BioMedR (version 1.2.1)

extrDrugCPSA: A Variety of Descriptors Combining Surface Area and Partial Charge Information

Description

A Variety of Descriptors Combining Surface Area and Partial Charge Information

Usage

extrDrugCPSA(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 29 columns:

• PPSA.1 - partial positive surface area -- sum of surface area on positive parts of molecule

• PPSA.2 - partial positive surface area * total positive charge on the molecule

• PPSA.3 - charge weighted partial positive surface area

• PNSA.1 - partial negative surface area -- sum of surface area on negative parts of molecule

• PNSA.2 - partial negative surface area * total negative charge on the molecule

• PNSA.3 - charge weighted partial negative surface area

• DPSA.1 - difference of PPSA.1 and PNSA.1

• DPSA.2 - difference of FPSA.2 and PNSA.2

• DPSA.3 - difference of PPSA.3 and PNSA.3

• FPSA.1 - PPSA.1 / total molecular surface area

• FFSA.2 - PPSA.2 / total molecular surface area

• FPSA.3 - PPSA.3 / total molecular surface area

• FNSA.1 - PNSA.1 / total molecular surface area

• FNSA.2 - PNSA.2 / total molecular surface area

• FNSA.3 - PNSA.3 / total molecular surface area

• WPSA.1 - PPSA.1 * total molecular surface area / 1000

• WPSA.2 - PPSA.2 * total molecular surface area /1000

• WPSA.3 - PPSA.3 * total molecular surface area / 1000

• WNSA.1 - PNSA.1 * total molecular surface area /1000

• WNSA.2 - PNSA.2 * total molecular surface area / 1000

• WNSA.3 - PNSA.3 * total molecular surface area / 1000

• RPCG - relative positive charge -- most positive charge / total positive charge

• RNCG - relative negative charge -- most negative charge / total negative charge

• RPCS - relative positive charge surface area -- most positive surface area * RPCG

• RNCS - relative negative charge surface area -- most negative surface area * RNCG

• THSA - sum of solvent accessible surface areas of atoms with absolute value of partial charges less than 0.2

• TPSA - sum of solvent accessible surface areas of atoms with absolute value of partial charges greater than or equal 0.2

• RHSA - THSA / total molecular surface area

• RPSA - TPSA / total molecular surface area

Details

Calculates 29 Charged Partial Surface Area (CPSA) descriptors. The CPSA's were developed by Stanton et al.

References

Stanton, D.T. and Jurs, P.C. , Development and Use of Charged Partial Surface Area Structural Descriptors in Computer Assissted Quantitative Structure Property Relationship Studies, Analytical Chemistry, 1990, 62:2323.2329.

Examples

# NOT RUN {
sdf = system.file('sysdata/test.sdf', package = 'BioMedR')
mol = readMolFromSDF(sdf)
dat = extrDrugCPSA(mol)
head(dat)

# }