Merge branch 'issue-#82/replace-libpopt-in-rbcavity' of github.com:CB…

…DD/rDock into issue-#82/replace-libpopt-in-rbcavity

rdock-utils/pyproject.toml

@@ -18,6 +18,7 @@ sdtether = "rdock_utils.sdtether.main:main"
 sdtether_old = "rdock_utils.sdtether_original:main"
 sdfilter = "rdock_utils.sdfilter.main:main"
 sdmodify = "rdock_utils.sdmodify:main"
+sdsort = "rdock_utils.sdsort:main"
 
 [project.urls]
 Repository = "https://github.com/CBDD/rDock.git"

rdock-utils/rdock_utils/common/SDFParser.py

@@ -107,3 +107,11 @@ def read_molecules(file: TextIO) -> Generator[FastSDMol, None, None]:
 
 def read_molecules_from_all_inputs(inputs: Iterable[TextIO]) -> Iterable[FastSDMol]:
     return itertools.chain.from_iterable(read_molecules(source) for source in inputs)
+
+
+def molecules_with_progress_log(molecules: Iterable[FastSDMol], count: int = 1000) -> Iterable[FastSDMol]:
+    for i, molecule in enumerate(molecules):
+        if i % count == 0:
+            logger.info(f"read {i} molecules")
+
+        yield molecule

rdock-utils/rdock_utils/common/__init__.py

@@ -1,5 +1,5 @@
 from .files import inputs_generator
-from .SDFParser import FastSDMol, read_molecules, read_molecules_from_all_inputs
+from .SDFParser import FastSDMol, molecules_with_progress_log, read_molecules, read_molecules_from_all_inputs
 from .superpose3d import MolAlignmentData, Superpose3D, update_coordinates
 from .types import (
     AtomsMapping,
@@ -19,6 +19,7 @@
     "FastSDMol",
     "read_molecules",
     "read_molecules_from_all_inputs",
+    "molecules_with_progress_log",
     # -- superpose3d --
     "update_coordinates",
     "MolAlignmentData",

rdock-utils/rdock_utils/common/files.py

@@ -2,7 +2,7 @@
 from typing import Generator, TextIO
 
 
-def inputs_generator(inputs: list[str]) -> Generator[TextIO, None, None]:
+def inputs_generator(inputs: list[str] | None) -> Generator[TextIO, None, None]:
     if not inputs:
         yield sys.stdin
     else: