pychnosz 1.1.1__cp310-cp310-win_amd64.whl

pychnosz/biomolecules/proteins.py

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+"""
+Protein functions for CHNOSZ.
+
+This module implements protein-related functions from CHNOSZ including
+add_protein, protein_length, protein_formula, protein_OBIGT, and protein_basis.
+"""
+
+import numpy as np
+import pandas as pd
+from typing import Union, Optional, List
+import warnings
+
+from ..core.thermo import thermo
+from ..utils.formula import i2A, as_chemical_formula, species_basis
+from ..biomolecules.ionize_aa import ionize_aa
+
+
+def pinfo(protein: Union[str, int, pd.DataFrame, List],
+          organism: Optional[str] = None,
+          residue: bool = False,
+          regexp: bool = False) -> Union[pd.DataFrame, np.ndarray, int]:
+    """
+    Get protein information from thermo().protein.
+
+    This function retrieves protein data from the thermodynamic database.
+    The behavior depends on the input type:
+    - DataFrame: returns the DataFrame (possibly per residue)
+    - int or list of ints: returns rows from thermo().protein
+    - str: searches for protein by name, returns row number(s)
+
+    Parameters
+    ----------
+    protein : str, int, DataFrame, or list
+        Protein identifier(s) or data
+    organism : str, optional
+        Organism identifier (used with protein name)
+    residue : bool, default False
+        Return per-residue amino acid composition
+    regexp : bool, default False
+        Use regular expression matching for protein search
+
+    Returns
+    -------
+    DataFrame, array, or int
+        Protein information or row numbers
+
+    Examples
+    --------
+    >>> # Get protein by name
+    >>> iprotein = pinfo("LYSC_CHICK")
+    >>> # Get protein data by row number
+    >>> protein_data = pinfo(iprotein)
+    """
+    t_p = thermo().protein
+
+    if t_p is None:
+        raise RuntimeError("Protein database not loaded. Run reset() first.")
+
+    # If input is a DataFrame, return it (possibly per residue)
+    if isinstance(protein, pd.DataFrame):
+        out = protein.copy()
+        if residue:
+            # Normalize by total amino acid count (columns 5:25)
+            row_sums = out.iloc[:, 5:25].sum(axis=1)
+            out.iloc[:, 4:24] = out.iloc[:, 4:24].div(row_sums, axis=0)
+        return out
+
+    # If input is numeric, get rows from thermo().protein
+    if isinstance(protein, (int, np.integer)):
+        protein = [protein]
+
+    if isinstance(protein, (list, np.ndarray)) and all(isinstance(x, (int, np.integer)) for x in protein):
+        # Get amino acid counts
+        iproteins = list(range(len(t_p)))
+        # Replace invalid indices with NaN
+        protein_clean = [p if p in iproteins else np.nan for p in protein]
+        # Filter out NaN values for indexing
+        valid_indices = [p for p in protein_clean if not np.isnan(p)]
+
+        if not valid_indices:
+            return pd.DataFrame()
+
+        out = t_p.iloc[valid_indices].copy()
+
+        # Compute per-residue counts if requested
+        if residue:
+            row_sums = out.iloc[:, 5:25].sum(axis=1)
+            out.iloc[:, 4:24] = out.iloc[:, 4:24].div(row_sums, axis=0)
+
+        return out
+
+    # If input is string or list of strings, search for protein
+    if isinstance(protein, str):
+        protein = [protein]
+
+    if isinstance(protein, list) and all(isinstance(x, str) for x in protein):
+        # Search for protein or protein_organism in thermo().protein
+        t_p_names = t_p['protein'] + '_' + t_p['organism']
+
+        if regexp:
+            # Use regular expression matching
+            matches = []
+            for prot in protein:
+                iprotein = t_p['protein'].str.contains(prot, regex=True, na=False)
+                if organism is not None:
+                    iorganism = t_p['organism'].str.contains(organism, regex=True, na=False)
+                    iprotein = iprotein & iorganism
+                indices = np.where(iprotein)[0]
+                if len(indices) > 0:
+                    matches.extend(indices.tolist())
+                else:
+                    matches.append(np.nan)
+
+            if len(matches) == 1:
+                if np.isnan(matches[0]):
+                    return np.nan
+                return int(matches[0])
+            return np.array(matches)
+        else:
+            # Exact matching
+            if organism is None:
+                my_names = protein
+            else:
+                my_names = [f"{p}_{organism}" for p in protein]
+
+            # Find matches
+            matches = []
+            for name in my_names:
+                idx = np.where(t_p_names == name)[0]
+                if len(idx) > 0:
+                    matches.append(idx[0])
+                else:
+                    matches.append(np.nan)
+
+            if len(matches) == 1:
+                if np.isnan(matches[0]):
+                    return np.nan
+                return int(matches[0])
+            return np.array(matches)
+
+    raise TypeError(f"Unsupported protein type: {type(protein)}")
+
+
+def add_protein(aa: pd.DataFrame, as_residue: bool = False) -> np.ndarray:
+    """
+    Add protein amino acid compositions to thermo().protein.
+
+    Parameters
+    ----------
+    aa : DataFrame
+        DataFrame with protein amino acid compositions.
+        Must have same columns as thermo().protein
+    as_residue : bool, default False
+        Normalize amino acid counts by protein length
+
+    Returns
+    -------
+    array
+        Row numbers of added/updated proteins in thermo().protein
+
+    Examples
+    --------
+    >>> import pandas as pd
+    >>> from pychnosz import *
+    >>> aa = pd.read_csv("POLG.csv")
+    >>> iprotein = add_protein(aa)
+    """
+    t = thermo()
+
+    if t.protein is None:
+        raise RuntimeError("Protein database not loaded. Run reset() first.")
+
+    # Check that columns match
+    if list(aa.columns) != list(t.protein.columns):
+        raise ValueError("'aa' does not have the same columns as thermo().protein")
+
+    # Check that new protein IDs are unique
+    po = aa['protein'] + '_' + aa['organism']
+    idup = po.duplicated()
+    if idup.any():
+        dup_proteins = po[idup].unique()
+        raise ValueError(f"some protein IDs are duplicated: {' '.join(dup_proteins)}")
+
+    # Normalize by protein length if as_residue = True
+    if as_residue:
+        pl = protein_length(aa)
+        aa.iloc[:, 4:24] = aa.iloc[:, 4:24].div(pl, axis=0)
+
+    # Find any protein IDs that are already present
+    ip = pinfo(po.tolist())
+    if isinstance(ip, (int, np.integer)):
+        ip = np.array([ip])
+    elif not isinstance(ip, np.ndarray):
+        ip = np.array([ip])
+
+    ip_present = ~np.isnan(ip)
+
+    # Now we're ready to go
+    tp_new = t.protein.copy()
+
+    # Add new proteins
+    if not all(ip_present):
+        new_proteins = aa[~ip_present].copy()
+        tp_new = pd.concat([tp_new, new_proteins], ignore_index=True)
+
+    # Update existing proteins
+    if any(ip_present):
+        valid_ip = ip[ip_present].astype(int)
+        tp_new.iloc[valid_ip] = aa[ip_present].values
+
+    # Update the protein database
+    tp_new.reset_index(drop=True, inplace=True)
+    t.protein = tp_new
+
+    # Return the new row numbers
+    ip_new = pinfo(po.tolist())
+    if isinstance(ip_new, (int, np.integer)):
+        ip_new = np.array([ip_new])
+
+    # Print messages
+    n_added = sum(~ip_present)
+    n_replaced = sum(ip_present)
+
+    if n_added > 0:
+        print(f"add_protein: added {n_added} new protein(s) to thermo().protein")
+    if n_replaced > 0:
+        print(f"add_protein: replaced {n_replaced} existing protein(s) in thermo().protein")
+
+    return ip_new
+
+
+def protein_length(protein: Union[int, List[int], pd.DataFrame],
+                   organism: Optional[str] = None) -> Union[int, np.ndarray]:
+    """
+    Calculate the length(s) of proteins.
+
+    Parameters
+    ----------
+    protein : int, list of int, or DataFrame
+        Protein identifier(s) or amino acid composition data
+    organism : str, optional
+        Organism identifier (used with protein number)
+
+    Returns
+    -------
+    int or array
+        Protein length(s) in amino acid residues
+
+    Examples
+    --------
+    >>> iprotein = pinfo("LYSC_CHICK")
+    >>> length = protein_length(iprotein)
+    """
+    # Get amino acid composition
+    aa = pinfo(pinfo(protein, organism))
+
+    if isinstance(aa, pd.DataFrame):
+        # Use sum on the columns containing amino acid counts (columns 5:25)
+        pl = aa.iloc[:, 5:25].sum(axis=1).values
+        return pl
+    else:
+        return 0
+
+
+def group_formulas() -> pd.DataFrame:
+    """
+    Return chemical formulas of amino acid residues.
+
+    This function returns a DataFrame with the chemical formulas of
+    H2O, the 20 amino acid sidechain groups, and the unfolded protein
+    backbone group [UPBB].
+
+    Returns
+    -------
+    DataFrame
+        Chemical formulas with elements C, H, N, O, S as columns
+        and residues as rows
+    """
+    # Chemical formulas as a numpy array
+    # Rows: water, [Ala], [Cys], [Asp], [Glu], [Phe], [Gly], [His], [Ile], [Lys], [Leu],
+    #       [Met], [Asn], [Pro], [Gln], [Arg], [Ser], [Thr], [Val], [Trp], [Tyr], [UPBB]
+    # Columns: C, H, N, O, S
+    A = np.array([
+        [0, 2, 0, 1, 0],      # H2O
+        [1, 3, 0, 0, 0],      # [Ala]
+        [1, 3, 0, 0, 1],      # [Cys]
+        [2, 3, 0, 2, 0],      # [Asp]
+        [3, 5, 0, 2, 0],      # [Glu]
+        [7, 7, 0, 0, 0],      # [Phe]
+        [0, 1, 0, 0, 0],      # [Gly]
+        [4, 5, 2, 0, 0],      # [His]
+        [4, 9, 0, 0, 0],      # [Ile]
+        [4, 10, 1, 0, 0],     # [Lys]
+        [4, 9, 0, 0, 0],      # [Leu]
+        [3, 7, 0, 0, 1],      # [Met]
+        [2, 4, 1, 1, 0],      # [Asn]
+        [3, 5, 0, 0, 0],      # [Pro]
+        [3, 6, 1, 1, 0],      # [Gln]
+        [4, 10, 3, 0, 0],     # [Arg]
+        [1, 3, 0, 1, 0],      # [Ser]
+        [2, 5, 0, 1, 0],      # [Thr]
+        [3, 7, 0, 0, 0],      # [Val]
+        [9, 8, 1, 0, 0],      # [Trp]
+        [7, 7, 0, 1, 0],      # [Tyr]
+        [2, 2, 1, 1, 0]       # [UPBB]
+    ])
+
+    rownames = ['H2O', '[Ala]', '[Cys]', '[Asp]', '[Glu]', '[Phe]', '[Gly]',
+                '[His]', '[Ile]', '[Lys]', '[Leu]', '[Met]', '[Asn]', '[Pro]',
+                '[Gln]', '[Arg]', '[Ser]', '[Thr]', '[Val]', '[Trp]', '[Tyr]',
+                '[UPBB]']
+
+    # Add [UPBB] to the sidechain groups to get residues
+    out = A.copy()
+    # Add [UPBB] (last row) to each sidechain group (rows 1-20)
+    out[1:21, :] = out[1:21, :] + A[21, :]
+
+    # Create DataFrame
+    df = pd.DataFrame(out[0:21, :],
+                     index=rownames[0:21],
+                     columns=['C', 'H', 'N', 'O', 'S'])
+
+    return df
+
+
+def protein_formula(protein: Union[int, List[int], pd.DataFrame],
+                   organism: Optional[str] = None,
+                   residue: bool = False) -> pd.DataFrame:
+    """
+    Calculate chemical formulas of proteins.
+
+    Parameters
+    ----------
+    protein : int, list of int, or DataFrame
+        Protein identifier(s) or amino acid composition data
+    organism : str, optional
+        Organism identifier (used with protein number)
+    residue : bool, default False
+        Return per-residue formula
+
+    Returns
+    -------
+    DataFrame
+        Chemical formulas with elements C, H, N, O, S as columns
+
+    Examples
+    --------
+    >>> iprotein = pinfo("LYSC_CHICK")
+    >>> formula = protein_formula(iprotein)
+    """
+    # Get amino acid composition
+    aa = pinfo(pinfo(protein, organism))
+
+    if not isinstance(aa, pd.DataFrame):
+        raise TypeError("Could not retrieve protein data")
+
+    # Get group formulas
+    rf = group_formulas()
+
+    # Matrix multiplication: amino acid counts * residue formulas
+    # Columns 5:25 contain amino acid counts (excluding chains column at 4)
+    # We need to add H2O (chains column) separately
+    aa_counts = aa.iloc[:, 5:25].values.astype(float)
+    chains = aa.iloc[:, 4].values.astype(float)
+    rf_values = rf.iloc[1:, :].values.astype(float)  # Skip H2O row, use amino acid residues
+    rf_H2O = rf.iloc[0, :].values.astype(float)  # H2O row
+
+    # Calculate protein formula: amino acids + H2O for chains
+    out = np.dot(aa_counts, rf_values) + np.outer(chains, rf_H2O)
+
+    # Normalize by residue if requested
+    if residue:
+        row_sums = aa.iloc[:, 5:25].sum(axis=1).values
+        out = out / row_sums[:, np.newaxis]
+
+    # Create DataFrame with protein names as index
+    protein_names = aa['protein'] + '_' + aa['organism']
+    # Make names unique if there are duplicates
+    if protein_names.duplicated().any():
+        counts = {}
+        unique_names = []
+        for name in protein_names:
+            if name in counts:
+                counts[name] += 1
+                unique_names.append(f"{name}.{counts[name]}")
+            else:
+                counts[name] = 0
+                unique_names.append(name)
+        protein_names = unique_names
+
+    result = pd.DataFrame(out,
+                         index=protein_names,
+                         columns=['C', 'H', 'N', 'O', 'S'])
+
+    return result
+
+
+def protein_OBIGT(protein: Union[int, List[int], pd.DataFrame],
+                 organism: Optional[str] = None,
+                 state: Optional[str] = None) -> pd.DataFrame:
+    """
+    Calculate protein properties using group additivity.
+
+    This function calculates thermodynamic properties of proteins
+    from amino acid composition using the group additivity approach.
+
+    Parameters
+    ----------
+    protein : int, list of int, or DataFrame
+        Protein identifier(s) or amino acid composition data
+    organism : str, optional
+        Organism identifier
+    state : str, optional
+        Physical state ('aq' or 'cr'). If None, uses thermo().opt['state']
+
+    Returns
+    -------
+    DataFrame
+        Thermodynamic properties in OBIGT format
+
+    Examples
+    --------
+    >>> iprotein = pinfo("LYSC_CHICK")
+    >>> props = protein_OBIGT(iprotein)
+    """
+    # Get amino acid composition
+    aa = pinfo(pinfo(protein, organism))
+
+    if not isinstance(aa, pd.DataFrame):
+        raise TypeError("Could not retrieve protein data")
+
+    # Get state
+    if state is None:
+        state = thermo().opt.get('state', 'aq')
+
+    # The names of the protein backbone groups depend on the state
+    # [UPBB] for aq or [PBB] for cr
+    if state == 'aq':
+        bbgroup = 'UPBB'
+    else:
+        bbgroup = 'PBB'
+
+    # Names of the AABB, sidechain and protein backbone groups
+    aa_cols = aa.columns[5:25].tolist()  # Get amino acid column names
+    groups = ['AABB'] + aa_cols + [bbgroup]
+
+    # Put brackets around the group names
+    groups = [f"[{g}]" for g in groups]
+
+    # The row numbers of the groups in thermo().OBIGT
+    from ..core.info import info
+
+    groups_state = [f"{g}" for g in groups]
+    obigt = thermo().obigt
+
+    # Find groups in OBIGT
+    igroup = []
+    for group_name in groups_state:
+        # Search for the group with the specified state
+        matches = obigt[(obigt['name'] == group_name) & (obigt['state'] == state)]
+        if len(matches) > 0:
+            igroup.append(matches.index[0])
+        else:
+            # Try without brackets if not found
+            group_alt = group_name.strip('[]')
+            matches = obigt[(obigt['name'] == group_alt) & (obigt['state'] == state)]
+            if len(matches) > 0:
+                igroup.append(matches.index[0])
+            else:
+                raise ValueError(f"Group {group_name} not found in OBIGT for state {state}")
+
+    # The properties are in columns 9:21 of thermo().OBIGT (G, H, S, Cp, V, etc.)
+    # Column indices: G=9, H=10, S=11, Cp=12, V=13, a1.a=14, a2.b=15, a3.c=16, a4.d=17, c1.e=18, c2.f=19, omega.lambda=20, z.T=21
+    groupprops = obigt.loc[igroup, obigt.columns[9:22]]
+
+    # The elements in each of the groups
+    groupelements = i2A(igroup)
+
+    results = []
+
+    # Process each protein
+    for idx in range(len(aa)):
+        aa_row = aa.iloc[idx]
+
+        # Numbers of groups: chains [=AABB], sidechains, protein backbone
+        nchains = float(aa_row.iloc[4])  # chains column
+        length = float(aa_row.iloc[5:25].sum())  # sum of amino acids
+        npbb = length - nchains
+
+        # Create ngroups array
+        ngroups = np.array([nchains] + aa_row.iloc[5:25].tolist() + [npbb], dtype=float)
+
+        # Calculate thermodynamic properties by group additivity
+        eos = (groupprops.values * ngroups[:, np.newaxis]).sum(axis=0)
+
+        # Calculate formula
+        f_in = (groupelements.values * ngroups[:, np.newaxis]).sum(axis=0).round(3)
+
+        # Remove elements that don't appear
+        element_names = groupelements.columns
+        f_dict = {elem: f_in[i] for i, elem in enumerate(element_names) if f_in[i] != 0}
+
+        # Turn it into a formula string
+        f = as_chemical_formula(f_dict)
+
+        # Species name
+        name = f"{aa_row['protein']}_{aa_row['organism']}"
+
+        # Print message
+        print(f"protein_OBIGT: found {name} ({f}, {round(length, 3)} residues)")
+
+        ref = aa_row['ref']
+
+        # Include 'model' column
+        model = 'HKF' if state == 'aq' else 'CGL'
+
+        # Create header
+        header = {
+            'name': name,
+            'abbrv': None,
+            'formula': f,
+            'state': state,
+            'ref1': ref,
+            'ref2': None,
+            'date': None,
+            'model': model,
+            'E_units': 'cal'
+        }
+
+        # Combine header and eos
+        eosout = {**header, **dict(zip(groupprops.columns, eos))}
+        results.append(eosout)
+
+    # Convert to DataFrame
+    out = pd.DataFrame(results)
+    out.reset_index(drop=True, inplace=True)
+
+    return out
+
+
+def protein_basis(protein: Union[int, List[int], pd.DataFrame],
+                 T: float = 25.0,
+                 normalize: bool = False) -> pd.DataFrame:
+    """
+    Calculate coefficients of basis species in protein formation reactions.
+
+    Parameters
+    ----------
+    protein : int, list of int, or DataFrame
+        Protein identifier(s) or amino acid composition data
+    T : float, default 25.0
+        Temperature in degrees Celsius
+    normalize : bool, default False
+        Normalize by protein length
+
+    Returns
+    -------
+    DataFrame
+        Coefficients of basis species
+
+    Examples
+    --------
+    >>> from pychnosz import *
+    >>> basis("CHNOSe")
+    >>> iprotein = pinfo("LYSC_CHICK")
+    >>> coeffs = protein_basis(iprotein)
+    """
+    # Get amino acid composition
+    aa = pinfo(pinfo(protein))
+
+    if not isinstance(aa, pd.DataFrame):
+        raise TypeError("Could not retrieve protein data")
+
+    # Get protein formulas
+    pf = protein_formula(aa)
+
+    # Calculate coefficients of basis species in formation reactions
+    sb = species_basis(pf)
+
+    # Calculate ionization states if H+ is a basis species
+    t = thermo()
+    if t.basis is not None:
+        basis_species = t.basis.index.tolist()
+        if 'H+' in basis_species:
+            iHplus = basis_species.index('H+')
+            pH = -t.basis.loc['H+', 'logact']
+            Z = ionize_aa(aa, T=T, pH=pH).iloc[0, :]
+            sb.iloc[:, iHplus] = sb.iloc[:, iHplus] + Z.values
+
+    # Normalize by length if requested
+    if normalize:
+        plen = protein_length(aa)
+        sb = sb.div(plen, axis=0)
+
+    return sb

pychnosz/core/__init__.py

@@ -0,0 +1,46 @@
+"""Core thermodynamic calculation functions for CHNOSZ."""
+
+from .thermo import ThermoSystem, thermo
+from .info import info, find_species, get_species_data, list_species
+from .basis import basis, get_basis, is_basis_defined, preset_basis, BasisError
+from .species import species, get_species, is_species_defined, n_species, SpeciesError
+from .retrieve import retrieve
+
+# Optional imports for modules that may not exist yet
+try:
+    from .subcrt import subcrt
+except ImportError:
+    subcrt = None
+
+try:
+    from .affinity import affinity
+except ImportError:
+    affinity = None
+
+try:
+    from .equilibrate import equilibrate
+except ImportError:
+    equilibrate = None
+
+try:
+    from .diagram import diagram
+except ImportError:
+    diagram = None
+
+__all__ = [
+    'ThermoSystem', 'thermo',
+    'info', 'find_species', 'get_species_data', 'list_species',
+    'basis', 'get_basis', 'is_basis_defined', 'preset_basis', 'BasisError',
+    'species', 'get_species', 'is_species_defined', 'n_species', 'SpeciesError',
+    'retrieve'
+]
+
+# Add optional functions if they exist
+if subcrt is not None:
+    __all__.append('subcrt')
+if affinity is not None:
+    __all__.append('affinity')
+if equilibrate is not None:
+    __all__.append('equilibrate')
+if diagram is not None:
+    __all__.append('diagram')