gemmi-protools 0.1.6__py3-none-any.whl → 0.1.8__py3-none-any.whl

gemmi_protools/utils/fixer.py

@@ -14,6 +14,7 @@ from typing import Union, Optional
 
 import pdbfixer
 from openmm import app
+import openmm
 from typeguard import typechecked
 
 from gemmi_protools.io.cif_opts import _is_cif
@@ -21,7 +22,21 @@ from gemmi_protools.io.pdb_opts import _is_pdb
 
 
 @typechecked
-def _load_by_pbdfixer(path: Union[str, pathlib.Path]) -> pdbfixer.PDBFixer:
+def _load_by_pbdfixer(path: Union[str, pathlib.Path], use_platform=True) -> pdbfixer.PDBFixer:
+    """
+
+    Args:
+        path:
+        use_platform: default True, if False, auto select platform
+
+    Returns:
+
+    """
+    if use_platform:
+        platform = openmm.Platform.getPlatformByName('CPU')
+    else:
+        platform = None
+
     cur_path = pathlib.Path(path)
     if _is_pdb(path) or _is_cif(path):
         s1 = cur_path.suffixes[-1]
@@ -29,15 +44,15 @@ def _load_by_pbdfixer(path: Union[str, pathlib.Path]) -> pdbfixer.PDBFixer:
 
         if s1 in [".pdb", ".cif"]:
             # s1 suffix
-            fixer = pdbfixer.PDBFixer(filename=path)
+            fixer = pdbfixer.PDBFixer(filename=path, platform=platform)
         else:
             # s2 suffix
             with gzip.open(path, "rb") as gz_handle:
                 with io.TextIOWrapper(gz_handle, encoding="utf-8") as text_io:
                     if s2 == ".pdb.gz":
-                        fixer = pdbfixer.PDBFixer(pdbfile=text_io)
+                        fixer = pdbfixer.PDBFixer(pdbfile=text_io, platform=platform)
                     else:
-                        fixer = pdbfixer.PDBFixer(pdbxfile=text_io)
+                        fixer = pdbfixer.PDBFixer(pdbxfile=text_io, platform=platform)
     else:
         raise ValueError("Only support .cif, .cif.gz, .pdb or .pdb.gz file, but got %s" % path)
     return fixer
@@ -50,7 +65,10 @@ def clean_structure(input_file: Union[str, pathlib.Path],
                     add_missing_atoms: str = "heavy",
                     keep_heterogens: str = "all",
                     replace_nonstandard: bool = True,
-                    ph: Union[float, int] = 7.0
+                    ph: Union[float, int] = 7.0,
+                    check_mode: bool = True,
+                    threshold: float = 0.3,
+                    use_platform=True
                     ):
     """
 
@@ -69,6 +87,10 @@ def clean_structure(input_file: Union[str, pathlib.Path],
             none: remove all heterogens
     :param replace_nonstandard: default True, replace all non-standard residues to standard ones
     :param ph: default 7.0, ph values to add missing hydrogen atoms
+    :param check_mode: default True to check the ratio of residues with missing atoms
+    :param threshold: float, default 0.3, only use when check_mode=True
+    :param use_platform: default True to use CPU platform, if False, auto select platform
+
     :return:
         str, status message of fixing
         if successful, return Finish, otherwise message of error
@@ -80,7 +102,16 @@ def clean_structure(input_file: Union[str, pathlib.Path],
         ######################################################
         # load structure
         ######################################################
-        fixer = _load_by_pbdfixer(input_file)
+        fixer = _load_by_pbdfixer(input_file, use_platform=use_platform)
+
+        ######################################################
+        # check
+        ######################################################
+        fixer.findMissingResidues()
+        fixer.findMissingAtoms()
+        ratio = len(fixer.missingAtoms) / fixer.topology.getNumResidues()
+        if ratio > threshold:
+            return dict(input=input_file, msg="Too many residues with missing atoms: %.2f" % ratio)
 
         ######################################################
         # replace non-standard residues

{gemmi_protools-0.1.6.dist-info → gemmi_protools-0.1.8.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: gemmi_protools
-Version: 0.1.6
+Version: 0.1.8
 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-0.1.6.dist-info → gemmi_protools-0.1.8.dist-info}/RECORD

@@ -11,10 +11,10 @@ gemmi_protools/io/struct_info.py,sha256=9nBj1Zer03S8_Wks7L7uRlc9PlbfCKzoaT32pKR5
 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=f1MAeYkFukijaBwTdINO0733Qbe5B9xSgRCE69nHkN4,8396
+gemmi_protools/utils/fixer.py,sha256=oiNtLCjQLFk4JHeO4exEkMH8QoEiKsJZIJRebkGGfBM,9545
 gemmi_protools/utils/ppi.py,sha256=VWYsdxWwQoS1xwEYj5KB96Zz3F8r5Eyuw6NT3ReD-wc,2330
-gemmi_protools-0.1.6.dist-info/licenses/LICENSE,sha256=JuQvKcgj6n11y5y6nXr9rABv3gJSswc4eTCd5WZBtSY,1062
-gemmi_protools-0.1.6.dist-info/METADATA,sha256=N8Os-XHbUKuRDyQw0Z3MjtYy5Z5fqLFpP1sxEZnoEbU,567
-gemmi_protools-0.1.6.dist-info/WHEEL,sha256=Nw36Djuh_5VDukK0H78QzOX-_FQEo6V37m3nkm96gtU,91
-gemmi_protools-0.1.6.dist-info/top_level.txt,sha256=P12mYJi5O5EKIn5u-RFaWxuix431CgLacSRD7rBid_U,15
-gemmi_protools-0.1.6.dist-info/RECORD,,
+gemmi_protools-0.1.8.dist-info/licenses/LICENSE,sha256=JuQvKcgj6n11y5y6nXr9rABv3gJSswc4eTCd5WZBtSY,1062
+gemmi_protools-0.1.8.dist-info/METADATA,sha256=j0xy5aqbEvdlqoNrEdCSiBpmLVOpe3URit-85PBWa1s,567
+gemmi_protools-0.1.8.dist-info/WHEEL,sha256=zaaOINJESkSfm_4HQVc5ssNzHCPXhJm0kEUakpsEHaU,91
+gemmi_protools-0.1.8.dist-info/top_level.txt,sha256=P12mYJi5O5EKIn5u-RFaWxuix431CgLacSRD7rBid_U,15
+gemmi_protools-0.1.8.dist-info/RECORD,,

{gemmi_protools-0.1.6.dist-info → gemmi_protools-0.1.8.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (80.7.1)
+Generator: setuptools (80.8.0)
 Root-Is-Purelib: true
 Tag: py3-none-any