aamutils 0.0.2__tar.gz → 0.0.4__tar.gz

{aamutils-0.0.2 → aamutils-0.0.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: aamutils
-Version: 0.0.2
+Version: 0.0.4
 Summary: Collection of atom-atom-mapping utility functions.
 Project-URL: homepage, https://github.com/klausweinbauer/AAMUtils
 Project-URL: source, https://github.com/klausweinbauer/AAMUtils
@@ -78,18 +78,18 @@ reported results can be reproduced by running the following commands:
 ### (1) Extend partial reaction center (50%, 75% and 100% missing atoms)  
 
 ```
-python3 benchmark.py --remove-mode rc --remove-ratio 0.5
+python3 benchmark.py --remove-mode rc --remove-ratio 0.5 --seed 42
 ```
 ```
-python3 benchmark.py --remove-mode rc --remove-ratio 0.75
+python3 benchmark.py --remove-mode rc --remove-ratio 0.75 --seed 42
 ```
 ```
-python3 benchmark.py --remove-mode rc --remove-ratio 1
+python3 benchmark.py --remove-mode rc --remove-ratio 1 --seed 42
 ```
 
 ### (2) Extend partial AAM with fully mapped RC 
 ```
-python3 benchmark.py --remove-mode keep_rc --remove-ratio 1
+python3 benchmark.py --remove-mode keep_rc --remove-ratio 1 --seed 42
 ```
 
 

{aamutils-0.0.2 → aamutils-0.0.4}/README.md

@@ -56,18 +56,18 @@ reported results can be reproduced by running the following commands:
 ### (1) Extend partial reaction center (50%, 75% and 100% missing atoms)  
 
 ```
-python3 benchmark.py --remove-mode rc --remove-ratio 0.5
+python3 benchmark.py --remove-mode rc --remove-ratio 0.5 --seed 42
 ```
 ```
-python3 benchmark.py --remove-mode rc --remove-ratio 0.75
+python3 benchmark.py --remove-mode rc --remove-ratio 0.75 --seed 42
 ```
 ```
-python3 benchmark.py --remove-mode rc --remove-ratio 1
+python3 benchmark.py --remove-mode rc --remove-ratio 1 --seed 42
 ```
 
 ### (2) Extend partial AAM with fully mapped RC 
 ```
-python3 benchmark.py --remove-mode keep_rc --remove-ratio 1
+python3 benchmark.py --remove-mode keep_rc --remove-ratio 1 --seed 42
 ```
 
 

{aamutils-0.0.2 → aamutils-0.0.4}/aamutils/utils.py

@@ -3,6 +3,7 @@ import numpy as np
 import networkx as nx
 import rdkit.Chem as Chem
 import rdkit.Chem.rdmolfiles as rdmolfiles
+import rdkit.Chem.rdDepictor as rdDepictor
 
 
 def mol_to_graph(mol: Chem.rdchem.Mol) -> nx.Graph:
@@ -26,6 +27,16 @@ def mol_to_graph(mol: Chem.rdchem.Mol) -> nx.Graph:
     return g
 
 
+def smiles_to_graph(smiles: str) -> nx.Graph | tuple[nx.Graph, nx.Graph]:
+    if ">>" in smiles:
+        smiles_token = smiles.split(">>")
+        g = mol_to_graph(rdmolfiles.MolFromSmiles(smiles_token[0]))
+        h = mol_to_graph(rdmolfiles.MolFromSmiles(smiles_token[1]))
+        return g, h
+    else:
+        return mol_to_graph(rdmolfiles.MolFromSmiles(smiles))
+
+
 def graph_to_mol(
     G: nx.Graph, symbol_key="symbol", aam_key="aam", bond_type_key="bond"
 ) -> Chem.rdchem.Mol:
@@ -37,13 +48,16 @@ def graph_to_mol(
         1.5: Chem.rdchem.BondType.AROMATIC,
     }
     rw_mol = Chem.rdchem.RWMol()
+    idx_map = {}
     for n, d in G.nodes(data=True):
         idx = rw_mol.AddAtom(Chem.rdchem.Atom(d[symbol_key]))
+        idx_map[n] = idx
         if aam_key in d.keys() and d[aam_key] >= 0:
             rw_mol.GetAtomWithIdx(idx).SetAtomMapNum(d[aam_key])
-        assert n == idx
     for n1, n2, d in G.edges(data=True):
-        rw_mol.AddBond(n1, n2, bond_order_map[d[bond_type_key]])
+        idx1 = idx_map[n1]
+        idx2 = idx_map[n2]
+        rw_mol.AddBond(idx1, idx2, bond_order_map[d[bond_type_key]])
     return rw_mol.GetMol()
 
 
@@ -123,3 +137,46 @@ def print_graph(graph):
             )
         )
     )
+
+
+def its2mol(its: nx.Graph, aam_key="aam", bond_key="bond") -> Chem.rdchem.Mol:
+    _its = its.copy()
+    for n in _its.nodes:
+        _its.nodes[n][aam_key] = n
+    for u, v in _its.edges():
+        _its[u][v][bond_key] = 1
+    return graph_to_mol(_its)
+
+
+def plot_its(its, ax, bond_key="bond", aam_key="aam", symbol_key="symbol"):
+    bond_char = {None: "∅", 1: "—", 2: "=", 3: "≡"}
+    mol = its2mol(its, aam_key=aam_key, bond_key=bond_key)
+
+    positions = {}
+    conformer = rdDepictor.Compute2DCoords(mol)
+    for i, atom in enumerate(mol.GetAtoms()):
+        aam = atom.GetAtomMapNum()
+        apos = mol.GetConformer(conformer).GetAtomPosition(i)
+        positions[aam] = [apos.x, apos.y]
+
+    ax.axis("equal")
+    ax.axis("off")
+
+    nx.draw_networkx_edges(its, positions, edge_color="#000000", ax=ax)
+    nx.draw_networkx_nodes(its, positions, node_color="#FFFFFF", node_size=500, ax=ax)
+
+    labels = {n: "{}:{}".format(d[symbol_key], n) for n, d in its.nodes(data=True)}
+    edge_labels = {}
+    for u, v, d in its.edges(data=True):
+        bc1 = d[bond_key][0]
+        bc2 = d[bond_key][1]
+        if bc1 == bc2:
+            continue
+        if bc1 in bond_char.keys():
+            bc1 = bond_char[bc1]
+        if bc2 in bond_char.keys():
+            bc2 = bond_char[bc2]
+        edge_labels[(u, v)] = "({},{})".format(bc1, bc2)
+
+    nx.draw_networkx_labels(its, positions, labels=labels, ax=ax)
+    nx.draw_networkx_edge_labels(its, positions, edge_labels=edge_labels, ax=ax)

{aamutils-0.0.2 → aamutils-0.0.4}/benchmark.py

@@ -50,7 +50,9 @@ def load_data():
     return data
 
 
-def run(n, remove_mode, remove_ratio):
+def run(n, remove_mode, remove_ratio, seed=None):
+    if seed is not None:
+        random.seed(seed)
     data = load_data()
     testcase_cnt = 0
     success_cnt = 0
@@ -136,6 +138,7 @@ if __name__ == "__main__":
     default_rm_mode = "rc"
     default_rm_ratio = 0.5
     default_n = 1000
+    default_seed = None
 
     parser = argparse.ArgumentParser(
         prog="benchmarks.py",
@@ -171,6 +174,13 @@ if __name__ == "__main__":
             + " Default: {}"
         ).format(default_rm_ratio),
     )
+    parser.add_argument(
+        "--seed",
+        default=default_seed,
+        help=(
+            "The seed used to initialize random number generation. " + "Default: {}"
+        ).format(default_seed),
+    )
 
     args = parser.parse_args()
-    run(args.n, args.remove_mode, args.remove_ratio)
+    run(args.n, args.remove_mode, args.remove_ratio, args.seed)

{aamutils-0.0.2 → aamutils-0.0.4}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "aamutils"
-version = "0.0.2"
+version = "0.0.4"
 authors = [
 	{name="Klaus Weinbauer", email="klaus@bioinf.uni-leipzig.de"}
 	]