tyche-tools 0.1.0__tar.gz

tyche_tools-0.1.0/LICENSE

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+MIT License
+
+Copyright (c) 2026 Robert Pollice
+
+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.

tyche_tools-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: tyche-tools
+Version: 0.1.0
+Summary: Extended cheminformatics toolkit: median molecules, chemical subspace enumeration, and evolutionary molecular optimization.
+Project-URL: Repository, https://git.lwp.rug.nl/pollice-research-group/artificial-design/tyche
+Requires-Python: >=3.8
+License-File: LICENSE
+Requires-Dist: tyche-core
+Requires-Dist: selfies<=2.1.2,>=2.0.0
+Requires-Dist: rdkit
+Requires-Dist: numpy
+Provides-Extra: nn
+Requires-Dist: torch; extra == "nn"
+Provides-Extra: all
+Requires-Dist: torch; extra == "all"
+Requires-Dist: pyyaml; extra == "all"
+Dynamic: license-file

tyche_tools-0.1.0/pyproject.toml

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+[build-system]
+requires = ["setuptools>=61.0"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "tyche-tools"
+version = "0.1.0"
+description = "Extended cheminformatics toolkit: median molecules, chemical subspace enumeration, and evolutionary molecular optimization."
+requires-python = ">=3.8"
+license-files = ["LICENSE"]
+dependencies = [
+    "tyche-core",
+    "selfies>=2.0.0,<=2.1.2",
+    "rdkit",
+    "numpy",
+]
+
+[project.optional-dependencies]
+nn = ["torch"]
+all = ["torch", "pyyaml"]
+
+[project.urls]
+Repository = "https://git.lwp.rug.nl/pollice-research-group/artificial-design/tyche"
+
+[tool.setuptools.packages.find]
+where = ["."]
+include = ["tyche_tools*"]

tyche_tools-0.1.0/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+

tyche_tools-0.1.0/tyche_tools/__init__.py

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+from tyche_tools.median import get_median_mols
+from tyche_tools.subspace import get_local_chemical_subspace
+from tyche_tools.optimize import optimize_molecules
+
+__all__ = [
+    "get_median_mols",
+    "get_local_chemical_subspace",
+    "optimize_molecules",
+]

tyche_tools-0.1.0/tyche_tools/_features.py

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+"""Molecular feature extraction for the optimizer's neural network classifier.
+
+Computes a 51-dimensional property vector for a given SMILES string. Features
+include atom-count ratios, RDKit descriptors, bond type ratios, and ring
+statistics.
+"""
+import inspect
+from collections import OrderedDict
+
+import numpy as np
+from rdkit import Chem, RDLogger
+from rdkit.Chem import Descriptors
+
+RDLogger.DisableLog('rdApp.*')
+
+_DESCRIPTOR_NAMES = [
+    "RingCount", "HallKierAlpha", "BalabanJ",
+    "NumAliphaticCarbocycles", "NumAliphaticHeterocycles", "NumAliphaticRings",
+    "NumAromaticCarbocycles", "NumAromaticHeterocycles", "NumAromaticRings",
+    "NumHAcceptors", "NumHDonors", "NumHeteroatoms",
+    "NumRadicalElectrons", "NumSaturatedCarbocycles", "NumSaturatedHeterocycles",
+    "NumSaturatedRings", "NumValenceElectrons",
+]
+
+_ROTATABLE_BOND_SMARTS = Chem.MolFromSmarts('*-&!@*')
+
+
+def _get_rot_bonds_posn(mol):
+    """Return atom-index pairs for all rotatable bonds in mol."""
+    return mol.GetSubstructMatches(_ROTATABLE_BOND_SMARTS)
+
+
+def _get_bond_indices(mol, rot):
+    """Convert rotatable bond atom pairs to bond indices."""
+    return [mol.GetBondBetweenAtoms(r[0], r[1]).GetIdx() for r in rot]
+
+
+def _obtain_rings(smi):
+    """Return a list of ring SMILES fragments from the input molecule.
+
+    Fragments the molecule on rotatable bonds and retains the pieces that
+    contain ring closures. Returns ``(None, None)`` for molecules with no
+    rotatable bonds (e.g. purely cyclic structures).
+    """
+    mol = Chem.MolFromSmiles(smi)
+    rot = _get_rot_bonds_posn(mol)
+    if len(rot) == 0:
+        return None, None
+    bond_idx = _get_bond_indices(mol, rot)
+    new_mol = Chem.FragmentOnBonds(mol, bond_idx, addDummies=False)
+    new_smi = Chem.MolToSmiles(new_mol)
+    return [s for s in new_smi.split('.') if '1' in s and Chem.MolFromSmiles(s) is not None]
+
+
+def _count_atoms(mol, atomic_num):
+    """Count atoms of a given atomic number in mol."""
+    pat = Chem.MolFromSmarts(f'[#{atomic_num}]')
+    return len(mol.GetSubstructMatches(pat))
+
+
+def _get_num_bond_types(mol):
+    """Return [single, double, triple, aromatic] bond counts as fractions of total."""
+    from rdkit.Chem import rdchem
+    counts = {
+        rdchem.BondType.SINGLE: 0,
+        rdchem.BondType.DOUBLE: 0,
+        rdchem.BondType.TRIPLE: 0,
+        rdchem.BondType.AROMATIC: 0,
+    }
+    total = 0
+    for bond in mol.GetBonds():
+        total += 1
+        bt = bond.GetBondType()
+        if bt in counts:
+            counts[bt] += 1
+    if total == 0:
+        return [0.0, 0.0, 0.0, 0.0]
+    return [counts[t] / total for t in [
+        rdchem.BondType.SINGLE, rdchem.BondType.DOUBLE,
+        rdchem.BondType.TRIPLE, rdchem.BondType.AROMATIC,
+    ]]
+
+
+def _count_conseq_double(mol):
+    """Count consecutive double bonds in mol."""
+    from rdkit.Chem import rdchem
+    prev = None
+    count = 0
+    for bond in mol.GetBonds():
+        curr = bond.GetBondType()
+        if prev == curr == rdchem.BondType.DOUBLE:
+            count += 1
+        prev = curr
+    return count
+
+
+def _size_ring_counter(ring_ls):
+    """Return a 19-element vector: [consecutive doubles in rings, ring counts by size 3–20].
+
+    Returns all zeros when ``ring_ls`` is ``(None, None)`` (no rotatable bonds).
+    """
+    if ring_ls == (None, None):
+        return [0] * 19
+    ring_mols = [Chem.MolFromSmiles(s) for s in ring_ls]
+    conseq = sum(_count_conseq_double(m) for m in ring_mols)
+    size_counts = [
+        sum(1 for m in ring_mols if m.GetNumAtoms() == sz)
+        for sz in range(3, 21)
+    ]
+    return [conseq] + size_counts
+
+
+def get_mol_info(smi):
+    """Compute a 51-dimensional molecular feature vector for classifier training.
+
+    Features (in order):
+    - 8 atom-count ratios relative to carbon (atoms, H, N, S, O, Cl, Br, F)
+    - 17 RDKit descriptor values
+    - 4 bond-type fractions (single, double, triple, aromatic)
+    - 2 ring summary features (ring count, triple bonds in rings)
+    - 19 ring-size histogram features
+
+    Parameters
+    ----------
+    smi : str
+        Valid SMILES string.
+
+    Returns
+    -------
+    numpy.ndarray of shape (51,)
+    """
+    mol = Chem.MolFromSmiles(smi)
+
+    num_atoms = mol.GetNumAtoms()
+    num_hydro = Chem.AddHs(mol).GetNumAtoms() - num_atoms
+    num_carbon = _count_atoms(mol, 6) or 0.0001  # avoid division by zero
+
+    basic_props = [
+        num_atoms / num_carbon,
+        num_hydro / num_carbon,
+        _count_atoms(mol, 7) / num_carbon,   # N
+        _count_atoms(mol, 16) / num_carbon,  # S
+        _count_atoms(mol, 8) / num_carbon,   # O
+        _count_atoms(mol, 17) / num_carbon,  # Cl
+        _count_atoms(mol, 35) / num_carbon,  # Br
+        _count_atoms(mol, 9) / num_carbon,   # F
+    ]
+
+    # 17 RDKit descriptors — selected by name from Descriptors module
+    calc_props = OrderedDict(inspect.getmembers(Descriptors, inspect.isfunction))
+    for key in list(calc_props.keys()):
+        if key.startswith('_') or key not in _DESCRIPTOR_NAMES:
+            del calc_props[key]
+    rdkit_features = []
+    for key, fn in calc_props.items():
+        try:
+            rdkit_features.append(fn(mol))
+        except Exception:
+            rdkit_features.append(0.0)
+
+    bond_info = _get_num_bond_types(mol)
+
+    ring_ls = _obtain_rings(smi)
+    num_triple_in_rings = 0
+    if ring_ls and ring_ls != (None, None) and len(ring_ls) > 0:
+        for item in ring_ls:
+            num_triple_in_rings += item.count('#')
+        bond_info.append(len(ring_ls))
+    else:
+        bond_info.append(0)
+    bond_info.append(num_triple_in_rings)
+    bond_info += _size_ring_counter(ring_ls)
+    bond_info.append(_count_conseq_double(mol))
+
+    return np.array(rdkit_features + basic_props + bond_info)

tyche_tools-0.1.0/tyche_tools/_network.py

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+"""Neural network classifier for guided molecular exploration.
+
+Trains a small MLP on previously evaluated (SMILES, fitness) pairs and uses it
+to predict which newly generated molecules are likely to score highly. This
+biases the exploration phase toward promising chemical space without requiring
+a full fitness evaluation for every candidate.
+
+Requires PyTorch. If PyTorch is not installed, import of this module will
+raise an ImportError; the optimizer falls back to random sampling in that case.
+"""
+import copy
+import multiprocessing
+from typing import List
+
+import numpy as np
+import torch
+import torch.nn as nn
+from torch.utils.data import DataLoader, TensorDataset
+
+from tyche_tools._features import get_mol_info
+
+
+# ── Feature extraction ─────────────────────────────────────────────────────────
+
+def _get_mol_feature(smi: str) -> np.ndarray:
+    return np.array(get_mol_info(smi))
+
+
+def obtain_features(smi_list: List[str], num_workers: int = 1) -> np.ndarray:
+    """Compute the 51-dim feature matrix for a list of SMILES.
+
+    Parameters
+    ----------
+    smi_list : list of str
+    num_workers : int
+        Number of parallel worker processes.
+
+    Returns
+    -------
+    numpy.ndarray of shape (N, 51)
+    """
+    if num_workers == 1:
+        return np.array([_get_mol_feature(s) for s in smi_list])
+    with multiprocessing.Pool(num_workers) as pool:
+        return np.array(pool.map(_get_mol_feature, smi_list))
+
+
+# ── Model architecture ─────────────────────────────────────────────────────────
+
+class MLP(nn.Module):
+    """Multi-layer perceptron with sigmoid activations throughout.
+
+    Parameters
+    ----------
+    h_sizes : list of int
+        Hidden layer widths.
+    n_input : int
+        Input dimensionality (51 for the default molecular features).
+    n_output : int
+        Output dimensionality (1 for binary classification).
+    """
+
+    def __init__(self, h_sizes: List[int], n_input: int, n_output: int):
+        super().__init__()
+        self.hidden = nn.ModuleList([nn.Linear(n_input, h_sizes[0])])
+        for i in range(len(h_sizes) - 1):
+            self.hidden.append(nn.Linear(h_sizes[i], h_sizes[i + 1]))
+        self.predict = nn.Linear(h_sizes[-1], n_output)
+
+    def forward(self, x):
+        for layer in self.hidden:
+            x = torch.sigmoid(layer(x))
+        return torch.sigmoid(self.predict(x))
+
+
+# ── Training utilities ─────────────────────────────────────────────────────────
+
+class _EarlyStopping:
+    """Monitor validation loss and restore best weights when improvement stalls."""
+
+    def __init__(self, patience: int = 500, min_delta: float = 1e-7):
+        self.patience = patience
+        self.min_delta = min_delta
+        self.best_val = np.inf
+        self.best_weights = None
+        self.best_epoch = 0
+        self.checkpoint = 0
+
+    def step(self, net, epoch: int, val_loss: float) -> bool:
+        """Update state. Returns True when training should stop."""
+        if val_loss + self.min_delta < self.best_val:
+            self.best_val = val_loss
+            self.best_weights = copy.deepcopy(net.state_dict())
+            self.best_epoch = epoch
+            self.checkpoint = 0
+        else:
+            self.checkpoint += 1
+        return self.checkpoint > self.patience
+
+    def restore_best(self, net) -> nn.Module:
+        print(f'        Early stopping at epoch {self.best_epoch}, val loss {self.best_val:.6f}')
+        net.load_state_dict(self.best_weights)
+        return net
+
+
+def _get_device(use_gpu: bool) -> str:
+    if use_gpu and torch.cuda.is_available():
+        return 'cuda'
+    if use_gpu:
+        print('No GPU available, defaulting to CPU.')
+    return 'cpu'
+
+
+def _train_valid_split(data_x, data_y, train_ratio=0.8, seed=30624700):
+    """Deterministic 80/20 train-validation split."""
+    n = data_x.shape[0]
+    train_n = int(np.floor(n * train_ratio))
+    idx = np.random.RandomState(seed=seed).permutation(n)
+    return (
+        data_x[idx[:train_n]], data_y[idx[:train_n]],
+        data_x[idx[train_n:]], data_y[idx[train_n:]],
+    )
+
+
+def _do_training(data_x, data_y, net, optimizer, loss_fn, steps=20000, batch_size=1024, device='cpu'):
+    """Train net for up to steps epochs with early stopping on validation loss."""
+    train_x, train_y, valid_x, valid_y = _train_valid_split(data_x, data_y)
+    train_x = torch.tensor(train_x, device=device, dtype=torch.float)
+    train_y = torch.tensor(train_y, device=device, dtype=torch.float)
+    valid_x = torch.tensor(valid_x, device=device, dtype=torch.float)
+    valid_y = torch.tensor(valid_y, device=device, dtype=torch.float)
+
+    loader = DataLoader(TensorDataset(train_x, train_y), batch_size=batch_size, shuffle=True)
+    valid_loader = DataLoader(TensorDataset(valid_x, valid_y), batch_size=batch_size)
+    early_stop = _EarlyStopping(patience=500, min_delta=1e-7)
+
+    net.train()
+    for epoch in range(steps):
+        for x, y in loader:
+            pred = net(x)
+            loss = loss_fn(pred, y)
+            optimizer.zero_grad()
+            loss.backward()
+            optimizer.step()
+
+        val_loss = 0.0
+        net.eval()
+        with torch.no_grad():
+            for x, y in valid_loader:
+                val_loss += loss_fn(net(x), y).item()
+        val_loss /= len(valid_loader)
+        net.train()
+
+        if epoch % 1000 == 0:
+            print(f'        Epoch {epoch}: train loss {loss.item():.6f}, val loss {val_loss:.6f}')
+
+        if early_stop.step(net, epoch, val_loss):
+            net = early_stop.restore_best(net)
+            break
+
+    return net
+
+
+# ── Public API ─────────────────────────────────────────────────────────────────
+
+def create_and_train_network(
+    smi_list: List[str],
+    targets: List[float],
+    n_hidden: List[int] = None,
+    use_gpu: bool = True,
+    num_workers: int = 1,
+) -> MLP:
+    """Featurize SMILES, build a binary MLP, and train it.
+
+    Labels are 1 for molecules at or above the 80th fitness percentile, 0 otherwise.
+    The trained model predicts which unseen molecules are likely to score highly.
+
+    Parameters
+    ----------
+    smi_list : list of str
+        SMILES of all previously evaluated molecules.
+    targets : list of float
+        Fitness values corresponding to each SMILES in smi_list.
+    n_hidden : list of int, default [100, 10]
+        Hidden layer widths of the MLP.
+    use_gpu : bool
+        Use CUDA if available.
+    num_workers : int
+        Parallel workers for feature extraction.
+
+    Returns
+    -------
+    MLP
+        Trained PyTorch model.
+    """
+    if n_hidden is None:
+        n_hidden = [100, 10]
+
+    dataset_x = obtain_features(smi_list, num_workers=num_workers)
+    threshold = np.percentile(targets, 80)
+    dataset_y = np.expand_dims(
+        [1.0 if t >= threshold else 0.0 for t in targets], axis=-1
+    )
+
+    device = _get_device(use_gpu)
+    net = MLP(n_hidden, dataset_x.shape[-1], dataset_y.shape[-1]).to(device)
+    optimizer = torch.optim.Adam(net.parameters(), lr=0.001, weight_decay=1e-4)
+    loss_fn = nn.BCELoss()
+
+    net = _do_training(
+        dataset_x, dataset_y, net, optimizer, loss_fn,
+        steps=20000, batch_size=1024, device=device,
+    )
+    return net
+
+
+def obtain_model_pred(
+    smi_list: List[str],
+    net: MLP,
+    use_gpu: bool = True,
+    num_workers: int = 1,
+    batch_size: int = 1024,
+) -> np.ndarray:
+    """Return classifier predictions for a list of SMILES.
+
+    Parameters
+    ----------
+    smi_list : list of str
+    net : MLP
+        Trained model from ``create_and_train_network``.
+    use_gpu : bool
+    num_workers : int
+    batch_size : int
+
+    Returns
+    -------
+    numpy.ndarray of shape (N, 1)
+        Predicted probability of belonging to the high-fitness class.
+    """
+    device = _get_device(use_gpu)
+    data_x = obtain_features(smi_list, num_workers=num_workers)
+    data_x = torch.tensor(data_x, device=device, dtype=torch.float)
+    loader = DataLoader(TensorDataset(data_x), batch_size=batch_size)
+
+    net.eval()
+    predictions = []
+    with torch.no_grad():
+        for (x,) in loader:
+            predictions.append(net(x).detach().cpu().numpy())
+    return np.concatenate(predictions, axis=0)

tyche_tools-0.1.0/tyche_tools/_utils.py

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+from rdkit import RDLogger
+from rdkit.Chem import MolFromSmiles as smi2mol
+from rdkit.Chem import MolToSmiles as mol2smi
+
+RDLogger.DisableLog('rdApp.*')
+
+
+def get_selfie_chars(selfie):
+    """Split a SELFIES string into a list of its tokens.
+
+    Parameters
+    ----------
+    selfie : str
+        A valid SELFIES string.
+
+    Returns
+    -------
+    list of str
+
+    Examples
+    --------
+    >>> get_selfie_chars('[C][=C][C][=C][C][=C][Ring1][Branch1_1]')
+    ['[C]', '[=C]', '[C]', '[=C]', '[C]', '[=C]', '[Ring1]', '[Branch1_1]']
+    """
+    chars = []
+    while selfie:
+        chars.append(selfie[selfie.find('['):selfie.find(']') + 1])
+        selfie = selfie[selfie.find(']') + 1:]
+    return chars
+
+
+def sanitize_smiles(smi):
+    """Return a canonical SMILES representation of the input string.
+
+    Parameters
+    ----------
+    smi : str
+
+    Returns
+    -------
+    mol : rdkit.Chem.rdchem.Mol or None
+    smi_canon : str or None
+        Canonical, non-isomeric SMILES string.
+    success : bool
+    """
+    try:
+        mol = smi2mol(smi, sanitize=True)
+        smi_canon = mol2smi(mol, isomericSmiles=False, canonical=True)
+        return mol, smi_canon, True
+    except Exception:
+        return None, None, False