connectivity: Calculate the Kier and Hall Chi Chain Indices of Orders 3, 4,...

In BioMedR: Generating Various Molecular Representations for Chemicals, Proteins, DNAs/RNAs and Their Interactions

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.

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.

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

Note

These descriptors are calculated using graph isomorphism to identify the various fragments. As a result calculations may be slow. In addition, recent versions of Molconn-Z use simplified fragment definitions (i.e., rings without branches etc.) whereas these descriptors use the older more complex fragment definitions.

These descriptors are calculated using graph isomorphism to identify the various fragments. As a result calculations may be slow. In addition, recent versions of Molconn-Z use simplified fragment definitions (i.e., rings without branches etc.) whereas these descriptors use the older more complex fragment definitions.

extrDrugChiPathCluster : These descriptors are calculated using graph isomorphism to identify the various fragments. As a result calculations may be slow. In addition, recent versions of Molconn-Z use simplified fragment definitions (i.e., rings without branches etc.) whereas these descriptors use the older more complex fragment definitions.

extrDrugChiPath: These descriptors are calculated using graph isomorphism to identify the various fragments. As a result calculations may be slow. In addition, recent versions of Molconn-Z use simplified fragment definitions (i.e., rings without branches etc.) whereas these descriptors use the older more complex fragment definitions.

Author(s)

Min-feng Zhu <[e-mail]>, Nan Xiao <http://r2s.name>

Examples

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)

BioMedR documentation built on Nov. 17, 2017, 10:08 a.m.