Rule

Rule objects and utilities for composing, applying, and modifying reaction rules.

Core

class synkit.Rule.syn_rule.SynRule(rc: Graph, name: str = 'rule', canonicaliser: GraphCanonicaliser | None = None, *, canon: bool = True, implicit_h: bool = True, format: Literal['typesGH', 'tuple'] | None = None)

Bases: object

classmethod from_gml(gml: str, name: str = 'rule', canonicaliser: GraphCanonicaliser | None = None, *, canon: bool = True, implicit_h: bool = True) → SynRule

classmethod from_smart(smart: str, name: str = 'rule', canonicaliser: GraphCanonicaliser | None = None, *, canon: bool = True, implicit_h: bool = True, format: Literal['typesGH', 'tuple'] = 'typesGH') → SynRule

help() → None

Compose

class synkit.Rule.Compose.compose_rule.ComposeRule

Bases: object

static filter_smallest_vertex(combo: List[object]) → List[object]

get_rule_comp(smart_1: str, smart_2: str) → str | None

static rule_cluster(graphs: List[Any]) → List[Any]

class synkit.Rule.Compose.rule_compose.RuleCompose

Bases: object

static filter_smallest_vertex(combo: List[object]) → List[object]

static rule_cluster(graphs: List) → List

static save_gml_from_text(gml_content: str, gml_file_path: str, rule_id: str, parent_ids: List[str]) → bool

class synkit.Rule.Compose.rule_mapping.RuleMapping

Bases: object

static enumerate_all_unique_mappings(child: Graph, parent: Graph) → List[Dict[Any, Any]]

fit(rule_1: str, rule_2: str, comp_rule: str) → Dict[Any, Any] | None

static get_child1_to_child2_mapping(mapping_child1_to_parent: Dict[Any, Any], mapping_child2_to_parent: Dict[Any, Any]) → Dict[Any, Any | None]

static graph_alignment(child: Graph, parent: Graph, node_label_names: List[str] = ['element'], node_label_default: List[str] = ['*'], edge_attribute: str = 'standard_order') → Tuple[bool, Dict[Any, Any] | None]

static keep_largest_component(graph: Graph) → Graph

static standardize_order(order_tuple: Tuple[float, ...]) → Tuple[float, ...] | None

static subtract_parent_from_child(child: Graph, parent: Graph, mapping: Dict[Any, Any]) → Graph

class synkit.Rule.Compose.seq_comp.SeqComp

Bases: object

static sequence_map(smarts: List[str]) → Dict[str, dict | None]

class synkit.Rule.Compose.valence_constrain.ValenceConstrain

Bases: object

check_rule(rule, verbose: bool = False, log_error: bool = False) → bool

split(rules: List) → Tuple[List, List]

valence(vertex) → int

Apply

class synkit.Rule.Apply.reactor_rule.ReactorRule

Bases: object

class synkit.Rule.Apply.retro_reactor.RetroReactor

Bases: object

backward_synthesis_search(product_smiles: str, known_precursor_smiles: str, rules: List[str], max_solutions: int = 1, fast_process: bool = True) → List[Dict[str, List]]

class synkit.Rule.Apply.rule_matcher.RuleMatcher(rsmi: str, rule: str | Graph, explicit_h: bool = True, electron_diagnostics: bool = False)

Bases: object

static all_in(a: List[str], b: List[str]) → bool

property diagnostics: list[dict]

get_result() → Tuple[str, Graph]

help() → None

class synkit.Rule.Apply.rule_rbl.RuleRBL

Bases: object

rbl(rsmi: str, gml_rule: str, remove_aam: bool = True) → List[str]

Modify

Note

synkit.Rule.Modify.implict_rule is currently omitted from this page because it fails to import in the uploaded repository due to an internal import error. Re-enable the directive below after that module is fixed.

class synkit.Rule.Modify.longest_path.LongestPath(G: Graph)

Bases: object

BFS(u: int) → Tuple[int, int]

LongestPathInDisconnectedGraph() → int

class synkit.Rule.Modify.molecule_rule.MoleculeRule

Bases: object

static generate_atom_map(smiles: str) → str | None

generate_molecule_rule(smiles: str, name: str = 'molecule', explicit_hydrogen: bool = True, sanitize: bool = True) → str | None

static generate_molecule_smart(smiles: str) → str | None

static remove_edges_from_left_right(input_str: str) → str

class synkit.Rule.Modify.prune_templates.PruneTemplate(templates: List[List[Dict[str, Any]]], graph_key: str)

Bases: object

fit() → List[List[Dict[str, Any]]]

static remove_edges_by_attribute(input_graph: Graph, attribute: str = 'standard_order', value: Any = 0) → Graph

synkit.Rule.Modify.rule_utils.filter_context(context_lines, relevant_nodes)

synkit.Rule.Modify.rule_utils.find_block(lines, keyword)

synkit.Rule.Modify.rule_utils.get_nodes_from_edges(block_lines)

synkit.Rule.Modify.rule_utils.parse_context(context_lines, node_regex=None, edge_regex=None)

synkit.Rule.Modify.rule_utils.strip_context(gml_text: str, remove_all: bool = True) → str

synkit.Rule.Modify.strip_rule.filter_context(context_lines, left_edges)

synkit.Rule.Modify.strip_rule.strip_context(gml_text: str, remove_all: bool = False) → str