Entropy #3
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added the handling of Outliers during Binding Mode agregation in FastOPTICS fixed the update of neighbors in RandomProjectedNeighborsAndDensities::getNeighbors()
…pulation BindingPopulation::Entropize() is now called only once all BindingModes are added to Population. This change has been made to prevent multiple unecessary calls to this function when handling outliers. This function recalculates the enthalpy and the entropy of each BindingMode upon each call. BindingMode and BindingPopulation are now friends of the FastOPTICS class
…TICS.cpp and FastOPTICS_cluster.c
implementation of generate_genetic_variants() almost finished. TO DO: modifiy the arguments to accept the vector<int> cCenters instead of the array of int currently implmenting generate_true_negatives_clusters()
… at least one generation is needed to proceed to the clustering part. Need to implement a way out, because each generation will add variability to the population, hindering the Ideal part of an IdealPopulation
…the clustering phase this is going to be used to test the clustering algorithm as FastOPTICS removed unused function in FOPTICS.cpp and FOPTICS.h removed conversion warnings in the FastOPTICS and BindingMode classes implementations and functions
…other algorithm linked to that.
…ell-defined BindingMode
…ealPopulation generates chromosomes. I don't know why, but FastOPTICS seems to underperform when compared to two-prior commit (db97ffc)
…other point. added RandomProjectedNeighborsAndDensities::accept_intraset_distance() to verify that all pairwise intra-set distances are below a dist_threshold. added comments in chrom vectorization function and commented Population 2 to 5 in FastOPTICS_cluster. added RandomProjectedNeighborsAndDensities::Randomly_Selected_Chromosome() to select a random chrom as projection instead of a Randomized_X_Vectors. added the output of inverseDensities[] to file.optics. added the possibility to ExpandClusterOrder() with shuffled chromosomes
…TICS. FastOPTICS is now functional for IdealPopulation cases (for some minPts values). The current version of the BindingMode classifier creates more clusters than necessary in IdealPopulation (need some merges) the current version of the BindingMode classifier still struggle with real life docking, too many or too few clusters
…lassification in FastOPTICS::Classify_Population commented lines of codes in BindingMode.x FOPTICS.x
edited : minor corrections to remove_BindingMode and Classify_BindingModes
modified round functions and oject-releated constructors calls commented update_ClusterOrdering_PriorityQueue_elements() since its compilation was problematic under VS2010 and VS2015 for Windows AND this function was not used in the final build for Mac OS X
modified calls to objects contructors added a definition for round if undef ommented update_ClusterOrdering_PriorityQueue_elements() since its compilation was problematic under VS2010 and VS2015 for Windows AND this function was not used in the final build for Mac OS X
…functions ordering entropy_cluster now evaluate twice the number_results
… in order to be in radians instead of degrees (as specified in math C functions)
…grid.cpp in order to be in radians instead of degrees (as specified in math C functions)" This reverts commit 4b4239d.
…n slice_grid.cpp in order to be in radians instead of degrees (as specified in math C functions)"" This reverts commit 5ddf56b.
…ting by fitness" This reverts commit 0274129.
…slice_grid.cpp in order to be in radians instead of degrees (as specified in math C functions) modified Entropy related files in top.c FOPTICS.cpp ColonyEnergy.cpp entropy_cluster.c
…ts and the atomtypes contributions
…energy file added further nan values error-checking in BindingMode::compute_entropy()
…lpy() to compute_complex_enthaly() and compute_energy() to compute_complex_energy() in BindingMode
…r.c, BindingMode.cpp, BindingMode.h.
added comments and fixed variable initialization in BindingPopulation::output_Population_energy() in BindingMode.cpp
…y functions to BindingMode.cpp and BindingMode.h still need to implement the core of the featured functions
…pute_energy() who called compute_enthalpy instead of compute_entropy() in -T∆S
…sed in entropy and solvation calculations.
…f/else blocks for faster runtime
…ons. Added SolvatedPartitionFunction and output_Population_energy in BindingPopulation changes MAX_NUM_RES from 250 to 500
…ee_ligand_entropy/enthalpy is now substracted from complex_entropy/enthalpy added FreeLigandEnergyComparator SolvatedEnergyComparator sorting functions in BindingPopulation
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Okay, just updating all branches together before next global commit. |
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