OEAtomSVGMarkupBase¶

class OEAtomSVGMarkupBase

OEAtomSVGMarkupBase is an abstract base class. Concrete classes derived from the base class define the markup of the atoms in .svg images that are generated when calling the OERenderMolecule function. Drawing elements representing atoms in the .svg images are grouped together in the following format in which the <group id> and <class name> strings can be defined in the derived concrete classes.

<g id='<group id>' class='<class name>'>
..
list of drawing elements
..
</g>

The following classes derive from this class:

OEAtomSVGAtomIdxMarkup

OEAtomSVGNoMarkup

OEAtomSVGResidueMarkup

See also

OE2DMolDisplayOptions.SetAtomSVGMarkupFunctor method
Generating Interactive SVG Images chapter

Note

User defined SVG atom marking can be implemented by deriving from this class and implementing all the methods listed below.

Example of using user defined SVG atom markings

class UserDataSVGAtomIdxMarkup(oedepict.OEAtomSVGMarkupBase):
    def GetClassName(self, atom):
        return "user-def-atom-class"

    def GetGroupId(self, atom):
        return "used-def-atom-{}".format(atom.GetIdx())

    def CreateCopy(self):
        return UserDataSVGAtomIdxMarkup().__disown__()


opts = oedepict.OE2DMolDisplayOptions(width, height, oedepict.OEScale_AutoScale)
opts.SetAtomSVGMarkupFunctor(UserDataSVGAtomIdxMarkup())
disp = oedepict.OE2DMolDisplay(mol, opts)

CreateCopy¶

OEAtomSVGMarkupBase *CreateCopy() const =0

Virtual const constructor which allows copying of concrete derived objects using a reference to this base class.

GetClassName¶

std::string GetClassName(const OEChem::OEAtomBase &) const =0

Returns the <class name> associated with a specific atom group in the .svg image. This is a virtual method that has to be implemented in the concrete derived classes. The return string will be verified by the OEIsValidSVGClassName function. Invalid SVG class names will be ignored.

GetGroupId¶

std::string GetGroupId(const OEChem::OEAtomBase &) const =0

Returns the <group id> associated with a specific atom group in the .svg image. This is a virtual method that has to be implemented in the concrete derived classes. The return string will be verified by the OEIsValidSVGGroupId function. Invalid SVG group ids will be ignored.