| add_impl_hydr | Add implicit hydrogens |
| add_mol_attribs | Add additional attributes to all atoms in all molecules in... |
| align_arun | Rigin alignment with Arun algorithm |
| align_mdb_template | Aligns molecular database mdb using template templ |
| alkans74.mdb | Molecular database with 74 Alkanes |
| allign_mdb_seal | Aligns molecular database mdb using template mol_t and... |
| apply_par_list | apply_par_list |
| build_krr_model | To build krr model |
| 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_plot_coverage_mean_error | Produce coverage - mean error plot for applicability domain... |
| cinf_plot_d2m_error | Produce distance to model - error plot for applicability... |
| cinf_plotxy | Scatter plot |
| 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... |
| 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... |
| cmf_coef_xyz_sv_ex_mopac | Computes coefficient at point (x,y,z) using support vectors... |
| cmf_coef_xyz_sv_ex_phch | Computes coefficient at point (x,y,z) using support vectors... |
| cmf_comp_mopac_kernels_all | Computes CMF kernel matrices for the combined set of... |
| cmf_comp_mopac_kernels_pred | Computes MOPAC kernel matrices for prediction and saves to... |
| cmf_comp_mopac_kernels_train | Computes MOPAC kernel matrices for the training set and saves... |
| cmf_ecvr_plot_coverage_mean_error | Producing plot "coverage - mean error" for applicability... |
| cmf_ecvr_plot_d2m_error | Producing plot "distance to model - error" for applicability... |
| 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... |
| 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... |
| cmf_kernel | Computation of the kernel that compares fields of two... |
| cmf_kernel_al | Computation of the kernel that compares fields of two... |
| cmf_kernel_matrix_tp | Computation of the kernel matrix between the training and... |
| cmf_kernel_matrix_tt | Computation of the kernel (Gram) matrix for the training set |
| cmf_kernels_interpolate | Linear interpolation of kernel values |
| cmf_krr_ecv | External n-fold cross-validation |
| cmf_krr_ecv_mem | External n-fold cross-validation in memory |
| 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_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... |
| comp_ind_kernels_pred | Computes indicator kernel matrices for prediction and saves... |
| comp_kernels_all | Computes CMF kernel matrices for the combined set of... |
| comp_kernels_pred | Computes CMF kernel matrices for prediction and saves them to... |
| comp_kernels_train | Computes CMF kernel matrices for training and saves to file |
| cv_krr | KRR with cross-validation |
| def_fcolors | Define default colors for physico-chemical molecular fields |
| del_expl_hydr | Delete explicit hydrogens |
| eucldist2 | Calculation of the square of the Euclidean distance between... |
| euler_orth | Generation of orthogonal rotation matrix for Euler angles... |
| extract_new | Extract rows from new data frame corresponding to compounds... |
| find_substr_isomorph | Finds all substructure isomorphisms |
| fr | fr |
| full_design | Produces data frame with full design |
| gen_atomlists | Generate atom lists |
| gen_atomlists_generic | Generate atom lists for generic molecular field |
| gen_atomlists_ind | Generate atom lists for continuous indicator field |
| gen_atomlists_mopac | Generate atom lists for MOPAC molecular field |
| gen_atomlists_phch | Generate atom lists for physico-chemical molecular field |
| get_mol_charge | Returns charge of molecule |
| get_prop | Get data frame with property values |
| get_prop_names | Get the list of property names |
| get_props | Get data frame with property values |
| get_prop_vec | Get property values |
| get_syb_types_list | Extracts list of sybyl types of atoms |
| get_syb_types_list_ex | Extended version of get_syb_types_list |
| grid_view_level | grid_view_level |
| grid_view_part | grid_view_part |
| grid_view_rlevel | grid_view_rlevel |
| make_atom_lists | Creation of atom lists |
| make_freq_table | Make frequency table |
| mdb_get_num_comp | Get the number of compounds in molecular database |
| mdb_get_prop_matr1 | Extract property one-column matrix by name |
| mdb_get_prop_names | Get the list of property names |
| mdb_get_prop_vect | Get property values |
| mdb_keep_matr_with_prop | Keep in matrix only rows and columns corresponding to... |
| mdb_keep_with_prop | Keep in molecular database only compounds containing values... |
| mlr | Build multiple linear regression model |
| mol2xyz | mol2xyz |
| mol_get_chelabs | Return array of chemical element labels |
| mol_get_ct | Return connection table for a molecule |
| mol_view_cpk | mol_view_cpk |
| mol_view_cylinders | mol_view_cylindres |
| mol_view_lines | mol_view_lines |
| normalize_gram | Normalization of the Gram matrix |
| pert_mdb | Perturbate molecular database |
| pert_mol | Perturbate molecule |
| plot_mlr_model | Makes scatter plot for MLR model |
| plot_regr | Plots regression |
| PT | Periodic Table |
| q2r | Converts quaternions to rotation mstrix |
| read_coordinates | read coordinates of atoms in molecule |
| read_integers | read ncount integers |
| read_lower_half_triangle | read lower half triangle |
| read_matrix | read rectangular matrix |
| read_mol2 | Read Sybyl mol2-file |
| read_mopac_out_file | Read mopac output file |
| read_reals | read ncount real numbers |
| read_sdf | Read sdf-file |
| read_strings | read ncount string tokens |
| read_tripos_ff | Reads TRIPOS force field |
| regr_param | Computes regression parameters: R2, RMSE, RMSE_pc, MAE |
| regr_param_ex | Computes extended set of regression parameters: R2ex |
| rmse4mol | rmse4mol |
| rmse4xyz | rmse4xyz |
| rnd_euler_orth | Generation of random orthogonal rotation matrix |
| rnd_rotmat_xyz | Generation of random rotation matrix |
| rnd_trans_vec | Random translation vector |
| rotmat_xyz | Generation of rotation matrix around x,y,z axes: alpha_(yaw),... |
| run_mopac | Run mopac executable |
| sample_subst | Produces data frame with samples of substitutions |
| substr_mask | Extract substructure from a molecule using mask |
| substruct | Extract substructure from a molecule |
| superpose_mol | Superposes moving molecule mol_m on templace molecule mol_t |
| superpose_mol_seal | superpose_mol_seal |
| test_isomorph | Finds mol2 in mol1 |
| transfer_props | Transfer properties from one mdb to another |
| transform_mol | transform_mol |
| transform_xyz | transform_xyz |
| try_current_hyper_params | Try current set of hyperparameters |
| write_mol2 | Write Sybyl mol2-file |
| write_mopac_input_file | Writes MOPAC inpout file with Cartesian coordinates |
| write_sdf | Write sdf-file |
| xyz2mol | xyz2mol |
