Constitutional: Calculates the Number of Amino Acids Descriptor

In wind22zhu/BioMedR: Generating Various Molecular Representations for Chemicals, Proteins, DNAs, RNAs and Their Interactions

Description

Calculates the Number of Amino Acids Descriptor

Calculates the Number of Aromatic Atoms Descriptor

Calculates the Number of Aromatic Bonds Descriptor

Calculates the Number of Atom Descriptor

Calculates the Descriptor Based on the Number of Bonds of a Certain Bond Order

Descriptor that Calculates the Number of Atoms in the Largest Chain

Descriptor that Calculates the Number of Atoms in the Largest Pi Chain

Descriptor that Calculates the Number of Atoms in the Longest Aliphatic Chain

Descriptor that Calculates the Number of Nonrotatable Bonds on A Molecule

Usage

extrDrugAminoAcidCount(molecules, silent = TRUE)

extrDrugAromaticAtomsCount(molecules, silent = TRUE)

extrDrugAromaticBondsCount(molecules, silent = TRUE)

extrDrugAtomCount(molecules, silent = TRUE)

extrDrugBondCount(molecules, silent = TRUE)

extrDrugLargestChain(molecules, silent = TRUE)

extrDrugLargestPiSystem(molecules, silent = TRUE)

extrDrugLongestAliphaticChain(molecules, silent = TRUE)

extrDrugRotatableBondsCount(molecules, silent = TRUE)

Arguments

molecules	Parsed molucule object.
silent	Logical. Whether the calculating process should be shown or not, default is TRUE.

Details

Calculates the number of each amino acids (total 20 types) found in the molecues.

Calculates the number of aromatic atoms of a molecule.

Calculates the number of aromatic bonds of a molecule.

Calculates the number of atoms of a certain element type in a molecule. By default it returns the count of all atoms.

Calculates the descriptor based on the number of bonds of a certain bond order.

This descriptor calculates the number of atoms in the largest chain. Note that a chain exists if there are two or more atoms. Thus single atom molecules will return 0.

This descriptor calculates the number of atoms in the largest pi chain.

This descriptor calculates the number of atoms in the longest aliphatic chain.

The number of rotatable bonds is given by the SMARTS specified by Daylight on SMARTS tutorial (http://www.daylight.com/dayhtml_tutorials/languages/smarts/smarts_examples.html#EXMPL)

Value

A data frame, each row represents one of the molecules, each column represents one feature. This function returns 20 columns named nA, nR, nN, nD, nC, nF, nQ, nE, nG, nH, nI, nP, nL nK, nM, nS, nT, nY nV, nW.

A data frame, each row represents one of the molecules, each column represents one feature. This function returns one column named naAromAtom.

Author(s)

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

Examples

# Calculates the Number of Amino Acids Descriptor
smi = system.file('vignettedata/test.smi', package = 'BioMedR')
mol = readMolFromSmi(smi, type = 'mol')
dat = extrDrugAminoAcidCount(mol)
head(dat)

# Calculates the Number of Aromatic Atoms Descriptor
smi = system.file('vignettedata/test.smi', package = 'BioMedR')
mol = readMolFromSmi(smi, type = 'mol')
dat = extrDrugAromaticAtomsCount(mol)
head(dat)

# Calculates the Number of Aromatic Bonds Descriptor
smi = system.file('vignettedata/test.smi', package = 'BioMedR')
mol = readMolFromSmi(smi, type = 'mol')
dat = extrDrugAromaticBondsCount(mol)
head(dat)

# Calculates the Number of Atom Descriptor
smi = system.file('vignettedata/test.smi', package = 'BioMedR')
mol = readMolFromSmi(smi, type = 'mol')
dat = extrDrugAtomCount(mol)
head(dat)

# Calculates the Descriptor Based on the Number of Bonds of a 
# Certain Bond Order
smi = system.file('vignettedata/test.smi', package = 'BioMedR')
mol = readMolFromSmi(smi, type = 'mol')
dat = extrDrugBondCount(mol)
head(dat)

# Descriptor that Calculates the Number of Atoms in the Largest Chain
smi = system.file('vignettedata/test.smi', package = 'BioMedR')
mol = readMolFromSmi(smi, type = 'mol')
dat = extrDrugLargestChain(mol)
head(dat)

# Descriptor that Calculates the Number of Atoms in the Largest Pi Chain
smi = system.file('vignettedata/test.smi', package = 'BioMedR')
mol = readMolFromSmi(smi, type = 'mol')
dat = extrDrugLargestPiSystem(mol)
head(dat)

# Descriptor that Calculates the Number of Atoms in the Longest Aliphatic Chain
smi = system.file('vignettedata/test.smi', package = 'BioMedR')
mol = readMolFromSmi(smi, type = 'mol')
dat = extrDrugLongestAliphaticChain(mol)
head(dat)

# Descriptor that Calculates the Number of Nonrotatable Bonds on A Molecule
smi = system.file('vignettedata/test.smi', package = 'BioMedR')
mol = readMolFromSmi(smi, type = 'mol')
dat = extrDrugRotatableBondsCount(mol)
head(dat)

wind22zhu/BioMedR documentation built on Oct. 21, 2019, 12:51 p.m.