From ba6feadfdea0b98fc44e4d4963a6fe8f136c84c3 Mon Sep 17 00:00:00 2001
From: Co Quach <43968221+daico007@users.noreply.github.com>
Date: Tue, 25 Oct 2022 14:14:37 -0500
Subject: [PATCH] Add smiles string conversion using pybel backend (#1056)

* add smiles string conversion using pybel backend

* add unit test for several smiles string conversion scenarios

* restrict python version, attempt to fix bleeding test
---
 environment-dev-win.yml       |  2 +-
 environment-dev.yml           |  2 +-
 environment.yml               |  2 +-
 mbuild/compound.py            | 16 ++++++++++++++++
 mbuild/conversion.py          | 29 +++++++++++++++++++++++++++++
 mbuild/tests/test_compound.py | 16 ++++++++++++++++
 6 files changed, 64 insertions(+), 3 deletions(-)

diff --git a/environment-dev-win.yml b/environment-dev-win.yml
index be6d07a0f..88e6bdb0c 100644
--- a/environment-dev-win.yml
+++ b/environment-dev-win.yml
@@ -25,6 +25,6 @@ dependencies:
   - pycifrw
   - pytest
   - pytest-cov
-  - python
+  - python<3.10
   - rdkit>=2021
   - scipy
diff --git a/environment-dev.yml b/environment-dev.yml
index 13a004b96..c4cd43fff 100644
--- a/environment-dev.yml
+++ b/environment-dev.yml
@@ -27,6 +27,6 @@ dependencies:
   - pytest
   - pytest-azurepipelines
   - pytest-cov
-  - python
+  - python<3.10
   - rdkit>=2021
   - scipy
diff --git a/environment.yml b/environment.yml
index 04d27a7b4..883dad7d5 100644
--- a/environment.yml
+++ b/environment.yml
@@ -7,6 +7,6 @@ dependencies:
   - packmol>=18
   - gmso>=0.9.0
   - parmed>=3.4.3
-  - python
+  - python<3.10
   - rdkit>=2021
   - scipy
diff --git a/mbuild/compound.py b/mbuild/compound.py
index beb9c8f90..fe5081f4d 100644
--- a/mbuild/compound.py
+++ b/mbuild/compound.py
@@ -2728,6 +2728,22 @@ def to_pybel(
             show_ports=show_ports,
         )
 
+    def to_smiles(self, backend="pybel"):
+        """Create a SMILES string from an mbuild compound.
+
+        Parameters
+        ----------
+        compound : mb.Compound.
+            The mbuild compound to be converted.
+        backend : str, optional, default="pybel"
+            Backend used to do the conversion.
+
+        Return
+        ------
+        smiles_string : str
+        """
+        return conversion.to_smiles(self, backend)
+
     def from_pybel(
         self,
         pybel_mol,
diff --git a/mbuild/conversion.py b/mbuild/conversion.py
index 22011e8e5..85a035158 100644
--- a/mbuild/conversion.py
+++ b/mbuild/conversion.py
@@ -1564,6 +1564,35 @@ def to_pybel(
     return pybelmol
 
 
+def to_smiles(compound, backend="pybel"):
+    """Create a SMILES string from an mbuild compound.
+
+    Parameters
+    ----------
+    compound : mb.Compound.
+        The mbuild compound to be converted.
+    backend : str, optional, default="pybel"
+        Backend used to do the conversion.
+
+    Return
+    ------
+    smiles_string : str
+    """
+    if backend == "pybel":
+        mol = to_pybel(compound)
+
+        warn(
+            "The bond orders will be guessed using pybel"
+            "OBMol.PerceviedBondOrders()"
+        )
+        mol.OBMol.PerceiveBondOrders()
+        smiles_string = mol.write("smi").replace("\t", " ").split(" ")[0]
+
+        return smiles_string
+    else:
+        raise NotImplementedError(f"Backend {backend} not implemented.")
+
+
 def to_networkx(compound, names_only=False):
     """Create a NetworkX graph representing the hierarchy of a Compound.
 
diff --git a/mbuild/tests/test_compound.py b/mbuild/tests/test_compound.py
index b284a1192..5e955e906 100644
--- a/mbuild/tests/test_compound.py
+++ b/mbuild/tests/test_compound.py
@@ -800,6 +800,22 @@ def test_reload(self):
         assert p3ht1.n_particles == 33
         assert p3ht1.n_bonds == 33
 
+    @pytest.mark.skipif(
+        not has_openbabel, reason="Open Bable package not installed"
+    )
+    def test_to_smiles(self, ethane, benzene):
+        # Test predefined molecule
+        eth_smiles = "CC"
+        benzene_smiles = "c1ccccc1"
+
+        assert ethane.to_smiles() == eth_smiles
+        assert benzene.to_smiles() == benzene_smiles
+
+        # Test molecules loaded in with smiles string
+        for smiles in ["CCO", "CC(O)O", "Cc1ccccc1"]:
+            compound = mb.load(smiles, smiles=True)
+            assert compound.to_smiles() == smiles
+
     @pytest.mark.parametrize(
         "extension", [(".xyz"), (".pdb"), (".mol2"), (".gro")]
     )