Merge pull request #249 from diogomart/clean_import_os

uniformize os.linesep as eol (no pathlib.os in Python 3.13)

meeko/analysis/fingerprint_interactions.py

@@ -4,8 +4,6 @@
 # Meeko
 #
 
-import os
-
 import numpy as np
 try:
     import pandas as pd

meeko/analysis/interactions.py

@@ -4,7 +4,6 @@
 # Meeko - Interactions
 #
 
-import os
 from abc import ABC, abstractmethod
 
 import numpy as np

meeko/bondtyper.py

@@ -4,11 +4,6 @@
 # Meeko bond typer
 #
 
-import os
-import sys
-from collections import defaultdict
-from operator import itemgetter
-
 
 class BondTyperLegacy:
 

meeko/cli/mk_export.py

@@ -7,6 +7,7 @@
 import gzip
 import pathlib
 import sys
+from os import linesep as eol
 import warnings
 import copy
 import numpy as np
@@ -143,10 +144,10 @@ def main():
                 iter_pose._positions = np.array([pdbqt_mol._positions[pose_id]])
                 iter_pose._pose_data['n_poses'] = 1  # Update the number of poses to reflect the reduction
                 iter_pose._current_pose = 0  # Reset to the first (and only) pose
-                pdb_string += "MODEL " + f"{model_nr:8}" + pathlib.os.linesep
+                pdb_string += "MODEL " + f"{model_nr:8}" + eol
                 pol_copy = copy.deepcopy(polymer)
                 pdb_string += export_pdb_updated_flexres(pol_copy, iter_pose)
-                pdb_string += "ENDMDL" + pathlib.os.linesep
+                pdb_string += "ENDMDL" + eol
             if write_pdb is None:
                 fn = pathlib.Path(filename).with_suffix("").name + f"{suffix}.pdb"
             else:

meeko/cli/mk_prepare_ligand.py

@@ -7,6 +7,7 @@
 from datetime import datetime
 import io
 import os
+from os import linesep as eol
 import sys
 import json
 import tarfile
@@ -333,7 +334,7 @@ def cmd_lineparser():
         sys.exit(2)
     is_covalent = num_required_covalent_args == 3
     if is_covalent and not _has_prody:
-        msg = "Covalent docking requires Prody which is not installed." + os.linesep
+        msg = "Covalent docking requires Prody which is not installed." + eol
         msg += "Installable from PyPI (pip install prody) or conda-forge (micromamba install prody)"
         print(_prody_import_error, file=sys.stderr)
         print(msg)

meeko/cli/mk_prepare_receptor.py

@@ -3,7 +3,7 @@
 import argparse
 import json
 import math
-from os import linesep as os_linesep
+from os import linesep as eol
 import pathlib
 import sys
 
@@ -265,19 +265,19 @@ def get_args():
     if args.read_pdb is None and args.read_with_prody is None:
         parser.print_help()
         msg = "Need input filename: use either -i/--read_with_prody or --read_pdb"
-        print(os_linesep + msg)
+        print(eol + msg)
         sys.exit(2)
 
     if args.read_pdb is not None and args.read_with_prody is not None:
         msg = "Can't use both -i/--read_with_prody and --read_pdb"
-        print(os_linesep + msg, file=sys.stderr)
+        print(eol + msg, file=sys.stderr)
         sys.exit(2)
 
     if args.write_gpf is not None and args.write_pdbqt is None:
         # there's a few of places that assume this condition has been checked
         msg = "--write_gpf requires --write_pdbqt because autogrid expects"
         msg += " the GPF file to point to the PDBQT file." 
-        print(os_linesep + msg)
+        print(eol + msg)
         sys.exit(2)
 
     skip_gpf = args.write_gpf is None and args.write_vina_box is None
@@ -397,7 +397,7 @@ def main():
             print(
                 "Command line error: repeated resname %s passed to --reactive_resname"
                 % resname
-                + os_linesep,
+                + eol,
                 file=sys.stderr,
             )
             sys.exit(2)
@@ -414,7 +414,7 @@ def main():
                 print(
                     "Command line error: repeated resid %s passed to --reactive_name_specific"
                     % res_id
-                    + os_linesep,
+                    + eol,
                     file=sys.stderr,
                 )
                 sys.exit(2)
@@ -439,7 +439,7 @@ def main():
     # Evaluate compatibility with other options
     if len(reactive_flexres) != 1 and args.box_center_off_reactive_res:
         msg = (
-            "--box_center_off_reactive_res can be used only with one reactive" + os_linesep
+            "--box_center_off_reactive_res can be used only with one reactive" + eol
         )
         msg += "residue, but %d reactive residues are set" % len(reactive_flexres_name)
         print("Command line error:" + msg, file=sys.stderr)
@@ -539,7 +539,7 @@ def main():
                 reactive_flexres_name[res_id] = reactive_atom[input_resname]
             else:
                 print("no default reactive name for %s, " % input_resname)
-                print("use --reactive_name or --reactive_name_specific" + os_linesep)
+                print("use --reactive_name or --reactive_name_specific" + eol)
                 sys.exit(2)
 
     # Print nonreactive and reactive flexible residues specs
@@ -680,12 +680,12 @@ def warn_flexres_outside_box(polymer, box_center, box_size):
                     continue
                 if gridbox.is_point_outside_box(atom.coord, box_center, box_size, spacing=1.0):
                     print(
-                        "WARNING: Flexible residue outside box." + os_linesep,
+                        "WARNING: Flexible residue outside box." + eol,
                         file=sys.stderr,
                     )
                     print(
                         "WARNING: Strongly recommended to use a box that encompasses flexible residues."
-                        + os_linesep,
+                        + eol,
                         file=sys.stderr,
                     )
                     break  # only need to warn once
@@ -850,7 +850,7 @@ def warn_flexres_outside_box(polymer, box_center, box_size):
                 any_lig_reac_types.append(reactive_typer.get_reactive_atype(t, order))
 
         rec_reac_types = []
-        for line in all_flex_pdbqt.split(os_linesep):
+        for line in all_flex_pdbqt.split(eol):
             if line.startswith("ATOM") or line.startswith("HETATM"):
                 atype = line[77:].strip()
                 basetype, _ = reactive_typer.get_basetype_and_order(atype)
@@ -869,7 +869,7 @@ def warn_flexres_outside_box(polymer, box_center, box_size):
         if len(collisions) > 0:
             collision_str = ""
             for t1, t2 in collisions:
-                collision_str += "%3s %3s" % (t1, t2) + os_linesep
+                collision_str += "%3s %3s" % (t1, t2) + eol
             collision_fn = str(outpath.with_suffix(".atype_collisions"))
             written_files_log["filename"].append(collision_fn)
             written_files_log["description"].append(
@@ -887,19 +887,19 @@ def warn_flexres_outside_box(polymer, box_center, box_size):
         all_types = []
         for basetype, reactypes in derivtypes.items():
             all_types.append(basetype)
-            map_block += "map %s.%s.map" % (map_prefix, basetype) + os_linesep
+            map_block += "map %s.%s.map" % (map_prefix, basetype) + eol
             for reactype in reactypes:
                 all_types.append(reactype)
-                map_block += "map %s.%s.map" % (map_prefix, basetype) + os_linesep
-        config = "ligand_types " + " ".join(all_types) + os_linesep
-        config += "fld %s.maps.fld" % map_prefix + os_linesep
+                map_block += "map %s.%s.map" % (map_prefix, basetype) + eol
+        config = "ligand_types " + " ".join(all_types) + eol
+        config += "fld %s.maps.fld" % map_prefix + eol
         config += map_block
 
         # in modpairs (dict): types are keys, parameters are values
         # now we will write a configuration file with nbp keywords
         # that AD-GPU reads using the --import_dpf flag
         # nbp stands for "non-bonded potential" or "non-bonded pairwise"
-        line = "intnbp_r_eps %8.6f %8.6f %3d %3d %4s %4s" + os_linesep
+        line = "intnbp_r_eps %8.6f %8.6f %3d %3d %4s %4s" + eol
         nbp_count = 0
         for (t1, t2), param in modpairs.items():
             config += line % (param["r_eq"], param["eps"], param["n"], param["m"], t1, t2)

meeko/gridbox.py

@@ -1,4 +1,4 @@
-from os import linesep as os_linesep
+from os import linesep as eol
 import pathlib
 import numpy as np
 
@@ -82,7 +82,7 @@ def box_to_pdb_string(box_center, npts, spacing=0.375):
     res = "BOX"
     chain = "X"
     pdb_out = ""
-    line = "ATOM  %5d %4s %3s %1s%4d    %8.3f%8.3f%8.3f  1.00 10.00          %1s" + os_linesep
+    line = "ATOM  %5d %4s %3s %1s%4d    %8.3f%8.3f%8.3f  1.00 10.00          %1s" + eol
     for idx in range(len(corners)):
         x = corners[idx][0]
         y = corners[idx][1]
@@ -93,18 +93,18 @@ def box_to_pdb_string(box_center, npts, spacing=0.375):
     # center
     pdb_out += line % (count+1, "Xe", res, chain, idx+1, center_x, center_y, center_z, "Xe")
 
-    pdb_out += "CONECT    1    2" + os_linesep
-    pdb_out += "CONECT    1    4" + os_linesep
-    pdb_out += "CONECT    1    5" + os_linesep
-    pdb_out += "CONECT    2    3" + os_linesep
-    pdb_out += "CONECT    2    6" + os_linesep
-    pdb_out += "CONECT    3    4" + os_linesep
-    pdb_out += "CONECT    3    7" + os_linesep
-    pdb_out += "CONECT    4    8" + os_linesep
-    pdb_out += "CONECT    5    6" + os_linesep
-    pdb_out += "CONECT    5    8" + os_linesep
-    pdb_out += "CONECT    6    7" + os_linesep
-    pdb_out += "CONECT    7    8" + os_linesep
+    pdb_out += "CONECT    1    2" + eol
+    pdb_out += "CONECT    1    4" + eol
+    pdb_out += "CONECT    1    5" + eol
+    pdb_out += "CONECT    2    3" + eol
+    pdb_out += "CONECT    2    6" + eol
+    pdb_out += "CONECT    3    4" + eol
+    pdb_out += "CONECT    3    7" + eol
+    pdb_out += "CONECT    4    8" + eol
+    pdb_out += "CONECT    5    6" + eol
+    pdb_out += "CONECT    5    8" + eol
+    pdb_out += "CONECT    6    7" + eol
+    pdb_out += "CONECT    7    8" + eol
     return pdb_out
 
 def is_point_outside_box(point, center, npts, spacing=0.375):
@@ -156,5 +156,5 @@ def box_to_vina_string(gridcenter, gridsizes):
     sizes_str = "\n".join([f"size_{d} = {gridsizes[i]:.3f}" for i, d in enumerate(dims)])
     return centers_str + "\n" + sizes_str
 
-boron_silicon_atompar  = "atom_par Si     4.10  0.200  35.8235  -0.00143  0.0  0.0  0  -1  -1  6" + os_linesep
-boron_silicon_atompar += "atom_par B      3.84  0.155  29.6478  -0.00152  0.0  0.0  0  -1  -1  0" + os_linesep
+boron_silicon_atompar  = "atom_par Si     4.10  0.200  35.8235  -0.00143  0.0  0.0  0  -1  -1  6" + eol
+boron_silicon_atompar += "atom_par B      3.84  0.155  29.6478  -0.00152  0.0  0.0  0  -1  -1  0" + eol