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

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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

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

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