calc_accuracy |
Calculate classification accuracy |
calc_af |
calc_af |
calc_balaccuracy |
Calculate classification balanced accuracy |
calc_distance_matrix |
Compute distance matrix from connection table |
calc_f1 |
Calculate classification F1-score |
calc_fukui |
calc_fukui |
calc_kappa |
Calculate kappa-statistics |
calc_matcorcoef |
Calculate Matthews correlation coefficient |
calc_mol2mol_transvec |
calc mol2mol transvec |
calc_mol_mopac |
calc_mol_mopac |
calc_precision |
Calculate classification precision |
calc_recall |
Calculate classification recall |
calc_sensitivity |
Calculate classification sensitivity |
calc_specificity |
Calculate classification specificity |
calc_wij |
calc_wij |
cinf_plotxy |
Scatter plot |
cinf_plot_coverage_mean_error |
Produce coverage - mean error plot for applicability domain studies |
cinf_plot_d2m_error |
Produce distance to model - error plot for applicability domain studies |
cmf_aa_ind_kernel |
Indicator fields |
cmf_aa_kernel |
Computation of the kernel that compares fields of two atoms |
cmf_calc_combined_kernels |
Kernel combination with linear interpolation |
cmf_calc_combined_kernels_1alpha |
Kernel combination with linear interpolation for fields with the same value of alpha |
cmf_calc_mdb_mopac |
cmf_calc_mdb_mopac |
cmf_calc_mdb_mopac_mem |
cmf_calc_mdb_mopac_mem |
cmf_coef_grid |
Computes coefficients for grid |
cmf_coef_grid_ex |
Computes coefficients for grid |
cmf_coef_grid_sv |
Computes coefficients for grid using support vectors |
cmf_coef_grid_sv_ex |
Computes coefficients for grid using support vectors |
cmf_coef_xyz |
Computes coefficient at point (x,y,z) |
cmf_coef_xyz_ex |
Computes coefficient at point (x,y,z) |
cmf_coef_xyz_sv |
Computes coefficient at point (x,y,z) using support vectors |
cmf_coef_xyz_sv_ex_ind |
Computes coefficient at point (x,y,z) using support vectors for continuous indicator field |
cmf_coef_xyz_sv_ex_mopac |
Computes coefficient at point (x,y,z) using support vectors for mopac molecular fields |
cmf_coef_xyz_sv_ex_phch |
Computes coefficient at point (x,y,z) using support vectors for physico-chemical molecular fields |
cmf_comp_mopac_kernels_all |
Computes CMF kernel matrices for the combined set of molecules and mopac fields |
cmf_comp_mopac_kernels_pred |
Computes MOPAC kernel matrices for prediction and saves to file |
cmf_comp_mopac_kernels_train |
Computes MOPAC kernel matrices for the training set and saves it to file |
cmf_ecvr_plot_coverage_mean_error |
Producing plot "coverage - mean error" for applicability domain studies Prediction variance is taken as distance to model |
cmf_ecvr_plot_d2m_error |
Producing plot "distance to model - error" for applicability domain studies Prediction variance is taken as distance to model |
cmf_extract_subkernels |
To extract subkernels |
cmf_fval_grid |
Computes field values for grid |
cmf_fval_xyz |
Computes field value at point (x,y,z) |
cmf_gen_grid |
Generation of grid for continuous molecular co-fields |
cmf_gen_grid_ex |
Generation of grid for continuous molecular co-fields Extended version with field families |
cmf_gen_grid_mopac |
Generation of grid for MOPAC molecular co-fields |
cmf_indicator_kernel |
Indicator kernel |
cmf_indicator_kernel_matrix |
Indicator kernel matrix |
cmf_indicator_kernel_matrix_pred |
Indicator kernel matrix predictor |
cmf_init_grid |
Initializes grid for a given step and margin around molecules from database |
cmf_kernel |
Computation of the kernel that compares fields of two molecules |
cmf_kernels_interpolate |
Linear interpolation of kernel values |
cmf_kernel_al |
Computation of the kernel that compares fields of two molecules with specified atom lists |
cmf_kernel_matrix_tp |
Computation of the kernel matrix between the training and prediction sets |
cmf_kernel_matrix_tt |
Computation of the kernel (Gram) matrix for the training set |
cmf_krr_ecv |
External n-fold cross-validation |
cmf_krr_ecvr |
External n-fold cross-validation with reshuffings |
cmf_krr_ecvr_mem |
External n-fold cross-validation with reshuffling in memory |
cmf_krr_ecvr_pred |
To make predictions using ecvr results |
cmf_krr_ecvr_pred_mem |
To make predictions using ecvr results in memory |
cmf_krr_ecv_mem |
External n-fold cross-validation in memory |
cmf_krr_pred |
To make predictions |
cmf_krr_pred_mem |
To meke predictions in memory |
cmf_krr_train |
To build model |
cmf_krr_train_mem |
To build model in memory |
cmf_merge_kernels |
Merging files with computed kernels |
cmf_moldim |
Returns dimensions of molecule |
cmf_multiply_fields |
Get product of two fields |
cmf_params_mopac |
Computing kernels based on MOPAC results |
cmf_params_tripos |
Parameters for CMF |
cmf_permute_kernels |
To permute kernel matrix using given permutation |
cmf_pred_anal |
Making predictions with analysis |
cmf_pred_anal_atoms |
Making predictions with analysus of ampacts of each atom |
cmf_view_mol_field_cofield |
View molecule, co-field and field |
cmf_view_mol_field_cofield_mopac |
View molecule, co-field and field |
comp_ind_kernels_all |
Computes CMF kernel matrices for the combined set of molecules and indicator fields |
comp_ind_kernels_pred |
Computes indicator kernel matrices for prediction and saves to file |
comp_kernels_all |
Computes CMF kernel matrices for the combined set of molecules |
comp_kernels_pred |
Computes CMF kernel matrices for prediction and saves them to file |
comp_kernels_train |
Computes CMF kernel matrices for training and saves to file |
cv_krr |
KRR with cross-validation |