im-rdkit-utilities 1.2.0__tar.gz

im_rdkit_utilities-1.2.0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2026 Informatics Matters Ltd
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

im_rdkit_utilities-1.2.0/MANIFEST.in

@@ -0,0 +1,4 @@
+include LICENSE
+# setup.py reads this to populate install_requires, so the sdist needs it
+# to be buildable (and therefore installable) on its own.
+include requirements.txt

im_rdkit_utilities-1.2.0/PKG-INFO

@@ -0,0 +1,164 @@
+Metadata-Version: 2.4
+Name: im-rdkit-utilities
+Version: 1.2.0
+Summary: RDKit utilities for Squonk2 Data Manager Jobs
+Home-page: https://github.com/informaticsmatters/squonk2-rdkit-utilities
+Author: Informatics Matters
+Author-email: info@informaticsmatters.com
+License: MIT
+Keywords: rdkit
+Platform: any
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Environment :: Other Environment
+Classifier: Intended Audience :: Developers
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Classifier: Topic :: Software Development :: Libraries :: Python Modules
+Classifier: Operating System :: POSIX :: Linux
+Requires-Python: >=3.10
+License-File: LICENSE
+Requires-Dist: rdkit>=2026.3.6
+Requires-Dist: im-data-manager-job-utilities>=1.3.0
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: home-page
+Dynamic: keywords
+Dynamic: license
+Dynamic: license-file
+Dynamic: platform
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
+
+Informatics Matters RDKit Utilities
+====================================
+
+.. image:: https://badge.fury.io/py/im-rdkit-utilities.svg
+   :target: https://badge.fury.io/py/im-rdkit-utilities
+   :alt: PyPI package (latest)
+
+.. image:: https://github.com/InformaticsMatters/squonk2-rdkit-utilities/actions/workflows/build.yaml/badge.svg
+   :target: https://github.com/InformaticsMatters/squonk2-rdkit-utilities/actions/workflows/build.yaml
+   :alt: Build
+
+.. image:: https://github.com/InformaticsMatters/squonk2-rdkit-utilities/actions/workflows/publish.yaml/badge.svg
+   :target: https://github.com/InformaticsMatters/squonk2-rdkit-utilities/actions/workflows/publish.yaml
+   :alt: Publish
+
+A Python package of RDKit-specific helpers shared by **Squonk2 Data Manager
+Jobs**: molecule readers/writers over SDF and delimited-SMILES text formats,
+fragment selection, and a handful of small molecule-inspection helpers.
+
+This consolidates the ``rdkit_utils.py`` module that had been copy-pasted,
+and had begun to diverge, across several Job repositories
+(``squonk2-desc-rdkit``, ``squonk2-desc-mordred``, ``squonk2-jaqpot`` and
+``virtual-screening``) into a single, tested, authoritative source.
+
+Installation (Python)
+======================
+
+The package is published on `PyPI`_ and can be installed from there::
+
+    pip install im-rdkit-utilities
+
+Once installed, import it as ``rdkit_utils`` (matching the module name it
+replaces, so existing call sites need no changes beyond the import path)::
+
+    >>> import rdkit_utils
+    >>> reader = rdkit_utils.create_reader('molecules.smi', delimiter='\t')
+
+Public surface
+==============
+
+- ``create_reader()`` / ``create_writer()`` — construct a reader/writer for
+  a .sdf, .sdf.gz or delimited-SMILES file, based on its extension.
+- ``SdfReader`` / ``SdfWriter`` / ``SmilesReader`` / ``SmilesWriter`` — the
+  underlying reader/writer implementations.
+- ``generate_headers()`` — build output headers for a tab/comma separated
+  file, given the ID column configuration.
+- ``fragment()`` — pick the largest fragment of a (typically salted)
+  molecule, by heavy-atom count or molecular weight.
+- ``fragmentAndFingerprint()`` — fragment a stream of molecules and
+  fingerprint the result.
+- ``get_num_chiral_centers()`` / ``get_num_sp3_centres()`` — small
+  molecule-inspection helpers.
+- ``check_molecules_are_3d()`` — check whether the molecules in a .sdf file
+  have 3D conformers.
+- ``rdk_read_single_mol()`` / ``rdk_read_mols()`` / ``rdk_read_molecule_files()``
+  / ``rdk_merge_mols()`` / ``rdk_mol_supplier()`` / ``sdf_record_gen()`` —
+  molecule-file reading helpers.
+- ``updateChargeFlagInAtomBlock()`` — adds the legacy charge-flag encoding
+  to a full CTAB molblock (counts line included), for tools such as rDock
+  that only understand the old syntax. This is **not** the same as
+  ``dm_job_utilities.utils.update_charge_flag_in_atom_block()``, which
+  operates on just the atom-block portion of a molblock (one line further
+  in) — the two take different input shapes and are not interchangeable.
+  This RDKit-oriented variant lives here because it's used directly
+  alongside the readers/writers above; the job-utilities function remains
+  the natural home for pure string manipulation with no RDKit dependency.
+
+Command-line helpers
+====================
+
+- ``add_common_molecule_io_args(parser)`` — adds the "Input/output options"
+  argument group shared by the molecule processing Jobs (``-i/--infile``,
+  ``-o/--outfile``, ``-d/--delimiter``, ``--id-column``, ``--mol-column``,
+  ``--read-header``, ``--write-header``, ``--read-records``,
+  ``-k/--omit-fields``, and optionally ``--y-column``), and returns the group
+  so more options can be added to it. Keyword arguments ``output_default``,
+  ``output_required`` and ``include_y_column`` cover the variations between
+  Jobs.
+- ``str_or_int()`` — an argparse ``type`` for a column specifier given either
+  as a zero-based index or as a field name.
+
+The group's namespace feeds ``create_reader()`` directly::
+
+    >>> import argparse, rdkit_utils
+    >>> from dm_job_utilities.utils import read_delimiter
+    >>> parser = argparse.ArgumentParser()
+    >>> _ = rdkit_utils.add_common_molecule_io_args(parser)
+    >>> args = parser.parse_args(['-i', 'molecules.smi', '-d', 'tab'])
+    >>> reader = rdkit_utils.create_reader(
+    ...     args.input,
+    ...     delimiter=read_delimiter(args.delimiter),
+    ...     read_header=args.read_header,
+    ...     id_column=args.id_column,
+    ...     mol_column=args.mol_column,
+    ...     read_records=args.read_records,
+    ... )
+
+``--infile`` and ``--outfile`` are the canonical long spellings. The parsed
+values are always available as ``args.input`` and ``args.output``.
+
+``--input`` and ``--output`` are **deprecated aliases**, retained only so that
+adopting the helper did not break existing Job manifests. They are due to be
+removed — see `issue #5
+<https://github.com/InformaticsMatters/squonk2-rdkit-utilities/issues/5>`_. Job
+Definitions should invoke ``-i``/``-o``: they are canonical, unaffected by that
+removal, and work against container images built before the Job adopted the
+helper.
+
+Defaults follow the ``create_reader()`` / ``create_writer()`` signatures rather
+than the values the Job scripts hand-type today — in particular ``--mol-column``
+defaults to ``None`` so that ``SmilesReader`` can infer it, where most Jobs
+currently pass an explicit ``0``.
+
+Progress and cost reporting (``--interval``, ``ProgressReporter``) is
+deliberately **not** here — that is a Data Manager logging concern and lives in
+`im-data-manager-job-utilities`_.
+
+.. _PyPI: https://pypi.org/project/im-rdkit-utilities
+.. _im-data-manager-job-utilities: https://pypi.org/project/im-data-manager-job-utilities
+
+Get in touch
+============
+
+- Report bugs, suggest features or view the source code `on GitHub`_.
+
+.. _on GitHub: https://github.com/informaticsmatters/squonk2-rdkit-utilities

im_rdkit_utilities-1.2.0/README.rst

@@ -0,0 +1,126 @@
+Informatics Matters RDKit Utilities
+====================================
+
+.. image:: https://badge.fury.io/py/im-rdkit-utilities.svg
+   :target: https://badge.fury.io/py/im-rdkit-utilities
+   :alt: PyPI package (latest)
+
+.. image:: https://github.com/InformaticsMatters/squonk2-rdkit-utilities/actions/workflows/build.yaml/badge.svg
+   :target: https://github.com/InformaticsMatters/squonk2-rdkit-utilities/actions/workflows/build.yaml
+   :alt: Build
+
+.. image:: https://github.com/InformaticsMatters/squonk2-rdkit-utilities/actions/workflows/publish.yaml/badge.svg
+   :target: https://github.com/InformaticsMatters/squonk2-rdkit-utilities/actions/workflows/publish.yaml
+   :alt: Publish
+
+A Python package of RDKit-specific helpers shared by **Squonk2 Data Manager
+Jobs**: molecule readers/writers over SDF and delimited-SMILES text formats,
+fragment selection, and a handful of small molecule-inspection helpers.
+
+This consolidates the ``rdkit_utils.py`` module that had been copy-pasted,
+and had begun to diverge, across several Job repositories
+(``squonk2-desc-rdkit``, ``squonk2-desc-mordred``, ``squonk2-jaqpot`` and
+``virtual-screening``) into a single, tested, authoritative source.
+
+Installation (Python)
+======================
+
+The package is published on `PyPI`_ and can be installed from there::
+
+    pip install im-rdkit-utilities
+
+Once installed, import it as ``rdkit_utils`` (matching the module name it
+replaces, so existing call sites need no changes beyond the import path)::
+
+    >>> import rdkit_utils
+    >>> reader = rdkit_utils.create_reader('molecules.smi', delimiter='\t')
+
+Public surface
+==============
+
+- ``create_reader()`` / ``create_writer()`` — construct a reader/writer for
+  a .sdf, .sdf.gz or delimited-SMILES file, based on its extension.
+- ``SdfReader`` / ``SdfWriter`` / ``SmilesReader`` / ``SmilesWriter`` — the
+  underlying reader/writer implementations.
+- ``generate_headers()`` — build output headers for a tab/comma separated
+  file, given the ID column configuration.
+- ``fragment()`` — pick the largest fragment of a (typically salted)
+  molecule, by heavy-atom count or molecular weight.
+- ``fragmentAndFingerprint()`` — fragment a stream of molecules and
+  fingerprint the result.
+- ``get_num_chiral_centers()`` / ``get_num_sp3_centres()`` — small
+  molecule-inspection helpers.
+- ``check_molecules_are_3d()`` — check whether the molecules in a .sdf file
+  have 3D conformers.
+- ``rdk_read_single_mol()`` / ``rdk_read_mols()`` / ``rdk_read_molecule_files()``
+  / ``rdk_merge_mols()`` / ``rdk_mol_supplier()`` / ``sdf_record_gen()`` —
+  molecule-file reading helpers.
+- ``updateChargeFlagInAtomBlock()`` — adds the legacy charge-flag encoding
+  to a full CTAB molblock (counts line included), for tools such as rDock
+  that only understand the old syntax. This is **not** the same as
+  ``dm_job_utilities.utils.update_charge_flag_in_atom_block()``, which
+  operates on just the atom-block portion of a molblock (one line further
+  in) — the two take different input shapes and are not interchangeable.
+  This RDKit-oriented variant lives here because it's used directly
+  alongside the readers/writers above; the job-utilities function remains
+  the natural home for pure string manipulation with no RDKit dependency.
+
+Command-line helpers
+====================
+
+- ``add_common_molecule_io_args(parser)`` — adds the "Input/output options"
+  argument group shared by the molecule processing Jobs (``-i/--infile``,
+  ``-o/--outfile``, ``-d/--delimiter``, ``--id-column``, ``--mol-column``,
+  ``--read-header``, ``--write-header``, ``--read-records``,
+  ``-k/--omit-fields``, and optionally ``--y-column``), and returns the group
+  so more options can be added to it. Keyword arguments ``output_default``,
+  ``output_required`` and ``include_y_column`` cover the variations between
+  Jobs.
+- ``str_or_int()`` — an argparse ``type`` for a column specifier given either
+  as a zero-based index or as a field name.
+
+The group's namespace feeds ``create_reader()`` directly::
+
+    >>> import argparse, rdkit_utils
+    >>> from dm_job_utilities.utils import read_delimiter
+    >>> parser = argparse.ArgumentParser()
+    >>> _ = rdkit_utils.add_common_molecule_io_args(parser)
+    >>> args = parser.parse_args(['-i', 'molecules.smi', '-d', 'tab'])
+    >>> reader = rdkit_utils.create_reader(
+    ...     args.input,
+    ...     delimiter=read_delimiter(args.delimiter),
+    ...     read_header=args.read_header,
+    ...     id_column=args.id_column,
+    ...     mol_column=args.mol_column,
+    ...     read_records=args.read_records,
+    ... )
+
+``--infile`` and ``--outfile`` are the canonical long spellings. The parsed
+values are always available as ``args.input`` and ``args.output``.
+
+``--input`` and ``--output`` are **deprecated aliases**, retained only so that
+adopting the helper did not break existing Job manifests. They are due to be
+removed — see `issue #5
+<https://github.com/InformaticsMatters/squonk2-rdkit-utilities/issues/5>`_. Job
+Definitions should invoke ``-i``/``-o``: they are canonical, unaffected by that
+removal, and work against container images built before the Job adopted the
+helper.
+
+Defaults follow the ``create_reader()`` / ``create_writer()`` signatures rather
+than the values the Job scripts hand-type today — in particular ``--mol-column``
+defaults to ``None`` so that ``SmilesReader`` can infer it, where most Jobs
+currently pass an explicit ``0``.
+
+Progress and cost reporting (``--interval``, ``ProgressReporter``) is
+deliberately **not** here — that is a Data Manager logging concern and lives in
+`im-data-manager-job-utilities`_.
+
+.. _PyPI: https://pypi.org/project/im-rdkit-utilities
+.. _im-data-manager-job-utilities: https://pypi.org/project/im-data-manager-job-utilities
+
+Get in touch
+============
+
+- Report bugs, suggest features or view the source code `on GitHub`_.
+
+.. _on GitHub: https://github.com/informaticsmatters/squonk2-rdkit-utilities

im_rdkit_utilities-1.2.0/im_rdkit_utilities.egg-info/PKG-INFO

@@ -0,0 +1,164 @@
+Metadata-Version: 2.4
+Name: im-rdkit-utilities
+Version: 1.2.0
+Summary: RDKit utilities for Squonk2 Data Manager Jobs
+Home-page: https://github.com/informaticsmatters/squonk2-rdkit-utilities
+Author: Informatics Matters
+Author-email: info@informaticsmatters.com
+License: MIT
+Keywords: rdkit
+Platform: any
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Environment :: Other Environment
+Classifier: Intended Audience :: Developers
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Classifier: Topic :: Software Development :: Libraries :: Python Modules
+Classifier: Operating System :: POSIX :: Linux
+Requires-Python: >=3.10
+License-File: LICENSE
+Requires-Dist: rdkit>=2026.3.6
+Requires-Dist: im-data-manager-job-utilities>=1.3.0
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: home-page
+Dynamic: keywords
+Dynamic: license
+Dynamic: license-file
+Dynamic: platform
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
+
+Informatics Matters RDKit Utilities
+====================================
+
+.. image:: https://badge.fury.io/py/im-rdkit-utilities.svg
+   :target: https://badge.fury.io/py/im-rdkit-utilities
+   :alt: PyPI package (latest)
+
+.. image:: https://github.com/InformaticsMatters/squonk2-rdkit-utilities/actions/workflows/build.yaml/badge.svg
+   :target: https://github.com/InformaticsMatters/squonk2-rdkit-utilities/actions/workflows/build.yaml
+   :alt: Build
+
+.. image:: https://github.com/InformaticsMatters/squonk2-rdkit-utilities/actions/workflows/publish.yaml/badge.svg
+   :target: https://github.com/InformaticsMatters/squonk2-rdkit-utilities/actions/workflows/publish.yaml
+   :alt: Publish
+
+A Python package of RDKit-specific helpers shared by **Squonk2 Data Manager
+Jobs**: molecule readers/writers over SDF and delimited-SMILES text formats,
+fragment selection, and a handful of small molecule-inspection helpers.
+
+This consolidates the ``rdkit_utils.py`` module that had been copy-pasted,
+and had begun to diverge, across several Job repositories
+(``squonk2-desc-rdkit``, ``squonk2-desc-mordred``, ``squonk2-jaqpot`` and
+``virtual-screening``) into a single, tested, authoritative source.
+
+Installation (Python)
+======================
+
+The package is published on `PyPI`_ and can be installed from there::
+
+    pip install im-rdkit-utilities
+
+Once installed, import it as ``rdkit_utils`` (matching the module name it
+replaces, so existing call sites need no changes beyond the import path)::
+
+    >>> import rdkit_utils
+    >>> reader = rdkit_utils.create_reader('molecules.smi', delimiter='\t')
+
+Public surface
+==============
+
+- ``create_reader()`` / ``create_writer()`` — construct a reader/writer for
+  a .sdf, .sdf.gz or delimited-SMILES file, based on its extension.
+- ``SdfReader`` / ``SdfWriter`` / ``SmilesReader`` / ``SmilesWriter`` — the
+  underlying reader/writer implementations.
+- ``generate_headers()`` — build output headers for a tab/comma separated
+  file, given the ID column configuration.
+- ``fragment()`` — pick the largest fragment of a (typically salted)
+  molecule, by heavy-atom count or molecular weight.
+- ``fragmentAndFingerprint()`` — fragment a stream of molecules and
+  fingerprint the result.
+- ``get_num_chiral_centers()`` / ``get_num_sp3_centres()`` — small
+  molecule-inspection helpers.
+- ``check_molecules_are_3d()`` — check whether the molecules in a .sdf file
+  have 3D conformers.
+- ``rdk_read_single_mol()`` / ``rdk_read_mols()`` / ``rdk_read_molecule_files()``
+  / ``rdk_merge_mols()`` / ``rdk_mol_supplier()`` / ``sdf_record_gen()`` —
+  molecule-file reading helpers.
+- ``updateChargeFlagInAtomBlock()`` — adds the legacy charge-flag encoding
+  to a full CTAB molblock (counts line included), for tools such as rDock
+  that only understand the old syntax. This is **not** the same as
+  ``dm_job_utilities.utils.update_charge_flag_in_atom_block()``, which
+  operates on just the atom-block portion of a molblock (one line further
+  in) — the two take different input shapes and are not interchangeable.
+  This RDKit-oriented variant lives here because it's used directly
+  alongside the readers/writers above; the job-utilities function remains
+  the natural home for pure string manipulation with no RDKit dependency.
+
+Command-line helpers
+====================
+
+- ``add_common_molecule_io_args(parser)`` — adds the "Input/output options"
+  argument group shared by the molecule processing Jobs (``-i/--infile``,
+  ``-o/--outfile``, ``-d/--delimiter``, ``--id-column``, ``--mol-column``,
+  ``--read-header``, ``--write-header``, ``--read-records``,
+  ``-k/--omit-fields``, and optionally ``--y-column``), and returns the group
+  so more options can be added to it. Keyword arguments ``output_default``,
+  ``output_required`` and ``include_y_column`` cover the variations between
+  Jobs.
+- ``str_or_int()`` — an argparse ``type`` for a column specifier given either
+  as a zero-based index or as a field name.
+
+The group's namespace feeds ``create_reader()`` directly::
+
+    >>> import argparse, rdkit_utils
+    >>> from dm_job_utilities.utils import read_delimiter
+    >>> parser = argparse.ArgumentParser()
+    >>> _ = rdkit_utils.add_common_molecule_io_args(parser)
+    >>> args = parser.parse_args(['-i', 'molecules.smi', '-d', 'tab'])
+    >>> reader = rdkit_utils.create_reader(
+    ...     args.input,
+    ...     delimiter=read_delimiter(args.delimiter),
+    ...     read_header=args.read_header,
+    ...     id_column=args.id_column,
+    ...     mol_column=args.mol_column,
+    ...     read_records=args.read_records,
+    ... )
+
+``--infile`` and ``--outfile`` are the canonical long spellings. The parsed
+values are always available as ``args.input`` and ``args.output``.
+
+``--input`` and ``--output`` are **deprecated aliases**, retained only so that
+adopting the helper did not break existing Job manifests. They are due to be
+removed — see `issue #5
+<https://github.com/InformaticsMatters/squonk2-rdkit-utilities/issues/5>`_. Job
+Definitions should invoke ``-i``/``-o``: they are canonical, unaffected by that
+removal, and work against container images built before the Job adopted the
+helper.
+
+Defaults follow the ``create_reader()`` / ``create_writer()`` signatures rather
+than the values the Job scripts hand-type today — in particular ``--mol-column``
+defaults to ``None`` so that ``SmilesReader`` can infer it, where most Jobs
+currently pass an explicit ``0``.
+
+Progress and cost reporting (``--interval``, ``ProgressReporter``) is
+deliberately **not** here — that is a Data Manager logging concern and lives in
+`im-data-manager-job-utilities`_.
+
+.. _PyPI: https://pypi.org/project/im-rdkit-utilities
+.. _im-data-manager-job-utilities: https://pypi.org/project/im-data-manager-job-utilities
+
+Get in touch
+============
+
+- Report bugs, suggest features or view the source code `on GitHub`_.
+
+.. _on GitHub: https://github.com/informaticsmatters/squonk2-rdkit-utilities

im_rdkit_utilities-1.2.0/im_rdkit_utilities.egg-info/SOURCES.txt

@@ -0,0 +1,18 @@
+LICENSE
+MANIFEST.in
+README.rst
+pyproject.toml
+requirements.txt
+setup.py
+im_rdkit_utilities.egg-info/PKG-INFO
+im_rdkit_utilities.egg-info/SOURCES.txt
+im_rdkit_utilities.egg-info/dependency_links.txt
+im_rdkit_utilities.egg-info/not-zip-safe
+im_rdkit_utilities.egg-info/requires.txt
+im_rdkit_utilities.egg-info/top_level.txt
+rdkit_utils/__init__.py
+rdkit_utils/_cli.py
+rdkit_utils/_core.py
+tests/test_cli.py
+tests/test_rdkit_utils.py
+tests/test_smiles_writer_columns.py

im_rdkit_utilities-1.2.0/im_rdkit_utilities.egg-info/dependency_links.txt

@@ -0,0 +1 @@
+

im_rdkit_utilities-1.2.0/im_rdkit_utilities.egg-info/not-zip-safe

@@ -0,0 +1 @@
+

im_rdkit_utilities-1.2.0/im_rdkit_utilities.egg-info/requires.txt

@@ -0,0 +1,2 @@
+rdkit>=2026.3.6
+im-data-manager-job-utilities>=1.3.0

im_rdkit_utilities-1.2.0/im_rdkit_utilities.egg-info/top_level.txt

@@ -0,0 +1 @@
+rdkit_utils

im_rdkit_utilities-1.2.0/pyproject.toml

@@ -0,0 +1,5 @@
+# The build system. The project metadata still lives in setup.py, which
+# takes the package version from GITHUB_REF_SLUG at publish time.
+[build-system]
+requires = ["setuptools >= 77"]
+build-backend = "setuptools.build_meta"

im_rdkit_utilities-1.2.0/rdkit_utils/__init__.py

@@ -0,0 +1,57 @@
+"""RDKit utilities for Squonk2 Data Manager Jobs.
+
+Everything in ``_core`` is re-exported here so callers can keep using the
+flat ``import rdkit_utils`` / ``rdkit_utils.create_reader(...)`` style that
+predates this package.
+"""
+
+from rdkit_utils._cli import add_common_molecule_io_args, str_or_int
+from rdkit_utils._core import (
+    ID_COL_NAME,
+    SMILES_COL_NAME,
+    SdfReader,
+    SdfWriter,
+    SmilesReader,
+    SmilesWriter,
+    check_molecules_are_3d,
+    create_reader,
+    create_writer,
+    fragment,
+    fragmentAndFingerprint,
+    generate_headers,
+    get_num_chiral_centers,
+    get_num_sp3_centres,
+    rdk_merge_mols,
+    rdk_mol_supplier,
+    rdk_read_molecule_files,
+    rdk_read_mols,
+    rdk_read_single_mol,
+    sdf_record_gen,
+    updateChargeFlagInAtomBlock,
+)
+
+__all__ = [
+    "ID_COL_NAME",
+    "SMILES_COL_NAME",
+    "SdfReader",
+    "SdfWriter",
+    "SmilesReader",
+    "SmilesWriter",
+    "add_common_molecule_io_args",
+    "check_molecules_are_3d",
+    "create_reader",
+    "create_writer",
+    "fragment",
+    "fragmentAndFingerprint",
+    "generate_headers",
+    "get_num_chiral_centers",
+    "get_num_sp3_centres",
+    "rdk_merge_mols",
+    "rdk_mol_supplier",
+    "rdk_read_molecule_files",
+    "rdk_read_mols",
+    "rdk_read_single_mol",
+    "sdf_record_gen",
+    "str_or_int",
+    "updateChargeFlagInAtomBlock",
+]