hillclimber 0.1.5a8__cp314-cp314-macosx_15_0_x86_64.whl

hillclimber/__init__.py

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+from hillclimber.actions import PrintAction
+from hillclimber.analysis import plot_cv_time_series, read_colvar, sum_hills
+from hillclimber.biases import LowerWallBias, RestraintBias, UpperWallBias
+from hillclimber.cvs import (
+    AngleCV,
+    CoordinationNumberCV,
+    DistanceCV,
+    RadiusOfGyrationCV,
+    TorsionCV,
+)
+from hillclimber.metadynamics import MetadBias, MetaDynamicsConfig, MetaDynamicsModel
+from hillclimber.opes import OPESBias, OPESConfig, OPESModel
+from hillclimber.selectors import IndexSelector, SMARTSSelector, SMILESSelector
+from hillclimber.virtual_atoms import VirtualAtom
+
+__all__ = [
+    "PrintAction",
+    "DistanceCV",
+    "AngleCV",
+    "CoordinationNumberCV",
+    "TorsionCV",
+    "RadiusOfGyrationCV",
+    "IndexSelector",
+    "SMILESSelector",
+    "SMARTSSelector",
+    "VirtualAtom",
+    "MetaDynamicsModel",
+    "MetadBias",
+    "MetaDynamicsConfig",
+    "OPESModel",
+    "OPESBias",
+    "OPESConfig",
+    "RestraintBias",
+    "UpperWallBias",
+    "LowerWallBias",
+    "sum_hills",
+    "read_colvar",
+    "plot_cv_time_series",
+]

hillclimber/actions.py

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+import dataclasses
+
+import ase
+
+from hillclimber.interfaces import CollectiveVariable, PlumedGenerator
+
+
+@dataclasses.dataclass
+class PrintAction(PlumedGenerator):
+    """PLUMED PRINT action for outputting collective variables.
+
+    This action prints the values of collective variables to a file during
+    the simulation. Multiple CVs can be printed to the same file.
+
+    Parameters
+    ----------
+    cvs : list[CollectiveVariable]
+        List of collective variables to print.
+    stride : int, optional
+        Print every N steps, by default 1.
+    file : str, optional
+        Output file name, by default "COLVAR".
+
+    Examples
+    --------
+    >>> import hillclimber as hc
+    >>> print_action = hc.PrintAction(
+    ...     cvs=[cv1, cv2, cv3],
+    ...     stride=100,
+    ...     file="COLVAR"
+    ... )
+
+    Resources
+    ---------
+    - https://www.plumed.org/doc-master/user-doc/html/PRINT/
+    """
+
+    cvs: list[CollectiveVariable]
+    stride: int = 1
+    file: str = "COLVAR"
+
+    def to_plumed(self, atoms: ase.Atoms) -> list[str]:
+        """Convert the action node to a PLUMED input string."""
+        all_labels = set()
+        for cv in self.cvs:
+            labels, _ = cv.to_plumed(atoms)
+            all_labels.update(labels)
+
+        # Create the PRINT command with the unique labels
+        print_command = f"PRINT ARG={','.join(sorted(all_labels))} STRIDE={self.stride} FILE={self.file}"
+
+        # Return the command as a list
+        return [print_command]

hillclimber/analysis.py

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+"""Analysis utilities for metadynamics simulations.
+
+This module provides tools for analyzing metadynamics simulations,
+including free energy surface reconstruction and other post-processing tasks.
+"""
+
+import re
+import subprocess
+import typing as t
+from pathlib import Path
+
+import numpy as np
+
+
+def _validate_multi_cv_params(
+    min_bounds: float | list[float] | None = None,
+    max_bounds: float | list[float] | None = None,
+    bin: int | list[int] | None = None,
+    spacing: float | list[float] | None = None,
+    sigma: float | list[float] | None = None,
+    idw: str | list[str] | None = None,
+) -> None:
+    """Validate that multi-CV parameters have consistent dimensions.
+
+    Parameters
+    ----------
+    min_bounds, max_bounds, bin, spacing, sigma, idw
+        Parameters from sum_hills that can be lists for multi-CV cases.
+
+    Raises
+    ------
+    ValueError
+        If list parameters have inconsistent lengths.
+    """
+    # Collect all list parameters and their lengths
+    list_params: dict[str, int] = {}
+
+    params_to_check = {
+        "min_bounds": min_bounds,
+        "max_bounds": max_bounds,
+        "bin": bin,
+        "spacing": spacing,
+        "sigma": sigma,
+        "idw": idw,
+    }
+
+    for name, value in params_to_check.items():
+        if isinstance(value, (list, tuple)):
+            list_params[name] = len(value)
+
+    # If no list parameters, nothing to validate (single CV case)
+    if not list_params:
+        return
+
+    # Check that all list parameters have the same length
+    lengths = set(list_params.values())
+    if len(lengths) > 1:
+        # Build a detailed error message
+        param_details = ", ".join(
+            f"{name}={length}" for name, length in list_params.items()
+        )
+        raise ValueError(
+            f"Inconsistent number of CVs in parameters. "
+            f"All list parameters must have the same length. "
+            f"Got: {param_details}"
+        )
+
+
+def sum_hills(
+    hills_file: str | Path,
+    # Boolean flags
+    negbias: bool = False,
+    nohistory: bool = False,
+    mintozero: bool = False,
+    # File/histogram options
+    histo: str | Path | None = None,
+    # Grid parameters
+    stride: int | None = None,
+    min_bounds: float | list[float] | None = None,
+    max_bounds: float | list[float] | None = None,
+    bin: int | list[int] | None = None,
+    spacing: float | list[float] | None = None,
+    # Variable selection
+    idw: str | list[str] | None = None,
+    # Output options
+    outfile: str | Path | None = None,
+    outhisto: str | Path | None = None,
+    # Integration parameters
+    kt: float | None = None,
+    sigma: float | list[float] | None = None,
+    # Format
+    fmt: str | None = None,
+    # Additional options
+    verbose: bool = True,
+    check: bool = True,
+) -> subprocess.CompletedProcess:
+    """Run PLUMED sum_hills to reconstruct free energy surfaces from metadynamics.
+
+    This function wraps the PLUMED ``sum_hills`` command-line tool, which analyzes
+    HILLS files from metadynamics simulations to reconstruct the free energy surface.
+
+    Parameters
+    ----------
+    hills_file : str or Path
+        Path to the HILLS file to analyze. This file is generated during
+        metadynamics simulations and contains the deposited Gaussian hills.
+    negbias : bool, default=False
+        Print the negative bias instead of the free energy.
+    nohistory : bool, default=False
+        To be used with ``stride``: splits the bias/histogram without previous history.
+    mintozero : bool, default=False
+        Translate all minimum values in bias/histogram to zero.
+    histo : str or Path, optional
+        Name of the file for histogram (a COLVAR/HILLS file is good).
+    stride : int, optional
+        Stride for integrating hills file. Default is 0 (never integrate).
+    min_bounds : float or list[float], optional
+        Lower bounds for the grid. For multi-dimensional CVs, provide a list with
+        one value per CV (e.g., ``[-3.14, -3.14]`` for two torsion angles).
+    max_bounds : float or list[float], optional
+        Upper bounds for the grid. For multi-dimensional CVs, provide a list with
+        one value per CV (e.g., ``[3.14, 3.14]`` for two torsion angles).
+    bin : int or list[int], optional
+        Number of bins for the grid. For multi-dimensional CVs, provide a list with
+        one value per CV (e.g., ``[250, 250]`` for two CVs with 250 bins each).
+    spacing : float or list[float], optional
+        Grid spacing, alternative to the number of bins. For multi-dimensional CVs,
+        provide a list with one value per CV.
+    idw : str or list[str], optional
+        Variables to be used for the free-energy/histogram. For multi-dimensional CVs,
+        provide a list with one variable name per CV (e.g., ``['phi', 'psi']``).
+    outfile : str or Path, optional
+        Output file for sum_hills. Default is ``fes.dat``.
+    outhisto : str or Path, optional
+        Output file for the histogram.
+    kt : float, optional
+        Temperature in energy units (kJ/mol) for integrating out variables.
+    sigma : float or list[float], optional
+        Sigma for binning (only needed when doing histogram). For multi-dimensional CVs,
+        provide a list with one value per CV.
+    fmt : str, optional
+        Output format specification.
+    verbose : bool, default=True
+        Print command output to stdout/stderr.
+    check : bool, default=True
+        Raise exception if command fails.
+
+    Returns
+    -------
+    subprocess.CompletedProcess
+        The completed process object from subprocess.run.
+
+    Raises
+    ------
+    FileNotFoundError
+        If the HILLS file cannot be found.
+    ValueError
+        If list-based parameters (``bin``, ``min_bounds``, ``max_bounds``, etc.)
+        have inconsistent lengths when using multiple CVs.
+    subprocess.CalledProcessError
+        If the PLUMED command fails and ``check=True``.
+
+    Examples
+    --------
+    Basic usage to reconstruct a 1D free energy surface:
+
+    >>> import hillclimber as hc
+    >>> hc.sum_hills("HILLS")
+
+    With custom grid resolution and output file:
+
+    >>> hc.sum_hills(
+    ...     "HILLS",
+    ...     bin=1000,
+    ...     outfile="custom_fes.dat"
+    ... )
+
+    For a 2D free energy surface with explicit bounds:
+
+    >>> hc.sum_hills(
+    ...     "HILLS",
+    ...     bin=[100, 100],
+    ...     min_bounds=[0.0, 0.0],
+    ...     max_bounds=[10.0, 10.0],
+    ...     outfile="fes_2d.dat"
+    ... )
+
+    For protein backbone torsion angles (phi and psi):
+
+    >>> hc.sum_hills(
+    ...     "HILLS",
+    ...     bin=[250, 250],
+    ...     min_bounds=[-3.14, -3.14],
+    ...     max_bounds=[3.14, 3.14],
+    ...     idw=["phi", "psi"],
+    ...     outfile="ramachandran.dat"
+    ... )
+
+    Resources
+    ---------
+    - https://www.plumed.org/doc-master/user-doc/html/sum_hills.html
+
+    Notes
+    -----
+    The HILLS file is automatically generated during metadynamics simulations
+    when using the METAD action. Each line in the file represents a deposited
+    Gaussian hill with its position, width (sigma), and height.
+
+    The free energy surface is reconstructed by summing all deposited hills:
+    F(s) = -V(s) where V(s) is the bias potential.
+
+    **Multi-CV Consistency:**
+    When using multiple collective variables (CVs), all list-based parameters
+    must have the same length. For example, if analyzing two CVs (phi and psi),
+    then ``bin``, ``min_bounds``, ``max_bounds``, and ``idw`` (if provided as lists)
+    must all have exactly 2 elements. The function will raise a ``ValueError``
+    if inconsistent list lengths are detected.
+    """
+    # Convert to Path object
+    hills_file = Path(hills_file)
+
+    # Verify HILLS file exists
+    if not hills_file.exists():
+        raise FileNotFoundError(f"HILLS file not found: {hills_file}")
+
+    # Validate multi-CV parameter consistency
+    _validate_multi_cv_params(
+        min_bounds=min_bounds,
+        max_bounds=max_bounds,
+        bin=bin,
+        spacing=spacing,
+        sigma=sigma,
+        idw=idw,
+    )
+
+    # Build command
+    cmd_parts = ["plumed", "sum_hills"]
+
+    # Add hills file
+    cmd_parts.extend(["--hills", str(hills_file)])
+
+    # Add boolean flags
+    if negbias:
+        cmd_parts.append("--negbias")
+    if nohistory:
+        cmd_parts.append("--nohistory")
+    if mintozero:
+        cmd_parts.append("--mintozero")
+
+    # Helper function to format list parameters
+    def format_param(value: t.Any) -> str:
+        if isinstance(value, (list, tuple)):
+            return ",".join(str(v) for v in value)
+        return str(value)
+
+    # Add optional parameters
+    if histo is not None:
+        cmd_parts.extend(["--histo", str(histo)])
+    if stride is not None:
+        cmd_parts.extend(["--stride", str(stride)])
+    if min_bounds is not None:
+        cmd_parts.extend(["--min", format_param(min_bounds)])
+    if max_bounds is not None:
+        cmd_parts.extend(["--max", format_param(max_bounds)])
+    if bin is not None:
+        cmd_parts.extend(["--bin", format_param(bin)])
+    if spacing is not None:
+        cmd_parts.extend(["--spacing", format_param(spacing)])
+    if idw is not None:
+        cmd_parts.extend(["--idw", format_param(idw)])
+    if outfile is not None:
+        cmd_parts.extend(["--outfile", str(outfile)])
+    if outhisto is not None:
+        cmd_parts.extend(["--outhisto", str(outhisto)])
+    if kt is not None:
+        cmd_parts.extend(["--kt", str(kt)])
+    if sigma is not None:
+        cmd_parts.extend(["--sigma", format_param(sigma)])
+    if fmt is not None:
+        cmd_parts.extend(["--fmt", str(fmt)])
+
+    # Run command
+    if verbose:
+        print(f"Running: {' '.join(cmd_parts)}")
+
+    result = subprocess.run(
+        cmd_parts,
+        capture_output=not verbose,
+        text=True,
+        check=check,
+    )
+
+    if verbose and result.returncode == 0:
+        print("sum_hills completed successfully")
+
+    return result
+
+
+def read_colvar(
+    colvar_file: str | Path,
+) -> dict[str, np.ndarray]:
+    """Read a PLUMED COLVAR file and parse its contents.
+
+    This function reads a COLVAR file produced by PLUMED, extracts the field names
+    from the header (which starts with ``#! FIELDS``), and returns the data as a
+    dictionary mapping field names to numpy arrays.
+
+    Parameters
+    ----------
+    colvar_file : str or Path
+        Path to the COLVAR file to read.
+
+    Returns
+    -------
+    dict[str, np.ndarray]
+        Dictionary mapping field names to 1D numpy arrays containing the data.
+        Keys correspond to the fields specified in the COLVAR header.
+
+    Raises
+    ------
+    FileNotFoundError
+        If the COLVAR file does not exist.
+    ValueError
+        If the COLVAR file does not contain a valid ``#! FIELDS`` header.
+
+    Examples
+    --------
+    >>> import hillclimber as hc
+    >>> data = hc.read_colvar("COLVAR")
+    >>> print(data.keys())
+    dict_keys(['time', 'phi', 'psi'])
+    >>> print(data['time'][:5])
+    [0. 1. 2. 3. 4.]
+
+    Notes
+    -----
+    The COLVAR file format from PLUMED starts with a header line:
+    ``#! FIELDS time cv1 cv2 ...``
+
+    All subsequent lines starting with ``#`` are treated as comments and ignored.
+    Data lines are parsed as whitespace-separated numeric values.
+
+    Resources
+    ---------
+    - https://www.plumed.org/doc-master/user-doc/html/colvar.html
+    """
+    colvar_file = Path(colvar_file)
+
+    if not colvar_file.exists():
+        raise FileNotFoundError(f"COLVAR file not found: {colvar_file}")
+
+    # Read the file
+    with open(colvar_file, "r") as f:
+        lines = f.readlines()
+
+    # Find and parse the header
+    field_names: list[str] | None = None
+    for line in lines:
+        if line.startswith("#! FIELDS"):
+            # Extract field names from the header
+            # Format: "#! FIELDS time phi psi ..."
+            fields_match = re.match(r"#!\s*FIELDS\s+(.+)", line)
+            if fields_match:
+                field_names = fields_match.group(1).split()
+                break
+
+    if field_names is None:
+        raise ValueError(
+            f"COLVAR file {colvar_file} does not contain a valid '#! FIELDS' header"
+        )
+
+    # Parse data lines (skip comments)
+    data_lines = []
+    for line in lines:
+        # Skip comments and empty lines
+        if line.startswith("#") or not line.strip():
+            continue
+        # Parse numeric data
+        values = line.split()
+        if len(values) == len(field_names):
+            data_lines.append([float(v) for v in values])
+
+    # Convert to numpy array
+    data_array = np.array(data_lines)
+
+    # Create dictionary mapping field names to columns
+    result = {name: data_array[:, i] for i, name in enumerate(field_names)}
+
+    return result
+
+
+def plot_cv_time_series(
+    colvar_file: str | Path,
+    cv_names: list[str] | None = None,
+    time_unit: str = "ps",
+    exclude_patterns: list[str] | None = None,
+    figsize: tuple[float, float] = (8, 5),
+    kde_width: str = "25%",
+    colors: list[str] | None = None,
+    alpha: float = 0.5,
+    marker: str = "x",
+    marker_size: float = 10,
+) -> tuple[t.Any, t.Any]:
+    """Plot collective variables over time with KDE distributions.
+
+    This function creates a visualization showing CV evolution over time as scatter
+    plots, with kernel density estimation (KDE) plots displayed on the right side
+    to show the distribution of each CV.
+
+    Parameters
+    ----------
+    colvar_file : str or Path
+        Path to the COLVAR file to plot.
+    cv_names : list[str], optional
+        List of CV names to plot. If None, automatically detects CVs by excluding
+        common non-CV fields like 'time', 'sigma_*', 'height', 'biasf'.
+    time_unit : str, default='ps'
+        Unit label for the time axis.
+    exclude_patterns : list[str], optional
+        Additional regex patterns for field names to exclude from auto-detection.
+        Default excludes: 'time', 'sigma_.*', 'height', 'biasf'.
+    figsize : tuple[float, float], default=(8, 5)
+        Figure size in inches (width, height).
+    kde_width : str, default='25%'
+        Width of the KDE subplot as a percentage of the main plot width.
+    colors : list[str], optional
+        List of colors to use for each CV. If None, uses default color cycle.
+    alpha : float, default=0.5
+        Transparency for scatter points.
+    marker : str, default='x'
+        Marker style for scatter points.
+    marker_size : float, default=10
+        Size of scatter markers.
+
+    Returns
+    -------
+    fig : matplotlib.figure.Figure
+        The matplotlib figure object.
+    axes : tuple
+        Tuple of (main_axis, kde_axis) matplotlib axes objects.
+
+    Raises
+    ------
+    ImportError
+        If matplotlib or seaborn is not installed.
+    FileNotFoundError
+        If the COLVAR file does not exist.
+
+    Examples
+    --------
+    Basic usage with auto-detected CVs:
+
+    >>> import hillclimber as hc
+    >>> fig, axes = hc.plot_cv_time_series("COLVAR")
+
+    Plot specific CVs:
+
+    >>> fig, axes = hc.plot_cv_time_series("COLVAR", cv_names=["phi", "psi"])
+
+    Customize appearance:
+
+    >>> fig, axes = hc.plot_cv_time_series(
+    ...     "COLVAR",
+    ...     figsize=(10, 6),
+    ...     colors=["blue", "red"],
+    ...     alpha=0.7
+    ... )
+
+    Notes
+    -----
+    This function requires matplotlib and seaborn to be installed.
+
+    The function automatically detects CVs by excluding common metadata fields
+    such as 'time', 'sigma_*', 'height', and 'biasf'. You can specify additional
+    exclusion patterns or explicitly provide the CV names to plot.
+
+    Resources
+    ---------
+    - https://www.plumed.org/doc-master/user-doc/html/colvar.html
+    """
+    try:
+        import matplotlib.pyplot as plt
+        import seaborn as sns
+        from mpl_toolkits.axes_grid1 import make_axes_locatable
+    except ImportError as e:
+        raise ImportError(
+            "matplotlib and seaborn are required for plotting. "
+            "Install them with: pip install matplotlib seaborn"
+        ) from e
+
+    # Read the COLVAR file
+    data = read_colvar(colvar_file)
+
+    # Auto-detect CVs if not specified
+    if cv_names is None:
+        # Default exclusion patterns
+        default_exclude = [
+            r"^time$",
+            r"^sigma_.*$",
+            r"^height$",
+            r"^biasf$",
+        ]
+        if exclude_patterns is not None:
+            default_exclude.extend(exclude_patterns)
+
+        # Filter field names
+        detected_cvs: list[str] = []
+        for field in data.keys():
+            # Check if field matches any exclusion pattern
+            exclude = False
+            for pattern in default_exclude:
+                if re.match(pattern, field):
+                    exclude = True
+                    break
+            if not exclude:
+                detected_cvs.append(field)
+
+        if not detected_cvs:
+            raise ValueError(
+                "No CVs detected in COLVAR file. "
+                "All fields were excluded by the exclusion patterns."
+            )
+        cv_names = detected_cvs
+
+    # Verify that all requested CVs exist
+    missing_cvs = [cv for cv in cv_names if cv not in data]
+    if missing_cvs:
+        raise ValueError(
+            f"CVs not found in COLVAR file: {missing_cvs}. "
+            f"Available fields: {list(data.keys())}"
+        )
+
+    # Get time data
+    if "time" not in data:
+        raise ValueError("COLVAR file must contain a 'time' field")
+    time = data["time"]
+
+    # Default colors if not provided
+    if colors is None:
+        colors = plt.cm.tab10.colors  # type: ignore
+
+    # Set seaborn style
+    sns.set(style="whitegrid")
+
+    # Create figure
+    fig, ax = plt.subplots(figsize=figsize)
+
+    # Plot each CV
+    for i, cv_name in enumerate(cv_names):
+        color = colors[i % len(colors)]
+        cv_data = data[cv_name]
+        ax.scatter(
+            time,
+            cv_data,
+            c=[color],
+            label=cv_name,
+            marker=marker,
+            s=marker_size,
+            alpha=alpha,
+        )
+
+    ax.set_xlabel(f"Time / {time_unit}")
+    ax.set_ylabel("CV value")
+    ax.legend()
+
+    # Create KDE subplot on the right
+    divider = make_axes_locatable(ax)
+    ax_kde = divider.append_axes("right", size=kde_width, pad=0.1, sharey=ax)
+
+    # Plot KDE for each CV
+    for i, cv_name in enumerate(cv_names):
+        color = colors[i % len(colors)]
+        cv_data = data[cv_name]
+        sns.kdeplot(
+            y=cv_data,
+            ax=ax_kde,
+            color=color,
+            fill=True,
+            alpha=0.3,
+            linewidth=1.5,
+            label=cv_name,
+        )
+
+    # Clean up KDE axis
+    ax_kde.set_xlabel("Density")
+    ax_kde.yaxis.set_tick_params(labelleft=False)
+
+    plt.tight_layout()
+
+    return fig, (ax, ax_kde)