IO

The synkit.IO module provides tools for converting chemical reaction representations between various formats:

• Reaction SMILES / SMARTS

• ITS (Internal Transformation Sequence) Graph

• GML (Graph Modeling Language)

Aldol Reaction Example

Below is the aldol condensation between an aldehyde and a ketone:

Figure: Aldol condensation between an aldehyde and a ketone.

Conversion to Reaction SMARTS

Use rsmi_to_rsmarts to transform a reaction SMILES into a reaction SMARTS template:

Converting Reaction SMILES to SMARTS

from synkit.IO import rsmi_to_rsmarts

template = (
    '[C:2]=[O:3].[C:4]([H:7])[H:8]'
    '>>'
    '[C:2]=[C:4].[O:3]([H:7])[H:8]'
)

smart = rsmi_to_rsmarts(template)
print("Reaction SMARTS:", smart)
# Reaction SMARTS: "[#6:2]=[#8:3].[#6:4](-[H:7])-[H:8]>>[#6:2]=[#6:4].[#8:3](-[H:7])-[H:8]"

Conversion to ITS Graph

Use rsmi_to_its to convert a reaction SMILES/SMARTS string into an ITS graph. Set core=True to restrict to the reaction center only.

Generating and Visualizing an ITS Graph

from synkit.IO import rsmi_to_its
from synkit.Vis import GraphVisualizer

rsmi = (
    '[CH3:1][CH:2]=[O:3].'
    '[CH:4]([H:7])([H:8])[CH:5]=[O:6]'
    '>>'
    '[CH3:1][CH:2]=[CH:4][CH:5]=[O:6].'
    '[O:3]([H:7])([H:8])'
)

# Full ITS graph
full_graph = rsmi_to_its(rsmi, core=False)
viz = GraphVisualizer()
viz.visualize_its(full_graph, use_edge_color=True)
# >> Figure A: Full ITS graph

# Reaction-center-only ITS graph
core_graph = rsmi_to_its(rsmi, core=True)
viz.visualize_its(core_graph, use_edge_color=True)
# >> Figure B: Reaction-center ITS graph

Figure: (A) Full ITS graph and (B) reaction-center-only ITS graph for the aldol condensation.

Conversion to DPO Rule (GML)

Convert a reaction SMARTS (or SMILES) template into a DPO rule in GML format:

• smart_to_gml(react_template, core=False, useSmile=False)

• its_to_gml(its_graph, core=False)

Set core=True to include only the reaction center, and useSmile=True to treat the input as SMILES.

Generating, Saving, and Loading a DPO Rule in GML

from synkit.IO import (
   rsmi_to_its,
   smart_to_gml,
   its_to_gml,
   save_text_as_gml,
   load_gml_as_text,
)

# Define the aldol reaction template
reaction = (
   '[CH3:1][CH:2]=[O:3].'
   '[CH:4]([H:7])([H:8])[CH:5]=[O:6]'
   '>>'
   '[CH3:1][CH:2]=[CH:4][CH:5]=[O:6].'
   '[O:3]([H:7])([H:8])'
)

# Option 1: Direct SMARTS → GML
gml_rule_1 = smart_to_gml(reaction, core=True, useSmiles=False)

# Option 2: SMILES → ITS → GML
its_graph = rsmi_to_its(reaction, core=True)
gml_rule_2 = its_to_gml(its_graph, core=True)

# Save to disk
save_text_as_gml(gml_text=gml_rule_2, file_path="aldol_rule.gml")

# Load back into text
loaded_rule = load_gml_as_text("aldol_rule.gml")
print(loaded_rule)

Example DPO Rule (GML)

rule [
  ruleID "aldol_rule"
  left [
    edge [ source 2 target 3 label "=" ]
    edge [ source 4 target 7 label "-" ]
    edge [ source 4 target 8 label "-" ]
  ]
  context [
    node [ id 2 label "C" ]
    node [ id 3 label "O" ]
    node [ id 4 label "C" ]
    node [ id 7 label "H" ]
    node [ id 8 label "H" ]
  ]
  right [
    edge [ source 2 target 4 label "=" ]
    edge [ source 3 target 7 label "-" ]
    edge [ source 3 target 8 label "-" ]
  ]
]

See Also

• synkit.Vis — visualization utilities

• synkit.Graph — graph data structures and transformations