diff --git a/tests/common/mod.rs b/tests/common/mod.rs
new file mode 100644
index 0000000..7e86dc2
--- /dev/null
+++ b/tests/common/mod.rs
@@ -0,0 +1,28 @@
+pub use rulett::{
+    model::{Model, ModelDecl},
+    netgen::NetGenerator,
+    ob_tm::ObTm,
+    surface,
+    theory::{Signature, SignatureDecl},
+    ty::Ty,
+};
+
+pub use expect_test::expect;
+
+/// Merges multiple signatures.
+pub fn merge_signatures(sigs: &[Signature]) -> Signature {
+    let mut merged = Signature::new();
+    for sig in sigs {
+        for sort in sig.sorts() {
+            if !merged.sorts().any(|s| s == sort) {
+                merged.add_sort(sort).unwrap();
+            }
+        }
+        for (op, dom, cod) in sig.operations() {
+            if merged.interface(&op).is_none() {
+                merged.add_operation(op, dom.clone(), cod.clone()).unwrap();
+            }
+        }
+    }
+    merged
+}
diff --git a/tests/emergent-sites.rs b/tests/emergent-sites.rs
new file mode 100644
index 0000000..ed5c354
--- /dev/null
+++ b/tests/emergent-sites.rs
@@ -0,0 +1,484 @@
+//! https://q.uiver.app/#q=WzAsMTEsWzEsMCwiVHlNb25vbWVyIl0sWzEsMSwiTnQgXFxvdGltZXMgUiBcXG90aW1lcyBDdCJdLFswLDQsIlJfMSJdLFsyLDQsIlJfMiJdLFsxLDMsIlIiXSxbMiwwLCJDdCBcXG90aW1lcyBOdCJdLFsyLDEsIkNOIl0sWzEsNywiU2l0ZVJfMVJfMSJdLFsxLDYsIlJfMSBcXG90aW1lcyBDTiBcXG90aW1lcyBSXzIiXSxbNCw2LCJTaXRlUl8xUl8xIFxcb3RpbWVzIFNpdGVDIl0sWzQsNywiSSJdLFsxLDAsIlxcaW90YV97YW1pbm9hY2lkfSIsMV0sWzIsNCwiXFxpb3RhX3tSXzF9IiwxXSxbMyw0LCJcXGlvdGFfe1JfMn0iLDFdLFs2LDUsImJvbmRfe3BlcHRpZGV9IiwxXSxbNyw4LCJcXGlvdGFfe1NpdGVSXzFSXzF9IiwxXSxbMTAsOSwiYm9uZCIsMV1d
+
+mod common;
+use common::*;
+use rulett::prelude::name;
+
+/// Base signature.
+fn base_signature() -> Signature {
+    Signature::parse([
+        // Sorts
+        SignatureDecl::sort("TyMonomer"),
+        SignatureDecl::sort("Nt"), // Think "Head"
+        SignatureDecl::sort("Ct"), // Think "Tail"
+        SignatureDecl::sort("R"),  // Think "some amino acid residue"
+        SignatureDecl::sort("R1"),
+        SignatureDecl::sort("R2"),
+        SignatureDecl::sort("CN"),
+        SignatureDecl::sort("SiteR1R1"),
+        SignatureDecl::sort("SiteNotR1R1"),
+        SignatureDecl::sort("SiteC"),
+        // Operations
+        SignatureDecl::operation(
+            "i_aminoacid",
+            [Ty::sort("Nt"), Ty::sort("R"), Ty::sort("Ct")],
+            Ty::sort("TyMonomer"),
+        ),
+        SignatureDecl::operation("i_R1", [Ty::sort("R1")], Ty::sort("R")),
+        SignatureDecl::operation("i_R2", [Ty::sort("R2")], Ty::sort("R")),
+        SignatureDecl::operation(
+            // think "CN bond"
+            "bond_peptide",
+            [Ty::sort("CN")],
+            Ty::tensor([Ty::sort("Ct"), Ty::sort("Nt")]),
+        ),
+        SignatureDecl::operation(
+            "i_SiteR1R1",
+            [Ty::sort("SiteR1R1")],
+            Ty::tensor([Ty::sort("R1"), Ty::sort("CN"), Ty::sort("R1")]),
+        ),
+        // SignatureDecl::operation(
+        // "i_SiteNotR1R1_1",
+        // Ty::sort("SiteNotR1R1"),
+        // Ty::tensor([Ty::sort("SiteR1"), Ty::sort("CN"), Ty::sort("SiteR2")]),
+        // ),
+        // SignatureDecl::operation(
+        // "i_SiteNotR1R1_2",
+        // Ty::sort("SiteNotR1R1"),
+        // Ty::tensor([Ty::sort("SiteR2"), Ty::sort("CN"), Ty::sort("SiteR1")]),
+        // ),
+        // SignatureDecl::operation(
+        // "i_SiteNotR1R1_3",
+        // Ty::sort("SiteNotR1R1"),
+        // Ty::tensor([Ty::sort("SiteR2"), Ty::sort("CN"), Ty::sort("SiteR2")]),
+        // ),
+    ])
+    .unwrap()
+}
+
+/// Grounding signature.
+fn grounding_signature() -> Signature {
+    Signature::parse([
+        // Sorts
+        SignatureDecl::sort("Nt"), // Think "Head"
+        SignatureDecl::sort("Ct"), // Think "Tail"
+        SignatureDecl::sort("SiteR1R1"),
+        SignatureDecl::sort("SiteNotR1R1"),
+        SignatureDecl::sort("SiteC"),
+        // Operations
+        SignatureDecl::operation("e_N", [], Ty::sort("Nt")),
+        SignatureDecl::operation("e_C", [], Ty::sort("Ct")),
+        SignatureDecl::operation("e_SiteR1R1", [], Ty::sort("SiteR1R1")),
+        SignatureDecl::operation("e_SiteNotR1R1", [], Ty::sort("SiteNotR1R1")),
+        SignatureDecl::operation("e_SiteC", [], Ty::sort("SiteC")),
+        SignatureDecl::operation(
+            // SiteR1R1 is an emergent site that can bind to SiteC
+            "bond",
+            [],
+            Ty::tensor([Ty::sort("SiteR1R1"), Ty::sort("SiteC")]),
+        ),
+    ])
+    .unwrap()
+}
+
+/// Full signature.
+fn signature() -> Signature {
+    let sig1 = base_signature();
+    let sig2 = grounding_signature();
+    merge_signatures(&[sig1, sig2])
+}
+
+// Declares Model.
+fn model_decl() -> [ModelDecl; 4] {
+    use crate::surface::*;
+    let polymer = PatTm::let_(
+        [ObTm::var("s1"), ObTm::var("s2")],
+        MorTm::app("bond_peptide", [MorTm::var("cn")]),
+        PatTm::tensor([
+            PatTm::res(
+                "M",
+                [MorTm::app("i_aminoacid", [MorTm::var("n"), MorTm::var("r"), MorTm::var("s1")])],
+            ),
+            PatTm::res(
+                "M",
+                [MorTm::app("i_aminoacid", [MorTm::var("s2"), MorTm::var("r'"), MorTm::var("c")])],
+            ),
+        ]),
+    );
+    let dimer = PatTm::let_(
+        [ObTm::var("cn"), ObTm::var("s4")],
+        MorTm::app("bond", []),
+        PatTm::tensor([polymer.clone(), PatTm::res("C", [MorTm::var("s4")])]),
+    );
+    [
+        ModelDecl::agent("M", [ObTm::var("m")], [Ty::sort("TyMonomer")]),
+        ModelDecl::agent("C", [ObTm::var("c")], [Ty::sort("SiteC")]),
+        // TODO: perhaps we could add a field `dep` to rules for dependencies that occur on both lhs and rhs?
+        ModelDecl::rule(
+            "polymerization",
+            [ObTm::var("c"), ObTm::var("r"), ObTm::var("r'"), ObTm::var("n"), ObTm::var("cn")],
+            [Ty::sort("Ct"), Ty::sort("R"), Ty::sort("R"), Ty::sort("Nt"), Ty::sort("CN")],
+            PatTm::tensor([
+                PatTm::res(
+                    "M",
+                    [MorTm::app(
+                        "i_aminoacid",
+                        [MorTm::var("n"), MorTm::var("r"), MorTm::app("e_C", [])],
+                    )],
+                ),
+                PatTm::res(
+                    "M",
+                    [MorTm::app(
+                        "i_aminoacid",
+                        [MorTm::app("e_N", []), MorTm::var("r"), MorTm::var("c")],
+                    )],
+                ),
+            ]),
+            polymer.clone(),
+        ), // Note that `polymer` contains the emergent site SiteR1R1
+        ModelDecl::rule(
+            "dimerization",
+            [ObTm::var("n"), ObTm::var("c")],
+            [Ty::sort("Nt"), Ty::sort("Ct")],
+            PatTm::tensor([
+                polymer.subst(&mut vec![(name("cn"), MorTm::app("e_SiteR1R1", []))]),
+                PatTm::res("C", [MorTm::app("e_SiteC", [])]),
+            ]),
+            dimer,
+        ),
+    ]
+}
+
+// Generates Model.
+fn model() -> Model {
+    let decls = model_decl();
+    Model::parse(signature(), decls).unwrap()
+}
+
+#[test]
+fn parse_signature() {
+    let expected = expect![[r#"
+        #/ sorts:
+        TyMonomer
+        Nt
+        Ct
+        R
+        R1
+        R2
+        CN
+        SiteR1R1
+        SiteNotR1R1
+        SiteC
+        #/ operations:
+        i_aminoacid : [Nt, R, Ct] → TyMonomer
+        i_R1 : [R1] → R
+        i_R2 : [R2] → R
+        bond_peptide : [CN] → ⊗ [Ct, Nt]
+        i_SiteR1R1 : [SiteR1R1] → ⊗ [R1, CN, R1]
+        e_N : [] → Nt
+        e_C : [] → Ct
+        e_SiteR1R1 : [] → SiteR1R1
+        e_SitenotR1R1 : [] → SiteNotR1R1
+        e_SiteC : [] → SiteC
+        bond : [] → ⊗ [SiteR1R1, SiteC]
+    "#]];
+    expected.assert_eq(&signature().to_string());
+}
+
+#[test]
+fn parse_model() {
+    let expected = expect![[r#"
+        #/ sorts:
+        TyMonomer
+        Nt
+        Ct
+        R
+        R1
+        R2
+        CN
+        SiteR1R1
+        SiteNotR1R1
+        SiteC
+        #/ operations:
+        i_aminoacid : [Nt, R, Ct] → TyMonomer
+        i_R1 : [R1] → R
+        i_R2 : [R2] → R
+        bond_peptide : [CN] → ⊗ [Ct, Nt]
+        i_SiteR1R1 : [SiteR1R1] → ⊗ [R1, CN, R1]
+        e_N : [] → Nt
+        e_C : [] → Ct
+        e_SiteR1R1 : [] → SiteR1R1
+        e_SitenotR1R1 : [] → SiteNotR1R1
+        e_SiteC : [] → SiteC
+        bond : [] → ⊗ [SiteR1R1, SiteC]
+        #/ agents:
+        [m] : [TyMonomer] ⊢ M [m]
+        [c] : [SiteC] ⊢ C [c]
+        #/ rules:
+        [c, r, r', n, cn] : [Ct, R, R, Nt, CN] ⊢
+          polymerization [c, r, r', n, cn]
+            : (M [i_aminoacid [n, r, e_C []]], M [i_aminoacid [e_N [], r, c]])
+            → let bond_peptide [cn] in
+              (M [i_aminoacid [n, r, 0.0]], M [i_aminoacid [0.1, r', c]])
+        [n, c] : [Nt, Ct] ⊢
+          dimerization [n, c]
+            : (
+              let bond_peptide [e_SiteR1R1 []] in
+                (M [i_aminoacid [n, r, 0.0]], M [i_aminoacid [0.1, r', c]]),
+              C [e_SiteC []]
+            )
+            → let bond [] in
+              (
+                let bond_peptide [0.0] in
+                  (M [i_aminoacid [n, r, 0.0]], M [i_aminoacid [0.1, r', c]]),
+                C [0.1]
+              )
+    "#]];
+    expected.assert_eq(&model().to_string());
+}
+
+// Test that four dimerization and one polymerization reaction are created
+#[test]
+fn generate_network() {
+    use itertools::Itertools;
+    let model = model();
+    let generator = NetGenerator::new(&model);
+
+    let species = expect![[r#"
+        C [e_SiteC []]
+        let i_SiteR1R1 [e_SiteR1R1 []] in
+          let bond_peptide [0.1] in
+            (
+              M [i_aminoacid [e_N [], i_R1 [1.0], e_C []]],
+              M [i_aminoacid [0.1, i_R1 [1.2], 0.0]]
+            )
+        let i_SiteR1R1 [e_SiteR1R1 []] in
+          let bond_peptide [0.1] in
+            (
+              M [i_aminoacid [e_N [], i_R1 [1.0], 0.0]],
+              M [i_aminoacid [0.1, i_R1 [1.2], e_C []]]
+            )
+        let i_SiteR1R1 [e_SiteR1R1 []] in
+          let bond_peptide [0.1] in
+            (
+              M [i_aminoacid [0.1, i_R1 [1.0], e_C []]],
+              M [i_aminoacid [e_N [], i_R1 [1.2], 0.0]]
+            )
+        let i_SiteR1R1 [e_SiteR1R1 []] in
+          let bond_peptide [0.1] in
+            (
+              M [i_aminoacid [0.1, i_R1 [1.0], 0.0]],
+              M [i_aminoacid [e_N [], i_R1 [1.2], e_C []]]
+            )"#]];
+    species.assert_eq(&generator.species(2).join("\n"));
+
+    let transitions = expect![[r#"
+        let i_SiteR1R1 [e_SiteR1R1 []] in
+            polymerization [e_C [], i_R1 [0.0], i_R1 [0.2], e_N [], 0.1]
+          : let i_SiteR1R1 [e_SiteR1R1 []] in
+            (
+              M [i_aminoacid [e_N [], i_R1 [0.0], e_C []]],
+              M [i_aminoacid [e_N [], i_R1 [0.0], e_C []]]
+            )
+          → let i_SiteR1R1 [e_SiteR1R1 []] in
+            let bond_peptide [0.1] in
+              (
+                M [i_aminoacid [e_N [], i_R1 [1.0], 0.0]],
+                M [i_aminoacid [0.1, i_R1 [1.2], e_C []]]
+              )
+        dimerization [e_N [], e_C []]
+          : (
+            let bond_peptide [e_SiteR1R1 []] in
+              (M [i_aminoacid [e_N [], r, 0.0]], M [i_aminoacid [0.1, r', e_C []]]),
+            C [e_SiteC []]
+          )
+          → let bond [] in
+            (
+              let bond_peptide [0.0] in
+                (M [i_aminoacid [e_N [], r, 0.0]], M [i_aminoacid [0.1, r', e_C []]]),
+              C [0.1]
+            )
+        let bond [] in
+            let i_SiteR1R1 [0.0] in
+              (C [1.1], polymerization [e_C [], i_R1 [0.0], i_R1 [0.2], e_N [], 0.1])
+          : let bond [] in
+            let i_SiteR1R1 [0.0] in
+              (
+                C [1.1],
+                (
+                  M [i_aminoacid [e_N [], i_R1 [0.0], e_C []]],
+                  M [i_aminoacid [e_N [], i_R1 [0.0], e_C []]]
+                )
+              )
+          → let bond [] in
+            let i_SiteR1R1 [0.0] in
+              (
+                C [1.1],
+                let bond_peptide [0.1] in
+                  (
+                    M [i_aminoacid [e_N [], i_R1 [1.0], 0.0]],
+                    M [i_aminoacid [0.1, i_R1 [1.2], e_C []]]
+                  )
+              )
+        let i_SiteR1R1 [e_SiteR1R1 []] in
+            let i_SiteR1R1 [e_SiteR1R1 []] in
+              (
+                polymerization [e_C [], i_R1 [0.0], i_R1 [1.0], e_N [], 0.1],
+                polymerization [e_C [], i_R1 [0.2], i_R1 [1.2], e_N [], 1.1]
+              )
+          : let i_SiteR1R1 [e_SiteR1R1 []] in
+            let i_SiteR1R1 [e_SiteR1R1 []] in
+              (
+                (
+                  M [i_aminoacid [e_N [], i_R1 [0.0], e_C []]],
+                  M [i_aminoacid [e_N [], i_R1 [0.0], e_C []]]
+                ),
+                (
+                  M [i_aminoacid [e_N [], i_R1 [0.2], e_C []]],
+                  M [i_aminoacid [e_N [], i_R1 [0.2], e_C []]]
+                )
+              )
+          → let i_SiteR1R1 [e_SiteR1R1 []] in
+            let i_SiteR1R1 [e_SiteR1R1 []] in
+              (
+                let bond_peptide [0.1] in
+                  (
+                    M [i_aminoacid [e_N [], i_R1 [1.0], 0.0]],
+                    M [i_aminoacid [0.1, i_R1 [2.0], e_C []]]
+                  ),
+                let bond_peptide [1.1] in
+                  (
+                    M [i_aminoacid [e_N [], i_R1 [1.2], 0.0]],
+                    M [i_aminoacid [0.1, i_R1 [2.2], e_C []]]
+                  )
+              )
+        let i_SiteR1R1 [e_SiteR1R1 []] in
+            let i_SiteR1R1 [e_SiteR1R1 []] in
+              (
+                polymerization [e_C [], i_R1 [1.0], i_R1 [0.0], e_N [], 0.1],
+                polymerization [e_C [], i_R1 [0.2], i_R1 [1.2], e_N [], 1.1]
+              )
+          : let i_SiteR1R1 [e_SiteR1R1 []] in
+            let i_SiteR1R1 [e_SiteR1R1 []] in
+              (
+                (
+                  M [i_aminoacid [e_N [], i_R1 [1.0], e_C []]],
+                  M [i_aminoacid [e_N [], i_R1 [1.0], e_C []]]
+                ),
+                (
+                  M [i_aminoacid [e_N [], i_R1 [0.2], e_C []]],
+                  M [i_aminoacid [e_N [], i_R1 [0.2], e_C []]]
+                )
+              )
+          → let i_SiteR1R1 [e_SiteR1R1 []] in
+            let i_SiteR1R1 [e_SiteR1R1 []] in
+              (
+                let bond_peptide [0.1] in
+                  (
+                    M [i_aminoacid [e_N [], i_R1 [2.0], 0.0]],
+                    M [i_aminoacid [0.1, i_R1 [1.0], e_C []]]
+                  ),
+                let bond_peptide [1.1] in
+                  (
+                    M [i_aminoacid [e_N [], i_R1 [1.2], 0.0]],
+                    M [i_aminoacid [0.1, i_R1 [2.2], e_C []]]
+                  )
+              )
+        let i_SiteR1R1 [e_SiteR1R1 []] in
+            let i_SiteR1R1 [e_SiteR1R1 []] in
+              (
+                polymerization [e_C [], i_R1 [0.0], i_R1 [0.2], e_N [], 1.1],
+                polymerization [e_C [], i_R1 [1.0], i_R1 [1.2], e_N [], 0.1]
+              )
+          : let i_SiteR1R1 [e_SiteR1R1 []] in
+            let i_SiteR1R1 [e_SiteR1R1 []] in
+              (
+                (
+                  M [i_aminoacid [e_N [], i_R1 [0.0], e_C []]],
+                  M [i_aminoacid [e_N [], i_R1 [0.0], e_C []]]
+                ),
+                (
+                  M [i_aminoacid [e_N [], i_R1 [1.0], e_C []]],
+                  M [i_aminoacid [e_N [], i_R1 [1.0], e_C []]]
+                )
+              )
+          → let i_SiteR1R1 [e_SiteR1R1 []] in
+            let i_SiteR1R1 [e_SiteR1R1 []] in
+              (
+                let bond_peptide [1.1] in
+                  (
+                    M [i_aminoacid [e_N [], i_R1 [1.0], 0.0]],
+                    M [i_aminoacid [0.1, i_R1 [1.2], e_C []]]
+                  ),
+                let bond_peptide [0.1] in
+                  (
+                    M [i_aminoacid [e_N [], i_R1 [2.0], 0.0]],
+                    M [i_aminoacid [0.1, i_R1 [2.2], e_C []]]
+                  )
+              )
+        let i_SiteR1R1 [e_SiteR1R1 []] in
+            let i_SiteR1R1 [e_SiteR1R1 []] in
+              (
+                polymerization [e_C [], i_R1 [0.0], i_R1 [1.0], e_N [], 1.1],
+                polymerization [e_C [], i_R1 [0.2], i_R1 [1.2], e_N [], 0.1]
+              )
+          : let i_SiteR1R1 [e_SiteR1R1 []] in
+            let i_SiteR1R1 [e_SiteR1R1 []] in
+              (
+                (
+                  M [i_aminoacid [e_N [], i_R1 [0.0], e_C []]],
+                  M [i_aminoacid [e_N [], i_R1 [0.0], e_C []]]
+                ),
+                (
+                  M [i_aminoacid [e_N [], i_R1 [0.2], e_C []]],
+                  M [i_aminoacid [e_N [], i_R1 [0.2], e_C []]]
+                )
+              )
+          → let i_SiteR1R1 [e_SiteR1R1 []] in
+            let i_SiteR1R1 [e_SiteR1R1 []] in
+              (
+                let bond_peptide [1.1] in
+                  (
+                    M [i_aminoacid [e_N [], i_R1 [1.0], 0.0]],
+                    M [i_aminoacid [0.1, i_R1 [2.0], e_C []]]
+                  ),
+                let bond_peptide [0.1] in
+                  (
+                    M [i_aminoacid [e_N [], i_R1 [1.2], 0.0]],
+                    M [i_aminoacid [0.1, i_R1 [2.2], e_C []]]
+                  )
+              )
+        let i_SiteR1R1 [e_SiteR1R1 []] in
+            let i_SiteR1R1 [e_SiteR1R1 []] in
+              (
+                polymerization [e_C [], i_R1 [1.0], i_R1 [0.0], e_N [], 1.1],
+                polymerization [e_C [], i_R1 [0.2], i_R1 [1.2], e_N [], 0.1]
+              )
+          : let i_SiteR1R1 [e_SiteR1R1 []] in
+            let i_SiteR1R1 [e_SiteR1R1 []] in
+              (
+                (
+                  M [i_aminoacid [e_N [], i_R1 [1.0], e_C []]],
+                  M [i_aminoacid [e_N [], i_R1 [1.0], e_C []]]
+                ),
+                (
+                  M [i_aminoacid [e_N [], i_R1 [0.2], e_C []]],
+                  M [i_aminoacid [e_N [], i_R1 [0.2], e_C []]]
+                )
+              )
+          → let i_SiteR1R1 [e_SiteR1R1 []] in
+            let i_SiteR1R1 [e_SiteR1R1 []] in
+              (
+                let bond_peptide [1.1] in
+                  (
+                    M [i_aminoacid [e_N [], i_R1 [2.0], 0.0]],
+                    M [i_aminoacid [0.1, i_R1 [1.0], e_C []]]
+                  ),
+                let bond_peptide [0.1] in
+                  (
+                    M [i_aminoacid [e_N [], i_R1 [1.2], 0.0]],
+                    M [i_aminoacid [0.1, i_R1 [2.2], e_C []]]
+                  )
+              )"#]];
+    transitions.assert_eq(&generator.transitions(2).join("\n"));
+}