mdprep 0.2.0__py3-none-any.whl

mdprep/workflows/selftest.py

@@ -0,0 +1,220 @@
+"""Quick package-level self-test."""
+
+from __future__ import annotations
+
+from dataclasses import dataclass
+from importlib import import_module
+from importlib.resources import as_file, files
+from pathlib import Path
+from tempfile import TemporaryDirectory
+
+from rich.console import Console
+from rich.table import Table
+
+import mdprep
+from mdprep.ambertools.mol2 import Mol2File, read_mol2
+from mdprep.ambertools.resp import write_amber_esp
+from mdprep.charges.esp_grid import generate_merz_kollman_grid
+from mdprep.config.loader import load_manifest
+from mdprep.external.discovery import optional_executable_report
+from mdprep.leap.forcefields import protein_leaprc, water_box, water_leaprc
+from mdprep.qm.pyscf_runner import pyscf_available
+from mdprep.validation.openmm_check import openmm_available
+from mdprep.validation.parmed_check import parmed_available
+import numpy as np
+
+
+OPTIONAL_EXECUTABLES = [
+    "tleap",
+    "antechamber",
+    "parmchk2",
+    "respgen",
+    "resp",
+    "propka3",
+    "propka",
+    "xtb",
+]
+
+
+@dataclass(frozen=True)
+class SelftestSummary:
+    passed: bool
+    checked_examples: int
+
+
+def _project_root() -> Path | None:
+    candidates = [
+        Path.cwd(),
+        Path(__file__).resolve().parents[3],
+    ]
+    for candidate in candidates:
+        if (candidate / "examples").is_dir():
+            return candidate
+    return None
+
+
+def _validate_example_manifests(root: Path | None) -> tuple[int, list[str]]:
+    if root is not None:
+        examples = sorted((root / "examples").glob("*.yaml"))
+        errors: list[str] = []
+        for example in examples:
+            try:
+                load_manifest(example)
+            except Exception as exc:
+                errors.append(f"{example.name}: {exc}")
+        return len(examples), errors
+
+    resource = files("mdprep").joinpath("_selftest_data/basic_protein.yaml")
+    with as_file(resource) as example:
+        try:
+            load_manifest(example)
+        except Exception as exc:
+            return 1, [f"{example.name}: {exc}"]
+    return 1, []
+
+
+def _read_mol2_fixture(root: Path | None) -> Mol2File:
+    if root is not None:
+        return read_mol2(root / "tests" / "data" / "ligands" / "ligand_sub.good.mol2")
+
+    resource = files("mdprep").joinpath("_selftest_data/ligand_sub.mol2")
+    with as_file(resource) as fixture:
+        return read_mol2(fixture)
+
+
+def _blocked_tokens() -> tuple[str, ...]:
+    return (
+        "".join(("open", "babel")),
+        "".join(("Open", "Babel")),
+        "".join(("py", "bel")),
+        "".join(("o", "babel")),
+    )
+
+
+def _source_has_blocked_tokens() -> list[Path]:
+    source_root = Path(__file__).resolve().parents[1]
+    blocked = _blocked_tokens()
+    matches: list[Path] = []
+    for path in source_root.rglob("*.py"):
+        text = path.read_text(encoding="utf-8")
+        if any(token in text for token in blocked):
+            matches.append(path)
+    return matches
+
+
+def run_selftest(*, quick: bool = False, console: Console | None = None) -> SelftestSummary:
+    out = console or Console()
+    root = _project_root()
+
+    out.print(f"mdprep {mdprep.__version__}")
+    out.print("Mode: quick" if quick else "Mode: standard")
+
+    checks: list[tuple[str, bool, str]] = []
+
+    try:
+        import_module("mdprep")
+        import_module("mdprep.config.loader")
+        import_module("mdprep.external.discovery")
+        checks.append(("Python imports", True, "ok"))
+    except Exception as exc:
+        checks.append(("Python imports", False, str(exc)))
+
+    example_count, example_errors = _validate_example_manifests(root)
+    checks.append(
+        (
+            "Example manifests",
+            not example_errors and example_count > 0,
+            f"{example_count} validated" if not example_errors else "; ".join(example_errors),
+        )
+    )
+
+    blocked_matches = _source_has_blocked_tokens()
+    checks.append(
+        (
+            "Prohibited toolkit source scan",
+            not blocked_matches,
+            "ok" if not blocked_matches else ", ".join(str(path) for path in blocked_matches),
+        )
+    )
+
+    try:
+        mol2 = _read_mol2_fixture(root)
+        checks.append(("mol2 parser fixture", len(mol2.atoms) == 2, f"{len(mol2.atoms)} atoms"))
+    except Exception as exc:
+        checks.append(("mol2 parser fixture", False, str(exc)))
+
+    try:
+        ok = (
+            protein_leaprc("ff19SB") == "leaprc.protein.ff19SB"
+            and water_leaprc("TIP3P") == "leaprc.water.tip3p"
+            and water_box("OPC") == "OPCBOX"
+        )
+        checks.append(("force-field mappings", ok, "ok" if ok else "unexpected mapping"))
+    except Exception as exc:
+        checks.append(("force-field mappings", False, str(exc)))
+
+    checks.append(("ParmEd import", True, "available" if parmed_available() else "not available"))
+    checks.append(("OpenMM import", True, "available" if openmm_available() else "not available"))
+    checks.append(("PySCF import", True, "available" if pyscf_available() else "not available"))
+
+    try:
+        coords = np.asarray([[0.0, 0.0, 0.0], [0.96, 0.0, 0.0]], dtype=float)
+        grid_a = generate_merz_kollman_grid(
+            elements=["O", "H"],
+            coordinates=coords,
+            vdw_scale_factors=[1.4],
+            point_density_per_square_angstrom=0.25,
+            exclude_inside_vdw_scale=1.4,
+            max_points=100,
+        )
+        grid_b = generate_merz_kollman_grid(
+            elements=["O", "H"],
+            coordinates=coords,
+            vdw_scale_factors=[1.4],
+            point_density_per_square_angstrom=0.25,
+            exclude_inside_vdw_scale=1.4,
+            max_points=100,
+        )
+        checks.append(("ESP grid determinism", bool(np.allclose(grid_a.points, grid_b.points)), f"{len(grid_a.points)} points"))
+    except Exception as exc:
+        checks.append(("ESP grid determinism", False, str(exc)))
+
+    try:
+        atom_coords = np.asarray([[0.0, 0.0, 0.0], [2.0, 0.0, 0.0]], dtype=float)
+        grid_coords = np.asarray(
+            [[0.0, 3.0, 0.0], [2.0, 3.0, 0.0], [1.0, 3.5, 0.0], [1.0, -3.0, 0.0]],
+            dtype=float,
+        )
+        esp = np.asarray([-0.1, 0.1, 0.0, 0.0], dtype=float)
+        with TemporaryDirectory(prefix="mdprep-selftest-") as temporary_dir:
+            path = write_amber_esp(
+                atom_coordinates_bohr=atom_coords,
+                grid_coordinates_bohr=grid_coords,
+                esp_values_au=esp,
+                path=Path(temporary_dir) / "test.esp",
+            )
+            lines = path.read_text(encoding="ascii").splitlines()
+        fixed_width_ok = lines[0] == "    2    4" and len(lines[1]) == 65 and len(lines[3]) == 65
+        checks.append(("Amber RESP ESP format", fixed_width_ok, "2 atoms, 4 grid points"))
+    except Exception as exc:
+        checks.append(("Amber RESP ESP format", False, str(exc)))
+
+    table = Table(title="mdprep self-test")
+    table.add_column("Check")
+    table.add_column("Status")
+    table.add_column("Detail")
+    for name, ok, detail in checks:
+        table.add_row(name, "PASS" if ok else "FAIL", detail)
+    out.print(table)
+
+    exec_table = Table(title="Optional executables")
+    exec_table.add_column("Executable")
+    exec_table.add_column("Path")
+    for name, path in optional_executable_report(OPTIONAL_EXECUTABLES).items():
+        exec_table.add_row(name, path or "not found")
+    out.print(exec_table)
+
+    return SelftestSummary(
+        passed=all(ok for _, ok, _ in checks),
+        checked_examples=example_count,
+    )

mdprep/workflows/validate.py

@@ -0,0 +1,30 @@
+"""Standalone prepared-system validation."""
+
+from __future__ import annotations
+
+from pathlib import Path
+
+from mdprep.validation.parmed_check import run_parmed_check
+
+
+def validate_system(prmtop: str | Path, inpcrd: str | Path) -> dict[str, object]:
+    topology = Path(prmtop)
+    coordinates = Path(inpcrd)
+    errors: list[str] = []
+    for label, path in [("prmtop", topology), ("inpcrd", coordinates)]:
+        if not path.exists():
+            errors.append(f"Missing {label}: {path}")
+        elif path.stat().st_size == 0:
+            errors.append(f"Empty {label}: {path}")
+    parmed = None
+    if not errors:
+        parmed = run_parmed_check(topology, coordinates)
+        if parmed.get("status") == "error":
+            errors.append(f"ParmEd validation failed: {parmed.get('error')}")
+    if errors:
+        raise ValueError("; ".join(errors))
+    return {
+        "prmtop": str(topology),
+        "inpcrd": str(coordinates),
+        "parmed": parmed,
+    }

mdprep-0.2.0.dist-info/METADATA

@@ -0,0 +1,264 @@
+Metadata-Version: 2.5
+Name: mdprep
+Version: 0.2.0
+Summary: Reproducible Amber preparation for proteins, ligands, metal centers, and OpenMM MD.
+Project-URL: Homepage, https://github.com/miqueleg/mdprep
+Project-URL: Issues, https://github.com/miqueleg/mdprep/issues
+Author: Miquel Estévez Gay
+License: MIT
+License-File: LICENSE
+Keywords: amber,ligand,mcpb,metal,molecular-dynamics,openmm,protein,pyscf,qmmm,resp
+Classifier: Development Status :: 3 - Alpha
+Classifier: Environment :: Console
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Chemistry
+Requires-Python: >=3.11
+Requires-Dist: numpy>=1.24
+Requires-Dist: pandas>=2
+Requires-Dist: pydantic-settings>=2
+Requires-Dist: pydantic>=2
+Requires-Dist: pyyaml>=6
+Requires-Dist: rich>=13
+Requires-Dist: scipy>=1.10
+Requires-Dist: typer>=0.12
+Provides-Extra: dev
+Requires-Dist: build>=1; extra == 'dev'
+Requires-Dist: mypy>=1.10; extra == 'dev'
+Requires-Dist: pytest>=8; extra == 'dev'
+Requires-Dist: ruff>=0.6; extra == 'dev'
+Requires-Dist: twine>=5; extra == 'dev'
+Provides-Extra: docs
+Requires-Dist: mkdocs>=1.6; extra == 'docs'
+Provides-Extra: md
+Requires-Dist: openmm>=8.1; extra == 'md'
+Provides-Extra: qm
+Requires-Dist: parmed>=4.2; extra == 'qm'
+Requires-Dist: pyscf>=2.6; extra == 'qm'
+Provides-Extra: test
+Requires-Dist: pytest>=8; extra == 'test'
+Description-Content-Type: text/markdown
+
+# mdprep
+
+`mdprep` 0.2.0 prepares reproducible Amber molecular-dynamics systems from a
+PDB structure and a validated YAML manifest. It supports standard proteins,
+independent ligands and cofactors, explicit metal models, optional active-site
+QM/MM refinement, final `tleap` assembly, validation, and an optional OpenMM
+equilibration/production stage.
+
+The manifest is the source of truth. Chemistry-sensitive decisions—ligand
+charge and multiplicity, catalytic protonation, metal oxidation/spin state,
+coordinating bonds, and QM components—must be supplied explicitly and are
+recorded in the output reports.
+
+## Highlights
+
+- ff14SB or ff19SB proteins with TIP3P or OPC water.
+- PropKa protonation, manual catalytic overrides, disulfides, and optional
+  GFN2-xTB/g-xTB HID–HIE selection.
+- Multiple GAFF or GAFF2 ligands/cofactors with AM1-BCC, user mol2/frcmod,
+  PySCF gas-phase RESP, or electrostatically embedded PySCF QMMESP charges.
+- Amber nonbonded metal models or bonded MCPB.py models with explicit
+  coordinating atoms, charges, and multiplicities.
+- MCPB Seminario Hessians from PySCF, GFN2-xTB, g-xTB, or MACE-POLAR-1;
+  PySCF supplies the embedded large-model ESP/RESP calculation.
+- Optional ASH/OpenMM active-site QM/MM refinement before final
+  parameterization.
+- Final `prmtop`, `inpcrd`, and PDB generation through `tleap`, followed by
+  topology, coordinate, charge, and optional OpenMM energy validation.
+- Optional Roe–Brooks OpenMM minimization, heating, density equilibration, and
+  manifest-sized production MD with GPU-first/CPU-fallback execution.
+
+## Installation
+
+Conda or Mamba is recommended because the real workflows use AmberTools,
+PropKa, xTB, OpenMM, ParmEd, and PySCF:
+
+```bash
+git clone https://github.com/miqueleg/mdprep.git
+cd mdprep
+mamba env create -f environment.yml
+conda activate mdprep
+mdprep selftest --quick
+```
+
+For a lighter Python-only installation, which does not install external
+chemistry executables:
+
+```bash
+python -m pip install .
+```
+
+Optional Python extras are available as `.[md]` for OpenMM and `.[qm]` for
+PySCF/ParmEd. External commands are discovered through `PATH`; manifests may
+also name a reviewed relative executable. No developer-machine path is embedded
+in the distributed examples.
+
+## Basic example
+
+Start from a standard protein PDB:
+
+```bash
+mdprep inspect input.pdb
+mdprep init input.pdb -o system.yaml
+```
+
+A minimal protein-only `system.yaml` is:
+
+```yaml
+project:
+  name: my_system
+  input_structure: input.pdb
+  output_dir: prepared/my_system
+
+structure:
+  keep_crystal_waters: true
+  altloc_policy: highest_occupancy
+  remove_unknown_heterogens: false
+  preserve_chain_ids: true
+  remove_input_hydrogens: true
+
+protein:
+  forcefield: ff14SB
+  water_model: TIP3P
+
+protonation:
+  ph: 7.0
+  method: manual_only
+  overrides: []
+
+disulfides:
+  auto_detect: true
+  detection_cutoff_angstrom: 2.2
+  force: []
+  forbid: []
+
+ligands: []
+metals: []
+
+solvation:
+  enabled: true
+  box: truncated_octahedron
+  buffer_angstrom: 10.0
+  neutralize: true
+  salt_concentration_molar: 0.15
+  positive_ion: Na+
+  negative_ion: Cl-
+
+validation:
+  run_openmm_energy_check: true
+  fail_on_warnings: false
+  fail_on_missing_parameters: true
+  fail_on_noninteger_ligand_charge: true
+
+molecular_dynamics:
+  enabled: false
+```
+
+The same validated manifest is available as
+[`examples/00_basic_protein.yaml`](examples/00_basic_protein.yaml).
+
+Validate and prepare it:
+
+```bash
+mdprep config-check system.yaml
+mdprep prepare system.yaml
+mdprep validate \
+  prepared/my_system/final/system.prmtop \
+  prepared/my_system/final/system.inpcrd
+```
+
+Relative paths are resolved from the manifest directory. Unknown heterogens
+are not deleted or guessed: configure them under `ligands` or `metals`, or
+explicitly request their removal.
+
+## Common workflows
+
+Generate a starter manifest using PropKa and ff19SB/OPC:
+
+```bash
+mdprep init input.pdb -o system.yaml \
+  --forcefield ff19SB \
+  --water-model OPC \
+  --protonation-method propka
+```
+
+Stop after a stage while reviewing a complex system:
+
+```bash
+mdprep prepare system.yaml --stop-after structure
+mdprep prepare system.yaml --stop-after protonation --overwrite
+mdprep prepare system.yaml --stop-after refinement --overwrite
+mdprep prepare system.yaml --stop-after ligands --overwrite
+mdprep prepare system.yaml --stop-after metals --overwrite
+mdprep prepare system.yaml --stop-after tleap --overwrite
+```
+
+Run the manifest-configured Roe–Brooks protocol from an existing Amber build:
+
+```bash
+mdprep run-md system.yaml \
+  --prmtop prepared/my_system/final/system.prmtop \
+  --inpcrd prepared/my_system/final/system.inpcrd
+```
+
+When `molecular_dynamics.enabled: true`, an ordinary `mdprep prepare` continues
+through MD. Production length and trajectory/state/checkpoint intervals are
+specified in steps in the manifest.
+
+## Where to go next
+
+| Task | Documentation | Example |
+| --- | --- | --- |
+| Manifest fields | [Manifest reference](docs/manifest_reference.md) | [All examples](examples/README.md) |
+| Protonation and histidines | [Protonation](docs/protonation.md) | `examples/02_manual_catalytic_protonation.yaml` |
+| Ligands, AM1-BCC, RESP, QMMESP | [Ligands](docs/ligands.md) and [QMMESP](docs/qmmesp_pyscf.md) | `examples/03_multi_ligand_am1bcc.yaml`, `04_qmmesp_pyscf_ligand.yaml` |
+| Metal centers and MCPB.py | [Metal centers](docs/metals.md) | `examples/08_nonbonded_zinc_1264.yaml`, `09_bonded_zinc_mcpb_prepare.yaml` |
+| Active-site QM/MM refinement | [QM/MM refinement](docs/qmmm_refinement.md) | `examples/10_qmmm_refinement_ash.yaml` |
+| Roe–Brooks OpenMM MD | [Molecular dynamics](docs/molecular_dynamics.md) | `examples/15_roe_brooks_openmm.yaml` |
+| Complete Fe(III) workflow | [7E07 tutorial](examples/tutorials/7E07_bonded_fe3/README.md) | `examples/tutorials/7E07_bonded_fe3/system.yaml` |
+
+All public example manifests are schema-validated in the test suite.
+
+## Outputs and reproducibility
+
+A complete run preserves:
+
+- the input and locked manifests;
+- normalized/protonated/refined intermediate PDBs;
+- ligand, QM, MCPB.py, and `tleap` inputs and logs;
+- final Amber topology, coordinates, and PDB;
+- structure, protonation, ligand, metal, `tleap`, and validation reports;
+- executable and Python-package version information;
+- optional MD PDBs, density history, trajectory, state log, and restarts.
+
+External failures are reported with command, working directory, return code,
+stdout, stderr, and runtime. mdprep does not silently fall back to another
+charge model, protonation, force field, QM method, or metal model.
+
+## Current limitations
+
+Version 0.2.0 does not support noncanonical amino acids inside peptide chains,
+covalent ligands, mmCIF input, automatic loop modeling, ORCA, Multiwfn,
+multiple independent bonded MCPB sites, or multi-chain MCPB protein inputs.
+Unsupported chemistry fails explicitly.
+
+## Development and release checks
+
+```bash
+mamba env create -f environment-dev.yml
+conda activate mdprep-dev
+pytest -q
+python -m mdprep.cli --help
+python -m mdprep.cli config-check examples/*.yaml
+python -m mdprep.cli selftest --quick
+python -m hatchling build
+```
+
+See [CONTRIBUTING.md](CONTRIBUTING.md), [CHANGELOG.md](CHANGELOG.md), and
+[CITATION.cff](CITATION.cff). mdprep is distributed under the MIT license.

mdprep-0.2.0.dist-info/RECORD

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mdprep-0.2.0.dist-info/WHEEL

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+Wheel-Version: 1.0
+Generator: hatchling 1.32.0
+Root-Is-Purelib: true
+Tag: py3-none-any

mdprep-0.2.0.dist-info/entry_points.txt

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+[console_scripts]
+mdprep = mdprep.cli:app

mdprep-0.2.0.dist-info/licenses/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2026 Miquel Estévez-Gay
+
+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.