fix doc build

MDAnalysis · Aug 14, 2020 · 4e49616 · 4e49616
1 parent d288e87
commit 4e49616
Showing 1 changed file with 35 additions and 32 deletions.
diff --git a/package/MDAnalysis/coordinates/RDKit.py b/package/MDAnalysis/coordinates/RDKit.py
@@ -24,24 +24,27 @@
 """RDKit molecule I/O --- :mod:`MDAnalysis.coordinates.RDKit`
 ================================================================
 
-Read coordinates data from an `RDKit <https://www.rdkit.org/docs/>`_ :class:`rdkit.Chem.rdchem.Mol` with
+Read coordinates data from an `RDKit <https://www.rdkit.org/docs/>`__ :class:`rdkit.Chem.rdchem.Mol` with
 :class:`RDKitReader` into an MDAnalysis Universe. Convert it back to a
 :class:`rdkit.Chem.rdchem.Mol` with :class:`RDKitConverter`.
 
 
 Example
 -------
 
->>> from rdkit import Chem
->>> import MDAnalysis as mda
->>> mol = Chem.MolFromMol2File("docking_poses.mol2", removeHs=False)
->>> u = mda.Universe(mol)
->>> u
-<Universe with 42 atoms>
->>> u.trajectory
-<RDKitReader with 10 frames of 42 atoms>
->>> u.atoms.convert_to("RDKIT")
-<rdkit.Chem.rdchem.Mol object at 0x7fcebb958148>
+To read an RDKit molecule and then convert the AtomGroup back to an RDKit
+molecule::
+
+    >>> from rdkit import Chem
+    >>> import MDAnalysis as mda
+    >>> mol = Chem.MolFromMol2File("docking_poses.mol2", removeHs=False)
+    >>> u = mda.Universe(mol)
+    >>> u
+    <Universe with 42 atoms>
+    >>> u.trajectory
+    <RDKitReader with 10 frames of 42 atoms>
+    >>> u.atoms.convert_to("RDKIT")
+    <rdkit.Chem.rdchem.Mol object at 0x7fcebb958148>
 
 
 Classes
@@ -599,27 +602,27 @@ def _standardize_patterns(mol, max_iter=200):
     -----
     The following functional groups are transformed in this order:
 
-    +---------------+-------------------------------------------------------------------------+
-    | Name          | Reaction                                                                |
-    +===============+=========================================================================+
-    | conjugated    | [*-;!O:1]-[*:2]=[*:3]-[*-:4]>>[*+0:1]=[*:2]-[*:3]=[*+0:4]               |
-    +---------------+-------------------------------------------------------------------------+
-    | conjugated-N+ | [N;X3;v3:1]-[*:2]=[*:3]-[*-:4]>>[N+:1]=[*:2]-[*:3]=[*+0:4]              |
-    +---------------+-------------------------------------------------------------------------+
-    | conjugated-O- | [O:1]=[#6:2]-[*:3]=[*:4]-[*-:5]>>[O-:1]-[*:2]=[*:3]-[*:4]=[*+0:5]       |
-    +---------------+-------------------------------------------------------------------------+
-    | Cterm         | [C-;X2:1]=[O:2]>>[C+0:1]=[O:2]                                          |
-    +---------------+-------------------------------------------------------------------------+
-    | Nterm         | [N-;X2;H1:1]>>[N+0:1]                                                   |
-    +---------------+-------------------------------------------------------------------------+
-    | keto-enolate  | [#6-:1]-[#6:2]=[O:3]>>[#6+0:1]=[#6:2]-[O-:3]                            |
-    +---------------+-------------------------------------------------------------------------+
-    | arginine      | [N;H1:1]-[C-;X3;H0:2](-[N;H2:3])-[N;H2:4]>>[N:1]-[C+0:2](-[N:3])=[N+:4] |
-    +---------------+-------------------------------------------------------------------------+
-    | sulfone       | [S;X4;v4:1](-[O-;X1:2])-[O-;X1:3]>>[S:1](=[O+0:2])=[O+0:3]              |
-    +---------------+-------------------------------------------------------------------------+
-    | nitro         | [N;X3;v3:1](-[O-;X1:2])-[O-;X1:3]>>[N+:1](-[O-:2])=[O+0:3]              |
-    +---------------+-------------------------------------------------------------------------+
+    +---------------+-----------------------------------------------------------------------------+
+    | Name          | Reaction                                                                    |
+    +===============+=============================================================================+
+    | conjugated    | ``[*-;!O:1]-[*:2]=[*:3]-[*-:4]>>[*+0:1]=[*:2]-[*:3]=[*+0:4]``               |
+    +---------------+-----------------------------------------------------------------------------+
+    | conjugated-N+ | ``[N;X3;v3:1]-[*:2]=[*:3]-[*-:4]>>[N+:1]=[*:2]-[*:3]=[*+0:4]``              |
+    +---------------+-----------------------------------------------------------------------------+
+    | conjugated-O- | ``[O:1]=[#6:2]-[*:3]=[*:4]-[*-:5]>>[O-:1]-[*:2]=[*:3]-[*:4]=[*+0:5]``       |
+    +---------------+-----------------------------------------------------------------------------+
+    | Cterm         | ``[C-;X2:1]=[O:2]>>[C+0:1]=[O:2]``                                          |
+    +---------------+-----------------------------------------------------------------------------+
+    | Nterm         | ``[N-;X2;H1:1]>>[N+0:1]``                                                   |
+    +---------------+-----------------------------------------------------------------------------+
+    | keto-enolate  | ``[#6-:1]-[#6:2]=[O:3]>>[#6+0:1]=[#6:2]-[O-:3]``                            |
+    +---------------+-----------------------------------------------------------------------------+
+    | arginine      | ``[N;H1:1]-[C-;X3;H0:2](-[N;H2:3])-[N;H2:4]>>[N:1]-[C+0:2](-[N:3])=[N+:4]`` |
+    +---------------+-----------------------------------------------------------------------------+
+    | sulfone       | ``[S;X4;v4:1](-[O-;X1:2])-[O-;X1:3]>>[S:1](=[O+0:2])=[O+0:3]``              |
+    +---------------+-----------------------------------------------------------------------------+
+    | nitro         | ``[N;X3;v3:1](-[O-;X1:2])-[O-;X1:3]>>[N+:1](-[O-:2])=[O+0:3]``              |
+    +---------------+-----------------------------------------------------------------------------+
 
     """