gemmi-protools 1.0.1__py3-none-any.whl → 1.0.3__py3-none-any.whl

gemmi_protools/io/reader.py

@@ -111,6 +111,23 @@ def parse_cif(path: str) -> dict:
 
     info_map = dict(st.info)
     pdb_code = info_map.get("_entry.id", "").lower()
+
+    v1 = block.find_value("_refine.ls_d_res_high")
+    v2 = block.find_value("_em_3d_reconstruction.resolution")
+
+    resolution = 0.0
+    if v1 not in [".", "?", None]:
+        resolution = v1
+    elif v2 not in [".", "?", None]:
+        resolution = v2
+
+    try:
+        resolution = float(resolution)
+    except:
+        resolution = 0.0
+
+    st.resolution = resolution
+
     info = dict(description={k: v for k, v in entityid2description.items() if v and v != "?"},
                 source=entityid2src,
                 resolution=st.resolution,
@@ -364,13 +381,24 @@ class StructureParser(object):
         return out
 
     def polymer_sequences(self, pdbx: bool = False):
+        """
+        entity sequences for polymers
+        :param pdbx:
+        :return:
+        """
         out = dict()
+        subchain_id2entity_id = self.subchain_id_to_entity_id
+        entity_dict = {ent.name: ent for ent in self.STRUCT.entities}
+
         for ch, polymer_type in self.polymer_types.items():
             polymer = self.get_chain(ch).get_polymer()
+            entity_id = subchain_id2entity_id[polymer.subchain_id()]
+            ent = entity_dict[entity_id]
+
             if pdbx:
-                s = gemmi.pdbx_one_letter_code(polymer.extract_sequence(), gemmi.sequence_kind(polymer_type))
+                s = gemmi.pdbx_one_letter_code(ent.full_sequence, gemmi.sequence_kind(polymer_type))
             else:
-                s = polymer.make_one_letter_sequence().replace("-", "")
+                s = "".join([gemmi.find_tabulated_residue(r).one_letter_code for r in ent.full_sequence]).upper()
             out[ch] = s
         return out
 
@@ -660,15 +688,18 @@ class StructureParser(object):
             raise ValueError("Chain %s not in found" % chain_name_2)
 
         flag = True
+        sw_name = ""
+
         while flag:
             characters = string.ascii_letters + string.digits
             sw_name = ''.join(random.choices(characters, k=4))
             if sw_name not in self.chain_ids:
                 flag = False
 
-        self.rename_chain(chain_name_1, sw_name)
-        self.rename_chain(chain_name_2, chain_name_1)
-        self.rename_chain(sw_name, chain_name_2)
+        if sw_name != "":
+            self.rename_chain(chain_name_1, sw_name)
+            self.rename_chain(chain_name_2, chain_name_1)
+            self.rename_chain(sw_name, chain_name_2)
 
     def make_one_letter_chain(self, only_uppercase: bool = True):
         uppercase_letters = list(string.ascii_uppercase)
@@ -695,7 +726,6 @@ class StructureParser(object):
 
         # not use yet
         letters_valid = [l for l in letters if l not in self.chain_ids]
-        chains2rename = [ch for ch in self.chain_ids if ch not in letters]
         mapper = {ch: letters_valid.pop() for ch in self.chain_ids if ch not in letters}
 
         for origin_name, target_name in mapper.items():

gemmi_protools/tools/pdb_annot.py

@@ -205,10 +205,7 @@ def annotate_pdb(struct_file: str):
     st.load_from_file(struct_file)
     st.clean_structure()
 
-    subchain_id2entity_id = dict()
-    for ent in st.STRUCT.entities:
-        for ch in ent.subchains:
-            subchain_id2entity_id[ch] = ent.name
+    subchain_id2entity_id = st.subchain_id_to_entity_id
 
     # Merge sequences
     polymers = dict()

{gemmi_protools-1.0.1.dist-info → gemmi_protools-1.0.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: gemmi_protools
-Version: 1.0.1
+Version: 1.0.3
 Summary: An Enhanced tool to process PDB structures based on Gemmi
 Author: Luo Jiejian
 Author-email: Luo Jiejian <luojiejian12@mails.ucas.ac.cn>

{gemmi_protools-1.0.1.dist-info → gemmi_protools-1.0.3.dist-info}/RECORD

@@ -6,14 +6,14 @@ gemmi_protools/data/MHC/MHC_combined.hmm.h3m,sha256=CvNMCsobQiX-wL7iB4CreNcbpnEl
 gemmi_protools/data/MHC/MHC_combined.hmm.h3p,sha256=-mK278pRedG3-KL-DtuVAQy7La9DgXg5FcP89D6X3Ck,78325
 gemmi_protools/io/__init__.py,sha256=F6e1xNT_7lZAWQgNIneH06o2qtWYrHNr_xPUPTwwx5E,29
 gemmi_protools/io/convert.py,sha256=A1i1vPgxG1LqMSUvWtegLl9LipgUQbfmKeGJ_f00UYo,3781
-gemmi_protools/io/reader.py,sha256=joQr_glerss3QcfIJGr0O6lw8Mc4N1-pVobMHqY1zi0,33255
+gemmi_protools/io/reader.py,sha256=-O9h5CIGPDnE1rDGMZqfApXk3_LRacNt_DaQ0zACkto,33992
 gemmi_protools/tools/__init__.py,sha256=F6e1xNT_7lZAWQgNIneH06o2qtWYrHNr_xPUPTwwx5E,29
 gemmi_protools/tools/align.py,sha256=oKHvpeDa62zEjLkPmuyBM6avYDl3HFeJVHeRX62I2f4,7085
 gemmi_protools/tools/dockq.py,sha256=baCuO5-GZCwrlS59T5UIXogpM44OIFIfXqksqRBAb0A,4428
 gemmi_protools/tools/mesh.py,sha256=73MuJYwS_ACJI15OsrooAAhB1Ti4fM8CJSBqFOBR7LU,6537
-gemmi_protools/tools/pdb_annot.py,sha256=EzgcntlERR04TfN0dIhf_GM9UCXEvUaH60Xohmbx_do,8253
-gemmi_protools-1.0.1.dist-info/licenses/LICENSE,sha256=JuQvKcgj6n11y5y6nXr9rABv3gJSswc4eTCd5WZBtSY,1062
-gemmi_protools-1.0.1.dist-info/METADATA,sha256=cdKO7zuEv4ZwwCrcBZcprXmDtLB4AbEFDKH887JRcTI,1034
-gemmi_protools-1.0.1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-gemmi_protools-1.0.1.dist-info/top_level.txt,sha256=P12mYJi5O5EKIn5u-RFaWxuix431CgLacSRD7rBid_U,15
-gemmi_protools-1.0.1.dist-info/RECORD,,
+gemmi_protools/tools/pdb_annot.py,sha256=enATyAHq0dE8TMsKQhsSbYj-baGrI33iviJdW2R7Hv8,8157
+gemmi_protools-1.0.3.dist-info/licenses/LICENSE,sha256=JuQvKcgj6n11y5y6nXr9rABv3gJSswc4eTCd5WZBtSY,1062
+gemmi_protools-1.0.3.dist-info/METADATA,sha256=mfEiC_hb27lnZzrW5f3EMpuEi_ri81w0xNsl1PXqVLE,1034
+gemmi_protools-1.0.3.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+gemmi_protools-1.0.3.dist-info/top_level.txt,sha256=P12mYJi5O5EKIn5u-RFaWxuix431CgLacSRD7rBid_U,15
+gemmi_protools-1.0.3.dist-info/RECORD,,