propy.CTD

Compute 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.

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: Dongsheng Cao and Yizeng Liang. Date: 2010.11.22 Email: oriental-cds@163.com

propy.CTD.CalculateC(ProteinSequence: str) → Dict[Any, Any][source]

Calculate all composition descriptors based seven different properties of AADs.

Parameters:ProteinSequence (str) – a pure protein sequence
Returns:result – contains all composition descriptors.
Return type:Dict[Any, Any]

Examples

>>> from propy.GetProteinFromUniprot import GetProteinSequence
>>> protein = GetProteinSequence(ProteinID="Q9NQ39")
>>> result = CalculateC(protein)
propy.CTD.CalculateCTD(ProteinSequence: str) → Dict[Any, Any][source]

Calculate all CTD descriptors based seven different properties of AADs.

Parameters:ProteinSequence (str) – a pure protein sequence
Returns:result – contains all CTD descriptors.
Return type:Dict[Any, Any]

Examples

>>> from propy.GetProteinFromUniprot import GetProteinSequence
>>> protein = GetProteinSequence(ProteinID="Q9NQ39")
>>> result = CalculateCTD(protein)
propy.CTD.CalculateComposition(ProteinSequence: str, AAProperty: Dict[Any, Any], AAPName: str) → Dict[Any, Any][source]

Compute composition descriptors.

Parameters:
  • ProteinSequence (str) – a pure protein sequence
  • AAProperty (Dict[Any, Any]) – contains classifciation of amino acids such as _Polarizability.
  • AAPName (str) – used for indicating a AAP name.
Returns:

result – contains composition descriptors based on the given property.

Return type:

Dict[Any, Any]

Examples

>>> from propy.GetProteinFromUniprot import GetProteinSequence
>>> protein = GetProteinSequence(ProteinID="Q9NQ39")
>>> AAProperty, AAPName = _Hydrophobicity, "_Hydrophobicity"
>>> result = CalculateComposition(protein, AAProperty, AAPName)
propy.CTD.CalculateCompositionCharge(ProteinSequence: str) → Dict[Any, Any][source]

Calculate composition descriptors based on Charge of AADs.

Parameters:ProteinSequence (str) – a pure protein sequence
Returns:result – contains Composition descriptors based on Charge.
Return type:Dict[Any, Any]

Examples

>>> from propy.GetProteinFromUniprot import GetProteinSequence
>>> protein = GetProteinSequence(ProteinID="Q9NQ39")
>>> result = CalculateCompositionCharge(protein)
propy.CTD.CalculateCompositionHydrophobicity(ProteinSequence: str)[source]

Calculate composition descriptors based on Hydrophobicity of AADs.

Parameters:ProteinSequence (str) – a pure protein sequence
Returns:result – contains Composition descriptors based on Hydrophobicity.
Return type:Dict[Any, Any]

Examples

>>> from propy.GetProteinFromUniprot import GetProteinSequence
>>> protein = GetProteinSequence(ProteinID="Q9NQ39")
>>> result = CalculateCompositionHydrophobicity(protein)
propy.CTD.CalculateCompositionNormalizedVDWV(ProteinSequence: str)[source]

Calculate composition descriptors based on NormalizedVDWV of AADs.

Parameters:ProteinSequence (str) – a pure protein sequence
Returns:result – contains Composition descriptors based on NormalizedVDWV.
Return type:Dict[Any, Any]

Examples

>>> from propy.GetProteinFromUniprot import GetProteinSequence
>>> protein = GetProteinSequence(ProteinID="Q9NQ39")
>>> result = CalculateCompositionNormalizedVDWV(protein)
propy.CTD.CalculateCompositionPolarity(ProteinSequence: str)[source]

Calculate composition descriptors based on Polarity of AADs.

Parameters:ProteinSequence (str) – a pure protein sequence
Returns:result – contains Composition descriptors based on Polarity.
Return type:Dict[Any, Any]

Examples

>>> from propy.GetProteinFromUniprot import GetProteinSequence
>>> protein = GetProteinSequence(ProteinID="Q9NQ39")
>>> result = CalculateCompositionPolarity(protein)
propy.CTD.CalculateCompositionPolarizability(ProteinSequence: str) → Dict[Any, Any][source]

Calculate composition descriptors based on Polarizability of AADs.

Parameters:ProteinSequence (str) – a pure protein sequence
Returns:result – contains Composition descriptors based on Polarizability.
Return type:Dict[Any, Any]

Examples

>>> from propy.GetProteinFromUniprot import GetProteinSequence
>>> protein = GetProteinSequence(ProteinID="Q9NQ39")
>>> result = CalculateCompositionPolarizability(protein)
propy.CTD.CalculateCompositionSecondaryStr(ProteinSequence: str) → Dict[Any, Any][source]

Calculate composition descriptors based on SecondaryStr of AADs.

Parameters:ProteinSequence (str) – a pure protein sequence
Returns:result – contains Composition descriptors based on SecondaryStr.
Return type:Dict[Any, Any]

Examples

>>> from propy.GetProteinFromUniprot import GetProteinSequence
>>> protein = GetProteinSequence(ProteinID="Q9NQ39")
>>> result = CalculateCompositionSecondaryStr(protein)
propy.CTD.CalculateCompositionSolventAccessibility(ProteinSequence: str) → Dict[Any, Any][source]

Clculate composition descriptors based on SolventAccessibility of AADs.

Parameters:ProteinSequence (str) – a pure protein sequence
Returns:result – contains Composition descriptors based on SolventAccessibility.
Return type:Dict[Any, Any]

Examples

>>> from propy.GetProteinFromUniprot import GetProteinSequence
>>> protein = GetProteinSequence(ProteinID="Q9NQ39")
>>> result = CalculateCompositionSolventAccessibility(protein)
propy.CTD.CalculateD(ProteinSequence: str) → Dict[Any, Any][source]

Calculate all distribution descriptors based seven different properties of AADs.

Parameters:ProteinSequence (str) – a pure protein sequence
Returns:result – contains all distribution descriptors.
Return type:Dict[Any, Any]

Examples

>>> from propy.GetProteinFromUniprot import GetProteinSequence
>>> protein = GetProteinSequence(ProteinID="Q9NQ39")
>>> result = CalculateD(protein)
propy.CTD.CalculateDistribution(ProteinSequence: str, AAProperty: Dict[Any, Any], AAPName: str) → Dict[Any, Any][source]

Compute distribution descriptors.

Parameters:
  • ProteinSequence (str) – a pure protein sequence.
  • AAProperty (Dict[Any, Any]) – contains classifciation of amino acids such as _Polarizability
  • AAPName (str) –
Returns:

result – contains Distribution descriptors based on the given property.

Return type:

Dict[Any, Any]

Examples

>>> from propy.GetProteinFromUniprot import GetProteinSequence
>>> protein = GetProteinSequence(ProteinID="Q9NQ39")
>>> AAProperty, AAPName = _Hydrophobicity, "_Hydrophobicity"
>>> result = CalculateDistribution(protein, AAProperty, AAPName)
propy.CTD.CalculateDistributionCharge(ProteinSequence: str) → Dict[Any, Any][source]

Calculate Distribution descriptors based on Charge of AADs.

Parameters:ProteinSequence (str) – a pure protein sequence
Returns:result – contains Distribution descriptors based on Charge.
Return type:Dict[Any, Any]

Examples

>>> from propy.GetProteinFromUniprot import GetProteinSequence
>>> protein = GetProteinSequence(ProteinID="Q9NQ39")
>>> result = CalculateDistributionCharge(protein)
propy.CTD.CalculateDistributionHydrophobicity(ProteinSequence: str) → Dict[Any, Any][source]

Calculate Distribution descriptors based on Hydrophobicity of AADs.

Parameters:ProteinSequence (str) – a pure protein sequence
Returns:result – contains Distribution descriptors based on Hydrophobicity.
Return type:Dict[Any, Any]

Examples

>>> from propy.GetProteinFromUniprot import GetProteinSequence
>>> protein = GetProteinSequence(ProteinID="Q9NQ39")
>>> result = CalculateDistributionHydrophobicity(protein)
propy.CTD.CalculateDistributionNormalizedVDWV(ProteinSequence: str) → Dict[Any, Any][source]

Calculate Distribution descriptors based on NormalizedVDWV of AADs.

Parameters:ProteinSequence (str) – a pure protein sequence
Returns:result – contains Distribution descriptors based on NormalizedVDWV.
Return type:Dict[Any, Any]

Examples

>>> from propy.GetProteinFromUniprot import GetProteinSequence
>>> protein = GetProteinSequence(ProteinID="Q9NQ39")
>>> result = CalculateDistributionNormalizedVDWV(protein)
propy.CTD.CalculateDistributionPolarity(ProteinSequence: str) → Dict[Any, Any][source]

Calculate Distribution descriptors based on Polarity of AADs.

Parameters:ProteinSequence (str) – a pure protein sequence
Returns:result – contains Distribution descriptors based on Polarity.
Return type:Dict[Any, Any]

Examples

>>> from propy.GetProteinFromUniprot import GetProteinSequence
>>> protein = GetProteinSequence(ProteinID="Q9NQ39")
>>> result = CalculateDistributionPolarity(protein)
propy.CTD.CalculateDistributionPolarizability(ProteinSequence: str) → Dict[Any, Any][source]

Calculate Distribution descriptors based on Polarizability of AADs.

Parameters:ProteinSequence (str) – a pure protein sequence
Returns:result – contains Distribution descriptors based on Polarizability.
Return type:Dict[Any, Any]

Examples

>>> from propy.GetProteinFromUniprot import GetProteinSequence
>>> protein = GetProteinSequence(ProteinID="Q9NQ39")
>>> result = CalculateDistributionPolarizability(protein)
propy.CTD.CalculateDistributionSecondaryStr(ProteinSequence: str) → Dict[Any, Any][source]

Calculate Distribution descriptors based on SecondaryStr of AADs.

Parameters:ProteinSequence (str) – a pure protein sequence
Returns:result – contains Distribution descriptors based on SecondaryStr.
Return type:Dict[Any, Any]

Examples

>>> from propy.GetProteinFromUniprot import GetProteinSequence
>>> protein = GetProteinSequence(ProteinID="Q9NQ39")
>>> result = CalculateDistributionSecondaryStr(protein)
propy.CTD.CalculateDistributionSolventAccessibility(ProteinSequence: str) → Dict[Any, Any][source]

Calculate Distribution descriptors based on SolventAccessibility of AADs.

Parameters:ProteinSequence (str) – a pure protein sequence
Returns:result – contains Distribution descriptors based on SolventAccessibility.
Return type:Dict[Any, Any]

Examples

>>> from propy.GetProteinFromUniprot import GetProteinSequence
>>> protein = GetProteinSequence(ProteinID="Q9NQ39")
>>> result = CalculateDistributionSolventAccessibility(protein)
propy.CTD.CalculateT(ProteinSequence: str) → Dict[Any, Any][source]

Calculate all transition descriptors based seven different properties of AADs.

Parameters:ProteinSequence (str) – a pure protein sequence
Returns:result – contains all transition descriptors.
Return type:Dict[Any, Any]

Examples

>>> from propy.GetProteinFromUniprot import GetProteinSequence
>>> protein = GetProteinSequence(ProteinID="Q9NQ39")
>>> result = CalculateT(protein)
propy.CTD.CalculateTransition(ProteinSequence: str, AAProperty: Dict[Any, Any], AAPName: str) → Dict[Any, Any][source]

Compute transition descriptors.

Parameters:
  • ProteinSequence (str) – a pure protein sequence
  • AAProperty (Dict[Any, Any]) – contains classifciation of amino acids such as _Polarizability.
  • AAPName (str) – used for indicating a AAP name.
Returns:

result – contains transition descriptors based on the given property.

Return type:

Dict[Any, Any]

Examples

>>> from propy.GetProteinFromUniprot import GetProteinSequence
>>> protein = GetProteinSequence(ProteinID="Q9NQ39")
>>> AAProperty, AAPName = _Hydrophobicity, "_Hydrophobicity"
>>> result = CalculateTransition(protein, AAProperty, AAPName)
propy.CTD.CalculateTransitionCharge(ProteinSequence: str) → Dict[Any, Any][source]

Calculate Transition descriptors based on Charge of AADs.

Parameters:ProteinSequence (str) – a pure protein sequence
Returns:result – contains Transition descriptors based on Charge.
Return type:Dict[Any, Any]

Examples

>>> from propy.GetProteinFromUniprot import GetProteinSequence
>>> protein = GetProteinSequence(ProteinID="Q9NQ39")
>>> result = CalculateTransitionCharge(protein)
propy.CTD.CalculateTransitionHydrophobicity(ProteinSequence: str) → Dict[Any, Any][source]

Calculate Transition descriptors based on Hydrophobicity of AADs.

Parameters:ProteinSequence (str) – a pure protein sequence
Returns:result – contains Transition descriptors based on Hydrophobicity.
Return type:Dict[Any, Any]

Examples

>>> from propy.GetProteinFromUniprot import GetProteinSequence
>>> protein = GetProteinSequence(ProteinID="Q9NQ39")
>>> result = CalculateTransitionHydrophobicity(protein)
propy.CTD.CalculateTransitionNormalizedVDWV(ProteinSequence: str) → Dict[Any, Any][source]

Calculate Transition descriptors based on NormalizedVDWV of AADs.

Parameters:ProteinSequence (str) – a pure protein sequence
Returns:result – contains Transition descriptors based on NormalizedVDWV.
Return type:Dict[Any, Any]

Examples

>>> from propy.GetProteinFromUniprot import GetProteinSequence
>>> protein = GetProteinSequence(ProteinID="Q9NQ39")
>>> result = CalculateTransitionNormalizedVDWV(protein)
propy.CTD.CalculateTransitionPolarity(ProteinSequence: str) → Dict[Any, Any][source]

Calculate Transition descriptors based on Polarity of AADs.

Parameters:ProteinSequence (str) – a pure protein sequence
Returns:result – contains Transition descriptors based on Polarity.
Return type:Dict[Any, Any]

Examples

>>> from propy.GetProteinFromUniprot import GetProteinSequence
>>> protein = GetProteinSequence(ProteinID="Q9NQ39")
>>> result = CalculateTransitionPolarity(protein)
propy.CTD.CalculateTransitionPolarizability(ProteinSequence: str) → Dict[Any, Any][source]

Calculate Transition descriptors based on Polarizability of AADs.

Parameters:ProteinSequence (str) – a pure protein sequence
Returns:result – contains Transition descriptors based on Polarizability.
Return type:Dict[Any, Any]

Examples

>>> from propy.GetProteinFromUniprot import GetProteinSequence
>>> protein = GetProteinSequence(ProteinID="Q9NQ39")
>>> result = CalculateTransitionPolarizability(protein)
propy.CTD.CalculateTransitionSecondaryStr(ProteinSequence: str) → Dict[Any, Any][source]

Calculate Transition descriptors based on SecondaryStr of AADs.

Parameters:ProteinSequence (str) – a pure protein sequence
Returns:result – contains Transition descriptors based on SecondaryStr.
Return type:Dict[Any, Any]

Examples

>>> from propy.GetProteinFromUniprot import GetProteinSequence
>>> protein = GetProteinSequence(ProteinID="Q9NQ39")
>>> result = CalculateTransitionSecondaryStr(protein)
propy.CTD.CalculateTransitionSolventAccessibility(ProteinSequence: str) → Dict[Any, Any][source]

Calculate Transition descriptors based on SolventAccessibility of AADs.

Parameters:ProteinSequence (str) – a pure protein sequence
Returns:result – contains Transition descriptors based on SolventAccessibility.
Return type:Dict[Any, Any]

Examples

>>> from propy.GetProteinFromUniprot import GetProteinSequence
>>> protein = GetProteinSequence(ProteinID="Q9NQ39")
>>> result = CalculateTransitionSolventAccessibility(protein)
propy.CTD.StringtoNum(ProteinSequence: str, AAProperty: Dict[Any, Any]) → str[source]

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

Parameters:
  • ProteinSequence (str) – a pure protein sequence
  • AAProperty (Dict[Any, Any]) – contains classifciation of amino acids such as _Polarizability.
Returns:

result – e.g. 123321222132111123222

Return type:

str

Examples

>>> from propy.GetProteinFromUniprot import GetProteinSequence
>>> protein = GetProteinSequence(ProteinID="Q9NQ39")
>>> AAProperty, AAPName = _Hydrophobicity, "_Hydrophobicity"
>>> result = StringtoNum(protein, AAProperty)