Electron-feature graph report

Electron Graph Figure Bundle

Browsable code-side assets for DPO diagrams, chemical companion views, EGML examples, and generated rule-composition records.

Images labelled RDKit view or Fragment view are clickable: click the image panel to switch between the chemical depiction and the electron-feature DOT representation.

7DPO cases 20molecules/states 12rule files 6applications 3compositions

Minimal Julia Snippets

Minimal Julia: apply an EGML rule

include("ElectronGraphs.jl")
using .ElectronGraphs
host = load_graph_egml("examples/graphs/methyl_radical_pair.egml")
rule = load_rule_egml("examples/rules/radical_recombination.egml")
app = apply_egml_rule(rule, host)
product = app.product

Minimal Julia: compose partial DPO rules

using AlgebraicRewriting
include("ElectronDPO.jl")
const D = ElectronDPO
first = D.open_rule_from_span(D.chlorine_h_abstraction_with_external_methyl_span_parts()...)
second = D.open_rule_from_span(D.radical_recombination_with_hcl_context_span_parts()...)
macro_open = composeV_(first, second)
macro_rule, _, L, _ = D.closed_rule_from_open_rule(macro_open)
host = D.radical_abstraction_recombination_host()
m = D.radical_abstraction_recombination_match(L, host)
product = rewrite_match(macro_rule, m; cat=D.EG.electron_cat())

Rules

Generated EGML rule spans. The visual rule panels below use clickable Fragment/DOT images where available; raw rule files remain in the appendix.

Rule file	Role
`exchange/rules/chlorine_h_abstraction.egml`	radical abstraction rule
`exchange/rules/chlorine_h_abstraction_with_external_methyl.egml`	context-complete rule input
`exchange/rules/diazomethane_azo_esterification_macro.egml`	composed macro rule
`exchange/rules/diazomethane_azo_proton_transfer.egml`	elementary proton-transfer rule
`exchange/rules/diazomethane_esterification_macro.egml`	composed macro rule
`exchange/rules/diazomethane_methyl_transfer.egml`	elementary methyl-transfer rule
`exchange/rules/diazomethane_methyl_transfer_after_azo_context.egml`	context-complete rule input
`exchange/rules/diazomethane_methyl_transfer_after_proton_context.egml`	context-complete rule input
`exchange/rules/diazomethane_proton_transfer.egml`	elementary proton-transfer rule
`exchange/rules/radical_abstraction_recombination_partial_macro.egml`	partial-overlap macro rule
`exchange/rules/radical_recombination_methyl.egml`	radical recombination rule
`exchange/rules/radical_recombination_with_hcl_context.egml`	context-complete rule input

Rule Composition

Composed rules and their concrete applications, including the partial-overlap radical-chain construction.

Partial DPO Composition Detail

chlorine_h_abstraction then radical_recombination_methyl, with only the produced methyl radical identified with one radical input of recombination.

Composition record: exchange/compositions/radical_abstraction_recombination_partial_composeV.egml
Composed rule: exchange/rules/radical_abstraction_recombination_partial_macro.egml
Direct application: exchange/applications/radical_abstraction_recombination_partial_macro_on_host.egml

Minimal Julia: compose and apply this rule

using AlgebraicRewriting
include("ElectronDPO.jl")
const D = ElectronDPO
first = D.open_rule_from_span(D.chlorine_h_abstraction_with_external_methyl_span_parts()...)
second = D.open_rule_from_span(D.radical_recombination_with_hcl_context_span_parts()...)
macro_open = composeV_(first, second)
macro_rule, _, L, _ = D.closed_rule_from_open_rule(macro_open)
host = D.radical_abstraction_recombination_host()
m = D.radical_abstraction_recombination_match(L, host)
product = rewrite_match(macro_rule, m; cat=D.EG.electron_cat())

Original rules before adding identity context

Rule	L	K	R
Rule 1: chlorine_h_abstraction	Fragment viewDOT viewclick image to switch representation	Fragment viewDOT viewclick image to switch representation	Fragment viewDOT viewclick image to switch representation
Rule 2: radical_recombination_methyl	Fragment viewDOT viewclick image to switch representation	Fragment viewDOT viewclick image to switch representation	Fragment viewDOT viewclick image to switch representation

Rule

Rule 1: chlorine_h_abstraction

Fragment viewDOT viewclick image to switch representation

Fragment viewDOT viewclick image to switch representation

Rule 1: chlorine_h_abstraction K Fragment

Fragment viewDOT viewclick image to switch representation

Rule 1: chlorine_h_abstraction R Fragment

Rule 2: radical_recombination_methyl

Fragment viewDOT viewclick image to switch representation

Rule 2: radical_recombination_methyl L DOT

Fragment viewDOT viewclick image to switch representation

Rule 2: radical_recombination_methyl K Fragment

Rule 2: radical_recombination_methyl K DOT

Fragment viewDOT viewclick image to switch representation

Rule 2: radical_recombination_methyl R Fragment

Rule 2: radical_recombination_methyl R DOT

Partial overlap

Overlap graph Meaning

Overlap graph	Meaning
Fragment viewDOT viewclick image to switch representation	The methyl radical produced by `chlorine_h_abstraction` is identified with one radical input of `radical_recombination_methyl`. The other methyl radical is carried as external context.

Fragment viewDOT viewclick image to switch representation

Partial overlap: produced methyl radical Fragment

Partial overlap: produced methyl radical DOT

The methyl radical produced by chlorine_h_abstraction is identified with one radical input of radical_recombination_methyl. The other methyl radical is carried as external context.

Context-complete open-rule inputs passed to `composeV_`

Rule	L	K	R
Rule 1 with external methyl context	Fragment viewDOT viewclick image to switch representation	Fragment viewDOT viewclick image to switch representation	Fragment viewDOT viewclick image to switch representation
Rule 2 with HCl context	Fragment viewDOT viewclick image to switch representation	Fragment viewDOT viewclick image to switch representation	Fragment viewDOT viewclick image to switch representation

Rule

Rule 1 with external methyl context

Fragment viewDOT viewclick image to switch representation

Rule 1 with external methyl context L DOT

Fragment viewDOT viewclick image to switch representation

Rule 1 with external methyl context K Fragment

Rule 1 with external methyl context K DOT

Fragment viewDOT viewclick image to switch representation

Rule 1 with external methyl context R Fragment

Rule 1 with external methyl context R DOT

Rule 2 with HCl context

Fragment viewDOT viewclick image to switch representation

Fragment viewDOT viewclick image to switch representation

Fragment viewDOT viewclick image to switch representation

Composed macro rule

Rule	L	K	R
Composed macro rule	Fragment viewDOT viewclick image to switch representation	Fragment viewDOT viewclick image to switch representation	Fragment viewDOT viewclick image to switch representation

Rule

Composed macro rule

Fragment viewDOT viewclick image to switch representation

Fragment viewDOT viewclick image to switch representation

Fragment viewDOT viewclick image to switch representation

Partial radical-chain DPO composition

RDKit molecule quick view

Host	Product
RDKit viewDOT viewclick image to switch representation	RDKit viewDOT viewclick image to switch representation

Host

Product

RDKit viewDOT viewclick image to switch representation

RDKit viewDOT viewclick image to switch representation

Chemistry: Cl radical + methane + methyl radical -> HCl + ethane

The first rule creates a methyl radical; the second overlaps only that produced methyl radical with one radical input of recombination.

Atom map: L1->H1, L2->H2, L3->H3, L4->H4, L5->H5, L6->H6, L7->H7, L8->H8, L9->H9, L10->H10

Feature map: L1->H1, L2->H2, L3->H3, L4->H6, L5->H7, L6->H8, L7->H4, L8->H5, L9->H9, L10->H10, L11->H11, L12->H12

Atom/H counts: L: atoms=10, H=7; K: atoms=10, H=7; R: atoms=10, H=7; H: atoms=10, H=7; D: atoms=10, H=7; H': atoms=10, H=7

Scope: L/K/R are rule fragments. H/D/H' are full application graphs, so hydrogens not shown in a rule fragment are preserved context atoms there.

Formal electron-feature DPO view

L rule fragment

K interface

R rule fragment

H full host

D pushout complement

H' full product

Chemical/DOT companion view

L rule fragment	K interface	R rule fragment
Fragment viewDOT viewclick image to switch representation	Fragment viewDOT viewclick image to switch representation	Fragment viewDOT viewclick image to switch representation
H full host	D pushout complement	H' full product
RDKit viewDOT viewclick image to switch representation	Fragment viewDOT viewclick image to switch representation	RDKit viewDOT viewclick image to switch representation

L rule fragment

K interface

R rule fragment

Fragment viewDOT viewclick image to switch representation

Fragment viewDOT viewclick image to switch representation

Fragment viewDOT viewclick image to switch representation

H full host

D pushout complement

H' full product

RDKit viewDOT viewclick image to switch representation

Fragment viewDOT viewclick image to switch representation

RDKit viewDOT viewclick image to switch representation

RDKit host/product views

Host	Product
RDKit viewDOT viewclick image to switch representation	RDKit viewDOT viewclick image to switch representation

Host

Product

RDKit viewDOT viewclick image to switch representation

Diazomethane composed macro DPO

RDKit molecule quick view

Host	Product
RDKit viewDOT viewclick image to switch representation	RDKit viewDOT viewclick image to switch representation

Host

Product

RDKit viewDOT viewclick image to switch representation

Chemistry: CH2N2 + RCO2H -> RCO2CH3 + N2

This macro rule is generated by vertical DPO composition of proton transfer and methyl transfer.

Atom map: L1->H1, L2->H2, L3->H3, L4->H12, L5->H13

Feature map: L1->H1, L2->H2, L3->H3, L4->H4, L5->H7, L6->H16

Atom/H counts: L: atoms=5, H=1; K: atoms=5, H=1; R: atoms=5, H=1; H: atoms=13, H=6; D: atoms=13, H=6; H': atoms=13, H=6

Scope: L/K/R are rule fragments. H/D/H' are full application graphs, so hydrogens not shown in a rule fragment are preserved context atoms there.

Formal electron-feature DPO view

L rule fragment

K interface

R rule fragment

H full host

D pushout complement

H' full product

Chemical/DOT companion view

L rule fragment	K interface	R rule fragment
Fragment viewDOT viewclick image to switch representation	Fragment viewDOT viewclick image to switch representation	Fragment viewDOT viewclick image to switch representation
H full host	D pushout complement	H' full product
RDKit viewDOT viewclick image to switch representation	Fragment viewDOT viewclick image to switch representation	RDKit viewDOT viewclick image to switch representation

L rule fragment

K interface

R rule fragment

Fragment viewDOT viewclick image to switch representation

H full host

D pushout complement

H' full product

RDKit viewDOT viewclick image to switch representation

Fragment viewDOT viewclick image to switch representation

RDKit viewDOT viewclick image to switch representation

RDKit host/product views

Host	Product
RDKit viewDOT viewclick image to switch representation	RDKit viewDOT viewclick image to switch representation

Host

Product

RDKit viewDOT viewclick image to switch representation

Diazomethane exact-azo composed macro DPO

RDKit molecule quick view

Host	Product
RDKit viewDOT viewclick image to switch representation	RDKit viewDOT viewclick image to switch representation

Host

Product

RDKit viewDOT viewclick image to switch representation

Chemistry: H2C=N+=N- + RCO2H -> RCO2CH3 + N2

This exact-resonance macro rule is generated by composing the azo-form proton-transfer step with context-complete methyl transfer.

Atom map: L1->H1, L2->H2, L3->H3, L4->H12, L5->H13

Feature map: L1->H1, L2->H3, L3->H4, L4->H7, L5->H2, L6->H8, L7->H16

Atom/H counts: L: atoms=5, H=1; K: atoms=5, H=1; R: atoms=5, H=1; H: atoms=13, H=6; D: atoms=13, H=6; H': atoms=13, H=6

Scope: L/K/R are rule fragments. H/D/H' are full application graphs, so hydrogens not shown in a rule fragment are preserved context atoms there.

Formal electron-feature DPO view

L rule fragment

K interface

R rule fragment

H full host

D pushout complement

H' full product

Chemical/DOT companion view

L rule fragment	K interface	R rule fragment
Fragment viewDOT viewclick image to switch representation	Fragment viewDOT viewclick image to switch representation	Fragment viewDOT viewclick image to switch representation
H full host	D pushout complement	H' full product
RDKit viewDOT viewclick image to switch representation	Fragment viewDOT viewclick image to switch representation	RDKit viewDOT viewclick image to switch representation

L rule fragment

K interface

R rule fragment

Fragment viewDOT viewclick image to switch representation

H full host

D pushout complement

H' full product

RDKit viewDOT viewclick image to switch representation

Fragment viewDOT viewclick image to switch representation

RDKit viewDOT viewclick image to switch representation

RDKit host/product views

Host	Product
RDKit viewDOT viewclick image to switch representation	RDKit viewDOT viewclick image to switch representation

Host

Product

RDKit viewDOT viewclick image to switch representation

Specific Chemical Examples

Elementary DPO applications over concrete chemical hosts.

Cyclopropanation DPO

RDKit molecule quick view

Host	Product
RDKit viewDOT viewclick image to switch representation	RDKit viewDOT viewclick image to switch representation

Host

Product

RDKit viewDOT viewclick image to switch representation

Chemistry: Cl2C: + C=C -> dichlorocyclopropane

The rule requires the singlet carbene lone-pair loop and consumes one alkene shared pair.

Atom map: L1->H1, L2->H2, L3->H3, L4->H4, L5->H5

Feature map: L1->H1, L2->H2, L3->H10, L4->H3, L5->H11

Atom/H counts: L: atoms=5, H=0; K: atoms=5, H=0; R: atoms=5, H=0; H: atoms=9, H=4; D: atoms=9, H=4; H': atoms=9, H=4

Scope: L/K/R are rule fragments. H/D/H' are full application graphs, so hydrogens not shown in a rule fragment are preserved context atoms there.

Formal electron-feature DPO view

L rule fragment

K interface

R rule fragment

H full host

D pushout complement

H' full product

Chemical/DOT companion view

L rule fragment	K interface	R rule fragment
Fragment viewDOT viewclick image to switch representation	Fragment viewDOT viewclick image to switch representation	Fragment viewDOT viewclick image to switch representation
H full host	D pushout complement	H' full product
RDKit viewDOT viewclick image to switch representation	Fragment viewDOT viewclick image to switch representation	RDKit viewDOT viewclick image to switch representation

L rule fragment

K interface

R rule fragment

Fragment viewDOT viewclick image to switch representation

H full host

D pushout complement

H' full product

RDKit viewDOT viewclick image to switch representation

Fragment viewDOT viewclick image to switch representation

RDKit viewDOT viewclick image to switch representation

RDKit host/product views

Host	Product
RDKit viewDOT viewclick image to switch representation	RDKit viewDOT viewclick image to switch representation

Host

Product

RDKit viewDOT viewclick image to switch representation

Diazomethane proton-transfer DPO

RDKit molecule quick view

Host	Product
RDKit viewDOT viewclick image to switch representation	RDKit viewDOT viewclick image to switch representation

Host

Product

RDKit viewDOT viewclick image to switch representation

Chemistry: CH2N2 + RCO2H -> [CH3N2+][RCO2-]

The rule consumes the diazomethane carbon lone-pair loop and the acid O-H shared pair.

Atom map: L1->H1, L2->H2, L3->H3, L4->H12, L5->H13

Feature map: L1->H1, L2->H2, L3->H3, L4->H4, L5->H7, L6->H16

Atom/H counts: L: atoms=5, H=1; K: atoms=5, H=1; R: atoms=5, H=1; H: atoms=13, H=6; D: atoms=13, H=6; H': atoms=13, H=6

Scope: L/K/R are rule fragments. H/D/H' are full application graphs, so hydrogens not shown in a rule fragment are preserved context atoms there.

Formal electron-feature DPO view

L rule fragment

K interface

R rule fragment

H full host

D pushout complement

H' full product

Chemical/DOT companion view

L rule fragment	K interface	R rule fragment
Fragment viewDOT viewclick image to switch representation	Fragment viewDOT viewclick image to switch representation	Fragment viewDOT viewclick image to switch representation
H full host	D pushout complement	H' full product
RDKit viewDOT viewclick image to switch representation	Fragment viewDOT viewclick image to switch representation	RDKit viewDOT viewclick image to switch representation

L rule fragment

K interface

R rule fragment

Fragment viewDOT viewclick image to switch representation

H full host

D pushout complement

H' full product

RDKit viewDOT viewclick image to switch representation

Fragment viewDOT viewclick image to switch representation

RDKit viewDOT viewclick image to switch representation

RDKit host/product views

Host	Product
RDKit viewDOT viewclick image to switch representation	RDKit viewDOT viewclick image to switch representation

Host

Product

RDKit viewDOT viewclick image to switch representation

Diazomethane azo-form proton-transfer DPO

RDKit molecule quick view

Host	Product
RDKit viewDOT viewclick image to switch representation	RDKit viewDOT viewclick image to switch representation

Host

Product

RDKit viewDOT viewclick image to switch representation

Chemistry: H2C=N+=N- + RCO2H -> CH3-N+=N + RCO2-

The exact azo-form rule deletes one C=N shared pair, one terminal-N lone-pair loop, and the acid O-H pair.

Atom map: L1->H1, L2->H2, L3->H3, L4->H12, L5->H13

Feature map: L1->H1, L2->H3, L3->H4, L4->H7, L5->H2, L6->H8, L7->H16

Atom/H counts: L: atoms=5, H=1; K: atoms=5, H=1; R: atoms=5, H=1; H: atoms=13, H=6; D: atoms=13, H=6; H': atoms=13, H=6

Scope: L/K/R are rule fragments. H/D/H' are full application graphs, so hydrogens not shown in a rule fragment are preserved context atoms there.

Formal electron-feature DPO view

L rule fragment

K interface

R rule fragment

H full host

D pushout complement

H' full product

Chemical/DOT companion view

L rule fragment	K interface	R rule fragment
Fragment viewDOT viewclick image to switch representation	Fragment viewDOT viewclick image to switch representation	Fragment viewDOT viewclick image to switch representation
H full host	D pushout complement	H' full product
RDKit viewDOT viewclick image to switch representation	Fragment viewDOT viewclick image to switch representation	RDKit viewDOT viewclick image to switch representation

L rule fragment

K interface

R rule fragment

Fragment viewDOT viewclick image to switch representation

H full host

D pushout complement

H' full product

RDKit viewDOT viewclick image to switch representation

Fragment viewDOT viewclick image to switch representation

RDKit viewDOT viewclick image to switch representation

RDKit host/product views

Host	Product
RDKit viewDOT viewclick image to switch representation	RDKit viewDOT viewclick image to switch representation

Host

Product

RDKit viewDOT viewclick image to switch representation

Diazomethane methyl-transfer DPO

RDKit molecule quick view

Host	Product
RDKit viewDOT viewclick image to switch representation	RDKit viewDOT viewclick image to switch representation

Host

Product

RDKit viewDOT viewclick image to switch representation

Chemistry: [CH3N2+][RCO2-] -> RCO2CH3 + N2

The rule consumes one carboxylate oxygen lone pair and the C-N shared pair, then restores a lone pair on the departing inner nitrogen.

Atom map: L1->H4, L2->H1, L3->H2, L4->H3

Feature map: L1->H2, L2->H3, L3->H4, L4->H5, L5->H1

Atom/H counts: L: atoms=4, H=0; K: atoms=4, H=0; R: atoms=4, H=0; H: atoms=13, H=6; D: atoms=13, H=6; H': atoms=13, H=6

Scope: L/K/R are rule fragments. H/D/H' are full application graphs, so hydrogens not shown in a rule fragment are preserved context atoms there.

Formal electron-feature DPO view

L rule fragment

K interface

R rule fragment

H full host

D pushout complement

H' full product

Chemical/DOT companion view

L rule fragment	K interface	R rule fragment
Fragment viewDOT viewclick image to switch representation	Fragment viewDOT viewclick image to switch representation	Fragment viewDOT viewclick image to switch representation
H full host	D pushout complement	H' full product
RDKit viewDOT viewclick image to switch representation	Fragment viewDOT viewclick image to switch representation	RDKit viewDOT viewclick image to switch representation

L rule fragment

K interface

R rule fragment

Fragment viewDOT viewclick image to switch representation

H full host

D pushout complement

H' full product

RDKit viewDOT viewclick image to switch representation

Fragment viewDOT viewclick image to switch representation

RDKit viewDOT viewclick image to switch representation

RDKit host/product views

Host	Product
RDKit viewDOT viewclick image to switch representation	RDKit viewDOT viewclick image to switch representation

Host

Product

RDKit viewDOT viewclick image to switch representation

Molecules And States

Each molecule/state panel is clickable and switches between the chemical depiction and the electron-feature DOT graph.

Diazomethane Pathway

Substrate, ion-pair intermediates, and esterification products.

Diazomethane plus acid

RDKit viewDOT viewclick image to switch representation

After diazomethane proton transfer

RDKit viewDOT viewclick image to switch representation

After diazomethane methyl transfer

RDKit viewDOT viewclick image to switch representation

Exact azo-form diazomethane plus acid

RDKit viewDOT viewclick image to switch representation

Exact azo-form diazomethane plus acid DOT

Radicals And Carbenes

Open-shell and carbene states used by the local and DPO rules.

Methylene singlet

RDKit viewDOT viewclick image to switch representation

Methylene triplet from rule

RDKit viewDOT viewclick image to switch representation

Chlorine radical plus methane

RDKit viewDOT viewclick image to switch representation

HCl plus methyl radical

RDKit viewDOT viewclick image to switch representation

Chlorine radical plus methane plus methyl radical

RDKit viewDOT viewclick image to switch representation

Chlorine radical plus methane plus methyl radical DOT

Radical chain after H abstraction

RDKit viewDOT viewclick image to switch representation

HCl plus ethane

RDKit viewDOT viewclick image to switch representation

Allyl radical start

RDKit viewDOT viewclick image to switch representation

Methyl radical pair

RDKit viewDOT viewclick image to switch representation

Ethane from radical recombination

RDKit viewDOT viewclick image to switch representation

Reference And Verification States

Closed-shell and charge-transfer examples used as sanity checks.

Formose host start

RDKit viewDOT viewclick image to switch representation

Formose after keto-enol step

RDKit viewDOT viewclick image to switch representation

Formose after aldol step

RDKit viewDOT viewclick image to switch representation

Hydronium/hydroxide ion pair

RDKit viewDOT viewclick image to switch representation

Two waters after neutralization

RDKit viewDOT viewclick image to switch representation

Other Molecule States

Additional generated states in the figure bundle.

Allyl radical shifted

RDKit viewDOT viewclick image to switch representation

Generated Exchange Files

graphs rules applications compositions

Raw EGML Appendix

Graphs

exchange/graphs/diazomethane_after_methyl_transfer.egml

graph [
  graphID "diazomethane_after_methyl_transfer"
  node [ id 1 label "O" ]
  node [ id 2 label "C" ]
  node [ id 3 label "N" ]
  node [ id 4 label "N" ]
  node [ id 5 label "H" ]
  node [ id 6 label "H" ]
  node [ id 7 label "H" ]
  node [ id 8 label "C" ]
  node [ id 9 label "H" ]
  node [ id 10 label "H" ]
  node [ id 11 label "H" ]
  node [ id 12 label "C" ]
  node [ id 13 label "O" ]
  edge [ id 1 source 3 target 4 label "pair" ]
  edge [ id 2 source 3 target 4 label "pair" ]
  edge [ id 3 source 3 target 4 label "pair" ]
  edge [ id 4 source 1 target 2 label "pair" ]
  loop [ id 5 node 3 label "lp" ]
  edge [ id 6 source 2 target 5 label "pair" ]
  edge [ id 7 source 2 target 6 label "pair" ]
  edge [ id 8 source 2 target 7 label "pair" ]
  loop [ id 9 node 4 label "lp" ]
  edge [ id 10 source 8 target 9 label "pair" ]
  edge [ id 11 source 8 target 10 label "pair" ]
  edge [ id 12 source 8 target 11 label "pair" ]
  edge [ id 13 source 8 target 12 label "pair" ]
  edge [ id 14 source 12 target 13 label "pair" ]
  edge [ id 15 source 12 target 13 label "pair" ]
  edge [ id 16 source 12 target 1 label "pair" ]
  loop [ id 17 node 13 label "lp" ]
  loop [ id 18 node 13 label "lp" ]
  loop [ id 19 node 1 label "lp" ]
  loop [ id 20 node 1 label "lp" ]
]

exchange/graphs/diazomethane_after_proton_transfer.egml

graph [
  graphID "diazomethane_after_proton_transfer"
  node [ id 1 label "C" ]
  node [ id 2 label "N" ]
  node [ id 3 label "N" ]
  node [ id 4 label "O" ]
  node [ id 5 label "H" ]
  node [ id 6 label "H" ]
  node [ id 7 label "H" ]
  node [ id 8 label "C" ]
  node [ id 9 label "H" ]
  node [ id 10 label "H" ]
  node [ id 11 label "H" ]
  node [ id 12 label "C" ]
  node [ id 13 label "O" ]
  edge [ id 1 source 1 target 2 label "pair" ]
  edge [ id 2 source 2 target 3 label "pair" ]
  edge [ id 3 source 2 target 3 label "pair" ]
  edge [ id 4 source 2 target 3 label "pair" ]
  loop [ id 5 node 4 label "lp" ]
  edge [ id 6 source 1 target 5 label "pair" ]
  edge [ id 7 source 1 target 6 label "pair" ]
  edge [ id 8 source 1 target 7 label "pair" ]
  loop [ id 9 node 3 label "lp" ]
  edge [ id 10 source 8 target 9 label "pair" ]
  edge [ id 11 source 8 target 10 label "pair" ]
  edge [ id 12 source 8 target 11 label "pair" ]
  edge [ id 13 source 8 target 12 label "pair" ]
  edge [ id 14 source 12 target 13 label "pair" ]
  edge [ id 15 source 12 target 13 label "pair" ]
  edge [ id 16 source 12 target 4 label "pair" ]
  loop [ id 17 node 13 label "lp" ]
  loop [ id 18 node 13 label "lp" ]
  loop [ id 19 node 4 label "lp" ]
  loop [ id 20 node 4 label "lp" ]
]

exchange/graphs/diazomethane_azo_after_proton_transfer.egml

graph [
  graphID "diazomethane_azo_after_proton_transfer"
  node [ id 1 label "C" ]
  node [ id 2 label "N" ]
  node [ id 3 label "N" ]
  node [ id 4 label "O" ]
  node [ id 5 label "H" ]
  node [ id 6 label "H" ]
  node [ id 7 label "H" ]
  node [ id 8 label "C" ]
  node [ id 9 label "H" ]
  node [ id 10 label "H" ]
  node [ id 11 label "H" ]
  node [ id 12 label "C" ]
  node [ id 13 label "O" ]
  edge [ id 1 source 1 target 2 label "pair" ]
  edge [ id 2 source 2 target 3 label "pair" ]
  edge [ id 3 source 2 target 3 label "pair" ]
  loop [ id 4 node 3 label "lp" ]
  edge [ id 5 source 2 target 3 label "pair" ]
  loop [ id 6 node 4 label "lp" ]
  edge [ id 7 source 1 target 5 label "pair" ]
  edge [ id 8 source 1 target 6 label "pair" ]
  edge [ id 9 source 1 target 7 label "pair" ]
  edge [ id 10 source 8 target 9 label "pair" ]
  edge [ id 11 source 8 target 10 label "pair" ]
  edge [ id 12 source 8 target 11 label "pair" ]
  edge [ id 13 source 8 target 12 label "pair" ]
  edge [ id 14 source 12 target 13 label "pair" ]
  edge [ id 15 source 12 target 13 label "pair" ]
  edge [ id 16 source 12 target 4 label "pair" ]
  loop [ id 17 node 13 label "lp" ]
  loop [ id 18 node 13 label "lp" ]
  loop [ id 19 node 4 label "lp" ]
  loop [ id 20 node 4 label "lp" ]
]

exchange/graphs/diazomethane_azo_esterification_host.egml

graph [
  graphID "diazomethane_azo_esterification_host"
  node [ id 1 label "C" ]
  node [ id 2 label "N" ]
  node [ id 3 label "N" ]
  node [ id 4 label "H" ]
  node [ id 5 label "H" ]
  node [ id 6 label "C" ]
  node [ id 7 label "H" ]
  node [ id 8 label "H" ]
  node [ id 9 label "H" ]
  node [ id 10 label "C" ]
  node [ id 11 label "O" ]
  node [ id 12 label "O" ]
  node [ id 13 label "H" ]
  edge [ id 1 source 1 target 2 label "pair" ]
  edge [ id 2 source 1 target 2 label "pair" ]
  edge [ id 3 source 2 target 3 label "pair" ]
  edge [ id 4 source 2 target 3 label "pair" ]
  edge [ id 5 source 1 target 4 label "pair" ]
  edge [ id 6 source 1 target 5 label "pair" ]
  loop [ id 7 node 3 label "lp" ]
  loop [ id 8 node 3 label "lp" ]
  edge [ id 9 source 6 target 7 label "pair" ]
  edge [ id 10 source 6 target 8 label "pair" ]
  edge [ id 11 source 6 target 9 label "pair" ]
  edge [ id 12 source 6 target 10 label "pair" ]
  edge [ id 13 source 10 target 11 label "pair" ]
  edge [ id 14 source 10 target 11 label "pair" ]
  edge [ id 15 source 10 target 12 label "pair" ]
  edge [ id 16 source 12 target 13 label "pair" ]
  loop [ id 17 node 11 label "lp" ]
  loop [ id 18 node 11 label "lp" ]
  loop [ id 19 node 12 label "lp" ]
  loop [ id 20 node 12 label "lp" ]
]

exchange/graphs/diazomethane_esterification_host.egml

graph [
  graphID "diazomethane_esterification_host"
  node [ id 1 label "C" ]
  node [ id 2 label "N" ]
  node [ id 3 label "N" ]
  node [ id 4 label "H" ]
  node [ id 5 label "H" ]
  node [ id 6 label "C" ]
  node [ id 7 label "H" ]
  node [ id 8 label "H" ]
  node [ id 9 label "H" ]
  node [ id 10 label "C" ]
  node [ id 11 label "O" ]
  node [ id 12 label "O" ]
  node [ id 13 label "H" ]
  edge [ id 1 source 1 target 2 label "pair" ]
  edge [ id 2 source 2 target 3 label "pair" ]
  edge [ id 3 source 2 target 3 label "pair" ]
  edge [ id 4 source 2 target 3 label "pair" ]
  edge [ id 5 source 1 target 4 label "pair" ]
  edge [ id 6 source 1 target 5 label "pair" ]
  loop [ id 7 node 1 label "lp" ]
  loop [ id 8 node 3 label "lp" ]
  edge [ id 9 source 6 target 7 label "pair" ]
  edge [ id 10 source 6 target 8 label "pair" ]
  edge [ id 11 source 6 target 9 label "pair" ]
  edge [ id 12 source 6 target 10 label "pair" ]
  edge [ id 13 source 10 target 11 label "pair" ]
  edge [ id 14 source 10 target 11 label "pair" ]
  edge [ id 15 source 10 target 12 label "pair" ]
  edge [ id 16 source 12 target 13 label "pair" ]
  loop [ id 17 node 11 label "lp" ]
  loop [ id 18 node 11 label "lp" ]
  loop [ id 19 node 12 label "lp" ]
  loop [ id 20 node 12 label "lp" ]
]

exchange/graphs/radical_chain_after_abstraction.egml

graph [
  graphID "radical_chain_after_abstraction"
  node [ id 1 label "Cl" ]
  node [ id 2 label "C" ]
  node [ id 3 label "H" ]
  node [ id 4 label "H" ]
  node [ id 5 label "H" ]
  node [ id 6 label "H" ]
  node [ id 7 label "C" ]
  node [ id 8 label "H" ]
  node [ id 9 label "H" ]
  node [ id 10 label "H" ]
  loop [ id 1 node 1 label "lp" ]
  loop [ id 2 node 1 label "lp" ]
  loop [ id 3 node 1 label "lp" ]
  edge [ id 4 source 2 target 4 label "pair" ]
  edge [ id 5 source 2 target 5 label "pair" ]
  edge [ id 6 source 2 target 6 label "pair" ]
  edge [ id 7 source 7 target 8 label "pair" ]
  edge [ id 8 source 7 target 9 label "pair" ]
  edge [ id 9 source 7 target 10 label "pair" ]
  halfedge [ id 10 node 7 label "rad" ]
  edge [ id 11 source 1 target 3 label "pair" ]
  halfedge [ id 12 node 2 label "rad" ]
]

exchange/graphs/radical_chain_host.egml

graph [
  graphID "radical_chain_host"
  node [ id 1 label "Cl" ]
  node [ id 2 label "C" ]
  node [ id 3 label "H" ]
  node [ id 4 label "H" ]
  node [ id 5 label "H" ]
  node [ id 6 label "H" ]
  node [ id 7 label "C" ]
  node [ id 8 label "H" ]
  node [ id 9 label "H" ]
  node [ id 10 label "H" ]
  loop [ id 1 node 1 label "lp" ]
  loop [ id 2 node 1 label "lp" ]
  loop [ id 3 node 1 label "lp" ]
  halfedge [ id 4 node 1 label "rad" ]
  edge [ id 5 source 2 target 3 label "pair" ]
  edge [ id 6 source 2 target 4 label "pair" ]
  edge [ id 7 source 2 target 5 label "pair" ]
  edge [ id 8 source 2 target 6 label "pair" ]
  edge [ id 9 source 7 target 8 label "pair" ]
  edge [ id 10 source 7 target 9 label "pair" ]
  edge [ id 11 source 7 target 10 label "pair" ]
  halfedge [ id 12 node 7 label "rad" ]
]

exchange/graphs/radical_chain_product.egml

graph [
  graphID "radical_chain_product"
  node [ id 1 label "Cl" ]
  node [ id 2 label "C" ]
  node [ id 3 label "H" ]
  node [ id 4 label "H" ]
  node [ id 5 label "H" ]
  node [ id 6 label "H" ]
  node [ id 7 label "C" ]
  node [ id 8 label "H" ]
  node [ id 9 label "H" ]
  node [ id 10 label "H" ]
  loop [ id 1 node 1 label "lp" ]
  loop [ id 2 node 1 label "lp" ]
  loop [ id 3 node 1 label "lp" ]
  edge [ id 4 source 2 target 4 label "pair" ]
  edge [ id 5 source 2 target 5 label "pair" ]
  edge [ id 6 source 2 target 6 label "pair" ]
  edge [ id 7 source 7 target 8 label "pair" ]
  edge [ id 8 source 7 target 9 label "pair" ]
  edge [ id 9 source 7 target 10 label "pair" ]
  edge [ id 10 source 1 target 3 label "pair" ]
  edge [ id 11 source 2 target 7 label "pair" ]
]

Rules

exchange/rules/chlorine_h_abstraction.egml

rule [
  ruleID "chlorine_h_abstraction"
  note "Consumes the chlorine radical halfedge and one methane C-H shared pair; creates H-Cl and a methyl radical halfedge."
  extension "loops encode lone pairs; halfedges encode radicals"
  interface [
    node [ id 1 label "Cl" ]
    node [ id 2 label "C" ]
    node [ id 3 label "H" ]
    node [ id 4 label "H" ]
    node [ id 5 label "H" ]
    node [ id 6 label "H" ]
    loop [ id 1 node 1 label "lp" ]
    loop [ id 2 node 1 label "lp" ]
    loop [ id 3 node 1 label "lp" ]
    edge [ id 4 source 2 target 4 label "pair" ]
    edge [ id 5 source 2 target 5 label "pair" ]
    edge [ id 6 source 2 target 6 label "pair" ]
  ]
  left [
    node [ id 1 label "Cl" ]
    node [ id 2 label "C" ]
    node [ id 3 label "H" ]
    node [ id 4 label "H" ]
    node [ id 5 label "H" ]
    node [ id 6 label "H" ]
    loop [ id 1 node 1 label "lp" ]
    loop [ id 2 node 1 label "lp" ]
    loop [ id 3 node 1 label "lp" ]
    edge [ id 4 source 2 target 4 label "pair" ]
    edge [ id 5 source 2 target 5 label "pair" ]
    edge [ id 6 source 2 target 6 label "pair" ]
    halfedge [ id 7 node 1 label "rad" ]
    edge [ id 8 source 2 target 3 label "pair" ]
  ]
  right [
    node [ id 1 label "Cl" ]
    node [ id 2 label "H" ]
    node [ id 3 label "C" ]
    node [ id 4 label "H" ]
    node [ id 5 label "H" ]
    node [ id 6 label "H" ]
    edge [ id 1 source 1 target 2 label "pair" ]
    loop [ id 2 node 1 label "lp" ]
    loop [ id 3 node 1 label "lp" ]
    loop [ id 4 node 1 label "lp" ]
    edge [ id 5 source 3 target 4 label "pair" ]
    edge [ id 6 source 3 target 5 label "pair" ]
    edge [ id 7 source 3 target 6 label "pair" ]
    halfedge [ id 8 node 3 label "rad" ]
  ]
  interfaceToLeft [
    atom [ interface 1 target 1 ]
    atom [ interface 2 target 2 ]
    atom [ interface 3 target 3 ]
    atom [ interface 4 target 4 ]
    atom [ interface 5 target 5 ]
    atom [ interface 6 target 6 ]
    feature [ interface 1 target 1 ]
    feature [ interface 2 target 2 ]
    feature [ interface 3 target 3 ]
    feature [ interface 4 target 4 ]
    feature [ interface 5 target 5 ]
    feature [ interface 6 target 6 ]
    attachment [ interface 1 target 1 ]
    attachment [ interface 2 target 2 ]
    attachment [ interface 3 target 3 ]
    attachment [ interface 4 target 4 ]
    attachment [ interface 5 target 5 ]
    attachment [ interface 6 target 6 ]
    attachment [ interface 7 target 7 ]
    attachment [ interface 8 target 8 ]
    attachment [ interface 9 target 9 ]
  ]
  interfaceToRight [
    atom [ interface 1 target 1 ]
    atom [ interface 2 target 3 ]
    atom [ interface 3 target 2 ]
    atom [ interface 4 target 4 ]
    atom [ interface 5 target 5 ]
    atom [ interface 6 target 6 ]
    feature [ interface 1 target 2 ]
    feature [ interface 2 target 3 ]
    feature [ interface 3 target 4 ]
    feature [ interface 4 target 5 ]
    feature [ interface 5 target 6 ]
    feature [ interface 6 target 7 ]
    attachment [ interface 1 target 3 ]
    attachment [ interface 2 target 4 ]
    attachment [ interface 3 target 5 ]
    attachment [ interface 4 target 6 ]
    attachment [ interface 5 target 7 ]
    attachment [ interface 6 target 8 ]
    attachment [ interface 7 target 9 ]
    attachment [ interface 8 target 10 ]
    attachment [ interface 9 target 11 ]
  ]
]

exchange/rules/chlorine_h_abstraction_with_external_methyl.egml

rule [
  ruleID "chlorine_h_abstraction_with_external_methyl"
  note "Chlorine abstraction rule with an external methyl radical carried as identity context for partial composition."
  extension "loops encode lone pairs; halfedges encode radicals"
  interface [
    node [ id 1 label "Cl" ]
    node [ id 2 label "C" ]
    node [ id 3 label "H" ]
    node [ id 4 label "H" ]
    node [ id 5 label "H" ]
    node [ id 6 label "H" ]
    node [ id 7 label "C" ]
    node [ id 8 label "H" ]
    node [ id 9 label "H" ]
    node [ id 10 label "H" ]
    loop [ id 1 node 1 label "lp" ]
    loop [ id 2 node 1 label "lp" ]
    loop [ id 3 node 1 label "lp" ]
    edge [ id 4 source 2 target 4 label "pair" ]
    edge [ id 5 source 2 target 5 label "pair" ]
    edge [ id 6 source 2 target 6 label "pair" ]
    edge [ id 7 source 7 target 8 label "pair" ]
    edge [ id 8 source 7 target 9 label "pair" ]
    edge [ id 9 source 7 target 10 label "pair" ]
    halfedge [ id 10 node 7 label "rad" ]
  ]
  left [
    node [ id 1 label "Cl" ]
    node [ id 2 label "C" ]
    node [ id 3 label "H" ]
    node [ id 4 label "H" ]
    node [ id 5 label "H" ]
    node [ id 6 label "H" ]
    node [ id 7 label "C" ]
    node [ id 8 label "H" ]
    node [ id 9 label "H" ]
    node [ id 10 label "H" ]
    loop [ id 1 node 1 label "lp" ]
    loop [ id 2 node 1 label "lp" ]
    loop [ id 3 node 1 label "lp" ]
    edge [ id 4 source 2 target 4 label "pair" ]
    edge [ id 5 source 2 target 5 label "pair" ]
    edge [ id 6 source 2 target 6 label "pair" ]
    halfedge [ id 7 node 1 label "rad" ]
    edge [ id 8 source 2 target 3 label "pair" ]
    edge [ id 9 source 7 target 8 label "pair" ]
    edge [ id 10 source 7 target 9 label "pair" ]
    edge [ id 11 source 7 target 10 label "pair" ]
    halfedge [ id 12 node 7 label "rad" ]
  ]
  right [
    node [ id 1 label "Cl" ]
    node [ id 2 label "H" ]
    node [ id 3 label "C" ]
    node [ id 4 label "H" ]
    node [ id 5 label "H" ]
    node [ id 6 label "H" ]
    node [ id 7 label "C" ]
    node [ id 8 label "H" ]
    node [ id 9 label "H" ]
    node [ id 10 label "H" ]
    edge [ id 1 source 1 target 2 label "pair" ]
    loop [ id 2 node 1 label "lp" ]
    loop [ id 3 node 1 label "lp" ]
    loop [ id 4 node 1 label "lp" ]
    edge [ id 5 source 3 target 4 label "pair" ]
    edge [ id 6 source 3 target 5 label "pair" ]
    edge [ id 7 source 3 target 6 label "pair" ]
    halfedge [ id 8 node 3 label "rad" ]
    edge [ id 9 source 7 target 8 label "pair" ]
    edge [ id 10 source 7 target 9 label "pair" ]
    edge [ id 11 source 7 target 10 label "pair" ]
    halfedge [ id 12 node 7 label "rad" ]
  ]
  interfaceToLeft [
    atom [ interface 1 target 1 ]
    atom [ interface 2 target 2 ]
    atom [ interface 3 target 3 ]
    atom [ interface 4 target 4 ]
    atom [ interface 5 target 5 ]
    atom [ interface 6 target 6 ]
    atom [ interface 7 target 7 ]
    atom [ interface 8 target 8 ]
    atom [ interface 9 target 9 ]
    atom [ interface 10 target 10 ]
    feature [ interface 1 target 1 ]
    feature [ interface 2 target 2 ]
    feature [ interface 3 target 3 ]
    feature [ interface 4 target 4 ]
    feature [ interface 5 target 5 ]
    feature [ interface 6 target 6 ]
    feature [ interface 7 target 9 ]
    feature [ interface 8 target 10 ]
    feature [ interface 9 target 11 ]
    feature [ interface 10 target 12 ]
    attachment [ interface 1 target 1 ]
    attachment [ interface 2 target 2 ]
    attachment [ interface 3 target 3 ]
    attachment [ interface 4 target 4 ]
    attachment [ interface 5 target 5 ]
    attachment [ interface 6 target 6 ]
    attachment [ interface 7 target 7 ]
    attachment [ interface 8 target 8 ]
    attachment [ interface 9 target 9 ]
    attachment [ interface 10 target 13 ]
    attachment [ interface 11 target 14 ]
    attachment [ interface 12 target 15 ]
    attachment [ interface 13 target 16 ]
    attachment [ interface 14 target 17 ]
    attachment [ interface 15 target 18 ]
    attachment [ interface 16 target 19 ]
  ]
  interfaceToRight [
    atom [ interface 1 target 1 ]
    atom [ interface 2 target 3 ]
    atom [ interface 3 target 2 ]
    atom [ interface 4 target 4 ]
    atom [ interface 5 target 5 ]
    atom [ interface 6 target 6 ]
    atom [ interface 7 target 7 ]
    atom [ interface 8 target 8 ]
    atom [ interface 9 target 9 ]
    atom [ interface 10 target 10 ]
    feature [ interface 1 target 2 ]
    feature [ interface 2 target 3 ]
    feature [ interface 3 target 4 ]
    feature [ interface 4 target 5 ]
    feature [ interface 5 target 6 ]
    feature [ interface 6 target 7 ]
    feature [ interface 7 target 9 ]
    feature [ interface 8 target 10 ]
    feature [ interface 9 target 11 ]
    feature [ interface 10 target 12 ]
    attachment [ interface 1 target 3 ]
    attachment [ interface 2 target 4 ]
    attachment [ interface 3 target 5 ]
    attachment [ interface 4 target 6 ]
    attachment [ interface 5 target 7 ]
    attachment [ interface 6 target 8 ]
    attachment [ interface 7 target 9 ]
    attachment [ interface 8 target 10 ]
    attachment [ interface 9 target 11 ]
    attachment [ interface 10 target 13 ]
    attachment [ interface 11 target 14 ]
    attachment [ interface 12 target 15 ]
    attachment [ interface 13 target 16 ]
    attachment [ interface 14 target 17 ]
    attachment [ interface 15 target 18 ]
    attachment [ interface 16 target 19 ]
  ]
]

exchange/rules/diazomethane_azo_esterification_macro.egml

rule [
  ruleID "diazomethane_azo_esterification_macro"
  note "Direct rule from exact H2C=N+=N- substrate form to ester plus N2 generated by AlgebraicRewriting.composeV_ from the exact azo-form proton-transfer step and the methyl-transfer step with preserved context."
  extension "loops encode lone pairs; halfedges encode radicals"
  interface [
    node [ id 1 label "C" ]
    node [ id 2 label "N" ]
    node [ id 3 label "N" ]
    node [ id 4 label "O" ]
    node [ id 5 label "H" ]
    edge [ id 1 source 2 target 3 label "pair" ]
    edge [ id 2 source 2 target 3 label "pair" ]
    loop [ id 3 node 3 label "lp" ]
  ]
  left [
    node [ id 1 label "C" ]
    node [ id 2 label "N" ]
    node [ id 3 label "N" ]
    node [ id 4 label "O" ]
    node [ id 5 label "H" ]
    edge [ id 1 source 1 target 2 label "pair" ]
    edge [ id 2 source 2 target 3 label "pair" ]
    edge [ id 3 source 2 target 3 label "pair" ]
    loop [ id 4 node 3 label "lp" ]
    edge [ id 5 source 1 target 2 label "pair" ]
    loop [ id 6 node 3 label "lp" ]
    edge [ id 7 source 4 target 5 label "pair" ]
  ]
  right [
    node [ id 1 label "C" ]
    node [ id 2 label "N" ]
    node [ id 3 label "N" ]
    node [ id 4 label "O" ]
    node [ id 5 label "H" ]
    edge [ id 1 source 2 target 3 label "pair" ]
    edge [ id 2 source 2 target 3 label "pair" ]
    edge [ id 3 source 2 target 3 label "pair" ]
    loop [ id 4 node 3 label "lp" ]
    edge [ id 5 source 1 target 5 label "pair" ]
    edge [ id 6 source 4 target 1 label "pair" ]
    loop [ id 7 node 2 label "lp" ]
  ]
  interfaceToLeft [
    atom [ interface 1 target 1 ]
    atom [ interface 2 target 2 ]
    atom [ interface 3 target 3 ]
    atom [ interface 4 target 4 ]
    atom [ interface 5 target 5 ]
    feature [ interface 1 target 2 ]
    feature [ interface 2 target 3 ]
    feature [ interface 3 target 4 ]
    attachment [ interface 1 target 3 ]
    attachment [ interface 2 target 4 ]
    attachment [ interface 3 target 5 ]
    attachment [ interface 4 target 6 ]
    attachment [ interface 5 target 7 ]
  ]
  interfaceToRight [
    atom [ interface 1 target 1 ]
    atom [ interface 2 target 2 ]
    atom [ interface 3 target 3 ]
    atom [ interface 4 target 4 ]
    atom [ interface 5 target 5 ]
    feature [ interface 1 target 1 ]
    feature [ interface 2 target 2 ]
    feature [ interface 3 target 4 ]
    attachment [ interface 1 target 1 ]
    attachment [ interface 2 target 2 ]
    attachment [ interface 3 target 3 ]
    attachment [ interface 4 target 4 ]
    attachment [ interface 5 target 7 ]
  ]
]

exchange/rules/diazomethane_azo_proton_transfer.egml

rule [
  ruleID "diazomethane_azo_proton_transfer"
  note "Exact H2C=N+=N- resonance-form proton transfer: consumes one C=N shared pair, one terminal-N lone-pair loop, and the acid O-H shared pair; creates the third N=N shared pair, an oxygen lone-pair loop, and a C-H shared pair."
  extension "loops encode lone pairs; halfedges encode radicals"
  interface [
    node [ id 1 label "C" ]
    node [ id 2 label "N" ]
    node [ id 3 label "N" ]
    node [ id 4 label "O" ]
    node [ id 5 label "H" ]
    edge [ id 1 source 1 target 2 label "pair" ]
    edge [ id 2 source 2 target 3 label "pair" ]
    edge [ id 3 source 2 target 3 label "pair" ]
    loop [ id 4 node 3 label "lp" ]
  ]
  left [
    node [ id 1 label "C" ]
    node [ id 2 label "N" ]
    node [ id 3 label "N" ]
    node [ id 4 label "O" ]
    node [ id 5 label "H" ]
    edge [ id 1 source 1 target 2 label "pair" ]
    edge [ id 2 source 2 target 3 label "pair" ]
    edge [ id 3 source 2 target 3 label "pair" ]
    loop [ id 4 node 3 label "lp" ]
    edge [ id 5 source 1 target 2 label "pair" ]
    loop [ id 6 node 3 label "lp" ]
    edge [ id 7 source 4 target 5 label "pair" ]
  ]
  right [
    node [ id 1 label "C" ]
    node [ id 2 label "N" ]
    node [ id 3 label "N" ]
    node [ id 4 label "O" ]
    node [ id 5 label "H" ]
    edge [ id 1 source 1 target 2 label "pair" ]
    edge [ id 2 source 2 target 3 label "pair" ]
    edge [ id 3 source 2 target 3 label "pair" ]
    loop [ id 4 node 3 label "lp" ]
    edge [ id 5 source 2 target 3 label "pair" ]
    loop [ id 6 node 4 label "lp" ]
    edge [ id 7 source 1 target 5 label "pair" ]
  ]
  interfaceToLeft [
    atom [ interface 1 target 1 ]
    atom [ interface 2 target 2 ]
    atom [ interface 3 target 3 ]
    atom [ interface 4 target 4 ]
    atom [ interface 5 target 5 ]
    feature [ interface 1 target 1 ]
    feature [ interface 2 target 2 ]
    feature [ interface 3 target 3 ]
    feature [ interface 4 target 4 ]
    attachment [ interface 1 target 1 ]
    attachment [ interface 2 target 2 ]
    attachment [ interface 3 target 3 ]
    attachment [ interface 4 target 4 ]
    attachment [ interface 5 target 5 ]
    attachment [ interface 6 target 6 ]
    attachment [ interface 7 target 7 ]
  ]
  interfaceToRight [
    atom [ interface 1 target 1 ]
    atom [ interface 2 target 2 ]
    atom [ interface 3 target 3 ]
    atom [ interface 4 target 4 ]
    atom [ interface 5 target 5 ]
    feature [ interface 1 target 1 ]
    feature [ interface 2 target 2 ]
    feature [ interface 3 target 3 ]
    feature [ interface 4 target 4 ]
    attachment [ interface 1 target 1 ]
    attachment [ interface 2 target 2 ]
    attachment [ interface 3 target 3 ]
    attachment [ interface 4 target 4 ]
    attachment [ interface 5 target 5 ]
    attachment [ interface 6 target 6 ]
    attachment [ interface 7 target 7 ]
  ]
]

exchange/rules/diazomethane_esterification_macro.egml

rule [
  ruleID "diazomethane_esterification_macro"
  note "Direct rule from substrate to ester plus N2 generated by AlgebraicRewriting.composeV_ from the two DPO steps."
  extension "loops encode lone pairs; halfedges encode radicals"
  interface [
    node [ id 1 label "C" ]
    node [ id 2 label "N" ]
    node [ id 3 label "N" ]
    node [ id 4 label "O" ]
    node [ id 5 label "H" ]
    edge [ id 1 source 2 target 3 label "pair" ]
    edge [ id 2 source 2 target 3 label "pair" ]
    edge [ id 3 source 2 target 3 label "pair" ]
  ]
  left [
    node [ id 1 label "C" ]
    node [ id 2 label "N" ]
    node [ id 3 label "N" ]
    node [ id 4 label "O" ]
    node [ id 5 label "H" ]
    edge [ id 1 source 1 target 2 label "pair" ]
    edge [ id 2 source 2 target 3 label "pair" ]
    edge [ id 3 source 2 target 3 label "pair" ]
    edge [ id 4 source 2 target 3 label "pair" ]
    loop [ id 5 node 1 label "lp" ]
    edge [ id 6 source 4 target 5 label "pair" ]
  ]
  right [
    node [ id 1 label "C" ]
    node [ id 2 label "N" ]
    node [ id 3 label "N" ]
    node [ id 4 label "O" ]
    node [ id 5 label "H" ]
    edge [ id 1 source 2 target 3 label "pair" ]
    edge [ id 2 source 2 target 3 label "pair" ]
    edge [ id 3 source 2 target 3 label "pair" ]
    edge [ id 4 source 1 target 5 label "pair" ]
    edge [ id 5 source 4 target 1 label "pair" ]
    loop [ id 6 node 2 label "lp" ]
  ]
  interfaceToLeft [
    atom [ interface 1 target 1 ]
    atom [ interface 2 target 2 ]
    atom [ interface 3 target 3 ]
    atom [ interface 4 target 4 ]
    atom [ interface 5 target 5 ]
    feature [ interface 1 target 2 ]
    feature [ interface 2 target 3 ]
    feature [ interface 3 target 4 ]
    attachment [ interface 1 target 3 ]
    attachment [ interface 2 target 4 ]
    attachment [ interface 3 target 5 ]
    attachment [ interface 4 target 6 ]
    attachment [ interface 5 target 7 ]
    attachment [ interface 6 target 8 ]
  ]
  interfaceToRight [
    atom [ interface 1 target 1 ]
    atom [ interface 2 target 2 ]
    atom [ interface 3 target 3 ]
    atom [ interface 4 target 4 ]
    atom [ interface 5 target 5 ]
    feature [ interface 1 target 1 ]
    feature [ interface 2 target 2 ]
    feature [ interface 3 target 3 ]
    attachment [ interface 1 target 1 ]
    attachment [ interface 2 target 2 ]
    attachment [ interface 3 target 3 ]
    attachment [ interface 4 target 4 ]
    attachment [ interface 5 target 5 ]
    attachment [ interface 6 target 6 ]
  ]
]

exchange/rules/diazomethane_methyl_transfer.egml

rule [
  ruleID "diazomethane_methyl_transfer"
  note "Consumes one carboxylate oxygen lone pair and the C-N shared pair; creates the O-C shared pair and restores a lone pair on the inner nitrogen."
  extension "loops encode lone pairs; halfedges encode radicals"
  interface [
    node [ id 1 label "O" ]
    node [ id 2 label "C" ]
    node [ id 3 label "N" ]
    node [ id 4 label "N" ]
    edge [ id 1 source 3 target 4 label "pair" ]
    edge [ id 2 source 3 target 4 label "pair" ]
    edge [ id 3 source 3 target 4 label "pair" ]
  ]
  left [
    node [ id 1 label "O" ]
    node [ id 2 label "C" ]
    node [ id 3 label "N" ]
    node [ id 4 label "N" ]
    edge [ id 1 source 3 target 4 label "pair" ]
    edge [ id 2 source 3 target 4 label "pair" ]
    edge [ id 3 source 3 target 4 label "pair" ]
    loop [ id 4 node 1 label "lp" ]
    edge [ id 5 source 2 target 3 label "pair" ]
  ]
  right [
    node [ id 1 label "O" ]
    node [ id 2 label "C" ]
    node [ id 3 label "N" ]
    node [ id 4 label "N" ]
    edge [ id 1 source 3 target 4 label "pair" ]
    edge [ id 2 source 3 target 4 label "pair" ]
    edge [ id 3 source 3 target 4 label "pair" ]
    edge [ id 4 source 1 target 2 label "pair" ]
    loop [ id 5 node 3 label "lp" ]
  ]
  interfaceToLeft [
    atom [ interface 1 target 1 ]
    atom [ interface 2 target 2 ]
    atom [ interface 3 target 3 ]
    atom [ interface 4 target 4 ]
    feature [ interface 1 target 1 ]
    feature [ interface 2 target 2 ]
    feature [ interface 3 target 3 ]
    attachment [ interface 1 target 1 ]
    attachment [ interface 2 target 2 ]
    attachment [ interface 3 target 3 ]
    attachment [ interface 4 target 4 ]
    attachment [ interface 5 target 5 ]
    attachment [ interface 6 target 6 ]
  ]
  interfaceToRight [
    atom [ interface 1 target 1 ]
    atom [ interface 2 target 2 ]
    atom [ interface 3 target 3 ]
    atom [ interface 4 target 4 ]
    feature [ interface 1 target 1 ]
    feature [ interface 2 target 2 ]
    feature [ interface 3 target 3 ]
    attachment [ interface 1 target 1 ]
    attachment [ interface 2 target 2 ]
    attachment [ interface 3 target 3 ]
    attachment [ interface 4 target 4 ]
    attachment [ interface 5 target 5 ]
    attachment [ interface 6 target 6 ]
  ]
]

exchange/rules/diazomethane_methyl_transfer_after_azo_context.egml

rule [
  ruleID "diazomethane_methyl_transfer_after_azo_context"
  note "Same methyl-transfer chemistry, but with the C-H pair and terminal-N lone-pair loop carried as preserved context so the exact azo-form proton-transfer result composes vertically."
  extension "loops encode lone pairs; halfedges encode radicals"
  interface [
    node [ id 1 label "C" ]
    node [ id 2 label "N" ]
    node [ id 3 label "N" ]
    node [ id 4 label "O" ]
    node [ id 5 label "H" ]
    edge [ id 1 source 2 target 3 label "pair" ]
    edge [ id 2 source 2 target 3 label "pair" ]
    edge [ id 3 source 2 target 3 label "pair" ]
    loop [ id 4 node 3 label "lp" ]
    edge [ id 5 source 1 target 5 label "pair" ]
  ]
  left [
    node [ id 1 label "C" ]
    node [ id 2 label "N" ]
    node [ id 3 label "N" ]
    node [ id 4 label "O" ]
    node [ id 5 label "H" ]
    edge [ id 1 source 1 target 2 label "pair" ]
    edge [ id 2 source 2 target 3 label "pair" ]
    edge [ id 3 source 2 target 3 label "pair" ]
    loop [ id 4 node 3 label "lp" ]
    edge [ id 5 source 2 target 3 label "pair" ]
    loop [ id 6 node 4 label "lp" ]
    edge [ id 7 source 1 target 5 label "pair" ]
  ]
  right [
    node [ id 1 label "C" ]
    node [ id 2 label "N" ]
    node [ id 3 label "N" ]
    node [ id 4 label "O" ]
    node [ id 5 label "H" ]
    edge [ id 1 source 2 target 3 label "pair" ]
    edge [ id 2 source 2 target 3 label "pair" ]
    edge [ id 3 source 2 target 3 label "pair" ]
    loop [ id 4 node 3 label "lp" ]
    edge [ id 5 source 1 target 5 label "pair" ]
    edge [ id 6 source 4 target 1 label "pair" ]
    loop [ id 7 node 2 label "lp" ]
  ]
  interfaceToLeft [
    atom [ interface 1 target 1 ]
    atom [ interface 2 target 2 ]
    atom [ interface 3 target 3 ]
    atom [ interface 4 target 4 ]
    atom [ interface 5 target 5 ]
    feature [ interface 1 target 2 ]
    feature [ interface 2 target 3 ]
    feature [ interface 3 target 5 ]
    feature [ interface 4 target 4 ]
    feature [ interface 5 target 7 ]
    attachment [ interface 1 target 3 ]
    attachment [ interface 2 target 4 ]
    attachment [ interface 3 target 5 ]
    attachment [ interface 4 target 6 ]
    attachment [ interface 5 target 8 ]
    attachment [ interface 6 target 9 ]
    attachment [ interface 7 target 7 ]
    attachment [ interface 8 target 11 ]
    attachment [ interface 9 target 12 ]
  ]
  interfaceToRight [
    atom [ interface 1 target 1 ]
    atom [ interface 2 target 2 ]
    atom [ interface 3 target 3 ]
    atom [ interface 4 target 4 ]
    atom [ interface 5 target 5 ]
    feature [ interface 1 target 1 ]
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    feature [ interface 3 target 3 ]
    feature [ interface 4 target 4 ]
    feature [ interface 5 target 5 ]
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    attachment [ interface 2 target 2 ]
    attachment [ interface 3 target 3 ]
    attachment [ interface 4 target 4 ]
    attachment [ interface 5 target 5 ]
    attachment [ interface 6 target 6 ]
    attachment [ interface 7 target 7 ]
    attachment [ interface 8 target 8 ]
    attachment [ interface 9 target 9 ]
  ]
]

exchange/rules/diazomethane_methyl_transfer_after_proton_context.egml

rule [
  ruleID "diazomethane_methyl_transfer_after_proton_context"
  note "Same methyl-transfer chemistry, but with the newly created C-H pair carried as preserved context so the rule can compose vertically with proton transfer."
  extension "loops encode lone pairs; halfedges encode radicals"
  interface [
    node [ id 1 label "C" ]
    node [ id 2 label "N" ]
    node [ id 3 label "N" ]
    node [ id 4 label "O" ]
    node [ id 5 label "H" ]
    edge [ id 1 source 2 target 3 label "pair" ]
    edge [ id 2 source 2 target 3 label "pair" ]
    edge [ id 3 source 2 target 3 label "pair" ]
    edge [ id 4 source 1 target 5 label "pair" ]
  ]
  left [
    node [ id 1 label "C" ]
    node [ id 2 label "N" ]
    node [ id 3 label "N" ]
    node [ id 4 label "O" ]
    node [ id 5 label "H" ]
    edge [ id 1 source 1 target 2 label "pair" ]
    edge [ id 2 source 2 target 3 label "pair" ]
    edge [ id 3 source 2 target 3 label "pair" ]
    edge [ id 4 source 2 target 3 label "pair" ]
    loop [ id 5 node 4 label "lp" ]
    edge [ id 6 source 1 target 5 label "pair" ]
  ]
  right [
    node [ id 1 label "C" ]
    node [ id 2 label "N" ]
    node [ id 3 label "N" ]
    node [ id 4 label "O" ]
    node [ id 5 label "H" ]
    edge [ id 1 source 2 target 3 label "pair" ]
    edge [ id 2 source 2 target 3 label "pair" ]
    edge [ id 3 source 2 target 3 label "pair" ]
    edge [ id 4 source 1 target 5 label "pair" ]
    edge [ id 5 source 4 target 1 label "pair" ]
    loop [ id 6 node 2 label "lp" ]
  ]
  interfaceToLeft [
    atom [ interface 1 target 1 ]
    atom [ interface 2 target 2 ]
    atom [ interface 3 target 3 ]
    atom [ interface 4 target 4 ]
    atom [ interface 5 target 5 ]
    feature [ interface 1 target 2 ]
    feature [ interface 2 target 3 ]
    feature [ interface 3 target 4 ]
    feature [ interface 4 target 6 ]
    attachment [ interface 1 target 3 ]
    attachment [ interface 2 target 4 ]
    attachment [ interface 3 target 5 ]
    attachment [ interface 4 target 6 ]
    attachment [ interface 5 target 7 ]
    attachment [ interface 6 target 8 ]
    attachment [ interface 7 target 10 ]
    attachment [ interface 8 target 11 ]
  ]
  interfaceToRight [
    atom [ interface 1 target 1 ]
    atom [ interface 2 target 2 ]
    atom [ interface 3 target 3 ]
    atom [ interface 4 target 4 ]
    atom [ interface 5 target 5 ]
    feature [ interface 1 target 1 ]
    feature [ interface 2 target 2 ]
    feature [ interface 3 target 3 ]
    feature [ interface 4 target 4 ]
    attachment [ interface 1 target 1 ]
    attachment [ interface 2 target 2 ]
    attachment [ interface 3 target 3 ]
    attachment [ interface 4 target 4 ]
    attachment [ interface 5 target 5 ]
    attachment [ interface 6 target 6 ]
    attachment [ interface 7 target 7 ]
    attachment [ interface 8 target 8 ]
  ]
]

exchange/rules/diazomethane_proton_transfer.egml

rule [
  ruleID "diazomethane_proton_transfer"
  note "Consumes the diazomethane carbon lone-pair loop and the acid O-H shared pair; creates an oxygen lone pair and a C-H shared pair."
  extension "loops encode lone pairs; halfedges encode radicals"
  interface [
    node [ id 1 label "C" ]
    node [ id 2 label "N" ]
    node [ id 3 label "N" ]
    node [ id 4 label "O" ]
    node [ id 5 label "H" ]
    edge [ id 1 source 1 target 2 label "pair" ]
    edge [ id 2 source 2 target 3 label "pair" ]
    edge [ id 3 source 2 target 3 label "pair" ]
    edge [ id 4 source 2 target 3 label "pair" ]
  ]
  left [
    node [ id 1 label "C" ]
    node [ id 2 label "N" ]
    node [ id 3 label "N" ]
    node [ id 4 label "O" ]
    node [ id 5 label "H" ]
    edge [ id 1 source 1 target 2 label "pair" ]
    edge [ id 2 source 2 target 3 label "pair" ]
    edge [ id 3 source 2 target 3 label "pair" ]
    edge [ id 4 source 2 target 3 label "pair" ]
    loop [ id 5 node 1 label "lp" ]
    edge [ id 6 source 4 target 5 label "pair" ]
  ]
  right [
    node [ id 1 label "C" ]
    node [ id 2 label "N" ]
    node [ id 3 label "N" ]
    node [ id 4 label "O" ]
    node [ id 5 label "H" ]
    edge [ id 1 source 1 target 2 label "pair" ]
    edge [ id 2 source 2 target 3 label "pair" ]
    edge [ id 3 source 2 target 3 label "pair" ]
    edge [ id 4 source 2 target 3 label "pair" ]
    loop [ id 5 node 4 label "lp" ]
    edge [ id 6 source 1 target 5 label "pair" ]
  ]
  interfaceToLeft [
    atom [ interface 1 target 1 ]
    atom [ interface 2 target 2 ]
    atom [ interface 3 target 3 ]
    atom [ interface 4 target 4 ]
    atom [ interface 5 target 5 ]
    feature [ interface 1 target 1 ]
    feature [ interface 2 target 2 ]
    feature [ interface 3 target 3 ]
    feature [ interface 4 target 4 ]
    attachment [ interface 1 target 1 ]
    attachment [ interface 2 target 2 ]
    attachment [ interface 3 target 3 ]
    attachment [ interface 4 target 4 ]
    attachment [ interface 5 target 5 ]
    attachment [ interface 6 target 6 ]
    attachment [ interface 7 target 7 ]
    attachment [ interface 8 target 8 ]
  ]
  interfaceToRight [
    atom [ interface 1 target 1 ]
    atom [ interface 2 target 2 ]
    atom [ interface 3 target 3 ]
    atom [ interface 4 target 4 ]
    atom [ interface 5 target 5 ]
    feature [ interface 1 target 1 ]
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    feature [ interface 3 target 3 ]
    feature [ interface 4 target 4 ]
    attachment [ interface 1 target 1 ]
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    attachment [ interface 4 target 4 ]
    attachment [ interface 5 target 5 ]
    attachment [ interface 6 target 6 ]
    attachment [ interface 7 target 7 ]
    attachment [ interface 8 target 8 ]
  ]
]

exchange/rules/radical_abstraction_recombination_partial_macro.egml

rule [
  ruleID "radical_abstraction_recombination_partial_macro"
  note "Direct Cl radical plus methane plus methyl radical to HCl plus ethane rule generated by composeV_ after partial overlap exposure."
  extension "loops encode lone pairs; halfedges encode radicals"
  interface [
    node [ id 1 label "Cl" ]
    node [ id 2 label "C" ]
    node [ id 3 label "H" ]
    node [ id 4 label "H" ]
    node [ id 5 label "H" ]
    node [ id 6 label "H" ]
    node [ id 7 label "C" ]
    node [ id 8 label "H" ]
    node [ id 9 label "H" ]
    node [ id 10 label "H" ]
    loop [ id 1 node 1 label "lp" ]
    loop [ id 2 node 1 label "lp" ]
    loop [ id 3 node 1 label "lp" ]
    edge [ id 4 source 2 target 4 label "pair" ]
    edge [ id 5 source 2 target 5 label "pair" ]
    edge [ id 6 source 2 target 6 label "pair" ]
    edge [ id 7 source 7 target 8 label "pair" ]
    edge [ id 8 source 7 target 9 label "pair" ]
    edge [ id 9 source 7 target 10 label "pair" ]
  ]
  left [
    node [ id 1 label "Cl" ]
    node [ id 2 label "C" ]
    node [ id 3 label "H" ]
    node [ id 4 label "H" ]
    node [ id 5 label "H" ]
    node [ id 6 label "H" ]
    node [ id 7 label "C" ]
    node [ id 8 label "H" ]
    node [ id 9 label "H" ]
    node [ id 10 label "H" ]
    loop [ id 1 node 1 label "lp" ]
    loop [ id 2 node 1 label "lp" ]
    loop [ id 3 node 1 label "lp" ]
    edge [ id 4 source 2 target 4 label "pair" ]
    edge [ id 5 source 2 target 5 label "pair" ]
    edge [ id 6 source 2 target 6 label "pair" ]
    halfedge [ id 7 node 1 label "rad" ]
    edge [ id 8 source 2 target 3 label "pair" ]
    edge [ id 9 source 7 target 8 label "pair" ]
    edge [ id 10 source 7 target 9 label "pair" ]
    edge [ id 11 source 7 target 10 label "pair" ]
    halfedge [ id 12 node 7 label "rad" ]
  ]
  right [
    node [ id 1 label "Cl" ]
    node [ id 2 label "H" ]
    node [ id 3 label "C" ]
    node [ id 4 label "H" ]
    node [ id 5 label "H" ]
    node [ id 6 label "H" ]
    node [ id 7 label "C" ]
    node [ id 8 label "H" ]
    node [ id 9 label "H" ]
    node [ id 10 label "H" ]
    edge [ id 1 source 1 target 2 label "pair" ]
    loop [ id 2 node 1 label "lp" ]
    loop [ id 3 node 1 label "lp" ]
    loop [ id 4 node 1 label "lp" ]
    edge [ id 5 source 3 target 4 label "pair" ]
    edge [ id 6 source 3 target 5 label "pair" ]
    edge [ id 7 source 3 target 6 label "pair" ]
    edge [ id 8 source 7 target 8 label "pair" ]
    edge [ id 9 source 7 target 9 label "pair" ]
    edge [ id 10 source 7 target 10 label "pair" ]
    edge [ id 11 source 3 target 7 label "pair" ]
  ]
  interfaceToLeft [
    atom [ interface 1 target 1 ]
    atom [ interface 2 target 2 ]
    atom [ interface 3 target 3 ]
    atom [ interface 4 target 4 ]
    atom [ interface 5 target 5 ]
    atom [ interface 6 target 6 ]
    atom [ interface 7 target 7 ]
    atom [ interface 8 target 8 ]
    atom [ interface 9 target 9 ]
    atom [ interface 10 target 10 ]
    feature [ interface 1 target 1 ]
    feature [ interface 2 target 2 ]
    feature [ interface 3 target 3 ]
    feature [ interface 4 target 4 ]
    feature [ interface 5 target 5 ]
    feature [ interface 6 target 6 ]
    feature [ interface 7 target 9 ]
    feature [ interface 8 target 10 ]
    feature [ interface 9 target 11 ]
    attachment [ interface 1 target 1 ]
    attachment [ interface 2 target 2 ]
    attachment [ interface 3 target 3 ]
    attachment [ interface 4 target 4 ]
    attachment [ interface 5 target 5 ]
    attachment [ interface 6 target 6 ]
    attachment [ interface 7 target 7 ]
    attachment [ interface 8 target 8 ]
    attachment [ interface 9 target 9 ]
    attachment [ interface 10 target 13 ]
    attachment [ interface 11 target 14 ]
    attachment [ interface 12 target 15 ]
    attachment [ interface 13 target 16 ]
    attachment [ interface 14 target 17 ]
    attachment [ interface 15 target 18 ]
  ]
  interfaceToRight [
    atom [ interface 1 target 1 ]
    atom [ interface 2 target 3 ]
    atom [ interface 3 target 2 ]
    atom [ interface 4 target 4 ]
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    atom [ interface 6 target 6 ]
    atom [ interface 7 target 7 ]
    atom [ interface 8 target 8 ]
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    atom [ interface 10 target 10 ]
    feature [ interface 1 target 2 ]
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    feature [ interface 3 target 4 ]
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    feature [ interface 5 target 6 ]
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    attachment [ interface 1 target 3 ]
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    attachment [ interface 3 target 5 ]
    attachment [ interface 4 target 6 ]
    attachment [ interface 5 target 7 ]
    attachment [ interface 6 target 8 ]
    attachment [ interface 7 target 9 ]
    attachment [ interface 8 target 10 ]
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    attachment [ interface 10 target 12 ]
    attachment [ interface 11 target 13 ]
    attachment [ interface 12 target 14 ]
    attachment [ interface 13 target 15 ]
    attachment [ interface 14 target 16 ]
    attachment [ interface 15 target 17 ]
  ]
]

exchange/rules/radical_recombination_methyl.egml

rule [
  ruleID "radical_recombination_methyl"
  note "Consumes two methyl radical halfedges and creates one C-C shared pair."
  extension "loops encode lone pairs; halfedges encode radicals"
  interface [
    node [ id 1 label "C" ]
    node [ id 2 label "H" ]
    node [ id 3 label "H" ]
    node [ id 4 label "H" ]
    node [ id 5 label "C" ]
    node [ id 6 label "H" ]
    node [ id 7 label "H" ]
    node [ id 8 label "H" ]
    edge [ id 1 source 1 target 2 label "pair" ]
    edge [ id 2 source 1 target 3 label "pair" ]
    edge [ id 3 source 1 target 4 label "pair" ]
    edge [ id 4 source 5 target 6 label "pair" ]
    edge [ id 5 source 5 target 7 label "pair" ]
    edge [ id 6 source 5 target 8 label "pair" ]
  ]
  left [
    node [ id 1 label "C" ]
    node [ id 2 label "H" ]
    node [ id 3 label "H" ]
    node [ id 4 label "H" ]
    node [ id 5 label "C" ]
    node [ id 6 label "H" ]
    node [ id 7 label "H" ]
    node [ id 8 label "H" ]
    edge [ id 1 source 1 target 2 label "pair" ]
    edge [ id 2 source 1 target 3 label "pair" ]
    edge [ id 3 source 1 target 4 label "pair" ]
    halfedge [ id 4 node 1 label "rad" ]
    edge [ id 5 source 5 target 6 label "pair" ]
    edge [ id 6 source 5 target 7 label "pair" ]
    edge [ id 7 source 5 target 8 label "pair" ]
    halfedge [ id 8 node 5 label "rad" ]
  ]
  right [
    node [ id 1 label "C" ]
    node [ id 2 label "H" ]
    node [ id 3 label "H" ]
    node [ id 4 label "H" ]
    node [ id 5 label "C" ]
    node [ id 6 label "H" ]
    node [ id 7 label "H" ]
    node [ id 8 label "H" ]
    edge [ id 1 source 1 target 2 label "pair" ]
    edge [ id 2 source 1 target 3 label "pair" ]
    edge [ id 3 source 1 target 4 label "pair" ]
    edge [ id 4 source 5 target 6 label "pair" ]
    edge [ id 5 source 5 target 7 label "pair" ]
    edge [ id 6 source 5 target 8 label "pair" ]
    edge [ id 7 source 1 target 5 label "pair" ]
  ]
  interfaceToLeft [
    atom [ interface 1 target 1 ]
    atom [ interface 2 target 2 ]
    atom [ interface 3 target 3 ]
    atom [ interface 4 target 4 ]
    atom [ interface 5 target 5 ]
    atom [ interface 6 target 6 ]
    atom [ interface 7 target 7 ]
    atom [ interface 8 target 8 ]
    feature [ interface 1 target 1 ]
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    feature [ interface 3 target 3 ]
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    feature [ interface 5 target 6 ]
    feature [ interface 6 target 7 ]
    attachment [ interface 1 target 1 ]
    attachment [ interface 2 target 2 ]
    attachment [ interface 3 target 3 ]
    attachment [ interface 4 target 4 ]
    attachment [ interface 5 target 5 ]
    attachment [ interface 6 target 6 ]
    attachment [ interface 7 target 8 ]
    attachment [ interface 8 target 9 ]
    attachment [ interface 9 target 10 ]
    attachment [ interface 10 target 11 ]
    attachment [ interface 11 target 12 ]
    attachment [ interface 12 target 13 ]
  ]
  interfaceToRight [
    atom [ interface 1 target 1 ]
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    feature [ interface 1 target 1 ]
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    feature [ interface 6 target 6 ]
    attachment [ interface 1 target 1 ]
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    attachment [ interface 6 target 6 ]
    attachment [ interface 7 target 7 ]
    attachment [ interface 8 target 8 ]
    attachment [ interface 9 target 9 ]
    attachment [ interface 10 target 10 ]
    attachment [ interface 11 target 11 ]
    attachment [ interface 12 target 12 ]
  ]
]

exchange/rules/radical_recombination_with_hcl_context.egml

rule [
  ruleID "radical_recombination_with_hcl_context"
  note "Methyl radical recombination rule with HCl carried as identity context for partial composition."
  extension "loops encode lone pairs; halfedges encode radicals"
  interface [
    node [ id 1 label "Cl" ]
    node [ id 2 label "H" ]
    node [ id 3 label "C" ]
    node [ id 4 label "H" ]
    node [ id 5 label "H" ]
    node [ id 6 label "H" ]
    node [ id 7 label "C" ]
    node [ id 8 label "H" ]
    node [ id 9 label "H" ]
    node [ id 10 label "H" ]
    edge [ id 1 source 1 target 2 label "pair" ]
    loop [ id 2 node 1 label "lp" ]
    loop [ id 3 node 1 label "lp" ]
    loop [ id 4 node 1 label "lp" ]
    edge [ id 5 source 3 target 4 label "pair" ]
    edge [ id 6 source 3 target 5 label "pair" ]
    edge [ id 7 source 3 target 6 label "pair" ]
    edge [ id 8 source 7 target 8 label "pair" ]
    edge [ id 9 source 7 target 9 label "pair" ]
    edge [ id 10 source 7 target 10 label "pair" ]
  ]
  left [
    node [ id 1 label "Cl" ]
    node [ id 2 label "H" ]
    node [ id 3 label "C" ]
    node [ id 4 label "H" ]
    node [ id 5 label "H" ]
    node [ id 6 label "H" ]
    node [ id 7 label "C" ]
    node [ id 8 label "H" ]
    node [ id 9 label "H" ]
    node [ id 10 label "H" ]
    edge [ id 1 source 1 target 2 label "pair" ]
    loop [ id 2 node 1 label "lp" ]
    loop [ id 3 node 1 label "lp" ]
    loop [ id 4 node 1 label "lp" ]
    edge [ id 5 source 3 target 4 label "pair" ]
    edge [ id 6 source 3 target 5 label "pair" ]
    edge [ id 7 source 3 target 6 label "pair" ]
    halfedge [ id 8 node 3 label "rad" ]
    edge [ id 9 source 7 target 8 label "pair" ]
    edge [ id 10 source 7 target 9 label "pair" ]
    edge [ id 11 source 7 target 10 label "pair" ]
    halfedge [ id 12 node 7 label "rad" ]
  ]
  right [
    node [ id 1 label "Cl" ]
    node [ id 2 label "H" ]
    node [ id 3 label "C" ]
    node [ id 4 label "H" ]
    node [ id 5 label "H" ]
    node [ id 6 label "H" ]
    node [ id 7 label "C" ]
    node [ id 8 label "H" ]
    node [ id 9 label "H" ]
    node [ id 10 label "H" ]
    edge [ id 1 source 1 target 2 label "pair" ]
    loop [ id 2 node 1 label "lp" ]
    loop [ id 3 node 1 label "lp" ]
    loop [ id 4 node 1 label "lp" ]
    edge [ id 5 source 3 target 4 label "pair" ]
    edge [ id 6 source 3 target 5 label "pair" ]
    edge [ id 7 source 3 target 6 label "pair" ]
    edge [ id 8 source 7 target 8 label "pair" ]
    edge [ id 9 source 7 target 9 label "pair" ]
    edge [ id 10 source 7 target 10 label "pair" ]
    edge [ id 11 source 3 target 7 label "pair" ]
  ]
  interfaceToLeft [
    atom [ interface 1 target 1 ]
    atom [ interface 2 target 2 ]
    atom [ interface 3 target 3 ]
    atom [ interface 4 target 4 ]
    atom [ interface 5 target 5 ]
    atom [ interface 6 target 6 ]
    atom [ interface 7 target 7 ]
    atom [ interface 8 target 8 ]
    atom [ interface 9 target 9 ]
    atom [ interface 10 target 10 ]
    feature [ interface 1 target 1 ]
    feature [ interface 2 target 2 ]
    feature [ interface 3 target 3 ]
    feature [ interface 4 target 4 ]
    feature [ interface 5 target 5 ]
    feature [ interface 6 target 6 ]
    feature [ interface 7 target 7 ]
    feature [ interface 8 target 9 ]
    feature [ interface 9 target 10 ]
    feature [ interface 10 target 11 ]
    attachment [ interface 1 target 1 ]
    attachment [ interface 2 target 2 ]
    attachment [ interface 3 target 3 ]
    attachment [ interface 4 target 4 ]
    attachment [ interface 5 target 5 ]
    attachment [ interface 6 target 6 ]
    attachment [ interface 7 target 7 ]
    attachment [ interface 8 target 8 ]
    attachment [ interface 9 target 9 ]
    attachment [ interface 10 target 10 ]
    attachment [ interface 11 target 11 ]
    attachment [ interface 12 target 13 ]
    attachment [ interface 13 target 14 ]
    attachment [ interface 14 target 15 ]
    attachment [ interface 15 target 16 ]
    attachment [ interface 16 target 17 ]
    attachment [ interface 17 target 18 ]
  ]
  interfaceToRight [
    atom [ interface 1 target 1 ]
    atom [ interface 2 target 2 ]
    atom [ interface 3 target 3 ]
    atom [ interface 4 target 4 ]
    atom [ interface 5 target 5 ]
    atom [ interface 6 target 6 ]
    atom [ interface 7 target 7 ]
    atom [ interface 8 target 8 ]
    atom [ interface 9 target 9 ]
    atom [ interface 10 target 10 ]
    feature [ interface 1 target 1 ]
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    feature [ interface 3 target 3 ]
    feature [ interface 4 target 4 ]
    feature [ interface 5 target 5 ]
    feature [ interface 6 target 6 ]
    feature [ interface 7 target 7 ]
    feature [ interface 8 target 8 ]
    feature [ interface 9 target 9 ]
    feature [ interface 10 target 10 ]
    attachment [ interface 1 target 1 ]
    attachment [ interface 2 target 2 ]
    attachment [ interface 3 target 3 ]
    attachment [ interface 4 target 4 ]
    attachment [ interface 5 target 5 ]
    attachment [ interface 6 target 6 ]
    attachment [ interface 7 target 7 ]
    attachment [ interface 8 target 8 ]
    attachment [ interface 9 target 9 ]
    attachment [ interface 10 target 10 ]
    attachment [ interface 11 target 11 ]
    attachment [ interface 12 target 12 ]
    attachment [ interface 13 target 13 ]
    attachment [ interface 14 target 14 ]
    attachment [ interface 15 target 15 ]
    attachment [ interface 16 target 16 ]
    attachment [ interface 17 target 17 ]
  ]
]

Applications

exchange/applications/diazomethane_azo_esterification_macro_on_substrate.egml

application [
  applicationID "diazomethane_azo_esterification_macro_on_substrate"
  ruleID "diazomethane_azo_esterification_macro"
  hostGraph "diazomethane_azo_esterification_host"
  resultGraph "diazomethane_after_methyl_transfer"
  note "This direct exact-resonance application reaches the ester product from the H2C=N+=N- substrate form in one composed macro step."
  match [
    atom [ rule 1 host 1 ]
    atom [ rule 2 host 2 ]
    atom [ rule 3 host 3 ]
    atom [ rule 4 host 12 ]
    atom [ rule 5 host 13 ]
    feature [ rule 1 host 1 ]
    feature [ rule 2 host 3 ]
    feature [ rule 3 host 4 ]
    feature [ rule 4 host 7 ]
    feature [ rule 5 host 2 ]
    feature [ rule 6 host 8 ]
    feature [ rule 7 host 16 ]
  ]
  deleted [
    item "pair(C_diazomethane,N_inner)"
    item "pair(C_diazomethane,N_inner)"
    item "lp(N_outer)"
    item "pair(O_acid,H_acid)"
  ]
  created [
    item "pair(N_inner,N_outer)"
    item "pair(C_diazomethane,H_acid)"
    item "pair(O_acid,C_diazomethane)"
    item "lp(N_inner)"
  ]
]

exchange/applications/diazomethane_azo_proton_transfer_on_acid.egml

application [
  applicationID "diazomethane_azo_proton_transfer_on_acid"
  ruleID "diazomethane_azo_proton_transfer"
  hostGraph "diazomethane_azo_esterification_host"
  resultGraph "diazomethane_azo_after_proton_transfer"
  note "This application follows the explicit [N-]=[N+]=C resonance form requested in the mechanism sketch."
  match [
    atom [ rule 1 host 1 ]
    atom [ rule 2 host 2 ]
    atom [ rule 3 host 3 ]
    atom [ rule 4 host 12 ]
    atom [ rule 5 host 13 ]
    feature [ rule 1 host 1 ]
    feature [ rule 2 host 3 ]
    feature [ rule 3 host 4 ]
    feature [ rule 4 host 7 ]
    feature [ rule 5 host 2 ]
    feature [ rule 6 host 8 ]
    feature [ rule 7 host 16 ]
  ]
  deleted [
    item "pair(C_diazomethane,N_inner)"
    item "lp(N_outer)"
    item "pair(O_acid,H_acid)"
  ]
  created [
    item "pair(N_inner,N_outer)"
    item "lp(O_carboxylate)"
    item "pair(C_diazomethane,H_acid)"
  ]
]

exchange/applications/diazomethane_esterification_macro_on_substrate.egml

application [
  applicationID "diazomethane_esterification_macro_on_substrate"
  ruleID "diazomethane_esterification_macro"
  hostGraph "diazomethane_esterification_host"
  resultGraph "diazomethane_after_methyl_transfer"
  note "This direct application reaches the ester product from the substrate in one macro step."
  match [
    atom [ rule 1 host 1 ]
    atom [ rule 2 host 2 ]
    atom [ rule 3 host 3 ]
    atom [ rule 4 host 12 ]
    atom [ rule 5 host 13 ]
    feature [ rule 1 host 1 ]
    feature [ rule 2 host 2 ]
    feature [ rule 3 host 3 ]
    feature [ rule 4 host 4 ]
    feature [ rule 5 host 7 ]
    feature [ rule 6 host 16 ]
  ]
  deleted [
    item "lp(C_diazomethane)"
    item "pair(O_acid,H_acid)"
    item "pair(C_methyl,N_inner)"
  ]
  created [
    item "pair(C_diazomethane,H_acid)"
    item "pair(O_acid,C_diazomethane)"
    item "lp(N_inner)"
  ]
]

exchange/applications/diazomethane_methyl_transfer_on_ion_pair.egml

application [
  applicationID "diazomethane_methyl_transfer_on_ion_pair"
  ruleID "diazomethane_methyl_transfer"
  hostGraph "diazomethane_after_proton_transfer"
  resultGraph "diazomethane_after_methyl_transfer"
  note "This second application reaches the ester product and neutral N2 from the ion-pair intermediate."
  match [
    atom [ rule 1 host 4 ]
    atom [ rule 2 host 1 ]
    atom [ rule 3 host 2 ]
    atom [ rule 4 host 3 ]
    feature [ rule 1 host 2 ]
    feature [ rule 2 host 3 ]
    feature [ rule 3 host 4 ]
    feature [ rule 4 host 5 ]
    feature [ rule 5 host 1 ]
  ]
  deleted [
    item "lp(O_carboxylate)"
    item "pair(C_methyl,N_inner)"
  ]
  created [
    item "pair(O_carboxylate,C_methyl)"
    item "lp(N_inner)"
  ]
]

exchange/applications/diazomethane_proton_transfer_on_acid.egml

application [
  applicationID "diazomethane_proton_transfer_on_acid"
  ruleID "diazomethane_proton_transfer"
  hostGraph "diazomethane_esterification_host"
  resultGraph "diazomethane_after_proton_transfer"
  note "This is the first application from the substrate graph."
  match [
    atom [ rule 1 host 1 ]
    atom [ rule 2 host 2 ]
    atom [ rule 3 host 3 ]
    atom [ rule 4 host 12 ]
    atom [ rule 5 host 13 ]
    feature [ rule 1 host 1 ]
    feature [ rule 2 host 2 ]
    feature [ rule 3 host 3 ]
    feature [ rule 4 host 4 ]
    feature [ rule 5 host 7 ]
    feature [ rule 6 host 16 ]
  ]
  deleted [
    item "lp(C_diazomethane)"
    item "pair(O_acid,H_acid)"
  ]
  created [
    item "lp(O_carboxylate)"
    item "pair(C_diazomethane,H_acid)"
  ]
]

exchange/applications/radical_abstraction_recombination_partial_macro_on_host.egml

application [
  applicationID "radical_abstraction_recombination_partial_macro_on_host"
  ruleID "radical_abstraction_recombination_partial_macro"
  hostGraph "radical_chain_host"
  resultGraph "radical_chain_product"
  note "This direct application maps Cl radical plus methane plus methyl radical to HCl plus ethane."
  match [
    atom [ rule 1 host 1 ]
    atom [ rule 2 host 2 ]
    atom [ rule 3 host 3 ]
    atom [ rule 4 host 4 ]
    atom [ rule 5 host 5 ]
    atom [ rule 6 host 6 ]
    atom [ rule 7 host 7 ]
    atom [ rule 8 host 8 ]
    atom [ rule 9 host 9 ]
    atom [ rule 10 host 10 ]
    feature [ rule 1 host 1 ]
    feature [ rule 2 host 2 ]
    feature [ rule 3 host 3 ]
    feature [ rule 4 host 6 ]
    feature [ rule 5 host 7 ]
    feature [ rule 6 host 8 ]
    feature [ rule 7 host 4 ]
    feature [ rule 8 host 5 ]
    feature [ rule 9 host 9 ]
    feature [ rule 10 host 10 ]
    feature [ rule 11 host 11 ]
    feature [ rule 12 host 12 ]
  ]
  deleted [
    item "rad(Cl)"
    item "pair(C_methane,H_abstracted)"
    item "rad(C_external_methyl)"
  ]
  created [
    item "pair(Cl,H_abstracted)"
    item "pair(C_methane,C_external_methyl)"
  ]
]

Compositions

exchange/compositions/diazomethane_azo_esterification_composeV.egml

composition [
  compositionID "diazomethane_azo_esterification_composeV"
  kind "vertical DPO rule composition"
  operation "AlgebraicRewriting.composeV_"
  firstRule "diazomethane_azo_proton_transfer"
  secondRule "diazomethane_methyl_transfer_after_azo_context"
  resultRule "diazomethane_azo_esterification_macro"
  intermediateCondition "right(firstRule) equals left(secondRule) after exposing preserved C-H and terminal-N lone-pair context"
  note "This is the exact resonance-form variant: R(firstRule) is exposed as L(secondRule), then the two open DPO rules are composed categorically."
]

exchange/compositions/diazomethane_esterification_composeV.egml

composition [
  compositionID "diazomethane_esterification_composeV"
  kind "vertical DPO rule composition"
  operation "AlgebraicRewriting.composeV_"
  firstRule "diazomethane_proton_transfer"
  secondRule "diazomethane_methyl_transfer_after_proton_context"
  resultRule "diazomethane_esterification_macro"
  intermediateCondition "right(firstRule) equals left(secondRule) after exposing preserved C-H context"
  note "This is a real categorical composition of open DPO rules, then projected back to a closed DPO rule for application to the substrate."
]

exchange/compositions/radical_abstraction_recombination_partial_composeV.egml

composition [
  compositionID "radical_abstraction_recombination_partial_composeV"
  kind "vertical DPO rule composition"
  operation "AlgebraicRewriting.composeV_"
  firstRule "chlorine_h_abstraction_with_external_methyl"
  secondRule "radical_recombination_with_hcl_context"
  resultRule "radical_abstraction_recombination_partial_macro"
  intermediateCondition "right(firstRule) equals left(secondRule) after adding identity contexts; original-rule overlap is only the produced methyl radical"
  note "This records the partial DPO composition: chlorine abstraction creates one methyl radical, which is identified with one radical input of recombination; HCl and the external methyl radical are carried as contexts."
]

Rules

Rule Composition

Partial DPO Composition Detail

Original rules before adding identity context

Partial overlap

Context-complete open-rule inputs passed to composeV_

Composed macro rule

Partial radical-chain DPO composition

RDKit molecule quick view

Formal electron-feature DPO view

Chemical/DOT companion view

RDKit host/product views

Diazomethane composed macro DPO

RDKit molecule quick view

Formal electron-feature DPO view

Chemical/DOT companion view

RDKit host/product views

Diazomethane exact-azo composed macro DPO

RDKit molecule quick view

Formal electron-feature DPO view

Chemical/DOT companion view

RDKit host/product views

Specific Chemical Examples

Cyclopropanation DPO

RDKit molecule quick view

Formal electron-feature DPO view

Chemical/DOT companion view

RDKit host/product views

Diazomethane proton-transfer DPO

RDKit molecule quick view

Formal electron-feature DPO view

Chemical/DOT companion view

RDKit host/product views

Diazomethane azo-form proton-transfer DPO

RDKit molecule quick view

Formal electron-feature DPO view

Chemical/DOT companion view

RDKit host/product views

Diazomethane methyl-transfer DPO

RDKit molecule quick view

Formal electron-feature DPO view

Chemical/DOT companion view

RDKit host/product views

Molecules And States

Diazomethane Pathway

Diazomethane plus acid

After diazomethane proton transfer

After diazomethane methyl transfer

Exact azo-form diazomethane plus acid

Radicals And Carbenes

Methylene singlet

Methylene triplet from rule

Chlorine radical plus methane

HCl plus methyl radical

Chlorine radical plus methane plus methyl radical

Radical chain after H abstraction

HCl plus ethane

Allyl radical start

Methyl radical pair

Ethane from radical recombination

Reference And Verification States

Formose host start

Formose after keto-enol step

Formose after aldol step

Hydronium/hydroxide ion pair

Two waters after neutralization

Other Molecule States

Allyl radical shifted

Generated Exchange Files

Raw EGML Appendix

Graphs

Rules

Applications

Compositions

Context-complete open-rule inputs passed to `composeV_`