ChimeraX Recipes

Make attributes from ViewDockX column information

Here is Python code that converts the column information from the ViewDockX table into corresponding model attributes, which could then be used in color byattribute or other ChimeraX functions that work on attributes. The names of the generated attrbutes will be shown in the log, and whether they are numeric or non-numeric attributes. Opening the vdx_attrs.py code in ChimeraX generates the attributes

open vdx_attrs.py

Here’s an example docking output, with the ligands colored based on their generated vdx_Energy_score attribute

Here is the vdx_attrs.py code:

from chimerax.core.utils import string_to_attr
attr_names = set()
numeric_attr_names = set()
for m in session.models:
	if hasattr(m, 'viewdockx_data'):
		for k, v in m.viewdockx_data.items():
			attr_name = string_to_attr(k, prefix='vdx_')
			if attr_name not in attr_names:
				if isinstance(v, (float, int)):
					kw = { 'attr_type': type(v) }
					numeric_attr_names.add(attr_name)
				else:
					kw = { 'attr_type': str }
				from chimerax.atomic import Structure
				Structure.register_attr(session, attr_name, "ViewDockX attribute script", **kw)
				attr_names.add(attr_name)
			setattr(m, attr_name, v)
session.logger.info("The following numeric ViewDockX attributes were registered: %s" % ", ".join(sorted(list(numeric_attr_names))))
session.logger.info("The following non-numeric ViewDockX attributes were registered: %s" % ", ".join(sorted(list(attr_names - numeric_attr_names))))