Basic tools for chemoinformatics


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Documentation for package ‘cinf’ version 0.0-19

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add_impl_hydr Add implicit hydrogens
add_mol_attribs Add additional attributes to all atoms in all molecules in molecular database
alkans74.mdb Molecular database with 74 Alkanes
calc_accuracy Calculate classification accuracy
calc_balaccuracy Calculate classification balanced accuracy
calc_distance_matrix Compute distance matrix from connection table
calc_f1 Calculate classification F1-score
calc_kappa Calculate kappa-statistics
calc_matcorcoef Calculate Matthews correlation coefficient
calc_precision Calculate classification precision
calc_recall Calculate classification recall
calc_sensitivity Calculate classification sensitivity
calc_specificity Calculate classification specificity
connect Compute Kier-Hall connectivity topological indices
del_expl_hydr Delete explicit hydrogens
elem Compute descriptors based on elemetal composition
extract_new Extract rows from new data frame corresponding to compounds not contained in old data frame
find_substr_isomorph Find all substructure isomorphisms
full_design Produces data frame with full design
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
inv_free_wilson Solve the inverse problem in Free-Wilson analysis
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
mol_get_chelabs Return array of chemical element labels
mol_get_ct Return connection table for a molecule
predict_free_wilson_mlr Make predictions for MLR model in the Free-Wilson approach
predict_table_free_wilson_mlr Makes predictions for data frame using MLR model in the Free-Wilson approach
process_free_wilson Process data table using the Free-Wilson approach
PT Periodic Table
read_mol2 Read Sybyl mol2-file
read_sdf Read sdf-file
sample_subst Produces data frame with samples of substitutions
substruct Extract substructure from a molecule
substr_mask Extract substructure from a molecule using mask
transfer_props Transfer properties from one mdb to another
write_mol2 Write Sybyl mol2-file
write_sdf Write sdf-file