msmbuilder.cfep.contact_reaction_coordinate¶

msmbuilder.cfep.contact_reaction_coordinate(trajectory, weights)[source]¶

Computes a residue-contact based reaction coordinate.

Specifically, the reaction coordinate is a weighted linear combination of the alpha carbon distances for each residue. Weights can take any value, including negative and zero values.

Parameters:	trajectory : msmbuilder trajectory The trajectory along which to compute the reaction coordinate value weights : nd_array, float The weights to apply to all the inter-residue (Ca-Ca) distances
Returns:	rc_value : nd_array, float The reaction coordinate value for each snapshot of trajectory