Miscellaneous Tools

This module defines miscellaneous functions dealing with protein data.

showProtein(*atoms, **kwargs)[source]

Show protein representation using Axes3D(). This function is designed for generating a quick view of the contents of a AtomGroup or Selection.

Protein atoms matching "calpha" selection are displayed using solid lines by picking a random and unique color per chain. Line with can be adjusted using lw argument, e.g. lw=12. Default width is 4. Chain colors can be overwritten using chain identifier as in A='green'.

Water molecule oxygen atoms are represented by red colored circles. Color can be changed using water keyword argument, e.g. water='aqua'. Water marker and size can be changed using wmarker and wsize keywords, defaults values are wmarker='.', wsize=6.

Hetero atoms matching "hetero and noh" selection are represented by circles and unique colors are picked at random on a per residue basis. Colors can be customized using residue name as in NAH='purple'. Note that this will color all distinct residues with the same name in the same color. Hetero atom marker and size can be changed using hmarker and hsize keywords, default values are hmarker='o', hsize=6.

ProDy will set the size of axis so the representation is not distorted when the shape of figure window is close to a square. Colors are picked at random, except for water oxygens which will always be colored red.

writePQR(filename, atoms)[source]

Write atoms in PQR format to a file with name filename. Only current coordinate set is written. Returns filename upon success. If filename ends with .gz, a compressed file will be written.