All functions
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PT
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Periodic Table |
add_impl_hydr()
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Add implicit hydrogens |
add_mol_attribs()
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Add additional attributes to all atoms in all molecules in molecular database |
align_arun()
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Rigin alignment with Arun algorithm |
align_mdb_template()
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Aligns molecular database mdb using template templ |
alkans74.mdb
|
Molecular database with 74 Alkanes |
align_mdb_seal()
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Aligns molecular database mdb using template mol_t and algorithm SEAL |
apply_par_list()
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apply_par_list |
build_krr_model()
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To build krr model |
calc_accuracy()
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Calculate classification accuracy |
calc_af()
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calc_af |
calc_balaccuracy()
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Calculate classification balanced accuracy |
calc_distance_matrix()
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Compute distance matrix from connection table |
calc_f1()
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Calculate classification F1-score |
calc_fukui
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calc_fukui |
calc_kappa()
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Calculate kappa-statistics |
calc_matcorcoef()
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Calculate Matthews correlation coefficient |
calc_mol2mol_transvec()
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calc mol2mol transvec |
calc_mol_mopac()
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calc_mol_mopac |
calc_precision()
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Calculate classification precision |
calc_recall()
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Calculate classification recall |
calc_sensitivity()
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Calculate classification sensitivity |
calc_specificity()
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Calculate classification specificity |
calc_wij
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calc_wij |
cinf_plot_coverage_mean_error()
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Produce coverage - mean error plot for applicability domain studies |
cinf_plot_d2m_error()
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Produce distance to model - error plot for applicability domain studies |
cinf_plotxy()
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Scatter plot |
cmf_aa_ind_kernel()
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Indicator fields |
cmf_aa_kernel()
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Computation of the kernel that compares fields of two atoms |
cmf_calc_combined_kernels()
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Kernel combination with linear interpolation |
cmf_calc_combined_kernels_1alpha()
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Kernel combination with linear interpolation for fields with the same value of alpha |
cmf_calc_mdb_mopac()
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cmf_calc_mdb_mopac |
cmf_calc_mdb_mopac_mem()
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cmf_calc_mdb_mopac_mem |
cmf_coef_grid()
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Computes coefficients for grid |
cmf_coef_grid_ex()
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Computes coefficients for grid |
cmf_coef_grid_sv()
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Computes coefficients for grid using support vectors |
cmf_coef_grid_sv_ex()
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Computes coefficients for grid using support vectors |
cmf_coef_xyz()
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Computes coefficient at point (x,y,z) |
cmf_coef_xyz_ex()
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Computes coefficient at point (x,y,z) |
cmf_coef_xyz_sv()
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Computes coefficient at point (x,y,z) using support vectors |
cmf_coef_xyz_sv_ex_ind()
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Computes coefficient at point (x,y,z) using support vectors
for continuous indicator field |
cmf_coef_xyz_sv_ex_mopac()
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Computes coefficient at point (x,y,z) using support vectors
for mopac molecular fields |
cmf_coef_xyz_sv_ex_phch()
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Computes coefficient at point (x,y,z) using support vectors
for physico-chemical molecular fields |
cmf_comp_mopac_kernels_all()
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Computes CMF kernel matrices for the combined set of molecules and mopac fields |
cmf_comp_mopac_kernels_pred()
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Computes MOPAC kernel matrices for prediction and saves to file |
cmf_comp_mopac_kernels_train()
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Computes MOPAC kernel matrices for the training set and saves it to file |
cmf_ecvr_plot_coverage_mean_error()
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Producing plot "coverage - mean error" for applicability domain studies
Prediction variance is taken as distance to model |
cmf_ecvr_plot_d2m_error()
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Producing plot "distance to model - error" for applicability domain studies
Prediction variance is taken as distance to model |
cmf_extract_subkernels()
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To extract subkernels |
cmf_fval_grid()
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Computes field values for grid |
cmf_fval_xyz()
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Computes field value at point (x,y,z) |
cmf_gen_grid()
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Generation of grid for continuous molecular co-fields |
cmf_gen_grid_ex()
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Generation of grid for continuous molecular co-fields
Extended version with field families |
cmf_gen_grid_mopac()
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Generation of grid for MOPAC molecular co-fields |
cmf_indicator_kernel()
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Indicator kernel |
cmf_indicator_kernel_matrix()
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Indicator kernel matrix |
cmf_indicator_kernel_matrix_pred()
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Indicator kernel matrix predictor |
cmf_init_grid()
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Initializes grid for a given step and margin around molecules from database |
cmf_kernel()
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Computation of the kernel that compares fields of two molecules |
cmf_kernel_al()
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Computation of the kernel that compares fields of two molecules
with specified atom lists |
cmf_kernel_matrix_tp()
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Computation of the kernel matrix between the training and prediction sets |
cmf_kernel_matrix_tt()
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Computation of the kernel (Gram) matrix for the training set |
cmf_kernels_interpolate()
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Linear interpolation of kernel values |
cmf_krr_ecv()
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External n-fold cross-validation |
cmf_krr_ecv_mem()
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External n-fold cross-validation in memory |
cmf_krr_ecvr()
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External n-fold cross-validation with reshuffings |
cmf_krr_ecvr_mem()
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External n-fold cross-validation with reshuffling in memory |
cmf_krr_ecvr_pred()
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To make predictions using ecvr results |
cmf_krr_ecvr_pred_mem()
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To make predictions using ecvr results in memory |
cmf_krr_pred()
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To make predictions |
cmf_krr_pred_mem()
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To meke predictions in memory |
cmf_krr_train()
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To build model |
cmf_krr_train_mem()
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To build model in memory |
cmf_merge_kernels()
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Merging files with computed kernels |
cmf_moldim()
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Returns dimensions of molecule |
cmf_multiply_fields()
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Get product of two fields |
cmf_params_mopac()
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Computing kernels based on MOPAC results |
cmf_params_tripos()
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Parameters for CMF |
cmf_permute_kernels()
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To permute kernel matrix using given permutation |
cmf_pred_anal()
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Making predictions with analysis |
cmf_pred_anal_atoms()
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Making predictions with analysus of ampacts of each atom |
cmf_view_mol_field_cofield()
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View molecule, co-field and field |
cmf_view_mol_field_cofield_mopac
|
View molecule, co-field and field |
comp_ind_kernels_all()
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Computes CMF kernel matrices for the combined set of molecules and indicator fields |
comp_ind_kernels_pred()
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Computes indicator kernel matrices for prediction and saves to file |
comp_kernels_all()
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Computes CMF kernel matrices for the combined set of molecules |
comp_kernels_pred()
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Computes CMF kernel matrices for prediction and saves them to file |
comp_kernels_train()
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Computes CMF kernel matrices for training and saves to file |
cv_krr()
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KRR with cross-validation |
def_fcolors()
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Define default colors for physico-chemical molecular fields |
del_expl_hydr()
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Delete explicit hydrogens |
eucldist2()
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Calculation of the square of the Euclidean distance between two atoms |
euler_orth()
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Generation of orthogonal rotation matrix for Euler angles phi, teta, psi |
extract_new()
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Extract rows from new data frame corresponding to compounds not contained in old data frame |
find_substr_isomorph()
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Finds all substructure isomorphisms |
fr()
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fr |
full_design()
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Produces data frame with full design |
gen_atomlists()
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Generate atom lists |
gen_atomlists_generic()
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Generate atom lists for generic molecular field |
gen_atomlists_ind()
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Generate atom lists for continuous indicator field |
gen_atomlists_mopac()
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Generate atom lists for MOPAC molecular field |
gen_atomlists_phch()
|
Generate atom lists for physico-chemical molecular field |
get_mol_charge()
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Returns charge of molecule |
get_prop()
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Get data frame with property values |
get_prop_names()
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Get the list of property names |
get_prop_vec()
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Get property values |
get_props()
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Get data frame with property values |
get_syb_types_list()
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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()
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Creation of atom lists |
make_freq_table()
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Make frequency table |
mdb_get_num_comp()
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Get the number of compounds in molecular database |
mdb_get_prop_matr1()
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Extract property one-column matrix by name |
mdb_get_prop_names()
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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 compounds possessing values of certain property |
mdb_keep_with_prop()
|
Keep in molecular database only compounds containing values of a certain property |
mlr()
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Build multiple linear regression model |
mol2xyz()
|
mol2xyz |
mol_get_chelabs()
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Return array of chemical element labels |
mol_get_ct()
|
Return connection table for a molecule |
mol_view_cpk()
|
mol_view_cpk |
mol_view_cylindres()
|
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()
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Makes scatter plot for MLR model |
plot_regr()
|
Plots regression |
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
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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()
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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), beta_(pitch), gamma_(roll) |
run_mopac()
|
Run mopac executable |
sample_subst()
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Produces data frame with samples of substitutions |
substr_mask()
|
Extract substructure from a molecule using mask |
substruct()
|
Extract substructure from a molecule |
superpose_mol()
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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 |