Merge branch 'main' of github.com:klausweinbauer/FGUtils into github_…

…main
klausweinbauer · Dec 16, 2024 · d4f64da · d4f64da
2 parents 41c63a3 + a9806f0
commit d4f64da
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diff --git a/doc/functional_groups.rst b/doc/functional_groups.rst
@@ -50,16 +50,17 @@ Functional Group Tree
 .. code-block::
 
     Functional Group                    Parents                  Pattern
-    --------------------------------------------------------------------------
+    ----------------------------------------------------------------------------
     ether                               [ROOT]                   ROR
     ├── ketal                           [ether]                  RC(OR)(OR)R
     │   ├── acetal                      [ketal]                  RC(OC)(OC)H
     │   └── hemiketal                   [ketal, alcohol]         RC(OH)(OR)R
     │       └── hemiacetal              [hemiketal]              RC(OC)(OH)H
+    ├── epoxid                          [ether]                  RC(R)1C(R)(R)O1
     ├── ester                           [ketone, ether]          RC(=O)OR
     │   ├── anhydride                   [ester]                  RC(=O)OC(=O)R
     │   ├── peroxy_acid                 [ester, peroxide]        RC(=O)OOH
-    │   ├── carbamate                   [ester, amide]           ROC(=O)N(R)R
+    │   ├── carbamate                   [amide, ester]           ROC(=O)N(R)R
     │   └── carboxylic_acid             [ester, alcohol]         RC(=O)OH
     ├── alcohol                         [ether]                  COH
     │   ├── hemiketal                   [ketal, alcohol]         RC(OH)(OR)R
@@ -76,18 +77,18 @@ Functional Group Tree
     └── thioester                       [ketone, thioether]      RC(=O)SR
     amine                               [ROOT]                   RN(R)R
     ├── amide                           [ketone, amine]          RC(=O)N(R)R
-    │   └── carbamate                   [ester, amide]           ROC(=O)N(R)R
+    │   └── carbamate                   [amide, ester]           ROC(=O)N(R)R
     └── anilin                          [amine]                  C:CN(R)R
     carbonyl                            [ROOT]                   C(=O)
     ├── ketene                          [carbonyl]               RC(R)=C=O
     └── ketone                          [carbonyl]               RC(=O)R
         ├── amide                       [ketone, amine]          RC(=O)N(R)R
-        │   └── carbamate               [ester, amide]           ROC(=O)N(R)R
+        │   └── carbamate               [amide, ester]           ROC(=O)N(R)R
         ├── thioester                   [ketone, thioether]      RC(=O)SR
         ├── ester                       [ketone, ether]          RC(=O)OR
         │   ├── anhydride               [ester]                  RC(=O)OC(=O)R
         │   ├── peroxy_acid             [ester, peroxide]        RC(=O)OOH
-        │   ├── carbamate               [ester, amide]           ROC(=O)N(R)R
+        │   ├── carbamate               [amide, ester]           ROC(=O)N(R)R
         │   └── carboxylic_acid         [ester, alcohol]         RC(=O)OH
         ├── acyl_chloride               [ketone]                 RC(=O)Cl
         └── aldehyde                    [ketone]                 RC(=O)H

diff --git a/fgutils/fgconfig.py b/fgutils/fgconfig.py
@@ -67,6 +67,7 @@
     {"name": "ketene", "pattern": "RC(R)=C=O", "group_atoms": [1, 3, 4]},
     {"name": "carbamate", "pattern": "ROC(=O)N(R)R", "group_atoms": [1, 2, 3, 4]},
     {"name": "acyl_chloride", "pattern": "RC(=O)Cl", "group_atoms": [1, 2, 3]},
+    {"name": "epoxid", "pattern": "RC(R)1C(R)(R)O1", "group_atoms": [1, 3, 6]},
 ]
 
 

diff --git a/fgutils/vis.py b/fgutils/vis.py
@@ -111,8 +111,12 @@ def plot_as_mol(g: nx.Graph, ax, use_mol_coords=True):
     nx.draw_networkx_edge_labels(g, positions, edge_labels=edge_labels, ax=ax)
 
 
-def get_rxn_img(smiles):
+def get_rxn_img(smiles, background_colour=None):
     drawer = rdMolDraw2D.MolDraw2DCairo(1600, 900)
+    opts = drawer.drawOptions()
+    if background_colour is None:
+        background_colour = (0.0, 0.0, 0.0, 0.0)
+    opts.setBackgroundColour(background_colour)
     if ">>" in smiles:
         rxn = rdChemReactions.ReactionFromSmarts(smiles, useSmiles=True)
         drawer.DrawReaction(rxn)
@@ -127,7 +131,7 @@ def get_rxn_img(smiles):
         (x, y)
         for x in range(img.size[0])
         for y in range(img.size[1])
-        if img.getdata()[x + y * img.size[0]] != (255, 255, 255)  # type: ignore
+        if img.getdata()[x + y * img.size[0]] != background_colour  # type: ignore
     ]
     rect = (
         min([x - 10 for x, _ in nonwhite_positions]),

diff --git a/pyproject.toml b/pyproject.toml
@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "fgutils"
-version = "0.1.2"
+version = "0.1.3"
 authors = [{name="Klaus Weinbauer", email="klaus@bioinf.uni-leipzig.de"}]
 description = "Library to get functional groups from molecular graphs."
 readme = "README.md"

diff --git a/test/test_query.py b/test/test_query.py
@@ -84,7 +84,8 @@ def test_get_functional_group_once():
         pytest.param(
             "C(O)(O)C=CO", ["hemiketal", "enol"], [[0, 1, 2], [3, 4, 5]], id="Hemiketal"
         ),
-        pytest.param("C=CO", ["enol"], [[0, 1, 2]], id="Enol")
+        pytest.param("C=CO", ["enol"], [[0, 1, 2]], id="Enol"),
+        pytest.param("C1CO1", ["epoxid"], [[0, 1, 2]], id="Epoxid")
         # pytest.param("", [""], [[]], id=""),
     ],
 )