extrDrugCPSA: A Variety of Descriptors Combining Surface Area and Partial...

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

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.

Details

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

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

Author(s)

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

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

sdf = system.file('sysdata/test.sdf', package = 'BioMedR')
mol = readMolFromSDF(sdf)
dat = extrDrugCPSA(mol)
head(dat)

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