OEPrepareAlignedDepictionFrom3D¶

bool OEPrepareAlignedDepictionFrom3D(OEChem::OEMolBase &fitmol2D,
                                     const OEChem::OEMolBase &fitmol3D,
                                     const OEChem::OEMolBase &refmol2D,
                                     const OEChem::OEMolBase &refmol3D,
                                     bool clearCoords=true, bool suppressH=true)

Generates the 2D coordinates of a molecule driven by the 3D overlay of the 3D reference and the 3D fit molecules and the orientation of the 2D reference molecule.

fitmol2D

The molecule for which 2D coordinates are generated.

refmol2D

The 2D molecule whose orientation drives the 2D coordinate generation.

fitmol3D, refmol3D

The 3D molecules whose overlay drives the 2D coordinate generation.

clearCoords

If false and the fitmol2D has 2D coordinates, then these coordinates are used for the alignment. Otherwise the 2D coordinates of the fitted molecule are generated by calling the OEPrepareDepictionFrom3D function.

suppressH

If true, then explicit hydrogens are suppressed when generating the 2D coordinates of the fitted molecule. Only hydrogens that are necessary to faithfully represent tetrahedral stereochemistry will be kept.

bool OEPrepareAlignedDepictionFrom3D(OEChem::OEMolBase &fitmol2D,
                                     const OEChem::OEMolBase &fitmol3D,
                                     const OEChem::OEMolBase &refmol2D,
                                     const OEChem::OEMolBase &refmol3D,
                                     const OEAlignedDepictionFrom3DOptions &opts)

fitmol2D

The molecule for which 2D coordinates are generated.

refmol2D

The 2D molecule whose orientation drives the 2D coordinate generation.

fitmol3D, refmol3D

The 3D molecules whose overlay drives the 2D coordinate generation.

opts

The OEAlignedDepictionFrom3DOptions object that stores options controlling the generation of 2D coordinates.

The following code snippet shows how to use the OEPrepareAlignedDepictionFrom3D function. See generated images in Table: 2D depiction based on 3D molecule overlay.

OEGraphMol refmol2D = new OEGraphMol(refmol3D);
OEGrapheme.OEPrepareDepictionFrom3D(refmol2D);

OEGraphMol fitmol2D = new OEGraphMol(fitmol3D);
OEGrapheme.OEPrepareAlignedDepictionFrom3D(fitmol2D, fitmol3D, refmol2D, refmol3D);


OE2DMolDisplayOptions opts = new OE2DMolDisplayOptions(width, height, OEScale.AutoScale);
double refscale = OEDepict.OEGetMoleculeScale(refmol2D, opts);
double fitscale = OEDepict.OEGetMoleculeScale(fitmol2D, opts);
opts.SetScale(Math.Min(refscale, fitscale));

OE2DMolDisplay refdisp = new OE2DMolDisplay(refmol2D, opts);
OEDepict.OERenderMolecule("OEPrepareAlignedDepictionFrom3D-ref-2D.png", refdisp);

OE2DMolDisplay fitdisp = new OE2DMolDisplay(fitmol2D, opts);
OEDepict.OERenderMolecule("OEPrepareAlignedDepictionFrom3D-fit-2D.png", fitdisp);

2D depiction based on 3D molecule overlay

3D reference molecule	3D molecule overlay	3D fit molecule
2D reference molecule (generated by OEPrepareDepictionFrom3D)		2D fit molecule (generated by OEPrepareAlignedDepictionFrom3D)