Structural Bioinformatics Library
Template C++ / Python API for developping structural bioinformatics applications.

Authors: F. Cazals and T. Dreyfus and D. Mazauric and C. Roth
This package provides methods to compare, from a geometric/structural standpoint, two ensembles of conformations.
Consider two conformational ensembles, also called samplings, as defined in section Conformational ensembles  aka samplings . Let be some distance between two conformations.
This package offers methods two compare these two ensembles in different ways:
computing the Hausdorff distance between ensembles
These functionalities are provided in the program .
A standard problem in analyzing ensembles of conformations consists of comparing two such ensembles. For example, one may wish to compare two sets of local minima, or two sets of structures selected for their relevance in a particular context.
To perform such an assessment, consider two sets of conformations, denoted for convenience (say the reference set), and . In the sequel, we consider a comparison criterion involving one distance for each conformation from and .
We do so by computing a minimal spanning forest of a weighted complete bipartite graph induced by the two sets and . More precisely, the nodes represent the conformations and there is an edge between every node representing a conformation and every node representing a conformation . The weight of an edge is the distance . The problem then consists of computing a minimum weight subset of edges such that every node of the bipartite graph is incident to at least one edge of this subset. This means that every conformation is associated with at least another one. More precisely, considering the aforementioned spanning forest as directed, each conformation is constrained to have exactly one outgoing edge, connecting it to the nearest conformation.
Note that the following pieces of information are returned:
High level statistics: the sum of weights of oriented arcs.
Low level statistics: the list of oriented edges and their weight that is a list of triples.
Comparing sets of minima using a Minimum Oriented Spanning Forest (MSF) Each conformation from a sampling picks the nearest neighbor in the second set. Note that the process is not symmetric: picks , but picks . 
To get a global criterion, we introduce the socalled Hausdorff distance, a type criterion.
Consider the previous sets of conformations and . To assess the coverage of the set by , we compute for every sample its nearest neighbor in :
We then report the following triple:
Note that the third entry in Eq. (eqhausdorfftriple) is the socalled onesided Hausdorff distance between and – the sample from which is the most isolated from .
One sided Hausdorff distance Given two sets of conformations, one seeks for each of them the sample located furthest in the second sampling. Maximizing this distance yields the one sided Hausdorff distance. 
Given two samplings and , two useful operations are to compute
the symmetric difference : and .
Note that the previous set operations are performed up to a userspecified tolerance on the distance .
The input is two conformational ensembles of the same molecule, and can be provided with several format:
6 x11 y11 z11 x12 y12 z12 6 x21 y21 z21 x22 y22 z22 6 x31 y31 z31 x32 y32 z32 ...
All comparisons are optional, so that they have to be specified in the commandline. For example, running Hausdorff comparison is done using the option –Hausdorff. Thus, a calculation is launched as follows:
> sblconfensemblecomparisonlrmsd.exe pointsfile data/bln69_sampling.txt pointsfile data/bln69_10_lowest_minima.txt Hausdorff symmetricdifference identitythreshold 0.01 exactsearch directory results verbose outputprefix log
File Name  Description 
BLN69 conformations file  Sampling done from sbllandexphybridBHTRRTBLN.exe 
BLN69 conformations file  Ten lowest local minima of BLN69 obtained by an external sampling method 
Preview  File Name  Description 
General: log file  
Log file  Log file containing high level information on the run of  
Module MSF analysis: Minimum spanning forest  
Conformation matches text file  List of edges of the MSF with the distance between the selected conformations  
Module symmetric difference analysis: intersection and symmetric difference  
Conformation matches text file  List the pair of indices of conformations that match 
It is easily shown that an optimal subset of edges induces a forest; i.e., a subgraph without cycles. A simple algorithm consists of choosing, for every node, the incident edge with the smallest weight. This strategy corresponds to the first step of 's algorithm for computing a minimum spanning tree in a graph [113] . (See also Boruvka's algorithm.) Note that if the weights are not all different, a correction step is necessary in order to avoid cycles.
Two strategies are offered to compute the nearest neighbor of each sample:
Brute force: a linear scan is used to find the exact nearest neighbor.
Approximate: data structures to perform approximate nearest neighbor searches are used, see package Spatial_search
The nearest neighbor of each sample is computed during the MSF calculations. This information is used to compute the Hausdorff triple of Eq. eqhausdorfftriple.
The programs of Conformational_ensemble_comparison described above are based upon generic C++ classes, so that additional versions can easily be developed.
In order to derive other versions, there are two important ingredients, that are the workflow class, and its traits class.
T_Conformational_ensemble_comparison_traits:
This class defines the main types used in the modules of the workflow. It is templated by the classes of the concepts required by these modules. This design makes it possible to use the same workflow within different(biophysical) contexts to make new programs. To use the workflow T_Conformational_ensemble_comparison_workflow , one needs to define:
GeometricKernel  Traits class defining various geometric objects, in particular the number type used for representing the coordinates of a conformation, and the base representation of a point in dimension D – see class CGAL::Cartesian_d from the CGAL library 
DistanceFunctor  Functor computing the distance between two conformations. It has to define the type Point representing the geometric representation of a conformation and the type FT representing the number type of the distance. 
T_Conformational_ensemble_comparison_interface_workflow: