Autocorrelation: Calculates the Moreau-Broto Autocorrelation Descriptors using...

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

Description

Calculates the Moreau-Broto Autocorrelation Descriptors using Partial Charges

Calculates the Moreau-Broto Autocorrelation Descriptors using Atomic Weight

Calculates the Moreau-Broto Autocorrelation Descriptors using Polarizability

Usage

extrDrugAutocorrelationcharge(molecules, silent = TRUE)

extrDrugAutocorrelationMass(molecules, silent = TRUE)

extrDrugAutocorrelationPolarizability(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 ATS autocorrelation descriptor, where the weight equal to the charges.

Calculates the ATS autocorrelation descriptor, where the weight equal to the scaled atomic mass.

Calculates the ATS autocorrelation descriptor using polarizability.

Value

A data frame, each row represents one of the molecules, each column represents one feature. This function returns 5 columns named ATSc1, ATSc2, ATSc3, ATSc4, ATSc5.

extrDrugAutocorrelationMass: This function returns 5 columns named ATSm1, ATSm2, ATSm3, ATSm4, ATSm5.

extrDrugAutocorrelationPolarizability: This function returns 5 columns named ATSp1, ATSp2, ATSp3, ATSp4, ATSp5.

Author(s)

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

References

Moreau, Gilles, and Pierre Broto. The autocorrelation of a topological structure: a new molecular descriptor. Nouv. J. Chim 4 (1980): 359-360.

Examples

# Calculates the Moreau-Broto Autocorrelation Descriptors using Partial Charges
smi = system.file('vignettedata/test.smi', package = 'BioMedR')
mol = readMolFromSmi(smi, type = 'mol')
dat = extrDrugAutocorrelationcharge(mol)
head(dat)
# Calculates the Moreau-Broto Autocorrelation Descriptors using Atomic Weight
dat = extrDrugAutocorrelationMass(mol)
head(dat)
# Calculates the Moreau-Broto Autocorrelation Descriptors using Polarizability
dat = extrDrugAutocorrelationPolarizability(mol)
head(dat)

Example output

OpenJDK 64-Bit Server VM warning: Can't detect primordial thread stack location - find_vma failed
                                                            ATSc1       ATSc2
c1ccc2c(c1)oc(=O)c(C(CC(=O)C)c1ccc([N+](=O)[O-])cc1)c2O 0.4881987 -0.18184066
c1(ccc(cc1)O)NC(=O)C                                    0.2162844 -0.09614005
c1ccccc1NC(=O)C                                         0.1610223 -0.07980602
                                                              ATSc3
c1ccc2c(c1)oc(=O)c(C(CC(=O)C)c1ccc([N+](=O)[O-])cc1)c2O 0.061389482
c1(ccc(cc1)O)NC(=O)C                                    0.005670185
c1ccccc1NC(=O)C                                         0.009036194
                                                               ATSc4
c1ccc2c(c1)oc(=O)c(C(CC(=O)C)c1ccc([N+](=O)[O-])cc1)c2O -0.178985322
c1(ccc(cc1)O)NC(=O)C                                    -0.008711630
c1ccccc1NC(=O)C                                         -0.004998613
                                                               ATSc5
c1ccc2c(c1)oc(=O)c(C(CC(=O)C)c1ccc([N+](=O)[O-])cc1)c2O  0.116421715
c1(ccc(cc1)O)NC(=O)C                                    -0.021083366
c1ccccc1NC(=O)C                                         -0.004347956
                                                           ATSm1    ATSm2
c1ccc2c(c1)oc(=O)c(C(CC(=O)C)c1ccc([N+](=O)[O-])cc1)c2O 31.00679 30.93357
c1(ccc(cc1)O)NC(=O)C                                    12.90892 11.99655
c1ccccc1NC(=O)C                                         11.13445 10.66446
                                                           ATSm3     ATSm4
c1ccc2c(c1)oc(=O)c(C(CC(=O)C)c1ccc([N+](=O)[O-])cc1)c2O 45.20222 49.645836
c1(ccc(cc1)O)NC(=O)C                                    16.04828 12.328640
c1ccccc1NC(=O)C                                         13.38410  9.664456
                                                            ATSm5
c1ccc2c(c1)oc(=O)c(C(CC(=O)C)c1ccc([N+](=O)[O-])cc1)c2O 51.360684
c1(ccc(cc1)O)NC(=O)C                                     9.162458
c1ccccc1NC(=O)C                                          7.830366
                                                            ATSp1    ATSp2
c1ccc2c(c1)oc(=O)c(C(CC(=O)C)c1ccc([N+](=O)[O-])cc1)c2O 1701.6065 2029.271
c1(ccc(cc1)O)NC(=O)C                                     495.8999  534.724
c1ccccc1NC(=O)C                                          455.5073  482.933
                                                            ATSp3     ATSp4
c1ccc2c(c1)oc(=O)c(C(CC(=O)C)c1ccc([N+](=O)[O-])cc1)c2O 2901.0350 3172.9837
c1(ccc(cc1)O)NC(=O)C                                     652.6119  515.8175
c1ccccc1NC(=O)C                                          564.9583  429.8833
                                                            ATSp5
c1ccc2c(c1)oc(=O)c(C(CC(=O)C)c1ccc([N+](=O)[O-])cc1)c2O 2944.2852
c1(ccc(cc1)O)NC(=O)C                                     326.0907
c1ccccc1NC(=O)C                                          276.8267

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