From 4e49616720feb27bf4609279e5e8d05968be9864 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?C=C3=A9dric=20Bouysset?= Date: Fri, 14 Aug 2020 19:28:44 +0200 Subject: [PATCH] fix doc build --- package/MDAnalysis/coordinates/RDKit.py | 67 +++++++++++++------------ 1 file changed, 35 insertions(+), 32 deletions(-) diff --git a/package/MDAnalysis/coordinates/RDKit.py b/package/MDAnalysis/coordinates/RDKit.py index 1de9b95e329..54184371912 100644 --- a/package/MDAnalysis/coordinates/RDKit.py +++ b/package/MDAnalysis/coordinates/RDKit.py @@ -24,7 +24,7 @@ """RDKit molecule I/O --- :mod:`MDAnalysis.coordinates.RDKit` ================================================================ -Read coordinates data from an `RDKit `_ :class:`rdkit.Chem.rdchem.Mol` with +Read coordinates data from an `RDKit `__ :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`. @@ -32,16 +32,19 @@ Example ------- ->>> from rdkit import Chem ->>> import MDAnalysis as mda ->>> mol = Chem.MolFromMol2File("docking_poses.mol2", removeHs=False) ->>> u = mda.Universe(mol) ->>> u - ->>> u.trajectory - ->>> u.atoms.convert_to("RDKIT") - +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 + + >>> u.trajectory + + >>> u.atoms.convert_to("RDKIT") + 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]`` | + +---------------+-----------------------------------------------------------------------------+ """