gemmi-protools 0.1.11__py3-none-any.whl → 0.1.13__py3-none-any.whl

gemmi_protools/io/reader.py

@@ -88,15 +88,7 @@ class StructureParser(object):
         resolution_remarks = ["%-80s" % "REMARK   2",
                               "%-80s" % rs]
 
-        resolution_remark_exist = False
-        for line in struct.raw_remarks:
-            if "REMARK   2 RESOLUTION" in line:
-                resolution_remark_exist = True
-
-        if not resolution_remark_exist:
-            struct.raw_remarks = resolution_remarks + struct.raw_remarks
-
-        struct.raw_remarks = compound_source + struct.raw_remarks
+        struct.raw_remarks = compound_source + resolution_remarks
         if write_minimal_pdb:
             struct.write_minimal_pdb(outfile)
         else:

gemmi_protools/utils/fixer.py

@@ -196,21 +196,17 @@ def repair_structure(input_file: str,
     ############################################################
     # Check and convert input_file to .pdb if not
     ############################################################
+    input_file = str(pathlib.Path(input_file).expanduser().resolve())
+    output_file = str(pathlib.Path(output_file).expanduser().resolve())
+    # input_file and output_file can't be the same path
+    assert input_file != output_file, "input_file and output_file can't be the same path"
+
     assert os.path.splitext(output_file)[1] == ".pdb", "output_file Not .pdb: %s" % output_file
     assert _is_cif(input_file) or _is_pdb(input_file), "Not .pdb or .cif or .pdb.gz or .cif.gz: %s" % input_file
 
-    # input_file and output_file can't be the same path
-    p_in = pathlib.Path(input_file).expanduser().resolve()
-    p_out = pathlib.Path(output_file).expanduser().resolve()
-
-    assert str(p_in) != str(p_out), "input_file and output_file can't be the same path"
     ############################################################
     # Config Path
     ############################################################
-    file_name = os.path.basename(input_file)
-    stem_name = os.path.splitext(file_name)[0]
-
-    in_dir = os.path.dirname(input_file)
     out_dir = os.path.dirname(output_file)
     if not os.path.isdir(out_dir):
         os.makedirs(out_dir)
@@ -220,16 +216,14 @@ def repair_structure(input_file: str,
         shutil.rmtree(temp_dir)
     os.makedirs(temp_dir)
 
-    if os.path.splitext(input_file)[1] != ".pdb":
-        # convert to .pdb
-        st = StructureParser()
-        st.load_from_file(input_file)
-        file_name_r = "%s.pdb" % stem_name
-        in_dir_r = temp_dir
-        st.to_pdb(os.path.join(in_dir_r, file_name_r))
-    else:
-        file_name_r = file_name
-        in_dir_r = in_dir
+    # for fix the filename bug of foldx
+    # rename the input always and save to .pdb
+    # convert to .pdb
+    st = StructureParser()
+    st.load_from_file(input_file)
+    file_name_r = "in.pdb"
+    in_dir_r = temp_dir
+    st.to_pdb(os.path.join(in_dir_r, file_name_r))
 
     foldx_path = shutil.which("foldx")
     if foldx_path is None:
@@ -250,7 +244,6 @@ def repair_structure(input_file: str,
         repair_cmd.append("--complexWithRNA true")
 
     command_settings = ["cd %s &&" % temp_dir] + repair_cmd + ["&& cd %s" % cwd_dir]
-
     start = time.time()
     try:
         result = subprocess.run(" ".join(command_settings), shell=True, check=True,
@@ -266,7 +259,7 @@ def repair_structure(input_file: str,
     else:
         if msg_str == "Finished":
             # just keep .pdb, ignore .fxout
-            result_file = os.path.join(temp_dir, "%s_Repair.pdb" % stem_name)
+            result_file = os.path.join(temp_dir, "in_Repair.pdb")
             if os.path.exists(result_file):
                 shutil.move(result_file, output_file)
             else:

{gemmi_protools-0.1.11.dist-info → gemmi_protools-0.1.13.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: gemmi_protools
-Version: 0.1.11
+Version: 0.1.13
 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-0.1.11.dist-info → gemmi_protools-0.1.13.dist-info}/RECORD

@@ -6,15 +6,15 @@ gemmi_protools/io/parse_pdb_header.py,sha256=UOGMsE3-d3APhO7zaAEE0NT31n-iqt55VpD
 gemmi_protools/io/parser.py,sha256=HFc4Kovr6rxEpLAEDUtF_e-RnA5OsWMeMFjuVNm7UYY,9507
 gemmi_protools/io/pdb_opts.py,sha256=laUqxlecOe6goax12q8EJGZuZbHyIGsXVucMV3gVrgg,5741
 gemmi_protools/io/peptide.py,sha256=a2wiEutJmvhl6gDCIzzqRCbmyknk2mwgy2FZ53lXclU,750
-gemmi_protools/io/reader.py,sha256=lI9JTXqsct3D719qVN7Dsvg-zHudElojpW5-odtXa8A,16527
+gemmi_protools/io/reader.py,sha256=2AXg1JdYT2LxL6jWVsJkLHQREwAoYR7V-g-hQVgSgGg,16237
 gemmi_protools/io/struct_info.py,sha256=9nBj1Zer03S8_Wks7L7uRlc9PlbfCKzoaT32pKR58X8,2769
 gemmi_protools/utils/__init__.py,sha256=F6e1xNT_7lZAWQgNIneH06o2qtWYrHNr_xPUPTwwx5E,29
 gemmi_protools/utils/align.py,sha256=CZcrvjy-ZbX2u7OAn-YGblbxaj9YFUDX4CFZcpbpnB8,6959
 gemmi_protools/utils/dockq.py,sha256=XmMwVEy-H4p6sH_HPcDWA3TP77OWdih0fE_BQJDr4pU,4189
-gemmi_protools/utils/fixer.py,sha256=RDmpoZpTrGdwuJQTTK1eif132MHV1I-T6Nt47ezgxTM,10236
+gemmi_protools/utils/fixer.py,sha256=WCk2BztM4tSKWp0EGoBFK4Rge330_7LPXNe2kmk-9f0,10046
 gemmi_protools/utils/ppi.py,sha256=VWYsdxWwQoS1xwEYj5KB96Zz3F8r5Eyuw6NT3ReD-wc,2330
-gemmi_protools-0.1.11.dist-info/licenses/LICENSE,sha256=JuQvKcgj6n11y5y6nXr9rABv3gJSswc4eTCd5WZBtSY,1062
-gemmi_protools-0.1.11.dist-info/METADATA,sha256=liLlq__4RA0P1MW4gE_HmpyGfqDPQPMF8n0E3sGpKN4,568
-gemmi_protools-0.1.11.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-gemmi_protools-0.1.11.dist-info/top_level.txt,sha256=P12mYJi5O5EKIn5u-RFaWxuix431CgLacSRD7rBid_U,15
-gemmi_protools-0.1.11.dist-info/RECORD,,
+gemmi_protools-0.1.13.dist-info/licenses/LICENSE,sha256=JuQvKcgj6n11y5y6nXr9rABv3gJSswc4eTCd5WZBtSY,1062
+gemmi_protools-0.1.13.dist-info/METADATA,sha256=pfbi9HsUmoRy6ABRoqTu5IrmaAs2ACc81On-37f1VuI,568
+gemmi_protools-0.1.13.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+gemmi_protools-0.1.13.dist-info/top_level.txt,sha256=P12mYJi5O5EKIn5u-RFaWxuix431CgLacSRD7rBid_U,15
+gemmi_protools-0.1.13.dist-info/RECORD,,