gemmi-protools 1.1.0__py3-none-any.whl

gemmi_protools/io/__init__.py

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+"""
+@Author: Luo Jiejian
+"""

gemmi_protools/io/convert.py

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+"""
+@Author: Luo Jiejian
+"""
+
+import gemmi
+import numpy as np
+from Bio.PDB.Structure import Structure as BioStructure
+from Bio.PDB.StructureBuilder import StructureBuilder
+
+
+def gemmi2bio(gemmi_structure: gemmi.Structure) -> BioStructure:
+    """
+    Convert gemmi structure to biopython structure
+    :param gemmi_structure:
+    :return:
+    return biopython structure
+    """
+    structure_builder = StructureBuilder()
+    structure_builder.init_structure(structure_id=gemmi_structure.name)
+
+    for model_idx, gemmi_model in enumerate(gemmi_structure):
+        structure_builder.init_model(model_idx)
+
+        for gemmi_chain in gemmi_model:
+            structure_builder.init_chain(gemmi_chain.name)
+
+            for gemmi_residue in gemmi_chain:
+                if gemmi_residue.het_flag == "H":
+                    if gemmi_residue.name in ["HOH", "WAT"]:
+                        het_flag = "W"
+                    else:
+                        het_flag = "H"
+                else:
+                    het_flag = " "
+
+                structure_builder.init_residue(resname=gemmi_residue.name, field=het_flag,
+                                               resseq=gemmi_residue.seqid.num, icode=gemmi_residue.seqid.icode)
+                for gemmi_atom in gemmi_residue:
+                    coord = np.array([gemmi_atom.pos.x, gemmi_atom.pos.y, gemmi_atom.pos.z])
+                    structure_builder.init_atom(name=gemmi_atom.name,
+                                                coord=coord,
+                                                b_factor=gemmi_atom.b_iso,
+                                                occupancy=gemmi_atom.occ,
+                                                altloc=gemmi_atom.altloc if gemmi_atom.has_altloc() else ' ',
+                                                fullname=gemmi_atom.name.center(4),
+                                                serial_number=gemmi_atom.serial,
+                                                element=gemmi_atom.element.name.upper())
+
+    bio_structure = structure_builder.get_structure()
+    return bio_structure
+
+
+def bio2gemmi(bio_structure: BioStructure) -> gemmi.Structure:
+    """
+    Convert biopython structure to gemmi structure
+    :param bio_structure:
+    :return:
+    return gemmi structure
+    """
+
+    g_structure = gemmi.Structure()
+    g_structure.name = bio_structure.id
+
+    for bio_model in bio_structure:
+        # bio model start from 0, gemmi model start from 1
+        g_model = gemmi.Model(bio_model.id + 1)
+        for bio_chain in bio_model:
+            g_chain = gemmi.Chain(bio_chain.id)
+            for bio_residue in bio_chain:
+                g_residue = gemmi.Residue()
+                g_residue.name = bio_residue.resname
+                het_flag, r_num, i_code = bio_residue.id
+                g_residue.seqid.num = r_num
+                g_residue.seqid.icode = i_code
+                g_residue.het_flag = "A" if het_flag == " " else "H"
+
+                for bio_atom in bio_residue:
+                    g_atom = gemmi.Atom()
+                    g_atom.name = bio_atom.name
+                    g_atom.b_iso = bio_atom.bfactor
+                    g_atom.occ = bio_atom.occupancy
+                    g_atom.altloc = "\x00" if bio_atom.altloc == " " else bio_atom.altloc
+                    g_atom.element = gemmi.Element(bio_atom.element)
+                    g_atom.serial = bio_atom.serial_number
+                    px, py, pz = bio_atom.coord
+                    g_atom.pos = gemmi.Position(px, py, pz)
+                    g_residue.add_atom(g_atom)
+                g_chain.add_residue(g_residue)
+            g_model.add_chain(g_chain)
+        g_structure.add_model(g_model)
+    g_structure.setup_entities()
+    g_structure.assign_het_flags()
+    return g_structure