Continuous molecular fields

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Documentation for package ‘conmolfields’ version 0.0-19

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A B C D E F G M N P Q R S T W X

-- A --

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_seal Aligns molecular database mdb using template mol_t and algorithm SEAL
align_mdb_template Aligns molecular database mdb using template templ
alkans74.mdb Molecular database with 74 Alkanes
apply_par_list apply_par_list

-- B --

build_krr_model To build krr model

-- C --

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

-- D --

def_fcolors Define default colors for physico-chemical molecular fields
del_expl_hydr Delete explicit hydrogens

-- E --

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

-- F --

find_substr_isomorph Finds all substructure isomorphisms
fr fr
full_design Produces data frame with full design

-- G --

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_props Get data frame with property values
get_prop_names Get the list of property names
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

-- M --

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

-- N --

normalize_gram Normalization of the Gram matrix

-- P --

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

-- Q --

q2r Converts quaternions to rotation mstrix

-- R --

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

-- S --

sample_subst Produces data frame with samples of substitutions
substruct Extract substructure from a molecule
substr_mask Extract substructure from a molecule using mask
superpose_mol Superposes moving molecule mol_m on templace molecule mol_t
superpose_mol_seal superpose_mol_seal

-- T --

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

-- W --

write_mol2 Write Sybyl mol2-file
write_mopac_input_file Writes MOPAC inpout file with Cartesian coordinates
write_sdf Write sdf-file

-- X --

xyz2mol xyz2mol