Depicting Topological Polar Surface Area

Problem

You want to depict the topological polar surface area (TPSA) of a molecule. See example in Figure 1.

../_images/psa2img.png — **Figure 1. Example of depiction of topological polar surface area**

Ingredients

OEChem TK - cheminformatics toolkit
MolProp TK - molecular property calculation and filtering toolkit
OEDepict TK - molecule depiction toolkit
Grapheme TK - molecule and property visualization toolkit

Difficulty Level

Solution

The code snippet below shows how to calculate the total polar surface area of a molecule along with the atom contributions by calling the OEGet2dPSA function. Each atom contribution is then attached to the relevant atom as generic data with the given tag.

def SetAtomProperties(mol, tag, minvalue=float("inf"), maxvalue=float("-inf"), SAndP=True):

    avals = oechem.OEFloatArray(mol.GetMaxAtomIdx())
    psa = oemolprop.OEGet2dPSA(mol, avals, SAndP)

    mol.SetTitle(mol.GetTitle() + "Topological Polar Surface Area = %.2f" % psa)

    for atom in mol.GetAtoms():
        val = avals[atom.GetIdx()]
        atom.SetData(tag, val)
        minvalue = min(minvalue, val)
        maxvalue = max(maxvalue, val)

    return minvalue, maxvalue

The PSAArcFxn class below shows how to project the atom contributions of the polar surface area into a molecule surface of an atom . The __call__ method of the class takes a OESurfaceArc object that stores data required for drawing the arcs of molecule surface. The color of the arc of the molecule surface is determined by the polar surface area value attached to atom (lines 19-21). The molecule surface is rendered by using the OEDrawEyelashSurfaceArc function that draws an “eyelash” style arc with the given parameters (lines 28-36). In this case the darker colors and longer spikes indicate larger polar surface area contributions.

class PSAArcFxn(oegrapheme.OESurfaceArcFxnBase):
    def __init__(self, colorg, tag, pen):
        oegrapheme.OESurfaceArcFxnBase.__init__(self)
        self.colorg = colorg
        self.tag = tag
        self.pen = pen

    def __call__(self, image, arc):

        adisp = arc.GetAtomDisplay()
        if adisp is None or not adisp.IsVisible():
            return False

        atom = adisp.GetAtom()
        atompsa = atom.GetData(self.tag)
        if atompsa == 0.0:
            return True

        pen = oedepict.OEPen(self.pen)
        color = self.colorg.GetColorAt(atompsa)
        pen.SetForeColor(color)

        center = arc.GetCenter()
        bgnAngle = arc.GetBgnAngle()
        endAngle = arc.GetEndAngle()
        radius = arc.GetRadius()

        edgeAngle = 10.0
        patternDirection = oegrapheme.OEPatternDirection_Outside
        patternAngle = 10.0
        minPatternWidthRatio = 0.05
        maxPatternWidthRatio = 0.70
        actPatternWidthRatio = min(maxPatternWidthRatio, atompsa * (maxPatternWidthRatio / 40.0))
        oegrapheme.OEDrawEyelashSurfaceArc(image, center, bgnAngle, endAngle, radius, pen,
                                           edgeAngle, patternDirection, patternAngle,
                                           minPatternWidthRatio, actPatternWidthRatio)
        return True

    def CreateCopy(self):
        return PSAArcFxn(self.colorg, self.tag, self.pen).__disown__()

The DepictMoleculeWithPSA function below shows how to render a molecule along with its molecule surface customized to visualize the atom contributions of the polar surface area. After assigning the atom contributions to each atom (lines 6-7), an OELinearColorGradient object is constructed using the minimum and maximum contributions. This color gradient is used by the PSAArcFxn class to color the molecule surfaces based on the polar surface area values. The PSAArcFxn class that defines the style how the molecule surface is rendered is the attached to each atom by calling the OESetSurfaceArcFxn function (lines 14-15). Finally, the molecule is rendered along with its molecule surface by calling the OEDraw2DSurface function (lines 17-19).

def DepictMoleculeWithPSA(image, mol, opts):

    scale = oegrapheme.OEGetMoleculeSurfaceScale(mol, opts)
    opts.SetScale(scale)

    tag = oechem.OEGetTag("PSA")
    minvalue, maxvalue = SetAtomProperties(mol, tag, True)

    ncolor = oechem.OEColorStop(minvalue, oechem.OEWhite)
    pcolor = oechem.OEColorStop(maxvalue, oechem.OEDarkBlue)
    colorg = oechem.OELinearColorGradient(ncolor, pcolor)

    arcfxn = PSAArcFxn(colorg, tag, opts.GetDefaultBondPen())
    for atom in mol.GetAtoms():
        oegrapheme.OESetSurfaceArcFxn(mol, atom, arcfxn)

    disp = oedepict.OE2DMolDisplay(mol, opts)
    oegrapheme.OEDraw2DSurface(disp)
    oedepict.OERenderMolecule(image, disp)

Hint

You can easily adapt this example to visualize other atom properties by writing your own SetAtomProperties function.

Download code

psa2img.py and psa_utils.py

Usage:

prompt > python3 psa2img.py molecule.ism psa.png

Discussion

The example above shows how to visualize the polar surface area for a single molecule, however you might want to visualize the polar surface area for a set of molecules.

The DepictMoleculesWithPSA function shows how the minimum and maximum polar surface area values are calculated for a set of molecules (lines 10-13). These values are then used to initialize the linear color gradient that is used to color the molecule surfaces base on the polar surface area (lines 15-19). The molecule surface is then calculated for each molecule (lines 23-24) and the molecule along with its molecule surface is rendered into a cell of an OEReport object (lines 26-30). The OEReport class is a layout manager that allows generation of multi-page images in a convenient way. You can see the generated multi-page PDF in Table 1.

def DepictMoleculesWithPSA(report, mollist, opts):

    molscale = float("inf")
    for mol in mollist:
        molscale = min(molscale, oegrapheme.OEGetMoleculeSurfaceScale(mol, opts))
    opts.SetScale(molscale)

    tag = oechem.OEGetTag("PSA")

    minvalue = float("inf")
    maxvalue = float("-inf")
    for mol in mollist:
        minvalue, maxvalue = SetAtomProperties(mol, tag, minvalue, maxvalue, True)

    ncolor = oechem.OEColorStop(minvalue, oechem.OEWhite)
    pcolor = oechem.OEColorStop(maxvalue, oechem.OEDarkBlue)
    colorg = oechem.OELinearColorGradient(ncolor, pcolor)

    arcfxn = PSAArcFxn(colorg, tag, opts.GetDefaultBondPen())

    for mol in mollist:

        for atom in mol.GetAtoms():
            oegrapheme.OESetSurfaceArcFxn(mol, atom, arcfxn)

        disp = oedepict.OE2DMolDisplay(mol, opts)
        oegrapheme.OEDraw2DSurface(disp)

        cell = report.NewCell()
        oedepict.OERenderMolecule(cell, disp)

**Table 1. Example of depiction of polar surface areas for a set of molecules** (The pages are reduced here for visualization convenience)
page 1	page 2	page 3

Download code

psa2pdf.py and psa_utils.py

Usage:

prompt > python3 psa2pdf.py molecule.sdf psa.pdf

Depicting Topological Polar Surface Area

Problem

Ingredients

Difficulty Level

Solution

Discussion

See also in OEChem TK manual

See also in MolProp TK manual

See also in OEDepict TK manual

See also in Grapheme^TM TK manual

Depicting Topological Polar Surface Area

Problem

Ingredients

Difficulty Level

Solution

Discussion

See also in OEChem TK manual

See also in MolProp TK manual

See also in OEDepict TK manual

See also in GraphemeTM TK manual

See also in Grapheme^TM TK manual