Source code for BigDFT.Interop.RDKitInterop

This module contains some wrappers for using OpenBabel to perform
various operations with RDKit.

[docs]def convert_system_to_rdkit(sys): """ Convert a BigDFT system to rdkit molecule. Args: sys (BigDFT.Systems.System): the system to convert. Returns: (rdkit.Chem.rdchem.Mol): an rdkit type molecule. """ from BigDFT.IO import write_mol2 from io import StringIO from rdkit import Chem ostr = StringIO() write_mol2(sys, ostr) rdmol = Chem.MolFromMol2Block(ostr.getvalue()) return rdmol
[docs]def compute_rdkit_matching(sys, rdsys, check_matching=True): """ Similar to the cannonical `compute matching` of the system class, this creates a lookup table mapping each atom in a system class to the index of the atom in a rdkit system. Args: sys (BigDFT.Systems.System): the bigdft system. bsys (rdkit.Chem.rdchem.Mol): the rdkit version of the system. check_matching (bool): if set to True, this will raise an error if we can't match all of the atoms in the system. Returns: (dict): a mapping from a system to indices in the atom list. If an atom is not in the list, an index value of -1 is assigned. """ from BigDFT.Atoms import Atom # Convert rdkit system to a list of atoms atm_list = [] conf = rdsys.GetConformer() for at in rdsys.GetAtoms(): sym = at.GetSymbol() idx = at.GetIdx() pos = [float(x) for x in list(conf.GetAtomPosition(idx))] newat = Atom({sym: pos, "units": "angstroem"}) atm_list.append(newat) # Run compute matching. return sys.compute_matching(atm_list, check_matching)
[docs]def rdkit_visualize(sys, colordict=None, format="SVG"): """ Visualize a molecule and its fragments using RDKit. Args: sys (BigDFT.Systems.System): the system to visualize. colordict (dict): a dictionary mapping fragments to colors. format (str): either SVG or Cairo. Returns: (str): the image to display. If it's SVG use SVG(result), Cairo Image(result). """ from rdkit.Chem import rdDepictor, Draw rdsys = convert_system_to_rdkit(sys) matching = compute_rdkit_matching(sys, rdsys, check_matching=False) # Setup the atom colors if colordict is not None: atcolor = {} for fragid, frag in sys.items(): for j, at in enumerate(frag): if at.sym == "H": continue idx = matching[fragid][j] atcolor[idx] = tuple(colordict[fragid]) dargs = {"highlightAtoms": range(rdsys.GetNumAtoms()), "highlightAtomColors": atcolor, "highlightBonds": None} else: dargs = {} # Do the drawing. if format == "Cairo": d2d = Draw.MolDraw2DCairo(-1, -1) elif format == "SVG": d2d = Draw.MolDraw2DSVG(-1, -1) else: raise ValueError("Wrong format for drawing") rdDepictor.Compute2DCoords(rdsys) d2d.DrawMolecule(rdsys, **dargs) d2d.FinishDrawing() return d2d.GetDrawingText()