gemmi-protools 0.1.7__py3-none-any.whl → 0.1.9__py3-none-any.whl

gemmi_protools/utils/fixer.py

@@ -6,22 +6,39 @@ import gzip
 import io
 import os
 import pathlib
+import re
 import shutil
 import subprocess
 import time
 import uuid
-from typing import Union, Optional
+from typing import Union
 
+import openmm
 import pdbfixer
 from openmm import app
 from typeguard import typechecked
 
+from gemmi_protools import StructureParser
 from gemmi_protools.io.cif_opts import _is_cif
 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], cpu_platform=True) -> pdbfixer.PDBFixer:
+    """
+
+    Args:
+        path:
+        cpu_platform: default True, if False, auto select platform
+
+    Returns:
+
+    """
+    if cpu_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 +46,15 @@ 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
@@ -51,8 +68,8 @@ def clean_structure(input_file: Union[str, pathlib.Path],
                     keep_heterogens: str = "all",
                     replace_nonstandard: bool = True,
                     ph: Union[float, int] = 7.0,
-                    check_mode: bool = True,
-                    threshold: float = 0.3,
+                    cpu_platform=True,
+                    clean_connect=True
                     ):
     """
 
@@ -71,8 +88,8 @@ 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 cpu_platform: default True to use CPU platform, if False, auto select platform
+    :param clean_connect: default True to clean CONECT lines in output pdb
 
     :return:
         str, status message of fixing
@@ -85,16 +102,14 @@ def clean_structure(input_file: Union[str, pathlib.Path],
         ######################################################
         # load structure
         ######################################################
-        fixer = _load_by_pbdfixer(input_file)
+        fixer = _load_by_pbdfixer(input_file, cpu_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)
+        ratio = "%.2f" % (len(fixer.missingAtoms) / fixer.topology.getNumResidues(),)
 
         ######################################################
         # replace non-standard residues
@@ -149,73 +164,94 @@ def clean_structure(input_file: Union[str, pathlib.Path],
         msg_str = "Finished"
     except Exception as e:
         msg_str = str(e)
+        ratio = "*"
+    else:
+        if clean_connect:
+            output_lines = []
+            with open(output_file, "r") as in_handle:
+                for line in in_handle:
+                    if not re.match("CONECT", line):
+                        output_lines.append(line)
+            with open(output_file, "w") as out_handle:
+                print("".join(output_lines), file=out_handle)
 
-    return dict(input=input_file, msg=msg_str)
+    return dict(input=input_file, msg=msg_str, res_ratio_with_missing_atoms=ratio)
 
 
 @typechecked
-def move_with_overwrite(src_folder: str, dst_folder: str, filename: str):
-    assert os.path.isdir(src_folder)
-    assert os.path.isdir(dst_folder)
-
-    src_path = os.path.join(src_folder, filename)
-    dst_path = os.path.join(dst_folder, filename)
-
-    if os.path.exists(dst_path):
-        os.remove(dst_path)
-    shutil.move(src_path, dst_folder)
-
+def repair_structure(input_file: str,
+                     output_file: str,
+                     complex_with_dna: bool = False,
+                     complex_with_rna: bool = False,
+                     timeout: Union[int, float] = 3600):
+    """
 
-@typechecked
-def repair_structure(input_file: Union[str, pathlib.Path],
-                     out_dir: Union[str, pathlib.Path],
-                     temp_dir: Union[str, pathlib.Path],
-                     foldx_path: Optional[str] = None,
-                     timeout=3600):
+    :param input_file: .pdb or .cif or .pdb.gz or .cif.gz
+    :param output_file: .pdb file
+    :param complex_with_dna: bool, default False, not debug yet
+    :param complex_with_rna: bool, default False, not debug yet
+    :param timeout: float or int
+    :return:
+    """
+    ############################################################
+    # Check and convert input_file to .pdb if not
+    ############################################################
+    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):
-        raise NotADirectoryError(out_dir)
-
-    if not os.path.isdir(temp_dir):
-        raise NotADirectoryError(temp_dir)
-
-    in_path = pathlib.Path(input_file).expanduser().resolve()
-    pdb_dir = str(in_path.parent)
-    pdb_file = str(in_path.name)
-    if not os.path.isfile(input_file):
-        raise FileNotFoundError(input_file)
-
-    assert pdb_dir != str(out_dir), "output directory can't be the directory of input_file"
+        os.makedirs(out_dir)
+
+    temp_dir = os.path.join(out_dir, "_RepairTemp_%s" % str(uuid.uuid4()))
+    if os.path.isdir(temp_dir):
+        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
 
-    stem_name = in_path.stem
+    foldx_path = shutil.which("foldx")
+    if foldx_path is None:
+        raise RuntimeError("path of foldx is not set or found in PATH")
 
-    # create temp dir
-    sub_temp_dir = os.path.join(temp_dir, "%s_%s" % (stem_name, str(uuid.uuid4())))
+    cwd_dir = os.getcwd()
 
-    if os.path.isdir(sub_temp_dir):
-        shutil.rmtree(sub_temp_dir)
+    repair_cmd = [foldx_path,
+                  "-c RepairPDB",
+                  "--pdb %s" % file_name_r,
+                  "--pdb-dir %s" % in_dir_r,
+                  "--output-dir %s" % temp_dir
+                  ]
+    if complex_with_dna:
+        repair_cmd.append("--complexWithDNA true")
 
-    os.makedirs(sub_temp_dir)
+    if complex_with_rna:
+        repair_cmd.append("--complexWithRNA true")
 
-    if foldx_path is None:
-        foldx_path = shutil.which("foldx")
-
-    if foldx_path is None:
-        raise RuntimeError("path of foldx is not set or found in PATH")
-
-    old_dir = os.getcwd()
-    command_settings = ["cd %s" % sub_temp_dir,
-                        "&&",
-                        foldx_path,
-                        "-c RepairPDB",
-                        "--pdb %s" % pdb_file,
-                        "--pdb-dir %s" % pdb_dir,
-                        "--output-dir %s" % sub_temp_dir,
-                        "&&",
-                        "cd %s" % old_dir
-                        ]
+    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,
                                 stdout=subprocess.PIPE, stderr=subprocess.PIPE,
@@ -224,22 +260,19 @@ def repair_structure(input_file: Union[str, pathlib.Path],
         if result.returncode == 0:
             msg_str = "Finished"
         else:
-            msg_str = result.stderr
-
-        result_file = os.path.join(sub_temp_dir, "%s_Repair.pdb" % stem_name)
-        fxout_file = os.path.join(sub_temp_dir, "%s_Repair.fxout" % stem_name)
-        if os.path.exists(result_file) and os.path.exists(fxout_file):
-            move_with_overwrite(sub_temp_dir, out_dir, "%s_Repair.pdb" % stem_name)
-            move_with_overwrite(sub_temp_dir, out_dir, "%s_Repair.fxout" % stem_name)
-    except subprocess.CalledProcessError as e:
-        # Handle errors in the called executable
-        msg_str = e.stderr
+            msg_str = str(result.stderr)
     except Exception as e:
-        # Handle other exceptions such as file not found or permissions issues
-        msg_str = str(e).encode()
+        msg_str = str(e)
+    else:
+        if msg_str == "Finished":
+            # just keep .pdb, ignore .fxout
+            result_file = os.path.join(temp_dir, "%s_Repair.pdb" % stem_name)
+            if os.path.exists(result_file):
+                shutil.move(result_file, output_file)
+            else:
+                msg_str = "result file not found"
     finally:
-        # clean sub temp
-        if os.path.isdir(sub_temp_dir):
-            shutil.rmtree(sub_temp_dir)
+        if os.path.isdir(temp_dir):
+            shutil.rmtree(temp_dir)
     end = time.time()
-    return dict(input=input_file, msg=msg_str, use_time=round(end - start, 1))
+    return dict(input=input_file, output=output_file, msg=msg_str, use_time=round(end - start, 1))

{gemmi_protools-0.1.7.dist-info → gemmi_protools-0.1.9.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: gemmi_protools
-Version: 0.1.7
+Version: 0.1.9
 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-0.1.7.dist-info → gemmi_protools-0.1.9.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=WUiIoK8dFPGUkXlK-wiiWyorYD8T71rN7WDE2psGSiE,9061
+gemmi_protools/utils/fixer.py,sha256=RDmpoZpTrGdwuJQTTK1eif132MHV1I-T6Nt47ezgxTM,10236
 gemmi_protools/utils/ppi.py,sha256=VWYsdxWwQoS1xwEYj5KB96Zz3F8r5Eyuw6NT3ReD-wc,2330
-gemmi_protools-0.1.7.dist-info/licenses/LICENSE,sha256=JuQvKcgj6n11y5y6nXr9rABv3gJSswc4eTCd5WZBtSY,1062
-gemmi_protools-0.1.7.dist-info/METADATA,sha256=tsp4fzE0T7lTsmPaRYK5UzgqS4OjrvOSfESFMqbkk0Y,567
-gemmi_protools-0.1.7.dist-info/WHEEL,sha256=zaaOINJESkSfm_4HQVc5ssNzHCPXhJm0kEUakpsEHaU,91
-gemmi_protools-0.1.7.dist-info/top_level.txt,sha256=P12mYJi5O5EKIn5u-RFaWxuix431CgLacSRD7rBid_U,15
-gemmi_protools-0.1.7.dist-info/RECORD,,
+gemmi_protools-0.1.9.dist-info/licenses/LICENSE,sha256=JuQvKcgj6n11y5y6nXr9rABv3gJSswc4eTCd5WZBtSY,1062
+gemmi_protools-0.1.9.dist-info/METADATA,sha256=OFqx1MONnQTZ7b65AspnNX0FIvtrE2gQVWT7yCTGhqE,567
+gemmi_protools-0.1.9.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+gemmi_protools-0.1.9.dist-info/top_level.txt,sha256=P12mYJi5O5EKIn5u-RFaWxuix431CgLacSRD7rBid_U,15
+gemmi_protools-0.1.9.dist-info/RECORD,,

{gemmi_protools-0.1.7.dist-info → gemmi_protools-0.1.9.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (80.8.0)
+Generator: setuptools (80.9.0)
 Root-Is-Purelib: true
 Tag: py3-none-any