Style Guide for ProDy


PEP 8, the Style Guide for Python Code, is adopted in the development of ProDy package. Contributions to ProDy shall follow PEP 8 and the specifications and additions provided in this addendum.

Code Layout


Use 4 spaces per indentation level in source code (.py) and never use tabs as a substitute.

In documentation files (.rst), use 2 spaces per indentation level.

Maximum line length

Limit all lines to a maximum of 79 characters in both source code and documentation files. Exceptions may be made when tabulating data in documentation files and strings. The length of lines in a paragraph may be much less than 79 characters if the line ends align better with the first line, as in this paragraph.


In cases where an encoding for a .py file needs to be specified, such as when characters like α, β, or Å are used in docstrings, use UTF-8 encoding, i.e. start the file with the following line:

# -*- coding: utf-8 -*-


In addition to PEP 8#imports recommendations regarding imports, the following should be applied:

  • relative intra-ProDy imports are discouraged, use from prody.atomic import AtomGroup not from atomic import AtomGroup
  • always import from second top level module, use from prody.atomic import AtomGroup and not from prody.atomic.atomgroup import AtomGroup, because file names may change or files that grow too big may be split into smaller modules, etc.

Here is a series of properly formatted imports following a module documentation string:

"""This module defines a function to calculate something interesting."""

import os.path
from collections import defaultdict
from time import time

import numpy as np

from prody.atomic import AtomGroup
from prody.measure import calcRMSD
from import openFile
from prody import LOGGER, SETTINGS

__all__ = ['calcSomething']


In addition to recommendations regarding whitespace use in Python code (PEP 8#whitespace-in-expressions-and-statements), two whitespace characters should follow a period in documentation files and strings to help reading documentation in terminal windows and text editors.

Naming Conventions

ProDy naming conventions aim at making the library suitable for interactive sessions, i.e. easy to remember and type.

Class names

Naming style for classes is CapitalizedWords (or CapWords, or CamelCase). Abbreviations and/or truncated names should be used to keep class names short. Some class name examples are:

  • ANM for Anisotropic Network Model
  • HierView for Hierarchical View

Exception names

Prefer using a suitable standard-library exception over defining a new one. If you absolutely need to define one, use the class naming convention. Use the suffix “Error” for exception names, when exception is an error:

Method and function names

Naming style for methods and functions is mixedCase, that differs from CapWords by initial lowercase character. Starting with a lowercase (no shift key) and using no underscore characters decreases the number of key strokes by half in many cases in interactive sessions.

Method and function names should start with a verb, suggestive on the action, and followed by one or two names, where the second name may start with a lower case letter. Some examples are moveAtoms(), wrapAtoms(), assignSecstr(), and calcSubspaceOverlap().

Abbreviations and/or truncated names should be used and obvious words should be omitted to limit number of names to 20 characters. For example, buildHessian() is preferred over buildHessianMatrix(). Another example is the change from using getResidueNames() to using AtomGroup.getResnames(). In fact, this was part of a series of major Release Notes aimed at refining the library for interactive usage.

In addition, the following should be applied to enable grouping of methods and functions based on their action and/or return value:

  • buildSomething(): methods and functions that calculate a matrix should start with build, e.g. GNM.buildKirchhoff() and buildDistMatrix()
  • calcSomething(): methods that calculate new data but does not necessarily return anything and especially those that take timely actions, should start with calc, e.g. PCA.calcModes()
  • getSomething(): methods, and sometimes functions, that return a copy of data should start with get, such as listReservedWords()
  • setSomething(): methods, and sometimes functions, that alter internal data should start with set

Variable Names

Variable names in functions and methods should contain only lower case letters, and may contain underscore characters to increase readability.