All functions

PT

Periodic Table

add_impl_hydr()

Add implicit hydrogens

add_mol_attribs()

Add additional attributes to all atoms in all molecules in molecular database

align_arun()

Rigin alignment with Arun algorithm

align_mdb_template()

Aligns molecular database mdb using template templ

alkans74.mdb

Molecular database with 74 Alkanes

align_mdb_seal()

Aligns molecular database mdb using template mol_t and algorithm SEAL

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 studies

cinf_plot_d2m_error()

Produce distance to model - error plot for applicability domain studies

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 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_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_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 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

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 two atoms

euler_orth()

Generation of orthogonal rotation matrix for Euler angles phi, teta, psi

extract_new()

Extract rows from new data frame corresponding to compounds not contained in old data frame

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_prop_vec()

Get property values

get_props()

Get data frame with 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 compounds possessing values of certain property

mdb_keep_with_prop()

Keep in molecular database only compounds containing values of a certain property

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_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()

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

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), beta_(pitch), gamma_(roll)

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