gemmi-protools 0.1.2__py3-none-any.whl → 0.1.4__py3-none-any.whl

gemmi_protools/peptide.py

@@ -0,0 +1,32 @@
+"""
+@Author: Luo Jiejian
+"""
+from copy import deepcopy
+
+from Bio.PDB.Polypeptide import nucleic_letters_3to1_extended, protein_letters_3to1_extended
+
+
+def strip_key_val(inputs):
+    outputs = dict()
+    for key, val in inputs.items():
+        outputs[key.strip()] = val.strip()
+    return outputs
+
+
+def __nucleic_3to1_mapper():
+    mapper = deepcopy(nucleic_letters_3to1_extended)
+    mapper["DN"] = "N"
+    mapper["N"] = "N"
+    new_mapper = strip_key_val(mapper)
+    return new_mapper
+
+
+def __protein_3to1_mapper():
+    mapper = deepcopy(protein_letters_3to1_extended)
+    mapper["UNK"] = "X"
+    new_mapper = strip_key_val(mapper)
+    return new_mapper
+
+
+nucleic_3to1_mapper = __nucleic_3to1_mapper()
+protein_3to1_mapper = __protein_3to1_mapper()

gemmi_protools/reader.py

@@ -2,7 +2,6 @@
 @Author: Luo Jiejian
 """
 import pathlib
-import re
 import string
 import warnings
 from copy import deepcopy
@@ -17,6 +16,7 @@ from .parser import (_assign_digital_entity_names, _ent_from_structure,
                      pdb_parser, cif_parser, _chain_type, _chain_names2one_letter,
                      _assert_unique_chain_names_in_models, get_assembly)
 from .pdb_opts import _compound_source_string, _is_pdb
+from .peptide import nucleic_3to1_mapper, protein_3to1_mapper
 from .struct_info import Info
 
 
@@ -42,6 +42,27 @@ class StructureParser(object):
         self.INFO.from_gemmi_structure_infomap(self.STRUCT.info)
         self.ENTITY = _ent_from_structure(self.STRUCT)
         self.update_entity()
+        self.update_full_sequences()
+
+    def update_full_sequences(self):
+        for ent_idx, ent in enumerate(self.STRUCT.entities):
+            # get full sequence
+            full_seq = ent.full_sequence
+
+            # when missing, construct from Residues
+            if not full_seq:
+                sel_ch_id = None
+                sel_ch_len = 0
+                for ch_id, ent_id in self.ENTITY.polymer2eid.items():
+                    if ent_id == ent.name:
+                        cur_len = len(self.polymer_sequences[ch_id])
+                        if cur_len > sel_ch_len:
+                            sel_ch_id = ch_id
+                            sel_ch_len = cur_len
+
+                if sel_ch_id is not None and sel_ch_len > 0:
+                    full_seq = [r.name for r in self.STRUCT[0][sel_ch_id].get_polymer() if not r.is_water()]
+                    self.STRUCT.entities[ent_idx].full_sequence = full_seq
 
     @typechecked
     def load_from_file(self, path: Union[str, pathlib.PosixPath]):
@@ -56,6 +77,7 @@ class StructureParser(object):
         self.STRUCT, self.ENTITY = struct, entity
         self.INFO.from_gemmi_structure_infomap(self.STRUCT.info)
         self.update_entity()
+        self.update_full_sequences()
 
     @typechecked
     def to_pdb(self, outfile: str, write_minimal_pdb=False):
@@ -131,7 +153,7 @@ class StructureParser(object):
             for chain in model:
                 ct = cts.get(chain.name, "other")
                 if ct != "other":
-                    out[chain.name] = re.sub("-", "", chain.get_polymer().make_one_letter_sequence())
+                    out[chain.name] = self.make_one_letter_sequence(chain.name)
         return out
 
     @property
@@ -152,12 +174,28 @@ class StructureParser(object):
                                                 for r in chain.get_polymer()], dtype=id_type)
         return out
 
-    @property
-    def chain_residues(self):
+    def chain_residues(self, polymer_only=True, with_water=False):
+        """
+        :param polymer_only, bool
+        :param with_water:
+        :return: dict of Three-letter codes of chain residues
+        """
+
         out = dict()
         for model in self.STRUCT:
             for chain in model:
-                out[chain.name] = [r.name for r in chain]
+                res_codes = []
+                for r in chain:
+                    if r.is_water():
+                        if with_water:
+                            res_codes.append(r.name)
+                    else:
+                        if polymer_only:
+                            if r.entity_type.name == "Polymer":
+                                res_codes.append(r.name)
+                        else:
+                            res_codes.append(r.name)
+                out[chain.name] = res_codes
         return out
 
     def update_entity(self):
@@ -369,3 +407,15 @@ class StructureParser(object):
             return np.array(coord, dtype=np.float32), np.array(atom_id, dtype=id_type)
         else:
             return np.empty(shape=(0, 3), dtype=np.float32), np.array(atom_id, dtype=id_type)
+
+    def make_one_letter_sequence(self, chain_id):
+        c_type = self.chain_types[chain_id]
+        residues = self.chain_residues(polymer_only=True, with_water=False)[chain_id]
+
+        if c_type == "protein":
+            one_letter_code = "".join([protein_3to1_mapper.get(r, "X") for r in residues])
+        elif c_type in ["dna", "rna"]:
+            one_letter_code = "".join([nucleic_3to1_mapper.get(r, "N") for r in residues])
+        else:
+            one_letter_code = ""
+        return one_letter_code

{gemmi_protools-0.1.2.dist-info → gemmi_protools-0.1.4.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: gemmi_protools
-Version: 0.1.2
+Version: 0.1.4
 Summary: An Enhanced tool to process PDB structures based on Gemmi
 Author-email: Luo Jiejian <luojiejian12@mails.ucas.ac.cn>
 License-Expression: MIT

{gemmi_protools-0.1.2.dist-info → gemmi_protools-0.1.4.dist-info}/RECORD

@@ -6,11 +6,12 @@ gemmi_protools/dockq.py,sha256=JGPQ7Xs7gz9wubVVT9WSP5lZsLnfgcUH-_nLJ3c8I3U,4172
 gemmi_protools/parse_pdb_header.py,sha256=UOGMsE3-d3APhO7zaAEE0NT31n-iqt55VpDh_RPOicI,14223
 gemmi_protools/parser.py,sha256=QIJCOfK8FaFbLMvBG82zTOAjIvQJcf2WRwuFSxj4zvc,8982
 gemmi_protools/pdb_opts.py,sha256=NbXLDNNVF7tuG_bUM0Infylf5aYnOCP2Pd-ndqm5bK4,5652
+gemmi_protools/peptide.py,sha256=a2wiEutJmvhl6gDCIzzqRCbmyknk2mwgy2FZ53lXclU,750
 gemmi_protools/ppi.py,sha256=nRzRWv28SDjVt6hMShRL_QYKFsBO1xA5jSGIQrN0JBg,2313
-gemmi_protools/reader.py,sha256=0VjMxOogqB1dccucQU2I703W5Ro4JYBakE2eXftUTPU,13194
+gemmi_protools/reader.py,sha256=u7872K-XeUW_sr0E1SaQWrPVWm88jPBUN8LLzf0flM0,15321
 gemmi_protools/struct_info.py,sha256=9nBj1Zer03S8_Wks7L7uRlc9PlbfCKzoaT32pKR58X8,2769
-gemmi_protools-0.1.2.dist-info/licenses/LICENSE,sha256=JuQvKcgj6n11y5y6nXr9rABv3gJSswc4eTCd5WZBtSY,1062
-gemmi_protools-0.1.2.dist-info/METADATA,sha256=XTB_XuZpn611rYsLD2GMq6qd_bwm-TDBtGcNr-NROzE,567
-gemmi_protools-0.1.2.dist-info/WHEEL,sha256=CmyFI0kx5cdEMTLiONQRbGQwjIoR1aIYB7eCAQ4KPJ0,91
-gemmi_protools-0.1.2.dist-info/top_level.txt,sha256=P12mYJi5O5EKIn5u-RFaWxuix431CgLacSRD7rBid_U,15
-gemmi_protools-0.1.2.dist-info/RECORD,,
+gemmi_protools-0.1.4.dist-info/licenses/LICENSE,sha256=JuQvKcgj6n11y5y6nXr9rABv3gJSswc4eTCd5WZBtSY,1062
+gemmi_protools-0.1.4.dist-info/METADATA,sha256=aKz2slj7fXafD3SnNaI0apr7PIxK87FFXnnwHcCVfvw,567
+gemmi_protools-0.1.4.dist-info/WHEEL,sha256=CmyFI0kx5cdEMTLiONQRbGQwjIoR1aIYB7eCAQ4KPJ0,91
+gemmi_protools-0.1.4.dist-info/top_level.txt,sha256=P12mYJi5O5EKIn5u-RFaWxuix431CgLacSRD7rBid_U,15
+gemmi_protools-0.1.4.dist-info/RECORD,,