rdkit-cli 0.3.1__tar.gz → 0.3.2__tar.gz

{rdkit_cli-0.3.1 → rdkit_cli-0.3.2}/CHANGELOG.md

@@ -5,6 +5,31 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [0.3.2] - 2026-04-03
+
+### Added
+
+- **stereo**: New command for stereochemistry analysis — CIP label assignment (R/S, E/Z), stereocenter perception, enhanced stereo group inspection, and stereo cleanup/canonicalization
+- **energy**: New command for force field energy calculations — single-point MMFF/UFF energy and structure minimization with convergence reporting
+- **pharmacophore**: New command for pharmacophore feature perception (Donor, Acceptor, Aromatic, etc.) and 2D pharmacophore fingerprint similarity search
+- **fingerprints**: Added Avalon, MHFP (MinHash), and 2D pharmacophore (Gobbi) fingerprint types
+- **descriptors**: Added 42 Molecular Quantum Numbers (MQN) and 10 3D shape descriptors (PMI, NPR, Asphericity, Eccentricity, SpherocityIndex, PBF); new `--mqn`, `--3d`, and `--generate-conformers` flags
+- **similarity**: Added 8 metrics (AllBit, Asymmetric, BraunBlanquet, Kulczynski, McConnaughey, OnBit, RogotGoldberg, Tversky with alpha/beta); new `shape` subcommand for 3D shape similarity (Tanimoto, Protrude, Tversky)
+- **filter**: Expanded structural alert catalogs — `--catalog` option supports PAINS, PAINS_A/B/C, Brenk, NIH, ZINC, and all combined; added `alerts` subcommand as alias
+- **conformers**: Added `constrained` subcommand for template-constrained 3D embedding and `torsion` subcommand for dihedral angle scanning with energy profiles
+- **reactions**: Added `map` subcommand for atom-atom mapping inspection (text/JSON) and `fingerprint` subcommand for reaction difference/structural fingerprints
+- **scaffold**: Added `network` subcommand for scaffold network construction (CSV/JSON output) using rdScaffoldNetwork
+- **props**: Added `charges` subcommand for Gasteiger partial charges and `crippen` subcommand for per-atom LogP/MR contributions
+- **fragment**: Added `brics-build` subcommand for recombining BRICS fragments into new molecules
+- **depict**: Added `highlight` subcommand for SMARTS-based atom/bond highlighting with custom RGB colors
+
+### Changed
+
+- Total command count increased from 29 to 32 (stereo, energy, pharmacophore)
+- Total fingerprint types increased from 6 to 9
+- Total descriptor count increased from ~133 to ~185
+- Similarity metrics increased from 5 to 13
+
 ## [0.3.1] - 2026-03-14
 
 ### Changed

{rdkit_cli-0.3.1 → rdkit_cli-0.3.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rdkit-cli
-Version: 0.3.1
+Version: 0.3.2
 Summary: A comprehensive CLI tool for RDKit cheminformatics operations
 Project-URL: Homepage, https://github.com/vitruves/rdkit-cli
 Project-URL: Repository, https://github.com/vitruves/rdkit-cli
@@ -41,7 +41,7 @@ Description-Content-Type: text/markdown
 
 A high-performance CLI for cheminformatics workflows, powered by native RDKit (C++ under the hood).
 
-**29 commands** | **5 I/O formats** (CSV, TSV, SMI, SDF, Parquet) | **multi-core parallel processing** | **~80ms startup**
+**32 commands** | **5 I/O formats** (CSV, TSV, SMI, SDF, Parquet) | **multi-core parallel processing** | **~80ms startup**
 
 ## Installation
 
@@ -81,6 +81,7 @@ Commands:
     depict         Generate molecular depictions (SVG/PNG)
     descriptors    Compute molecular descriptors
     diversity      Analyze and select diverse molecules
+    energy         Force field energy calculations
     enumerate      Enumerate stereoisomers and tautomers
     filter         Filter by substructure, properties, drug-likeness, PAINS
     fingerprints   Compute fingerprints (Morgan, MACCS, RDKit, AtomPair, Torsion)
@@ -89,6 +90,7 @@ Commands:
     mcs            Find Maximum Common Substructure
     merge          Merge multiple molecule files
     mmp            Matched Molecular Pairs analysis
+    pharmacophore  Pharmacophore feature analysis
     props          Property column operations (add, rename, drop, keep)
     protonate      Enumerate protonation states
     reactions      Apply SMIRKS transformations and enumerate products
@@ -102,6 +104,7 @@ Commands:
     split          Split files into smaller chunks
     standardize    Standardize and canonicalize molecules
     stats          Calculate dataset statistics
+    stereo         Analyze and manipulate stereochemistry
     validate       Validate molecular structures
 
 Use 'rdkit-cli <command> --help' for command-specific options.

{rdkit_cli-0.3.1 → rdkit_cli-0.3.2}/README.md

@@ -7,7 +7,7 @@
 
 A high-performance CLI for cheminformatics workflows, powered by native RDKit (C++ under the hood).
 
-**29 commands** | **5 I/O formats** (CSV, TSV, SMI, SDF, Parquet) | **multi-core parallel processing** | **~80ms startup**
+**32 commands** | **5 I/O formats** (CSV, TSV, SMI, SDF, Parquet) | **multi-core parallel processing** | **~80ms startup**
 
 ## Installation
 
@@ -47,6 +47,7 @@ Commands:
     depict         Generate molecular depictions (SVG/PNG)
     descriptors    Compute molecular descriptors
     diversity      Analyze and select diverse molecules
+    energy         Force field energy calculations
     enumerate      Enumerate stereoisomers and tautomers
     filter         Filter by substructure, properties, drug-likeness, PAINS
     fingerprints   Compute fingerprints (Morgan, MACCS, RDKit, AtomPair, Torsion)
@@ -55,6 +56,7 @@ Commands:
     mcs            Find Maximum Common Substructure
     merge          Merge multiple molecule files
     mmp            Matched Molecular Pairs analysis
+    pharmacophore  Pharmacophore feature analysis
     props          Property column operations (add, rename, drop, keep)
     protonate      Enumerate protonation states
     reactions      Apply SMIRKS transformations and enumerate products
@@ -68,6 +70,7 @@ Commands:
     split          Split files into smaller chunks
     standardize    Standardize and canonicalize molecules
     stats          Calculate dataset statistics
+    stereo         Analyze and manipulate stereochemistry
     validate       Validate molecular structures
 
 Use 'rdkit-cli <command> --help' for command-specific options.

{rdkit_cli-0.3.1 → rdkit_cli-0.3.2}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "rdkit-cli"
-version = "0.3.1"
+version = "0.3.2"
 description = "A comprehensive CLI tool for RDKit cheminformatics operations"
 readme = "README.md"
 license = "Apache-2.0"

{rdkit_cli-0.3.1 → rdkit_cli-0.3.2}/src/rdkit_cli/__init__.py

@@ -1,4 +1,4 @@
 """rdkit-cli: A comprehensive CLI tool for RDKit cheminformatics operations."""
 
-__version__ = "0.3.1"
+__version__ = "0.3.2"
 __author__ = "Vitruves"

{rdkit_cli-0.3.1 → rdkit_cli-0.3.2}/src/rdkit_cli/cli.py

@@ -146,6 +146,7 @@ def _register_commands(subparsers):
         depict,
         descriptors,
         diversity,
+        energy,
         enumerate,
         filter,
         fingerprints,
@@ -154,6 +155,7 @@ def _register_commands(subparsers):
         mcs,
         merge,
         mmp,
+        pharmacophore,
         props,
         protonate,
         reactions,
@@ -167,6 +169,7 @@ def _register_commands(subparsers):
         split,
         standardize,
         stats,
+        stereo,
         validate,
     )
 
@@ -178,6 +181,7 @@ def _register_commands(subparsers):
     depict.register_parser(subparsers)
     descriptors.register_parser(subparsers)
     diversity.register_parser(subparsers)
+    energy.register_parser(subparsers)
     enumerate.register_parser(subparsers)
     filter.register_parser(subparsers)
     fingerprints.register_parser(subparsers)
@@ -186,6 +190,7 @@ def _register_commands(subparsers):
     mcs.register_parser(subparsers)
     merge.register_parser(subparsers)
     mmp.register_parser(subparsers)
+    pharmacophore.register_parser(subparsers)
     props.register_parser(subparsers)
     protonate.register_parser(subparsers)
     reactions.register_parser(subparsers)
@@ -199,6 +204,7 @@ def _register_commands(subparsers):
     split.register_parser(subparsers)
     standardize.register_parser(subparsers)
     stats.register_parser(subparsers)
+    stereo.register_parser(subparsers)
     validate.register_parser(subparsers)
 
 

{rdkit_cli-0.3.1 → rdkit_cli-0.3.2}/src/rdkit_cli/commands/conformers.py

@@ -120,6 +120,74 @@ def register_parser(subparsers):
     )
     opt_parser.set_defaults(func=run_optimize)
 
+    # conformers constrained
+    const_parser = conf_subparsers.add_parser(
+        "constrained",
+        help="Embed molecules constrained to a reference template",
+        formatter_class=RdkitHelpFormatter,
+    )
+    add_common_io_options(const_parser)
+    add_common_processing_options(const_parser)
+    const_parser.add_argument(
+        "-r", "--reference",
+        required=True,
+        metavar="FILE",
+        help="Reference molecule file with 3D coords (SDF, MOL, PDB)",
+    )
+    const_parser.add_argument(
+        "-f", "--force-field",
+        choices=["mmff", "uff"],
+        default="mmff",
+        help="Force field for optimization (default: mmff)",
+    )
+    const_parser.add_argument(
+        "--seed",
+        type=int,
+        default=42,
+        help="Random seed (default: 42)",
+    )
+    const_parser.set_defaults(func=run_constrained)
+
+    # conformers torsion
+    torsion_parser = conf_subparsers.add_parser(
+        "torsion",
+        help="Scan torsion angles and compute energy profile",
+        formatter_class=RdkitHelpFormatter,
+    )
+    add_common_io_options(torsion_parser)
+    add_common_processing_options(torsion_parser)
+    torsion_parser.add_argument(
+        "--atoms",
+        required=True,
+        metavar="I,J,K,L",
+        help="Comma-separated atom indices for the dihedral",
+    )
+    torsion_parser.add_argument(
+        "--start",
+        type=float,
+        default=-180.0,
+        help="Start angle in degrees (default: -180)",
+    )
+    torsion_parser.add_argument(
+        "--end",
+        type=float,
+        default=180.0,
+        help="End angle in degrees (default: 180)",
+    )
+    torsion_parser.add_argument(
+        "--step",
+        type=float,
+        default=10.0,
+        help="Step size in degrees (default: 10)",
+    )
+    torsion_parser.add_argument(
+        "-f", "--force-field",
+        choices=["mmff", "uff"],
+        default="mmff",
+        help="Force field (default: mmff)",
+    )
+    torsion_parser.set_defaults(func=run_torsion)
+
     # Set default for main parser
     parser.set_defaults(func=lambda args: parser.print_help() or 1)
 
@@ -218,3 +286,109 @@ def run_optimize(args) -> int:
         )
 
     return 0 if result.failed == 0 else 1
+
+
+def run_constrained(args) -> int:
+    """Run constrained embedding."""
+    from rdkit_cli.core.conformers import ConstrainedEmbedder
+    from rdkit_cli.io import create_reader, create_writer, FileFormat
+
+    try:
+        embedder = ConstrainedEmbedder(
+            reference_file=args.reference,
+            force_field=args.force_field,
+            random_seed=args.seed,
+        )
+    except ValueError as e:
+        print(f"Error: {e}", file=sys.stderr)
+        return 1
+
+    input_path = Path(args.input)
+    if not input_path.exists():
+        print(f"Error: Input file not found: {input_path}", file=sys.stderr)
+        return 1
+
+    reader = create_reader(
+        input_path,
+        smiles_column=args.smiles_column,
+        name_column=args.name_column,
+        has_header=not args.no_header,
+    )
+
+    output_path = Path(args.output)
+    writer = create_writer(output_path, format_override=FileFormat.SDF)
+
+    # Single-threaded: ConstrainedEmbed not picklable
+    records = list(reader)
+    succeeded = 0
+    failed = 0
+    with writer:
+        for record in records:
+            result = embedder.embed(record)
+            if result is not None:
+                writer.write_row(result)
+                succeeded += 1
+            else:
+                failed += 1
+
+    if not args.quiet:
+        total = succeeded + failed
+        print(
+            f"Embedded {succeeded}/{total} molecules "
+            f"({failed} failed)",
+            file=sys.stderr,
+        )
+
+    return 0
+
+
+def run_torsion(args) -> int:
+    """Run torsion angle scan."""
+    from rdkit_cli.core.conformers import TorsionScanner
+    from rdkit_cli.io import create_reader, create_writer
+
+    try:
+        indices = tuple(int(x) for x in args.atoms.split(","))
+        if len(indices) != 4:
+            raise ValueError("Need exactly 4 atom indices")
+    except ValueError as e:
+        print(f"Error: {e}", file=sys.stderr)
+        return 1
+
+    scanner = TorsionScanner(
+        atom_indices=indices,
+        start_angle=args.start,
+        end_angle=args.end,
+        step=args.step,
+        force_field=args.force_field,
+    )
+
+    input_path = Path(args.input)
+    if not input_path.exists():
+        print(f"Error: Input file not found: {input_path}", file=sys.stderr)
+        return 1
+
+    reader = create_reader(
+        input_path,
+        smiles_column=args.smiles_column,
+        name_column=getattr(args, "name_column", None),
+        has_header=not args.no_header,
+    )
+    output_path = Path(args.output)
+    writer = create_writer(output_path)
+
+    count = 0
+    with writer:
+        for record in reader:
+            result = scanner.scan(record)
+            if result is not None:
+                writer.write_row(result)
+                count += 1
+
+    if not args.quiet:
+        print(
+            f"Scanned torsion for {count} molecules",
+            file=sys.stderr,
+        )
+
+    return 0

{rdkit_cli-0.3.1 → rdkit_cli-0.3.2}/src/rdkit_cli/commands/depict.py

@@ -274,6 +274,48 @@ def register_parser(subparsers):
     )
     grid_parser.set_defaults(func=run_grid)
 
+    # depict highlight
+    hl_parser = depict_subparsers.add_parser(
+        "highlight",
+        help="Depict with SMARTS-based highlighting",
+        formatter_class=RdkitHelpFormatter,
+    )
+    hl_parser.add_argument(
+        "smiles",
+        metavar="SMILES",
+        help="SMILES string of molecule to depict",
+    )
+    hl_parser.add_argument(
+        "-s", "--smarts",
+        required=True,
+        metavar="PATTERN",
+        help="SMARTS pattern to highlight",
+    )
+    hl_parser.add_argument(
+        "-o", "--output",
+        required=True,
+        metavar="FILE",
+        help="Output image file (SVG or PNG)",
+    )
+    hl_parser.add_argument(
+        "--width",
+        type=int,
+        default=400,
+        help="Image width (default: 400)",
+    )
+    hl_parser.add_argument(
+        "--height",
+        type=int,
+        default=300,
+        help="Image height (default: 300)",
+    )
+    hl_parser.add_argument(
+        "--color",
+        default="1.0,0.0,0.0",
+        help="Highlight color as R,G,B floats (default: 1.0,0.0,0.0)",
+    )
+    hl_parser.set_defaults(func=run_highlight)
+
     # Set default for main parser
     parser.set_defaults(func=lambda args: parser.print_help() or 1)
 
@@ -431,3 +473,72 @@ def run_grid(args) -> int:
         print(f"Wrote grid image to {output_path}", file=sys.stderr)
 
     return 0
+
+
+def run_highlight(args) -> int:
+    """Depict molecule with SMARTS-based highlighting."""
+    from rdkit import Chem
+    from rdkit.Chem.Draw import rdMolDraw2D
+
+    mol = Chem.MolFromSmiles(args.smiles)
+    if mol is None:
+        print(f"Error: Invalid SMILES: {args.smiles}", file=sys.stderr)
+        return 1
+
+    pattern = Chem.MolFromSmarts(args.smarts)
+    if pattern is None:
+        print(f"Error: Invalid SMARTS: {args.smarts}", file=sys.stderr)
+        return 1
+
+    # Find matching atoms/bonds
+    matches = mol.GetSubstructMatches(pattern)
+    if not matches:
+        print("Warning: No substructure match found", file=sys.stderr)
+
+    highlight_atoms = []
+    highlight_bonds = []
+    for match in matches:
+        highlight_atoms.extend(match)
+        for i in range(len(match)):
+            for j in range(i + 1, len(match)):
+                bond = mol.GetBondBetweenAtoms(match[i], match[j])
+                if bond is not None:
+                    highlight_bonds.append(bond.GetIdx())
+
+    # Parse color
+    try:
+        rgb = tuple(float(c) for c in args.color.split(","))
+    except (ValueError, TypeError):
+        rgb = (1.0, 0.0, 0.0)
+
+    atom_colors = {a: rgb for a in highlight_atoms}
+    bond_colors = {b: rgb for b in highlight_bonds}
+
+    output_path = Path(args.output)
+    fmt = output_path.suffix.lower().lstrip(".")
+
+    if fmt == "svg":
+        drawer = rdMolDraw2D.MolDraw2DSVG(args.width, args.height)
+    else:
+        drawer = rdMolDraw2D.MolDraw2DCairo(args.width, args.height)
+
+    drawer.DrawMolecule(
+        mol,
+        highlightAtoms=highlight_atoms,
+        highlightBonds=highlight_bonds,
+        highlightAtomColors=atom_colors,
+        highlightBondColors=bond_colors,
+    )
+    drawer.FinishDrawing()
+
+    data = drawer.GetDrawingText()
+    mode = "w" if fmt == "svg" else "wb"
+    with open(output_path, mode) as f:
+        f.write(data)
+
+    print(
+        f"Wrote highlighted image to {output_path} "
+        f"({len(highlight_atoms)} atoms highlighted)",
+        file=sys.stderr,
+    )
+    return 0

{rdkit_cli-0.3.1 → rdkit_cli-0.3.2}/src/rdkit_cli/commands/descriptors.py

@@ -17,6 +17,8 @@ DESCRIPTOR_CATEGORIES = [
     "electronic",
     "geometric",
     "molecular",
+    "mqn",
+    "3d",
 ]
 
 
@@ -90,6 +92,17 @@ def register_parser(subparsers):
         action="store_true",
         help="Compute drug-likeness descriptors",
     )
+    desc_group.add_argument(
+        "--mqn",
+        action="store_true",
+        help="Compute 42 Molecular Quantum Numbers",
+    )
+    desc_group.add_argument(
+        "--3d",
+        action="store_true",
+        dest="compute_3d_set",
+        help="Compute 3D shape descriptors (PMI, NPR, Asphericity, etc.)",
+    )
     desc_group.add_argument(
         "--category",
         choices=DESCRIPTOR_CATEGORIES,
@@ -117,10 +130,9 @@ def register_parser(subparsers):
         help="Value to use for failed calculations (default: NaN)",
     )
     compute_parser.add_argument(
-        "--3d",
+        "--generate-conformers",
         action="store_true",
-        dest="compute_3d",
-        help="Include 3D descriptors (requires 3D coordinates)",
+        help="Auto-generate 3D coordinates for 3D descriptors",
     )
     compute_parser.add_argument(
         "--no-smiles",
@@ -209,6 +221,8 @@ def run_compute(args) -> int:
         COMMON_DESCRIPTORS,
         LIPINSKI_DESCRIPTORS,
         DRUGLIKE_DESCRIPTORS,
+        MQN_DESCRIPTORS,
+        THREE_D_DESCRIPTORS,
     )
     from rdkit_cli.io import create_reader, create_writer
     from rdkit_cli.parallel.batch import process_molecules
@@ -224,6 +238,10 @@ def run_compute(args) -> int:
         descriptor_names = LIPINSKI_DESCRIPTORS
     elif args.druglike:
         descriptor_names = DRUGLIKE_DESCRIPTORS
+    elif args.mqn:
+        descriptor_names = MQN_DESCRIPTORS
+    elif args.compute_3d_set:
+        descriptor_names = THREE_D_DESCRIPTORS
     elif args.compute_category:
         descs = list_descriptors(category=args.compute_category)
         descriptor_names = [d.name for d in descs]
@@ -249,6 +267,7 @@ def run_compute(args) -> int:
             include_name=not args.no_name,
             precision=args.precision,
             error_value=args.error_value,
+            generate_conformers=getattr(args, "generate_conformers", False),
         )
     except ValueError as e:
         print(f"Error: {e}", file=sys.stderr)

rdkit_cli-0.3.2/src/rdkit_cli/commands/energy.py

@@ -0,0 +1,151 @@
+"""Energy command implementation."""
+
+import sys
+from pathlib import Path
+
+from rdkit_cli.cli import (
+    RdkitHelpFormatter,
+    add_common_io_options,
+    add_common_processing_options,
+)
+
+
+def register_parser(subparsers):
+    """Register the energy command and subcommands."""
+    parser = subparsers.add_parser(
+        "energy",
+        help="Force field energy calculations",
+        description="Compute MMFF/UFF energies and minimize structures.",
+        formatter_class=RdkitHelpFormatter,
+    )
+
+    energy_sub = parser.add_subparsers(
+        title="Subcommands",
+        dest="subcommand",
+        metavar="<subcommand>",
+    )
+
+    # energy compute
+    compute_parser = energy_sub.add_parser(
+        "compute",
+        help="Compute single-point energy",
+        formatter_class=RdkitHelpFormatter,
+    )
+    add_common_io_options(compute_parser)
+    add_common_processing_options(compute_parser)
+    compute_parser.add_argument(
+        "-f", "--force-field",
+        choices=["mmff", "uff"],
+        default="mmff",
+        help="Force field (default: mmff)",
+    )
+    compute_parser.set_defaults(func=run_compute)
+
+    # energy minimize
+    minimize_parser = energy_sub.add_parser(
+        "minimize",
+        help="Minimize and report energy",
+        formatter_class=RdkitHelpFormatter,
+    )
+    add_common_io_options(minimize_parser)
+    add_common_processing_options(minimize_parser)
+    minimize_parser.add_argument(
+        "-f", "--force-field",
+        choices=["mmff", "uff"],
+        default="mmff",
+        help="Force field (default: mmff)",
+    )
+    minimize_parser.add_argument(
+        "--max-iter",
+        type=int,
+        default=500,
+        help="Maximum iterations (default: 500)",
+    )
+    minimize_parser.set_defaults(func=run_minimize)
+
+    parser.set_defaults(func=lambda args: parser.print_help() or 1)
+
+
+def run_compute(args) -> int:
+    """Compute single-point energies."""
+    from rdkit_cli.core.energy import EnergyCalculator
+    from rdkit_cli.io import create_reader, create_writer
+    from rdkit_cli.parallel.batch import process_molecules
+
+    calculator = EnergyCalculator(force_field=args.force_field)
+
+    input_path = Path(args.input)
+    if not input_path.exists():
+        print(f"Error: Input file not found: {input_path}", file=sys.stderr)
+        return 1
+
+    reader = create_reader(
+        input_path,
+        smiles_column=args.smiles_column,
+        name_column=getattr(args, "name_column", None),
+        has_header=not args.no_header,
+    )
+    output_path = Path(args.output)
+    writer = create_writer(output_path)
+
+    with reader, writer:
+        result = process_molecules(
+            reader=reader,
+            writer=writer,
+            processor=calculator.compute,
+            n_workers=1,  # 3D generation not picklable
+            quiet=args.quiet,
+        )
+
+    if not args.quiet:
+        print(
+            f"Computed energy for "
+            f"{result.successful}/{result.total_processed} molecules "
+            f"in {result.elapsed_time:.1f}s",
+            file=sys.stderr,
+        )
+    return 0
+
+
+def run_minimize(args) -> int:
+    """Minimize structures."""
+    from rdkit_cli.core.energy import EnergyMinimizer
+    from rdkit_cli.io import create_reader, create_writer
+    from rdkit_cli.parallel.batch import process_molecules
+
+    minimizer = EnergyMinimizer(
+        force_field=args.force_field,
+        max_iterations=args.max_iter,
+    )
+
+    input_path = Path(args.input)
+    if not input_path.exists():
+        print(f"Error: Input file not found: {input_path}", file=sys.stderr)
+        return 1
+
+    reader = create_reader(
+        input_path,
+        smiles_column=args.smiles_column,
+        name_column=getattr(args, "name_column", None),
+        has_header=not args.no_header,
+    )
+    output_path = Path(args.output)
+    writer = create_writer(output_path)
+
+    with reader, writer:
+        result = process_molecules(
+            reader=reader,
+            writer=writer,
+            processor=minimizer.minimize,
+            n_workers=1,
+            quiet=args.quiet,
+        )
+
+    if not args.quiet:
+        print(
+            f"Minimized "
+            f"{result.successful}/{result.total_processed} molecules "
+            f"in {result.elapsed_time:.1f}s",
+            file=sys.stderr,
+        )
+    return 0