From 0487621e0bdeeebc43264d07ec927ad0e3fad858 Mon Sep 17 00:00:00 2001
From: Cole Mathis <cole.mathis.ool@gmail.com>
Date: Fri, 25 Jul 2025 16:33:13 -0700
Subject: [PATCH 1/5] Adding script to pull data for condensed poly-aromatric
 rings, downsampling the data based on reasonable compute times, and data that
 we need, converting to mol files and saving in  with meta data

---
 scripts/ring-data.py | 62 ++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 62 insertions(+)
 create mode 100644 scripts/ring-data.py

diff --git a/scripts/ring-data.py b/scripts/ring-data.py
new file mode 100644
index 00000000..cbf5a19b
--- /dev/null
+++ b/scripts/ring-data.py
@@ -0,0 +1,62 @@
+import requests
+import pandas as pd
+from pathlib import Path
+
+import rdkit
+from rdkit import Chem
+from rdkit.Chem import rdMolDescriptors
+
+def download_compas_csv(save_path="compas-3x.csv"):
+    url = "https://gitlab.com/porannegroup/compas/-/raw/32b1a7904ebc525ec0095edc41daba0b9a2b3436/COMPAS-3/compas-3x.csv"
+    response = requests.get(url)
+    
+    if response.status_code == 200:
+        with open(save_path, "wb") as f:
+            f.write(response.content)
+        print(f"Downloaded to {save_path}")
+    else:
+        raise Exception(f"Failed to download file: {response.status_code}")
+
+def count_double_bonds(mol):
+    rdkit.Chem.Kekulize(mol)
+    double_bond_count = 0
+    for bond in mol.GetBonds():
+        if bond.GetBondType() == Chem.BondType.DOUBLE:
+            double_bond_count += 1
+    return double_bond_count
+
+def read_and_reduce_compas_3x():
+    compas_df = pd.read_csv("compas-3x.csv")
+    compas_df = compas_df.query("n_rings <= 8")
+    compas_df["mol"] = compas_df["smiles"].apply(Chem.MolFromSmiles)
+    compas_df["formula"] = compas_df["mol"].apply(Chem.rdMolDescriptors.CalcMolFormula)
+    compas_df["bonds"] = [c.GetNumBonds() for c in compas_df["mol"]]
+    compas_df["double_bonds"] = compas_df["mol"].apply(count_double_bonds)
+    compas_df["atoms"] = [c.GetNumAtoms() for c in compas_df["mol"]]
+
+    reduced_df = compas_df[["smiles",
+                        "mol",
+                        "n_rings",
+                        "double_bonds",
+                        "bonds",
+                        "atoms"]].reset_index()
+    return reduced_df
+
+def write_mols_to_file(compas_df):
+    Path("../data/polycyclic_hydrocarbons/").mkdir(parents=True, exist_ok=True)
+
+    compas_df["filename"] = compas_df.index.to_series().map(lambda x: f"../data/polycyclic_hydrocarbons/pah_{x}.mol")
+    compas_df.apply(lambda row: Chem.MolToMolFile(row["mol"], row["filename"]), axis=1)
+    meta_data_file = "../data/polycyclic_hydrocarbons/selected_compas_3x.csv"
+    compas_df[["filename", "n_rings", "double_bonds", "bonds", "atoms"]].to_csv(meta_data_file)
+
+if __name__ == "__main__":
+    # Grab COMPAS-3 Data from gitlab 
+    # Cite as A. Wahab and R. Gershoni-Poranne, COMPAS-3, DOI: 10.1039/D4CP01027B
+    download_compas_csv()
+    
+    # Read and reduce data
+    reduced_compas = read_and_reduce_compas_3x()
+
+    # Generate filenames for mol and write to file
+    write_mols_to_file(reduced_compas)
\ No newline at end of file

From 2dc0c7f5a708f361fa2a59051d98c3cbdbc26c76 Mon Sep 17 00:00:00 2001
From: Cole Mathis <cole.mathis.ool@gmail.com>
Date: Fri, 25 Jul 2025 16:34:01 -0700
Subject: [PATCH 2/5] Sampling random branched alkenes with bond counts derived
 from the ring data

---
 scripts/alkene-sampling.py | 115 +++++++++++++++++++++++++++++++++++++
 1 file changed, 115 insertions(+)
 create mode 100644 scripts/alkene-sampling.py

diff --git a/scripts/alkene-sampling.py b/scripts/alkene-sampling.py
new file mode 100644
index 00000000..ff057d6e
--- /dev/null
+++ b/scripts/alkene-sampling.py
@@ -0,0 +1,115 @@
+# This script depends on having already run ring-data.csv
+# It will inspect the output of that script and generate a control dataset
+# This dataset will have the same number of molecules, but all molecules will be free
+# from rings entirely. Each molecule in this dataset will have a number of 
+# bonds and double bonds corresponding to the number of bonds/double bonds in the ring data. 
+
+import random
+import networkx as nx
+import pandas as pd
+from rdkit import Chem
+from rdkit.Chem import RWMol
+from pathlib import Path
+
+def random_tree_prufer(n, max_degree=4):
+    """Generate a random tree with n nodes using Prüfer sequence. Reject if any node exceeds max_degree."""
+    while True:
+        seq = [random.randint(0, n - 1) for _ in range(n - 2)]
+        deg = [1] * n
+        for v in seq:
+            deg[v] += 1
+        if any(d > max_degree for d in deg):
+            # print("rejecting sequence")
+            continue
+        
+        G = nx.from_prufer_sequence(seq)
+        
+        return G
+
+
+def assign_double_bonds(G, D, max_valence=4):
+    """Randomly assign D double bonds to edges of G while obeying valence constraint."""
+    edges = list(G.edges())
+    if D > len(edges):
+        return None  # impossible
+    elif D == 0:
+        return []
+    for _ in range(10*D):
+        candidate_edges = set(random.sample(edges, D))
+        # Count valence
+        bond_counts = {node: 0 for node in G.nodes()}
+        for u, v in G.edges():
+            bond_order = 2 if (u, v) in candidate_edges or (v, u) in candidate_edges else 1
+            bond_counts[u] += bond_order
+            bond_counts[v] += bond_order
+        if all(val <= max_valence for val in bond_counts.values()):
+            # print("Double bond success")
+            return candidate_edges
+        else:
+            # print('rejecting double bond configuration')
+            continue
+
+
+def graph_to_smiles_with_double(G, double_edges):
+    mol = RWMol()
+    for _ in G.nodes():
+        mol.AddAtom(Chem.Atom("C"))
+    for u, v in G.edges():
+        btype = Chem.BondType.DOUBLE if (u, v) in double_edges or (v, u) in double_edges else Chem.BondType.SINGLE
+        mol.AddBond(int(u), int(v), btype)
+    m = mol.GetMol()
+    Chem.SanitizeMol(m)
+    return Chem.MolToSmiles(m)
+
+
+def sample_acyclic_hydrocarbons(B, D):
+    """Sample n_samples of acyclic hydrocarbons with B total bonds, D of which are double bonds."""
+    assert B >= 1, "At least one bond required"
+    assert D <= B, "Double bonds must be ≤ total bonds"
+    n_carbons = B + 1  # from tree: nodes = edges + 1
+
+    smiles_set = set()
+    while len(smiles_set) < 1:
+        G = random_tree_prufer(n_carbons, max_degree=4)
+        double_bonds = assign_double_bonds(G, D, max_valence=4)
+        if double_bonds is None:
+            continue
+        try:
+            smi = graph_to_smiles_with_double(G, double_bonds)
+            smiles_set.add(smi)
+        except Exception:
+            continue  # skip invalid molecules
+    return list(smiles_set)[0]
+
+def get_pah_metadata():
+    pah_data = pd.read_csv("../data/polycyclic_hydrocarbons/selected_compas_3x.csv")
+    # Take the parameters we need for the control
+    return pah_data[["bonds", "double_bonds", "atoms"]]
+
+def sample_acyclic_smiles(bond_metadata):
+    smiles = bond_metadata.apply(lambda row: 
+                                    sample_acyclic_hydrocarbons(row["bonds"], 
+                                                                row["double_bonds"]), 
+                                                                axis=1)
+    return smiles
+
+def write_mols_to_file(ach_df):
+
+    Path("../data/acyclic_hydrocarbons/").mkdir(parents=True, exist_ok=True)
+
+    ach_df["mol"] = ach_df["smiles"].apply(Chem.MolFromSmiles)
+    ach_df["filename"] = ach_df.index.to_series().map(lambda x: f"../data/acyclic_hydrocarbons/ach_{x}.mol")
+    ach_df.apply(lambda row: Chem.MolToMolFile(row["mol"], row["filename"]), axis=1)
+    metadata_file = "../data/acyclic_hydrocarbons/sampled_ach.csv"
+    ach_df[["filename", "double_bonds", "bonds", "atoms"]].to_csv(metadata_file)
+
+if __name__ == "__main__":
+    # Set random seed for sampling
+    random.seed(137)
+    # Get controls from ring data
+    ach_data = get_pah_metadata()
+    # Sample acyclic smiles
+    ach_data["smiles"] = sample_acyclic_smiles(ach_data)
+    # Write data and meta data to file
+    write_mols_to_file(ach_data)
+    
\ No newline at end of file

From fc497cde929fdfea5a573b4c0d584fb793af078a Mon Sep 17 00:00:00 2001
From: Cole Mathis <cole.mathis.ool@gmail.com>
Date: Fri, 25 Jul 2025 16:43:44 -0700
Subject: [PATCH 3/5] Update readme for new sceripts

---
 scripts/README.md | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/scripts/README.md b/scripts/README.md
index 144ac2dc..2a42c10f 100644
--- a/scripts/README.md
+++ b/scripts/README.md
@@ -69,3 +69,10 @@ Calculate assembly indices using:
 We do not package its source code or its executable with our library, but it can be obtained [on GitHub](https://github.com/croningp/assembly_go) if non-self-referential ground truth is desired.
 [`assembly_cpp`] is the current state-of-the-art algorithm by Seet et al. (2024) and was provided to us by its authors on the condition that it remains private and is used only for this ground-truth generation.
 Otherwise, a release build of `assembly-theory` is created and used.
+
+### `ring-data.py`
+
+Rings present a challenge to any assembly index algorithm because the number of subgraphs grows quickly with the number of rings. This script will download a file from the [COMPAS project](https://pubs.rsc.org/en/content/articlehtml/2024/cp/d4cp01027b) of Polybenzenoid hydrocarbons (PBHs), these are fused benzene rings. We select molecules with 8 rings or fewer, and save them to mol files. This results in 415 molecules saved to `polycyclic_hydrocarbons` along with metadata. 
+
+### `alkene-sampling.py`
+See information in about `ring-data` above. This script will generate a complementary data set of molecules that have the same number of bonds and double bonds as the molecules generated by `ring data`. This is a useful control experiment to understand the impact of rings on performance characteristics. These molecules are generated though a hierachical rejection sampler, first sampling randomly labelled trees with a maximum degree of 4, and then sampling edges to convert to double bonds and verifying that labelling does not violate valence rules. The rejection sampling involved is somewhat slow. This results in 415 molecules saved to `data/acyclic_hydrocarbons` along with a csv of metadata. 
\ No newline at end of file

From b8bc5c5eaecf208574a7df31fe0be53562465cdb Mon Sep 17 00:00:00 2001
From: Cole Mathis <cole.mathis.ool@gmail.com>
Date: Fri, 25 Jul 2025 16:49:43 -0700
Subject: [PATCH 4/5] Add ring data

---
 data/polycyclic_hydrocarbons/pah_0.mol        |   3 +
 data/polycyclic_hydrocarbons/pah_1.mol        |   3 +
 data/polycyclic_hydrocarbons/pah_10.mol       |   3 +
 data/polycyclic_hydrocarbons/pah_100.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_101.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_102.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_103.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_104.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_105.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_106.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_107.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_108.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_109.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_11.mol       |   3 +
 data/polycyclic_hydrocarbons/pah_110.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_111.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_112.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_113.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_114.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_115.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_116.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_117.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_118.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_119.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_12.mol       |   3 +
 data/polycyclic_hydrocarbons/pah_120.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_121.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_122.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_123.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_124.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_125.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_126.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_127.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_128.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_129.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_13.mol       |   3 +
 data/polycyclic_hydrocarbons/pah_130.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_131.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_132.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_133.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_134.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_135.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_136.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_137.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_138.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_139.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_14.mol       |   3 +
 data/polycyclic_hydrocarbons/pah_140.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_141.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_142.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_143.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_144.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_145.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_146.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_147.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_148.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_149.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_15.mol       |   3 +
 data/polycyclic_hydrocarbons/pah_150.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_151.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_152.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_153.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_154.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_155.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_156.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_157.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_158.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_159.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_16.mol       |   3 +
 data/polycyclic_hydrocarbons/pah_160.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_161.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_162.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_163.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_164.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_165.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_166.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_167.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_168.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_169.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_17.mol       |   3 +
 data/polycyclic_hydrocarbons/pah_170.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_171.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_172.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_173.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_174.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_175.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_176.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_177.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_178.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_179.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_18.mol       |   3 +
 data/polycyclic_hydrocarbons/pah_180.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_181.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_182.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_183.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_184.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_185.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_186.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_187.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_188.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_189.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_19.mol       |   3 +
 data/polycyclic_hydrocarbons/pah_190.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_191.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_192.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_193.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_194.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_195.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_196.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_197.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_198.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_199.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_2.mol        |   3 +
 data/polycyclic_hydrocarbons/pah_20.mol       |   3 +
 data/polycyclic_hydrocarbons/pah_200.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_201.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_202.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_203.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_204.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_205.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_206.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_207.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_208.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_209.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_21.mol       |   3 +
 data/polycyclic_hydrocarbons/pah_210.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_211.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_212.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_213.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_214.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_215.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_216.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_217.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_218.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_219.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_22.mol       |   3 +
 data/polycyclic_hydrocarbons/pah_220.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_221.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_222.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_223.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_224.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_225.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_226.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_227.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_228.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_229.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_23.mol       |   3 +
 data/polycyclic_hydrocarbons/pah_230.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_231.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_232.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_233.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_234.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_235.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_236.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_237.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_238.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_239.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_24.mol       |   3 +
 data/polycyclic_hydrocarbons/pah_240.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_241.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_242.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_243.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_244.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_245.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_246.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_247.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_248.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_249.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_25.mol       |   3 +
 data/polycyclic_hydrocarbons/pah_250.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_251.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_252.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_253.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_254.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_255.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_256.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_257.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_258.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_259.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_26.mol       |   3 +
 data/polycyclic_hydrocarbons/pah_260.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_261.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_262.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_263.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_264.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_265.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_266.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_267.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_268.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_269.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_27.mol       |   3 +
 data/polycyclic_hydrocarbons/pah_270.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_271.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_272.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_273.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_274.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_275.mol      |   3 +
 data/polycyclic_hydrocarbons/pah_276.mol      |   3 +
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 .../selected_compas_3x.csv                    | 417 ++++++++++++++++++
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From 7676159ca22dcf1b9fe6711cfaee611ff9fadf59 Mon Sep 17 00:00:00 2001
From: Cole Mathis <cole.mathis.ool@gmail.com>
Date: Fri, 25 Jul 2025 16:50:02 -0700
Subject: [PATCH 5/5] Add tree data

---
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 data/acyclic_hydrocarbons/ach_1.mol       |   3 +
 data/acyclic_hydrocarbons/ach_10.mol      |   3 +
 data/acyclic_hydrocarbons/ach_100.mol     |   3 +
 data/acyclic_hydrocarbons/ach_101.mol     |   3 +
 data/acyclic_hydrocarbons/ach_102.mol     |   3 +
 data/acyclic_hydrocarbons/ach_103.mol     |   3 +
 data/acyclic_hydrocarbons/ach_104.mol     |   3 +
 data/acyclic_hydrocarbons/ach_105.mol     |   3 +
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 data/acyclic_hydrocarbons/ach_107.mol     |   3 +
 data/acyclic_hydrocarbons/ach_108.mol     |   3 +
 data/acyclic_hydrocarbons/ach_109.mol     |   3 +
 data/acyclic_hydrocarbons/ach_11.mol      |   3 +
 data/acyclic_hydrocarbons/ach_110.mol     |   3 +
 data/acyclic_hydrocarbons/ach_111.mol     |   3 +
 data/acyclic_hydrocarbons/ach_112.mol     |   3 +
 data/acyclic_hydrocarbons/ach_113.mol     |   3 +
 data/acyclic_hydrocarbons/ach_114.mol     |   3 +
 data/acyclic_hydrocarbons/ach_115.mol     |   3 +
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 data/acyclic_hydrocarbons/ach_117.mol     |   3 +
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 data/acyclic_hydrocarbons/ach_120.mol     |   3 +
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 data/acyclic_hydrocarbons/ach_122.mol     |   3 +
 data/acyclic_hydrocarbons/ach_123.mol     |   3 +
 data/acyclic_hydrocarbons/ach_124.mol     |   3 +
 data/acyclic_hydrocarbons/ach_125.mol     |   3 +
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 data/acyclic_hydrocarbons/ach_204.mol     |   3 +
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 data/acyclic_hydrocarbons/ach_206.mol     |   3 +
 data/acyclic_hydrocarbons/ach_207.mol     |   3 +
 data/acyclic_hydrocarbons/ach_208.mol     |   3 +
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