OEPrepareAlignedDepictionFrom3D¶

**The overloaded versions of the OERenderActiveSite function**¶
Link	Description
OEPrepareAlignedDepictionFrom3D(fitmol2D, fitmol3D, refmol2D, refmol3D)	2D molecule alignment based on 3D
OEPrepareAlignedDepictionFrom3D(fitmol2D, fitmol3D,, refmol2D, refmol3D, opts)	2D molecule alignment based on 3D with options
OEPrepareAlignedDepictionFrom3D(fitmol2D, fitmol3D, shapequery)	2D molecule alignment to 3D shape query

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 molecule 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)

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.
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.

refmol2D = oechem.OEGraphMol(refmol3D)
oegrapheme.OEPrepareDepictionFrom3D(refmol2D)

fitmol2D = oechem.OEGraphMol(fitmol3D)
oegrapheme.OEPrepareAlignedDepictionFrom3D(fitmol2D, fitmol3D, refmol2D, refmol3D)

width, height = 300, 300
opts = oedepict.OE2DMolDisplayOptions(width, height, oedepict.OEScale_AutoScale)
refscale = oedepict.OEGetMoleculeScale(refmol2D, opts)
fitscale = oedepict.OEGetMoleculeScale(fitmol2D, opts)
opts.SetScale(min(refscale, fitscale))

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

fitdisp = oedepict.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)

bool OEPrepareAlignedDepictionFrom3D(OEChem::OEMolBase& fitmol2D,
                                     const OEChem::OEMolBase& fitmol3D,
                                     const OEShapeQueryDisplay& qdisp);

Generates the 2D coordinates of a molecule driven by the 3D overlay of the shape query display object.

fitmol2D: The molecule for which 2D coordinates are generated.
refmol2D: The 2D molecule whose orientation drives the 2D coordinate generation.
qdisp: The OEShapeQueryDisplay object that drives the layout of the 2D coordinate generation.