27 orientational entropy

[skfegan]

Summary

This pull request adds the basic orientational entropy calculation.

Changes

Adding Neighbours to Levels:

• Functions for counting the number of neighbours (two methods available - RAD and grid)
• Function for guessing symmetry number using RDKit structure matching functions
• Function for identifying linear molecules using RDKit labels of hybridization types for molecules with more than two united atom beads

Orientational Entropy Calculation:

• Adds the orientational term to the entropy calculation

Conformational Entropy:

• Fixing a small bug in conformational entropy by removing one equals sign in the identifying of peaks.

Documentation

• Update to science.rst to describe the orientational entropy calculation
• Update to conf.rst to include the neighbours search_type option

Impact

• The orientational entropy term is now included to give a more complete entropy value.
• The conformational entropy is improved by not identifying extraneous peaks in the histogram.
• Documentation expanded to cover the orientational entropy theory.