cinf: Basic tools for chemoinformatics
Version 0.0-19

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

Browse man pages Browse package API and functions Browse package files

AuthorIgor Baskin [aut, cre]
Date of publication2013-01-27 18:41:45
MaintainerIgor Baskin <igbaskin@gmail.com>
LicenseGPL (>= 2)
Version0.0-19
Package repositoryView on R-Forge
InstallationInstall the latest version of this package by entering the following in R:
install.packages("cinf", repos="http://R-Forge.R-project.org")

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

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

Files

DESCRIPTION
NAMESPACE
R
R/cinf-classperf.R
R/cinf-descr-connect.R
R/cinf-descr-elem.R
R/cinf-filters.R
R/cinf-free-wilson.R
R/cinf-getprops.R
R/cinf-hydrogens.R
R/cinf-isomorph.R
R/cinf-mdb.R
R/cinf-metals.R
R/cinf-mol.R
R/cinf-mol2.R
R/cinf-molattribs.R
R/cinf-regression.R
R/cinf-sdf.R
data
data/PT.RData
data/alkans74.RData
data/free-wilson-boehm.txt.gz
man
man/PT.Rd
man/add_impl_hydr.Rd
man/add_mol_attribs.Rd
man/alkans74.mdb.Rd
man/calc_accuracy.Rd
man/calc_balaccuracy.Rd
man/calc_distance_matrix.Rd
man/calc_f1.Rd
man/calc_kappa.Rd
man/calc_matcorcoef.Rd
man/calc_precision.Rd
man/calc_recall.Rd
man/calc_sensitivity.Rd
man/calc_specificity.Rd
man/connect.Rd
man/del_expl_hydr.Rd
man/elem.Rd
man/extract_new.Rd
man/find_substr_isomorph.Rd
man/full_design.Rd
man/get_prop.Rd
man/get_prop_names.Rd
man/get_prop_vec.Rd
man/get_props.Rd
man/inv_free_wilson.Rd
man/make_freq_table.Rd
man/mdb_get_num_comp.Rd
man/mdb_get_prop_matr1.Rd
man/mdb_get_prop_names.Rd
man/mdb_get_prop_vect.Rd
man/mdb_keep_matr_with_prop.Rd
man/mdb_keep_with_prop.Rd
man/mol_get_chelabs.Rd
man/mol_get_ct.Rd
man/predict_free_wilson_mlr.Rd
man/predict_table_free_wilson_mlr.Rd
man/process_free_wilson.Rd
man/read_mol2.Rd
man/read_sdf.Rd
man/sample_subst.Rd
man/substr_mask.Rd
man/substruct.Rd
man/transfer_props.Rd
man/write_mol2.Rd
man/write_sdf.Rd
cinf documentation built on May 21, 2017, 12:58 a.m.