first version

script/mutagenesis.py

@@ -0,0 +1,66 @@
+# 定义残基突变函数
+from pymol import cmd
+from pathlib import Path
+def Mutagenesis_site(filename: Path, mutation_type: str, site: int, outfile: Path = None) -> Path:
+    """Mutagenesis_site Mutagenesis residue in site
+        residue site have mutil conformations, need to select one conformations, some error accured.
+        pass
+    _extended_summary_
+
+    Arguments:
+        filename {str} -- PDB file format
+        mutation_type {str} -- 'VAL' for ALA TO VAL; 'ALA' for any/not ALA to ALA; 'GLY' for ALA to GLY
+        site {int} -- residue site in pdbfile
+
+    Keyword Arguments:
+        outfile {str} -- _description_ (default: {None})
+
+    Raises:
+        ValueError: not one object in PDBs,need to fix
+
+    Returns:
+        str -- save mutagenesis file path
+    """
+    p = Path(filename)
+    savename = p.stem + f"_{site}_mutation.pdb"
+    _out_file = Path(outfile) if outfile else p.absolute().parent.joinpath(savename)
+    if not _out_file.absolute().parent.exists(): _out_file.absolute().parent.mkdir(parents=True)
+    cmd.reinitialize('everything')  # ! clean up
+    cmd.load(filename.as_posix())
+    PDBs = cmd.get_names()
+    # Get the ID numbers of c-alpha (CA) atoms of all residues
+    if len(PDBs) == 1:
+        PDB = PDBs[0]
+    else:
+        raise ValueError(f'this pdb have more than one object!PDBs:{PDBs}')
+    CAindex = cmd.identify(f"{PDB} and name CA")
+    pdbstrList = [cmd.get_pdbstr("%s and id %s" % (PDB, CAid)).splitlines() for CAid in CAindex]
+    ProtChainResiList = [[PDB, i[0][21], i[0][22:26].strip()] for i in pdbstrList]
+    for i, j, k in ProtChainResiList:
+        if int(k) == int(site):
+            cmd.wizard("mutagenesis")
+            # print(i,j,k)
+            cmd.refresh_wizard()
+            cmd.get_wizard().set_mode(mutation_type)
+            ##Possible mutation_type could be:
+            ##'VAL' for ALA TO VAL
+            ##'ALA' for any/not ALA to ALA
+            ##'GLY' for ALA to GLY
+            # 'selection' will select each residue that you have selected
+            # on ProtChainResiList above using the PDBid,chain,and residue
+            # present on your pdb file.If you didn't select a range on
+            # ProteinChainResiList, it will do the mutation on all the residues
+            # present in your protein.
+            selection = f"/{i}//{j}/{k}"
+            # Print selection to check the output
+            # print(selection)
+            # Selects where to place the mutation
+            cmd.get_wizard().do_select(selection)
+            ##Applies mutation
+            cmd.get_wizard().apply()
+    # Save each mutation and reinitialize the session before the next mutation
+    ##to have pdb files only with the residue-specific single-point mutation you were interested.
+    cmd.set_wizard("done")
+    cmd.save(_out_file.as_posix(), f"{PDB}")
+    cmd.reinitialize('everything')  # Reinitialize PyMOL to default settings.
+    return _out_file