cinf: Basic tools for chemoinformatics

The package provides basics tools for chemoinformatics: manipulation with chemical structures, reading/writing files with chemical structures, etc

AuthorIgor Baskin [aut, cre]
Date of publication2013-01-27 18:41:45
MaintainerIgor Baskin <igbaskin@gmail.com>
LicenseGPL (>= 2)
Version0.0-19

View on R-Forge

Man pages

add_impl_hydr: Add implicit hydrogens

add_mol_attribs: Add additional attributes to all atoms in all molecules in...

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...

find_substr_isomorph: Find all substructure isomorphisms

full_design: Produces data frame with full design

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

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...

mdb_keep_with_prop: Keep in molecular database only compounds containing values...

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...

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

substr_mask: Extract substructure from a molecule using mask

substruct: Extract substructure from a molecule

transfer_props: Transfer properties from one mdb to another

write_mol2: Write Sybyl mol2-file

write_sdf: Write sdf-file

Functions

add_impl_hydr Man page
add_mol_attribs Man page
alkans74.mdb Man page
calc_accuracy Man page
calc_balaccuracy Man page
calc_distance_matrix Man page
calc_f1 Man page
calc_kappa Man page
calc_matcorcoef Man page
calc_precision Man page
calc_recall Man page
calc_sensitivity Man page
calc_specificity Man page
connect Man page
del_expl_hydr Man page
elem Man page
extract_new Man page
find_substr_isomorph Man page
full_design Man page
get_prop Man page
get_prop_names Man page
get_props Man page
get_prop_vec Man page
inv_free_wilson Man page
make_freq_table Man page
mdb_get_num_comp Man page
mdb_get_prop_matr1 Man page
mdb_get_prop_names Man page
mdb_get_prop_vect Man page
mdb_keep_matr_with_prop Man page
mdb_keep_with_prop Man page
mol_get_chelabs Man page
mol_get_ct Man page
predict_free_wilson_mlr Man page
predict_table_free_wilson_mlr Man page
process_free_wilson Man page
PT Man page
read_mol2 Man page
read_sdf Man page
sample_subst Man page
substr_mask Man page
substruct Man page
transfer_props Man page
write_mol2 Man page
write_sdf Man page

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.