synkit 1.1.2__tar.gz → 1.2__tar.gz

{synkit-1.1.2 → synkit-1.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: synkit
-Version: 1.1.2
+Version: 1.2
 Summary: Utility for reaction modeling using graph grammar
 Project-URL: homepage, https://github.com/TieuLongPhan/SynKit
 Project-URL: source, https://github.com/TieuLongPhan/SynKit
@@ -22,6 +22,7 @@ Requires-Dist: scikit-learn>=1.4.0
 Requires-Dist: seaborn>=0.13.2
 Provides-Extra: all
 Requires-Dist: numpy>=2.2.0; extra == 'all'
+Requires-Dist: sympy>=1.13.1; extra == 'all'
 Requires-Dist: torch>=2.2.0; extra == 'all'
 Provides-Extra: docs
 Requires-Dist: graphviz; extra == 'docs'

{synkit-1.1.2 → synkit-1.2}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "synkit"
-version = "1.1.2"
+version = "1.2"
 description = "Utility for reaction modeling using graph grammar"
 readme = "README.md"
 long-description = { file = "CHANGELOG.md" }
@@ -31,7 +31,7 @@ dependencies = [
 ]
 
 [project.optional-dependencies]
-all = ["numpy>=2.2.0", "torch>=2.2.0"]
+all = ["numpy>=2.2.0", "torch>=2.2.0", "sympy>=1.13.1"]
 docs = [
   # Core Sphinx
   "sphinx>=6.0",

synkit-1.2/synkit/CRN/Construct/__init__.py

@@ -0,0 +1,16 @@
+from .builder import CRNExpand, build_crn_from_smarts
+from .flattener import ReactionDeltaFlattener
+from .state import DerivationState
+from .strategy import ConstructionStrategy, FrontierStrategy
+from .derivation import DerivationRecord, DerivationLog
+
+__all__ = [
+    "CRNExpand",
+    "ReactionDeltaFlattener",
+    "build_crn_from_smarts",
+    "DerivationState",
+    "ConstructionStrategy",
+    "FrontierStrategy",
+    "DerivationRecord",
+    "DerivationLog",
+]

synkit-1.2/synkit/CRN/Construct/arity.py

@@ -0,0 +1,36 @@
+from __future__ import annotations
+
+from typing import Any, Optional
+
+
+def count_lhs_components(text: str) -> Optional[int]:
+    if not text:
+        return None
+    lhs = text.split(">>", 1)[0].strip() if ">>" in text else text.strip()
+    parts = [p for p in lhs.split(".") if p.strip()]
+    return len(parts) if parts else None
+
+
+def infer_rule_arity(rule: Any) -> int:
+    ar: Optional[int] = None
+    if isinstance(rule, str):
+        ar = count_lhs_components(rule)
+    else:
+        for attr in ("smarts", "smirks", "template"):
+            if not hasattr(rule, attr):
+                continue
+            try:
+                ar = count_lhs_components(str(getattr(rule, attr)))
+                if ar is not None:
+                    break
+            except Exception:
+                continue
+        if ar is None:
+            try:
+                ar = count_lhs_components(repr(rule))
+            except Exception:
+                ar = None
+
+    if ar is None or ar < 1:
+        ar = 2
+    return int(ar)

synkit-1.2/synkit/CRN/Construct/builder.py

@@ -0,0 +1,539 @@
+from __future__ import annotations
+
+from collections import Counter
+from dataclasses import dataclass, field
+from typing import Any, Dict, Iterable, Iterator, List, Optional, Set, Tuple
+import logging
+from concurrent.futures import ProcessPoolExecutor
+
+import networkx as nx
+
+from .arity import infer_rule_arity
+from .keys import make_dedup_key
+from .smiles import Chem, standardize_smiles_rdkit
+from .worker import apply_rule_worker
+from .state import DerivationState
+from .strategy import FrontierStrategy
+from .derivation import DerivationLog
+
+logger = logging.getLogger(__name__)
+
+
+@dataclass
+class CRNExpand:
+    rules: List[Any]
+    repeats: int = 50
+
+    explicit_h: bool = False
+    implicit_temp: bool = False
+    strategy: Optional[str] = None
+    keep_aam: bool = True
+
+    max_components: int = 3
+    use_frontier: bool = True
+    max_mixtures_per_rule_step: int = 50_000
+    max_tasks_per_step: int = 200_000
+    allow_self_mixtures: bool = False
+
+    skip_no_change: bool = True
+    allow_empty_side: bool = False
+
+    dedup_delta: bool = True
+    dedup_across_rules: bool = False
+
+    graph: nx.DiGraph = field(init=False)
+
+    _species_index: Dict[str, int] = field(init=False)
+    _next_node_id: int = field(init=False)
+    _smiles_cache: Dict[str, Optional[str]] = field(init=False)
+    _app_counter: Dict[int, int] = field(init=False)
+
+    _seen_attempts: Set[Tuple[int, Tuple[str, ...]]] = field(init=False)
+    _seen_delta: Set[Tuple[Optional[int], Tuple[str, ...], Tuple[str, ...]]] = field(
+        init=False
+    )
+    _rule_arity_cache: Dict[int, int] = field(init=False)
+    _warned_no_rdkit: bool = field(init=False)
+    state: DerivationState = field(init=False, repr=False)
+    strategy_engine: FrontierStrategy = field(init=False, repr=False)
+    derivations: DerivationLog = field(init=False, repr=False)
+
+    def __post_init__(self) -> None:
+        if self.max_components < 1:
+            raise ValueError("max_components must be >= 1")
+        self.state = DerivationState()
+        self.strategy_engine = FrontierStrategy()
+        self.derivations = DerivationLog()
+        self.reset()
+
+    def reset(self) -> None:
+        self.graph = nx.DiGraph()
+        self._species_index = {}
+        self._next_node_id = 1
+        self._smiles_cache = {}
+        self._app_counter = {}
+
+        self._seen_attempts = set()
+        self._seen_delta = set()
+        self._rule_arity_cache = {}
+        self._warned_no_rdkit = False
+        self.state.set_initial(pool_keys=set(), frontier_keys=set())
+        self.derivations.clear()
+
+    def _alloc_node_id(self) -> int:
+        nid = self._next_node_id
+        self._next_node_id += 1
+        return nid
+
+    def _next_app_index(self, *, rule_index: int) -> int:
+        cur = self._app_counter.get(rule_index, 0) + 1
+        self._app_counter[rule_index] = cur
+        return cur
+
+    def _standardize_smiles(self, smiles: str) -> Optional[str]:
+        if smiles in self._smiles_cache:
+            return self._smiles_cache[smiles]
+
+        out = standardize_smiles_rdkit(smiles, keep_aam=self.keep_aam)
+        self._smiles_cache[smiles] = out
+
+        if Chem is None and out is not None and not self._warned_no_rdkit:
+            logger.warning(
+                "RDKit not available; SMILES standardization is a passthrough."
+            )
+            self._warned_no_rdkit = True
+
+        return out
+
+    def _standardize_product_mixture(self, prod_mix: str) -> List[str]:
+        out: List[str] = []
+        for s in (prod_mix or "").split("."):
+            if not s:
+                continue
+            std = self._standardize_smiles(s)
+            if std is None:
+                continue
+            out.append(std)
+        return out
+
+    def _infer_rule_arity(self, rule: Any, rule_index: int) -> int:
+        if rule_index in self._rule_arity_cache:
+            return self._rule_arity_cache[rule_index]
+        arity = infer_rule_arity(rule)
+        self._rule_arity_cache[rule_index] = int(arity)
+        return int(arity)
+
+    def _add_species_node(self, smiles: str) -> Optional[int]:
+        std = self._standardize_smiles(smiles)
+        if std is None:
+            return None
+
+        if std in self._species_index:
+            return self._species_index[std]
+
+        nid = self._alloc_node_id()
+        self._species_index[std] = nid
+        self.graph.add_node(
+            nid,
+            kind="species",
+            smiles=std,
+            label=std,
+        )
+        return nid
+
+    def _add_rxn_event_node(self, *, step: int, rule_index: int) -> int:
+        app_index = self._next_app_index(rule_index=rule_index)
+        label = f"r@{rule_index}@{app_index}"
+
+        eid = self._alloc_node_id()
+        self.graph.add_node(
+            eid,
+            kind="rule",
+            label=label,
+            step=step,
+            rule_index=rule_index,
+            app_index=app_index,
+            rule_repr=repr(self.rules[rule_index]),
+        )
+        return eid
+
+    def _delta_keep_smiles(
+        self,
+        reactant_ids: List[int],
+        products_std_all: List[str],
+    ) -> Tuple[List[int], List[str], Tuple[str, ...], Tuple[str, ...]]:
+        r_smiles_all = [self.graph.nodes[rid]["smiles"] for rid in reactant_ids]
+        unchanged = set(r_smiles_all) & set(products_std_all)
+
+        r_keep_ids = [
+            rid for rid, rs in zip(reactant_ids, r_smiles_all) if rs not in unchanged
+        ]
+        p_keep_smiles = [ps for ps in products_std_all if ps not in unchanged]
+
+        r_keep_keys = tuple(
+            sorted(self.graph.nodes[rid]["smiles"] for rid in r_keep_ids)
+        )
+        p_keep_keys = tuple(sorted(p_keep_smiles))
+
+        return r_keep_ids, p_keep_smiles, r_keep_keys, p_keep_keys
+
+    def _iter_mixtures_for_rule(
+        self,
+        pool_keys: List[str],
+        frontier_keys: List[str],
+        *,
+        arity: int,
+        cap: int,
+    ) -> Iterator[Tuple[str, ...]]:
+        return self.strategy_engine.iter_mixtures(
+            pool_keys=pool_keys,
+            frontier_keys=frontier_keys,
+            arity=arity,
+            use_frontier=self.use_frontier,
+            allow_self_mixtures=self.allow_self_mixtures,
+            cap=cap,
+            max_components=self.max_components,
+        )
+
+    def build(
+        self,
+        seeds: Iterable[str],
+        *,
+        parallel: bool = False,
+        max_workers: Optional[int] = None,
+        reset: bool = True,
+    ) -> nx.DiGraph:
+        if reset:
+            self.reset()
+
+        pool_keys, frontier_keys = self._init_pool(seeds)
+        self.state.set_initial(pool_keys=pool_keys, frontier_keys=frontier_keys)
+        if not pool_keys:
+            return self.graph
+
+        for step in range(1, self.repeats + 1):
+            self.state.begin_step(step)
+            if self.use_frontier and not frontier_keys:
+                break
+
+            tasks = self._make_tasks_for_step(pool_keys, frontier_keys)
+            if not tasks:
+                break
+
+            results = self._run_tasks(tasks, parallel=parallel, max_workers=max_workers)
+            next_frontier = self._integrate_results(results, pool_keys, step)
+
+            frontier_keys = next_frontier
+            self.state.advance(next_frontier)
+            if self.use_frontier and not frontier_keys:
+                break
+
+        return self.graph
+
+    def _init_pool(self, seeds: Iterable[str]) -> Tuple[Set[str], Set[str]]:
+        pool_keys: Set[str] = set()
+        frontier_keys: Set[str] = set()
+
+        for s in seeds:
+            sid = self._add_species_node(s)
+            if sid is None:
+                continue
+            k = self.graph.nodes[sid]["smiles"]
+            pool_keys.add(k)
+            frontier_keys.add(k)
+
+        return pool_keys, frontier_keys
+
+    def _make_tasks_for_step(
+        self,
+        pool_keys: Set[str],
+        frontier_keys: Set[str],
+    ) -> List[Tuple[int, Any, str, bool, bool, Optional[str], Tuple[str, ...]]]:
+        budget = int(self.max_tasks_per_step)
+        tasks: List[
+            Tuple[int, Any, str, bool, bool, Optional[str], Tuple[str, ...]]
+        ] = []
+
+        for ridx, rule in enumerate(self.rules):
+            if budget <= 0:
+                break
+
+            arity = self._infer_rule_arity(rule, ridx)
+            if arity > self.max_components:
+                continue
+
+            cap = min(int(self.max_mixtures_per_rule_step), budget)
+            mix_iter = self._iter_mixtures_for_rule(
+                list(pool_keys),
+                list(frontier_keys),
+                arity=arity,
+                cap=cap,
+            )
+
+            for mix_keys in mix_iter:
+                if budget <= 0:
+                    break
+                task = self._task_from_mix(
+                    ridx=ridx,
+                    rule=rule,
+                    mix_keys=mix_keys,
+                )
+                if task is None:
+                    continue
+                tasks.append(task)
+                budget -= 1
+
+        return tasks
+
+    def _task_from_mix(
+        self,
+        *,
+        ridx: int,
+        rule: Any,
+        mix_keys: Tuple[str, ...],
+    ) -> Optional[Tuple[int, Any, str, bool, bool, Optional[str], Tuple[str, ...]]]:
+        app_key = (int(ridx), mix_keys)
+        if app_key in self._seen_attempts:
+            return None
+        self._seen_attempts.add(app_key)
+
+        substrate = ".".join(mix_keys)
+        return (
+            int(ridx),
+            rule,
+            substrate,
+            self.explicit_h,
+            self.implicit_temp,
+            self.strategy,
+            mix_keys,
+        )
+
+    def _run_tasks(
+        self,
+        tasks: List[Tuple[int, Any, str, bool, bool, Optional[str], Tuple[str, ...]]],
+        *,
+        parallel: bool,
+        max_workers: Optional[int],
+    ) -> List[Tuple[int, Tuple[str, ...], List[str]]]:
+        results: List[Tuple[int, Tuple[str, ...], List[str]]] = []
+
+        if parallel and len(tasks) > 1:
+            with ProcessPoolExecutor(max_workers=max_workers) as ex:
+                for idx, mix_keys, products_list in ex.map(apply_rule_worker, tasks):
+                    results.append((idx, mix_keys, products_list))
+            return results
+
+        for t in tasks:
+            results.append(apply_rule_worker(t))
+        return results
+
+    def _integrate_results(
+        self,
+        results: List[Tuple[int, Tuple[str, ...], List[str]]],
+        pool_keys: Set[str],
+        step: int,
+    ) -> Set[str]:
+        next_frontier: Set[str] = set()
+
+        for rule_index, mix_keys, products_list in results:
+            if not products_list:
+                continue
+            self._integrate_one_result(
+                rule_index=rule_index,
+                mix_keys=mix_keys,
+                products_list=products_list,
+                pool_keys=pool_keys,
+                next_frontier=next_frontier,
+                step=step,
+            )
+
+        return next_frontier
+
+    def _integrate_one_result(
+        self,
+        *,
+        rule_index: int,
+        mix_keys: Tuple[str, ...],
+        products_list: List[str],
+        pool_keys: Set[str],
+        next_frontier: Set[str],
+        step: int,
+    ) -> None:
+        reactant_ids = [self._species_index.get(k) for k in mix_keys]
+        if any(nid is None for nid in reactant_ids):
+            return
+        reactant_ids_int = [int(nid) for nid in reactant_ids if nid is not None]
+
+        seen_prod_mix: Set[str] = set()
+        for prod_mix in products_list:
+            prod_mix = (prod_mix or "").strip()
+            if not prod_mix or prod_mix in seen_prod_mix:
+                continue
+            seen_prod_mix.add(prod_mix)
+
+            products_std_all = self._standardize_product_mixture(prod_mix)
+            if not products_std_all:
+                continue
+
+            r_keep, p_keep_smiles, r_keep_keys, p_keep_keys = self._delta_keep_smiles(
+                reactant_ids_int,
+                products_std_all,
+            )
+
+            if self.skip_no_change and (not r_keep and not p_keep_smiles):
+                continue
+            if (not self.allow_empty_side) and (not r_keep or not p_keep_smiles):
+                continue
+
+            if self.dedup_delta:
+                dkey = make_dedup_key(
+                    dedup_across_rules=self.dedup_across_rules,
+                    rule_index=int(rule_index),
+                    r_keep_keys=r_keep_keys,
+                    p_keep_keys=p_keep_keys,
+                )
+                if dkey in self._seen_delta:
+                    continue
+                self._seen_delta.add(dkey)
+
+            eid = self._add_rxn_event_node(step=step, rule_index=int(rule_index))
+            nd = self.graph.nodes[eid]
+            self._add_reactant_edges(
+                reactant_ids=r_keep,
+                eid=eid,
+                step=step,
+                rule_index=int(rule_index),
+            )
+            self._add_product_edges(
+                product_smiles=p_keep_smiles,
+                eid=eid,
+                step=step,
+                rule_index=int(rule_index),
+            )
+
+            self.derivations.append(
+                event_id=eid,
+                label=str(nd.get("label")),
+                step=int(step),
+                rule_index=int(rule_index),
+                reactants=tuple(
+                    sorted(self.graph.nodes[rid]["smiles"] for rid in r_keep)
+                ),
+                products=tuple(sorted(p_keep_smiles)),
+            )
+
+            self._update_pool_with_products(
+                products_std_all=products_std_all,
+                pool_keys=pool_keys,
+                next_frontier=next_frontier,
+            )
+
+    def _add_reactant_edges(
+        self,
+        *,
+        reactant_ids: List[int],
+        eid: int,
+        step: int,
+        rule_index: int,
+    ) -> None:
+        for rid, stoich in Counter(reactant_ids).items():
+            self.graph.add_edge(
+                rid,
+                eid,
+                step=step,
+                rule_index=rule_index,
+                rxn_id=eid,
+                role="reactant",
+                stoich=int(stoich),
+            )
+
+    def _add_product_edges(
+        self,
+        *,
+        product_smiles: List[str],
+        eid: int,
+        step: int,
+        rule_index: int,
+    ) -> None:
+        for ps, stoich in Counter(product_smiles).items():
+            pid = self._add_species_node(ps)
+            if pid is None:
+                continue
+            self.graph.add_edge(
+                eid,
+                pid,
+                step=step,
+                rule_index=rule_index,
+                rxn_id=eid,
+                role="product",
+                stoich=int(stoich),
+            )
+
+    def _update_pool_with_products(
+        self,
+        *,
+        products_std_all: List[str],
+        pool_keys: Set[str],
+        next_frontier: Set[str],
+    ) -> None:
+        for ps in set(products_std_all):
+            pid = self._add_species_node(ps)
+            if pid is None:
+                continue
+            pk = self.graph.nodes[pid]["smiles"]
+            if pk not in pool_keys:
+                pool_keys.add(pk)
+                next_frontier.add(pk)
+
+    @property
+    def species_nodes(self) -> List[int]:
+        return [n for n, d in self.graph.nodes(data=True) if d.get("kind") == "species"]
+
+    @property
+    def rxn_nodes(self) -> List[int]:
+        return [n for n, d in self.graph.nodes(data=True) if d.get("kind") == "rule"]
+
+    @property
+    def derivation_records(self) -> List[Dict[str, object]]:
+        return self.derivations.as_dicts()
+
+
+def build_crn_from_smarts(
+    rules: List[str],
+    seeds: List[str],
+    *,
+    repeats: int = 50,
+    explicit_h: bool = False,
+    implicit_temp: bool = False,
+    strategy: Optional[str] = None,
+    keep_aam: bool = True,
+    parallel: bool = False,
+    max_workers: Optional[int] = None,
+    max_components: int = 3,
+    use_frontier: bool = True,
+    max_mixtures_per_rule_step: int = 50_000,
+    max_tasks_per_step: int = 200_000,
+    allow_self_mixtures: bool = False,
+    skip_no_change: bool = True,
+    allow_empty_side: bool = False,
+    dedup_delta: bool = True,
+    dedup_across_rules: bool = False,
+) -> nx.DiGraph:
+    crn = CRNExpand(
+        rules=rules,
+        repeats=repeats,
+        explicit_h=explicit_h,
+        implicit_temp=implicit_temp,
+        strategy=strategy,
+        keep_aam=keep_aam,
+        max_components=max_components,
+        use_frontier=use_frontier,
+        max_mixtures_per_rule_step=max_mixtures_per_rule_step,
+        max_tasks_per_step=max_tasks_per_step,
+        allow_self_mixtures=allow_self_mixtures,
+        skip_no_change=skip_no_change,
+        allow_empty_side=allow_empty_side,
+        dedup_delta=dedup_delta,
+        dedup_across_rules=dedup_across_rules,
+    )
+    return crn.build(seeds, parallel=parallel, max_workers=max_workers)

synkit-1.2/synkit/CRN/Construct/derivation.py

@@ -0,0 +1,63 @@
+from __future__ import annotations
+
+from dataclasses import dataclass, field
+from typing import Dict, List, Tuple
+
+
+@dataclass(frozen=True)
+class DerivationRecord:
+    """
+    Abstract direct derivation record.
+
+    This stores the reaction event as multisets of standardized species without
+    changing the public NetworkX CRN representation.
+    """
+
+    event_id: int
+    label: str
+    step: int
+    rule_index: int
+    reactants: Tuple[str, ...]
+    products: Tuple[str, ...]
+
+
+@dataclass
+class DerivationLog:
+    records: List[DerivationRecord] = field(default_factory=list)
+
+    def clear(self) -> None:
+        self.records.clear()
+
+    def append(
+        self,
+        *,
+        event_id: int,
+        label: str,
+        step: int,
+        rule_index: int,
+        reactants: Tuple[str, ...],
+        products: Tuple[str, ...],
+    ) -> None:
+        self.records.append(
+            DerivationRecord(
+                event_id=int(event_id),
+                label=str(label),
+                step=int(step),
+                rule_index=int(rule_index),
+                reactants=tuple(reactants),
+                products=tuple(products),
+            )
+        )
+
+    def as_dicts(self) -> List[Dict[str, object]]:
+        return [
+            {
+                "event_id": r.event_id,
+                "label": r.label,
+                "step": r.step,
+                "rule_index": r.rule_index,
+                "reactants": list(r.reactants),
+                "products": list(r.products),
+            }
+            for r in self.records
+        ]