Depicting Polar Hydrogens

Problem

You want to depict your molecule with explicit polar hydrogens. See example in Figure 1.

../_images/DepictPolarHydrogens1.png

Figure 1. Example of depicting polar hydrogens

Ingredients

Difficulty Level

../_images/chilly1.png

Solution

Before rendering a molecule, the OEPrepareDepiction function should be called which prepares the molecule for depiction. This function perceives atom and bond stereo information and suppresses or adds hydrogens if necessary. By default, the explicit hydrogens are suppressed by the OEPrepareDepiction function, see example (A) in Table: Example of default molecule depiction. Only hydrogens that are necessary to faithfully represent tetrahedral stereochemistry are added, see example (B) in Table 1.

Table 1. Example of default molecule depiction
( A ) ( B )
../_images/DepictDefault.png ../_images/DepictDefault-StereoH.png

If the molecule has only implicit hydrogens then you can add the polar hydrogens by calling the OEAddExplicitHydrogens function with the polarOnly = True parameter (lines 3-4), before preparing the molecule for depiction. It is important to call the OEPrepareDepiction function with clearcoords = True and suppressH = False parameters (lines 6-8).

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def DepictMoleculeWithPolarHydrogens(mol, opts, filename):

    polarOnly = True
    oechem.OEAddExplicitHydrogens(mol, polarOnly)

    clearcoords = True
    suppressH = False
    oedepict.OEPrepareDepiction(mol, clearcoords, suppressH)

    disp = oedepict.OE2DMolDisplay(mol, opts)
    oedepict.OERenderMolecule(filename, disp)

Discussion

If the molecule already has explicit hydrogens then you can suppress all non polar hydrogens by calling the OESuppressHydrogens function with retainPolar = True parameter (lines 3-4), prior to preparing the molecule for depiction.

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def DepictMoleculeOnlyPolarHydrogens(mol, opts, filename):

    retainPolar = True
    oechem.OESuppressHydrogens(mol, retainPolar)

    clearcoords = True
    suppressH = False
    oedepict.OEPrepareDepiction(mol, clearcoords, suppressH)

    disp = oedepict.OE2DMolDisplay(mol, opts)
    oedepict.OERenderMolecule(filename, disp)

See Also in OEChem TK Manual

API

See Also in OEDepict TK Manual

Theory

API