenced to both self and shallow.
+        This may be due to overriding the residue and chain classes so may not be a bug in biopython.
+
+        When copying the child_list in the loop, I use the list to iterate over instead of the dictionary.
+        This preserves the ordering of the children.
+        """
+        shallow = copy(self)
+        shallow.child_list = (
+            []
+        )  # copy(self.child_list) # I have removed this explicit copy.
+        shallow.child_dict = {}  # copy(self.child_dict)
+        shallow.xtra = copy(self.xtra)
+        shallow.detach_parent()
+
+        # Order preserving copy
+        for child in self.get_list():
+            assert (
+                child.get_id() in self.child_dict
+            ), "child id not in the child_dict keys: this is unexpected and bad :("
+            shallow.add(child.copy())
+        return shallow

stcrpy/tcr_processing/Fragment.py

@@ -0,0 +1,58 @@
+"""
+Created on 9 May 2017
+@author: leem
+Modified version of the ABDB.AbPDB.Fragment class
+"""
+
+from .Entity import Entity
+from Bio.PDB.PDBExceptions import PDBConstructionException
+
+
+class Fragment(Entity):
+    """
+    A modified Entity class that can be thought of as a way of grouping children:
+        e.g. TCR (TCR object) -> TCRchain (TCRchain object) -> Fragment CDRB3 (Fragment object)
+                                                            -> Residue  B110  (Residue object)
+    Does not modify the parent/child attributes of its children.
+    For instance, one might define a fragment and add residues to it in order to visualise them.
+    """
+
+    def __init__(self, id):
+        self._id = id
+        Entity.__init__(self, id)
+        self.level = "F"
+
+    def __repr__(self):
+        if hasattr(self, "chain_type"):
+            return "<Fragment %s TCRchain: %s>" % (self.id, self.parent.parent.id)
+        else:
+            return "<Fragment %s>" % self.id
+
+    def add(self, entity):
+        "Add a child to the Entity."
+        entity_id = entity.get_id()
+        if self.has_id(entity_id):
+            raise PDBConstructionException("%s defined twice" % str(entity_id))
+
+        # parent of child is not changed
+        self.child_list.append(entity)
+        self.child_dict[entity_id] = entity
+
+    def insert(self, pos, entity):
+        "Add a child to the Entity at a specified position."
+        entity_id = entity.get_id()
+        if self.has_id(entity_id):
+            raise PDBConstructionException("%s defined twice" % str(entity_id))
+
+        # parent of child is not changed
+        self.child_list[pos:pos] = [entity]
+        self.child_dict[entity_id] = entity
+
+    def get_residues(self):
+        for residue in self:
+            yield residue
+
+    def get_atoms(self):
+        for residue in self.get_residues():
+            for atom in residue:
+                yield atom

stcrpy/tcr_processing/Holder.py

@@ -0,0 +1,24 @@
+"""
+Created on 9 May 2017
+@author: leem
+
+A generic holder class that can be used to contain individual chains, etc.
+
+"""
+
+from .Entity import Entity
+
+
+class Holder(Entity):
+    def __init__(self, identifier):
+        Entity.__init__(self, identifier)
+        self.level = "H"
+
+    def __repr__(self):
+        if len(self.child_list):
+            return "<Holder %s chains: %s>" % (
+                self.id,
+                ",".join([child.id for child in self]),
+            )
+        else:
+            return "<Holder %s chains: None>" % (self.id)