propy.Autocorrelation

This module is used for computing the Autocorrelation descriptors based different properties of AADs. You can also input your properties of AADs, then it can help you to compute Autocorrelation descriptors based on the property of AADs. Currently, you can get 720 descriptors for a given protein sequence based on our provided physicochemical properties of AADs.

References

[1]http://www.genome.ad.jp/dbget/aaindex.html
[2]Feng, Z.P. and Zhang, C.T. (2000) Prediction of membrane protein types based on the hydrophobic index of amino acids. J Protein Chem, 19, 269-275.
[3]Horne, D.S. (1988) Prediction of protein helix content from an autocorrelation analysis of sequence hydrophobicities. Biopolymers, 27, 451-477.
[4]Sokal, R.R. and Thomson, B.A. (2006) Population structure inferred by local spatial autocorrelation: an Usage from an Amerindian tribal population. Am J Phys Anthropol, 129, 121-131.

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

propy.Autocorrelation.CalculateAutoTotal(ProteinSequence: str) → Dict[Any, Any][source]

Compute all autocorrelation descriptors based on 8 properties of AADs.

Parameters:ProteinSequence (str) – a pure protein sequence
Returns:
  • result contains 30*8*3=720 normalized Moreau Broto, Moran, and Geary
  • autocorrelation descriptors based on the given properties(i.e.,
  • _AAPropert).

Examples

>>> from propy.GetProteinFromUniprot import GetProteinSequence
>>> protein = GetProteinSequence(ProteinID="Q9NQ39")
>>> result = CalculateGearyAutoTotal(protein)
propy.Autocorrelation.CalculateEachGearyAuto(ProteinSequence, AAP: Dict[Any, Any], AAPName) → Dict[Any, Any][source]

Compute GearyAuto descriptors for different properties based on AADs.

Parameters:
  • ProteinSequence (str) – a pure protein sequence.
  • AAP (Dict[Any, Any]) – contains the properties of 20 amino acids (e.g., _AvFlexibility).
  • AAPName (str) – used for indicating the property (e.g., ‘_AvFlexibility’).
Returns:

result – contains 30 Geary autocorrelation descriptors based on the given property.

Return type:

Dict[Any, Any]

Examples

>>> from propy.GetProteinFromUniprot import GetProteinSequence
>>> protein = GetProteinSequence(ProteinID="Q9NQ39")
>>> AAP, AAPName = _Hydrophobicity, "_Hydrophobicity"
>>> result = CalculateEachGearyAuto(protein, AAP, AAPName)
propy.Autocorrelation.CalculateEachMoranAuto(ProteinSequence: str, AAP: Dict[Any, Any], AAPName: str) → Dict[Any, Any][source]

Compute MoranAuto descriptors for different properties based on AADs.

Parameters:
  • ProteinSequence (str) – a pure protein sequence.
  • AAP (Dict[Any, Any]) – contains the properties of 20 amino acids (e.g., _AvFlexibility).
  • AAPName (str) – used for indicating the property (e.g., ‘_AvFlexibility’).
Returns:

  • result contains 30 Moran autocorrelation descriptors based on the given
  • property.

Examples

>>> from propy.GetProteinFromUniprot import GetProteinSequence
>>> protein = GetProteinSequence(ProteinID="Q9NQ39")
>>> AAP, AAPName = _Hydrophobicity, "_Hydrophobicity"
>>> result = CalculateEachMoranAuto(protein, AAP, AAPName)
propy.Autocorrelation.CalculateEachNormalizedMoreauBrotoAuto(ProteinSequence: str, AAP: Dict[Any, Any], AAPName: str) → Dict[str, float][source]

Compute MoreauBrotoAuto descriptors for different properties based on AADs.

Parameters:
  • ProteinSequence (str) – a pure protein sequence
  • AAP (Dict[Any, Any]) – contains the properties of 20 amino acids (e.g., _AvFlexibility).
  • AAPName (str) – used for indicating the property (e.g., ‘_AvFlexibility’).
Returns:

result – contains 30 Normalized Moreau-Broto autocorrelation descriptors based on the given property.

Return type:

Dict[str, float]

Examples

>>> from propy.GetProteinFromUniprot import GetProteinSequence
>>> protein = GetProteinSequence(ProteinID="Q9NQ39")
>>> AAP, AAPName = _Hydrophobicity, "_Hydrophobicity"
>>> result = CalculateEachNormalizedMoreauBrotoAuto(protein, AAP, AAPName)
propy.Autocorrelation.CalculateGearyAuto(ProteinSequence, AAProperty, AAPropertyName) → Dict[Any, Any][source]

A method used for computing GearyAuto for all properties.

Parameters:
  • ProteinSequence (str) – a pure protein sequence
  • AAProperty (list or tuple form) – contains the properties of 20 amino acids (e.g., _AAProperty).
  • AAPName (list or tuple form) – used for indicating the property (e.g., ‘_AAPropertyName’).
Returns:

  • result contains 30*p Geary autocorrelation descriptors based on the given
  • properties.

Examples

>>> from propy.GetProteinFromUniprot import GetProteinSequence
>>> protein = GetProteinSequence(ProteinID="Q9NQ39")
>>> AAP, AAPName = _Hydrophobicity, "_Hydrophobicity"
>>> result = CalculateGearyAuto(protein, AAP, AAPName)
propy.Autocorrelation.CalculateGearyAutoAvFlexibility(ProteinSequence: str)[source]

Calculte the Geary Autocorrelation descriptors based on AvFlexibility.

Parameters:ProteinSequence (str) – a pure protein sequence.
Returns:result – contains 30 Geary Autocorrelation descriptors based on AvFlexibility.
Return type:Dict

Examples

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

Calculte the Geary Autocorrelation descriptors based on FreeEnergy.

Parameters:ProteinSequence (str) – a pure protein sequence
Returns:
Return type:result contains 30 Geary Autocorrelation descriptors based on FreeEnergy.

Examples

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

Calculte the Geary Autocorrelation descriptors based on hydrophobicity.

Parameters:ProteinSequence (str) – a pure protein sequence
Returns:
  • result contains 30 Geary Autocorrelation descriptors based on
  • hydrophobicity.

Examples

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

Calculte the Geary Autocorrelation descriptors based on Mutability.

Parameters:ProteinSequence (str) – a pure protein sequence
Returns:
Return type:result contains 30 Geary Autocorrelation descriptors based on Mutability.

Examples

>>> from propy.GetProteinFromUniprot import GetProteinSequence
>>> protein = GetProteinSequence(ProteinID="Q9NQ39")
>>> result = CalculateGearyAutoMutability(protein)
propy.Autocorrelation.CalculateGearyAutoPolarizability(ProteinSequence: str)[source]

Calculte the Geary Autocorrelation descriptors based on Polarizability.

Parameters:ProteinSequence (str) – a pure protein sequence.
Returns:result – contains 30 Geary Autocorrelation descriptors based on Polarizability.
Return type:Dict

Examples

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

Calculte the Geary Autocorrelation descriptors based on ResidueASA.

Parameters:ProteinSequence (str) – a pure protein sequence
Returns:
Return type:result contains 30 Geary Autocorrelation descriptors based on ResidueASA.

Examples

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

Calculte the Geary Autocorrelation descriptors based on ResidueVol.

Parameters:ProteinSequence (str) – a pure protein sequence
Returns:
Return type:result contains 30 Geary Autocorrelation descriptors based on ResidueVol.

Examples

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

Calculte the Geary Autocorrelation descriptors based on Steric.

Parameters:ProteinSequence (str) – a pure protein sequence
Returns:
Return type:result contains 30 Geary Autocorrelation descriptors based on Steric.

Examples

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

Compute Geary autocorrelation descriptors based on 8 properties of AADs.

Parameters:ProteinSequence (str) – a pure protein sequence
Returns:
  • result contains 30*8=240 Geary autocorrelation descriptors based on the
  • given properties(i.e., _AAPropert).

Examples

>>> from propy.GetProteinFromUniprot import GetProteinSequence
>>> protein = GetProteinSequence(ProteinID="Q9NQ39")
>>> result = CalculateGearyAutoTotal(protein)
propy.Autocorrelation.CalculateMoranAuto(ProteinSequence, AAProperty, AAPropertyName) → Dict[Any, Any][source]

A method used for computing MoranAuto for all properties.

Parameters:
  • ProteinSequence (str) – a pure protein sequence
  • AAProperty (list or tuple form) – contains the properties of 20 amino acids (e.g., _AAProperty).
  • AAPName (list or tuple form) – used for indicating the property (e.g., ‘_AAPropertyName’).
Returns:

  • result contains 30*p Moran autocorrelation descriptors based on the given
  • properties.

Examples

>>> from propy.GetProteinFromUniprot import GetProteinSequence
>>> protein = GetProteinSequence(ProteinID="Q9NQ39")
>>> AAP, AAPName = _Hydrophobicity, "_Hydrophobicity"
>>> result = CalculateMoranAuto(protein, AAP, AAPName)
propy.Autocorrelation.CalculateMoranAutoAvFlexibility(ProteinSequence: str) → Dict[Any, Any][source]

Calculte the MoranAuto Autocorrelation descriptors based on AvFlexibility.

Parameters:ProteinSequence (str) – a pure protein sequence
Returns:
  • result contains 30 Moran Autocorrelation descriptors based on
  • AvFlexibility.

Examples

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

Calculte the MoranAuto Autocorrelation descriptors based on FreeEnergy.

Parameters:ProteinSequence (str) – a pure protein sequence
Returns:
Return type:result contains 30 Moran Autocorrelation descriptors based on FreeEnergy.

Examples

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

Calculte the MoranAuto Autocorrelation descriptors based on hydrophobicity.

Parameters:ProteinSequence (str) – a pure protein sequence
Returns:
  • result contains 30 Moran Autocorrelation descriptors based on
  • hydrophobicity.

Examples

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

Calculte the MoranAuto Autocorrelation descriptors based on Mutability.

Parameters:ProteinSequence (str) – a pure protein sequence
Returns:
Return type:result contains 30 Moran Autocorrelation descriptors based on Mutability.

Examples

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

Calculte the MoranAuto Autocorrelation descriptors based on Polarizability.

Parameters:ProteinSequence (str) – a pure protein sequence
Returns:
  • result contains 30 Moran Autocorrelation descriptors based on
  • Polarizability.

Examples

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

Calculte the MoranAuto Autocorrelation descriptors based on ResidueASA.

Parameters:ProteinSequence (str) – a pure protein sequence
Returns:
Return type:result contains 30 Moran Autocorrelation descriptors based on ResidueASA.

Examples

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

Calculte the MoranAuto Autocorrelation descriptors based on ResidueVol.

Parameters:ProteinSequence (str) – a pure protein sequence
Returns:
Return type:result contains 30 Moran Autocorrelation descriptors based on ResidueVol.

Examples

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

Calculte the MoranAuto Autocorrelation descriptors based on AutoSteric.

Parameters:ProteinSequence (str) – a pure protein sequence
Returns:
Return type:result contains 30 Moran Autocorrelation descriptors based on AutoSteric.

Examples

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

Compute Moran autocorrelation descriptors based on 8 properties of AADs.

Parameters:ProteinSequence (str) – a pure protein sequence
Returns:
  • result contains 30*8=240 Moran autocorrelation descriptors based on the
  • given properties(i.e., _AAPropert).

Examples

>>> from propy.GetProteinFromUniprot import GetProteinSequence
>>> protein = GetProteinSequence(ProteinID="Q9NQ39")
>>> result = CalculateMoranAutoTotal(protein)
propy.Autocorrelation.CalculateNormalizedMoreauBrotoAuto(ProteinSequence, AAProperty, AAPropertyName) → Dict[Any, Any][source]

A method used for computing MoreauBrotoAuto for all properties.

Parameters:
  • ProteinSequence (str) – a pure protein sequence
  • AAProperty (a list or tuple form) – contains the properties of 20 amino acids (e.g., _AAProperty).
  • AAPName (a list or tuple form) – used for indicating the property (e.g., ‘_AAPropertyName’).
Returns:

  • result contains 30*p Normalized Moreau-Broto autocorrelation descriptors
  • based on the given properties.

Examples

>>> from propy.GetProteinFromUniprot import GetProteinSequence
>>> protein = GetProteinSequence(ProteinID="Q9NQ39")
>>> AAP, AAPName = _Hydrophobicity, "_Hydrophobicity"
>>> result = CalculateNormalizedMoreauBrotoAuto(protein, AAP, AAPName)
propy.Autocorrelation.CalculateNormalizedMoreauBrotoAutoAvFlexibility(ProteinSequence: str) → Dict[Any, Any][source]

Calculte the NormalizedMoreauBorto Autocorrelation descriptors based on AvFlexibility.

Parameters:ProteinSequence (str) – a pure protein sequence
Returns:
  • result contains 30 Normalized Moreau-Broto Autocorrelation descriptors
  • based on AvFlexibility.

Examples

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

Calculte the NormalizedMoreauBorto Autocorrelation descriptors based on FreeEnergy.

Parameters:ProteinSequence (str) – a pure protein sequence
Returns:
  • result contains 30 Normalized Moreau-Broto Autocorrelation descriptors
  • based on FreeEnergy.

Examples

>>> from propy.GetProteinFromUniprot import GetProteinSequence
>>> protein = GetProteinSequence(ProteinID="Q9NQ39")
>>> result = CalculateNormalizedMoreauBrotoAutoFreeEnergy(protein)
propy.Autocorrelation.CalculateNormalizedMoreauBrotoAutoHydrophobicity(ProteinSequence) → Dict[Any, Any][source]

Calculte the NormalizedMoreauBorto Autocorrelation descriptors based on hydrophobicity.

Parameters:ProteinSequence (str) – a pure protein sequence
Returns:
  • result contains 30 Normalized Moreau-Broto Autocorrelation descriptors
  • based on Hydrophobicity.

Examples

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

Calculte the NormalizedMoreauBorto Autocorrelation descriptors based on Mutability.

Parameters:ProteinSequence (str) – a pure protein sequence
Returns:
  • result contains 30 Normalized Moreau-Broto Autocorrelation descriptors
  • based on Mutability.

Examples

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

Calculte the NormalizedMoreauBorto Autocorrelation descriptors based on Polarizability.

Parameters:ProteinSequence (str) – a pure protein sequence
Returns:
  • result contains 30 Normalized Moreau-Broto Autocorrelation descriptors
  • based on Polarizability.

Examples

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

Calculte the NormalizedMoreauBorto Autocorrelation descriptors based on ResidueASA.

Parameters:ProteinSequence (str) – a pure protein sequence
Returns:
  • result contains 30 Normalized Moreau-Broto Autocorrelation descriptors
  • based on ResidueASA.

Examples

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

Calculte the NormalizedMoreauBorto Autocorrelation descriptors based on ResidueVol.

Parameters:ProteinSequence (str) – a pure protein sequence
Returns:
  • result contains 30 Normalized Moreau-Broto Autocorrelation descriptors
  • based on ResidueVol.

Examples

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

Calculte the NormalizedMoreauBorto Autocorrelation descriptors based on Steric.

Parameters:ProteinSequence (str) – a pure protein sequence
Returns:
  • result contains 30 Normalized Moreau-Broto Autocorrelation descriptors
  • based on Steric.

Examples

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

Compute normalized Moreau Broto autocorrelation descriptors based on 8 proterties of AADs.

Parameters:ProteinSequence (str) – a pure protein sequence
Returns:
  • result contains 30*8=240 normalized Moreau Broto autocorrelation
  • descriptors based on the given properties(i.e., _AAPropert).

Examples

>>> from propy.GetProteinFromUniprot import GetProteinSequence
>>> protein = GetProteinSequence(ProteinID="Q9NQ39")
>>> result = CalculateNormalizedMoreauBrotoAutoTotal(protein)
propy.Autocorrelation.NormalizeEachAAP(AAP: Dict[Any, Any]) → Dict[Any, Any][source]

Centralizes and standardizes all amino acid indices before the calculation

Parameters:AAP (Dict[Any, Any]) – contains the properties of 20 amino acids
Returns:result – contains the normalized properties of 20 amino acids
Return type:Dict