BioMedR (version 1.2.1)

connectivity: Calculate the Kier and Hall Chi Chain Indices of Orders 3, 4, 5, 6 and 7

Description

Calculate the Kier and Hall Chi Chain Indices of Orders 3, 4, 5, 6 and 7

Evaluates the Kier and Hall Chi cluster indices of orders 3, 4, 5 and 6

the Kier and Hall Chi Path Cluster Indices of Orders 4, 5 and 6

Calculate the Kier and Hall Chi Path Indices of Orders 0 to 7

Usage

extrDrugChiChain(molecules, silent = TRUE)
extrDrugChiCluster(molecules, silent = TRUE)
extrDrugChiPathCluster(molecules, silent = TRUE)
extrDrugChiPath(molecules, silent = TRUE)

Arguments

molecules

Parsed molucule object.

silent

Logical. Whether the calculating process should be shown or not, default is TRUE.

Value

A data frame, each row represents one of the molecules, each column represents one feature. This function returns 10 columns, in the following order:

• SCH.3 - Simple chain, order 3

• SCH.4 - Simple chain, order 4

• SCH.5 - Simple chain, order 5

• SCH.6 - Simple chain, order 6

• SCH.7 - Simple chain, order 7

• VCH.3 - Valence chain, order 3

• VCH.4 - Valence chain, order 4

• VCH.5 - Valence chain, order 5

• VCH.6 - Valence chain, order 6

• VCH.7 - Valence chain, order 7

extrDrugChiCluster: This function returns 8 columns, the order and names of the columns returned is:

• SC.3 - Simple cluster, order 3

• SC.4 - Simple cluster, order 4

• SC.5 - Simple cluster, order 5

• SC.6 - Simple cluster, order 6

• VC.3 - Valence cluster, order 3

• VC.4 - Valence cluster, order 4

• VC.5 - Valence cluster, order 5

• VC.6 - Valence cluster, order 6

extrDrugChiPathCluster: This function returns 6 columns named SPC.4, SPC.5, SPC.6, VPC.4, VPC.5, VPC.6:

• SPC.4 - Simple path cluster, order 4

• SPC.5 - Simple path cluster, order 5

• SPC.6 - Simple path cluster, order 6

• VPC.4 - Valence path cluster, order 4

• VPC.5 - Valence path cluster, order 5

• VPC.6 - Valence path cluster, order 6

extrDrugChiPath: This function returns 16 columns, The order and names of the columns returned is:

• SP.0, SP.1, ..., SP.7 - Simple path, orders 0 to 7

• VP.0, VP.1, ..., VP.7 - Valence path, orders 0 to 7

Details

Evaluates chi chain descriptors. The code currently evluates the simple and valence chi chain descriptors of orders 3, 4, 5, 6 and 7. It utilizes the graph isomorphism code of the CDK to find fragments matching SMILES strings representing the fragments corresponding to each type of chain.

Evaluates chi cluster descriptors. It utilizes the graph isomorphism code of the CDK to find fragments matching SMILES strings representing the fragments corresponding to each type of chain.

Evaluates chi path cluster descriptors. The code currently evluates the simple and valence chi chain descriptors of orders 4, 5 and 6. It utilizes the graph isomorphism code of the CDK to find fragments matching SMILES strings representing the fragments corresponding to each type of chain.

Evaluates chi path descriptors. This function utilizes the graph isomorphism code of the CDK to find fragments matching SMILES strings representing the fragments corresponding to each type of chain.

Examples

# NOT RUN {
smi = system.file('vignettedata/test.smi', package = 'BioMedR')
mol = readMolFromSmi(smi, type = 'mol')
# Calculate the Kier and Hall Chi Chain Indices of Orders 3, 4, 5, 6 and 7
dat = extrDrugChiChain(mol)
head(dat)

# Evaluates the Kier and Hall Chi cluster indices of orders 3, 4, 5 and 6
dat = extrDrugChiCluster(mol)
head(dat)

# Calculate the Kier and Hall Chi Path Cluster Indices of Orders 4, 5 and 6
dat = extrDrugChiPathCluster(mol)
head(dat)

# Calculate the Kier and Hall Chi Path Indices of Orders 0 to 7
dat = extrDrugChiPath(mol)
head(dat)

# }