CTD module

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This module is used for computing the composition, transition and distribution

descriptors based on the different properties of AADs. The AADs with the same

properties is marked as the same number. You can get 147 descriptors for a given

protein sequence. You can freely use and distribute it. If you hava any problem,

you could contact with us timely!

References:

[1]: Inna Dubchak, Ilya Muchink, Stephen R.Holbrook and Sung-Hou Kim. Prediction

of protein folding class using global description of amino acid sequence. Proc.Natl.

Acad.Sci.USA, 1995, 92, 8700-8704.

[2]:Inna Dubchak, Ilya Muchink, Christopher Mayor, Igor Dralyuk and Sung-Hou Kim.

Recognition of a Protein Fold in the Context of the SCOP classification. Proteins:

Structure, Function and Genetics,1999,35,401-407.

Authors: Zhijiang Yao and Dongsheng Cao.

Date: 2016.06.04

Email: gadsby@163.com

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CTD.CalculateC(ProteinSequence)

Calculate all composition descriptors based seven different properties of AADs.

Usage:

result=CalculateC(protein)

Input:protein is a pure protein sequence.

CTD.CalculateCTD(ProteinSequence)

Calculate all CTD descriptors based seven different properties of AADs.

Usage:

result=CalculateCTD(protein)

Input:protein is a pure protein sequence.

CTD.CalculateComposition(ProteinSequence, AAProperty, AAPName)

A method used for computing composition descriptors.

Usage:

result=CalculateComposition(protein,AAProperty,AAPName)

Input: protein is a pure protein sequence.

AAProperty is a dict form containing classifciation of amino acids such as _Polarizability.

AAPName is a string used for indicating a AAP name.

CTD.CalculateCompositionCharge(ProteinSequence)

A method used for calculating composition descriptors based on Charge of

AADs.

Usage:

result=CalculateCompositionCharge(protein)

Input:protein is a pure protein sequence.

CTD.CalculateCompositionHydrophobicity(ProteinSequence)

A method used for calculating composition descriptors based on Hydrophobicity of

AADs.

Usage:

result=CalculateCompositionHydrophobicity(protein)

Input:protein is a pure protein sequence.

CTD.CalculateCompositionNormalizedVDWV(ProteinSequence)

A method used for calculating composition descriptors based on NormalizedVDWV of

AADs.

Usage:

result=CalculateCompositionNormalizedVDWV(protein)

Input:protein is a pure protein sequence.

CTD.CalculateCompositionPolarity(ProteinSequence)

A method used for calculating composition descriptors based on Polarity of

AADs.

Usage:

result=CalculateCompositionPolarity(protein)

Input:protein is a pure protein sequence.

CTD.CalculateCompositionPolarizability(ProteinSequence)

A method used for calculating composition descriptors based on Polarizability of

AADs.

Usage:

result=CalculateCompositionPolarizability(protein)

Input:protein is a pure protein sequence.

CTD.CalculateCompositionSecondaryStr(ProteinSequence)

A method used for calculating composition descriptors based on SecondaryStr of

AADs.

Usage:

result=CalculateCompositionSecondaryStr(protein)

Input:protein is a pure protein sequence.

CTD.CalculateCompositionSolventAccessibility(ProteinSequence)

A method used for calculating composition descriptors based on SolventAccessibility

of AADs.

Usage:

result=CalculateCompositionSolventAccessibility(protein)

Input:protein is a pure protein sequence.

CTD.CalculateD(ProteinSequence)

Calculate all distribution descriptors based seven different properties of AADs.

Usage:

result=CalculateD(protein)

Input:protein is a pure protein sequence.

CTD.CalculateDistribution(ProteinSequence, AAProperty, AAPName)

A method used for computing distribution descriptors.

Usage:

result=CalculateDistribution(protein,AAProperty,AAPName)

Input:protein is a pure protein sequence.

AAProperty is a dict form containing classifciation of amino acids such as _Polarizability.

AAPName is a string used for indicating a AAP name.

CTD.CalculateDistributionCharge(ProteinSequence)

A method used for calculating Distribution descriptors based on Charge of

AADs.

Usage:

result=CalculateDistributionCharge(protein)

Input:protein is a pure protein sequence.

CTD.CalculateDistributionHydrophobicity(ProteinSequence)

A method used for calculating Distribution descriptors based on Hydrophobicity of

AADs.

Usage:

result=CalculateDistributionHydrophobicity(protein)

Input:protein is a pure protein sequence.

CTD.CalculateDistributionNormalizedVDWV(ProteinSequence)

A method used for calculating Distribution descriptors based on NormalizedVDWV of

AADs.

Usage:

result=CalculateDistributionNormalizedVDWV(protein)

Input:protein is a pure protein sequence.

CTD.CalculateDistributionPolarity(ProteinSequence)

A method used for calculating Distribution descriptors based on Polarity of

AADs.

Usage:

result=CalculateDistributionPolarity(protein)

Input:protein is a pure protein sequence.

CTD.CalculateDistributionPolarizability(ProteinSequence)

A method used for calculating Distribution descriptors based on Polarizability of

AADs.

Usage:

result=CalculateDistributionPolarizability(protein)

Input:protein is a pure protein sequence.

CTD.CalculateDistributionSecondaryStr(ProteinSequence)

A method used for calculating Distribution descriptors based on SecondaryStr of

AADs.

Usage:

result=CalculateDistributionSecondaryStr(protein)

Input:protein is a pure protein sequence.

CTD.CalculateDistributionSolventAccessibility(ProteinSequence)

A method used for calculating Distribution descriptors based on SolventAccessibility

of AADs.

Usage:

result=CalculateDistributionSolventAccessibility(protein)

Input:protein is a pure protein sequence.

CTD.CalculateT(ProteinSequence)

Calculate all transition descriptors based seven different properties of AADs.

Usage:

result=CalculateT(protein)

Input:protein is a pure protein sequence.

CTD.CalculateTransition(ProteinSequence, AAProperty, AAPName)

A method used for computing transition descriptors

Usage:

result=CalculateTransition(protein,AAProperty,AAPName)

Input:protein is a pure protein sequence.

AAProperty is a dict form containing classifciation of amino acids such as _Polarizability.

AAPName is a string used for indicating a AAP name.

CTD.CalculateTransitionCharge(ProteinSequence)

A method used for calculating Transition descriptors based on Charge of

AADs.

Usage:

result=CalculateTransitionCharge(protein)

Input:protein is a pure protein sequence.

CTD.CalculateTransitionHydrophobicity(ProteinSequence)

A method used for calculating Transition descriptors based on Hydrophobicity of

AADs.

Usage:

result=CalculateTransitionHydrophobicity(protein)

Input:protein is a pure protein sequence.

CTD.CalculateTransitionNormalizedVDWV(ProteinSequence)

A method used for calculating Transition descriptors based on NormalizedVDWV of

AADs.

Usage:

result=CalculateTransitionNormalizedVDWV(protein)

Input:protein is a pure protein sequence.

CTD.CalculateTransitionPolarity(ProteinSequence)

A method used for calculating Transition descriptors based on Polarity of

AADs.

Usage:

result=CalculateTransitionPolarity(protein)

Input:protein is a pure protein sequence.

CTD.CalculateTransitionPolarizability(ProteinSequence)

A method used for calculating Transition descriptors based on Polarizability of

AADs.

Usage:

result=CalculateTransitionPolarizability(protein)

Input:protein is a pure protein sequence.

CTD.CalculateTransitionSecondaryStr(ProteinSequence)

A method used for calculating Transition descriptors based on SecondaryStr of

AADs.

Usage:

result=CalculateTransitionSecondaryStr(protein)

Input:protein is a pure protein sequence.

CTD.CalculateTransitionSolventAccessibility(ProteinSequence)

A method used for calculating Transition descriptors based on SolventAccessibility

of AADs.

Usage:

result=CalculateTransitionSolventAccessibility(protein)

Input:protein is a pure protein sequence.

CTD.StringtoNum(ProteinSequence, AAProperty)

Tranform the protein sequence into the string form such as 32123223132121123.

Usage:

result=StringtoNum(protein,AAProperty)

Input: protein is a pure protein sequence.

AAProperty is a dict form containing classifciation of amino acids such as _Polarizability.