cinf: Basic tools for chemoinformatics

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

Author
Igor Baskin [aut, cre]
Date of publication
2013-01-27 18:41:45
Maintainer
Igor Baskin <igbaskin@gmail.com>
License
GPL (>= 2)
Version
0.0-19

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

Files in this package

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