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changeset 30:921004017f3c draft

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author jose_duarte
date Mon, 13 Dec 2021 11:19:01 +0000
parents c36c8a144219
children 3d94608aea7a
files local_ctd.py
diffstat 1 files changed, 0 insertions(+), 324 deletions(-) [+]
line wrap: on
line diff
--- a/local_ctd.py	Sun Dec 12 10:50:31 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,324 +0,0 @@
-# -*- coding: utf-8 -*-
-"""
-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
-"""
-
-# Core Library
-import copy
-import math
-from typing import Any, Dict
-
-_Hydrophobicity = {"1": "RKEDQN", "2": "GASTPHY", "3": "CLVIMFW"}
-# '1'stand for Polar; '2'stand for Neutral, '3' stand for Hydrophobicity
-
-_NormalizedVDWV = {"1": "GASTPDC", "2": "NVEQIL", "3": "MHKFRYW"}
-# '1'stand for (0-2.78); '2'stand for (2.95-4.0), '3' stand for (4.03-8.08)
-
-_Polarity = {"1": "LIFWCMVY", "2": "PATGS", "3": "HQRKNED"}
-# '1'stand for (4.9-6.2); '2'stand for (8.0-9.2), '3' stand for (10.4-13.0)
-
-_Charge = {"1": "KR", "2": "ANCQGHILMFPSTWYV", "3": "DE"}
-# '1'stand for Positive; '2'stand for Neutral, '3' stand for Negative
-
-_SecondaryStr = {"1": "EALMQKRH", "2": "VIYCWFT", "3": "GNPSD"}
-# '1'stand for Helix; '2'stand for Strand, '3' stand for coil
-
-_SolventAccessibility = {"1": "ALFCGIVW", "2": "RKQEND", "3": "MPSTHY"}
-# '1'stand for Buried; '2'stand for Exposed, '3' stand for Intermediate
-
-_Polarizability = {"1": "GASDT", "2": "CPNVEQIL", "3": "KMHFRYW"}
-# '1'stand for (0-0.108); '2'stand for (0.128-0.186), '3' stand for (0.219-0.409)
-
-
-# You can continuely add other properties of AADs to compute descriptors of
-# protein sequence.
-
-_AATProperty = (
-    _Hydrophobicity,
-    _NormalizedVDWV,
-    _Polarity,
-    _Charge,
-    _SecondaryStr,
-    _SolventAccessibility,
-    _Polarizability,
-)
-
-_AATPropertyName = (
-    "_Hydrophobicity",
-    "_NormalizedVDWV",
-    "_Polarity",
-    "_Charge",
-    "_SecondaryStr",
-    "_SolventAccessibility",
-    "_Polarizability",
-)
-
-
-def StringtoNum(ProteinSequence: str, AAProperty: Dict[Any, Any]) -> str:
-    hardProteinSequence = copy.deepcopy(ProteinSequence)
-    for k, m in list(AAProperty.items()):
-        for index in m:
-            hardProteinSequence = hardProteinSequence.replace(index, k)
-    TProteinSequence = hardProteinSequence
-
-    return TProteinSequence
-
-
-def CalculateComposition(
-    ProteinSequence: str, AAProperty: Dict[Any, Any], AAPName: str) -> Dict[Any, Any]:
-    TProteinSequence = StringtoNum(ProteinSequence, AAProperty)
-    result = {}
-    num = len(TProteinSequence)
-    result[AAPName + "C" + "1"] = round(float(TProteinSequence.count("1")) / num, 3)
-    result[AAPName + "C" + "2"] = round(float(TProteinSequence.count("2")) / num, 3)
-    result[AAPName + "C" + "3"] = round(float(TProteinSequence.count("3")) / num, 3)
-    return result
-
-
-def CalculateTransition(
-    ProteinSequence: str, AAProperty: Dict[Any, Any], AAPName: str
-) -> Dict[Any, Any]:
-    TProteinSequence = StringtoNum(ProteinSequence, AAProperty)
-    Result = {}
-    num = len(TProteinSequence)
-    CTD = TProteinSequence
-    Result[AAPName + "T" + "12"] = round(
-        float(CTD.count("12") + CTD.count("21")) / (num - 1), 3
-    )
-    Result[AAPName + "T" + "13"] = round(
-        float(CTD.count("13") + CTD.count("31")) / (num - 1), 3
-    )
-    Result[AAPName + "T" + "23"] = round(
-        float(CTD.count("23") + CTD.count("32")) / (num - 1), 3
-    )
-    return Result
-
-
-def CalculateDistribution(
-    ProteinSequence: str, AAProperty: Dict[Any, Any], AAPName: str
-) -> Dict[Any, Any]:
-    TProteinSequence = StringtoNum(ProteinSequence, AAProperty)
-    Result: Dict[str, float] = {}
-    Num = len(TProteinSequence)
-    for i in ("1", "2", "3"):
-        num = TProteinSequence.count(i)
-        ink = 1
-        indexk = 0
-        cds = []
-        while ink <= num:
-            indexk = TProteinSequence.find(i, indexk) + 1
-            cds.append(indexk)
-            ink = ink + 1
-
-        if cds == []:
-            Result[AAPName + "D" + i + "001"] = 0
-            Result[AAPName + "D" + i + "025"] = 0
-            Result[AAPName + "D" + i + "050"] = 0
-            Result[AAPName + "D" + i + "075"] = 0
-            Result[AAPName + "D" + i + "100"] = 0
-        else:
-            Result[AAPName + "D" + i + "001"] = round(float(cds[0]) / Num * 100, 3)
-            Result[AAPName + "D" + i + "025"] = round(
-                float(cds[int(math.floor(num * 0.25)) - 1]) / Num * 100, 3
-            )
-            Result[AAPName + "D" + i + "050"] = round(
-                float(cds[int(math.floor(num * 0.5)) - 1]) / Num * 100, 3
-            )
-            Result[AAPName + "D" + i + "075"] = round(
-                float(cds[int(math.floor(num * 0.75)) - 1]) / Num * 100, 3
-            )
-            Result[AAPName + "D" + i + "100"] = round(float(cds[-1]) / Num * 100, 3)
-
-    return Result
-
-
-def CalculateCompositionHydrophobicity(ProteinSequence: str):
-    return CalculateComposition(ProteinSequence, _Hydrophobicity, "_Hydrophobicity")
-
-
-def CalculateCompositionNormalizedVDWV(ProteinSequence: str):
-    return CalculateComposition(ProteinSequence, _NormalizedVDWV, "_NormalizedVDWV")
-
-
-def CalculateCompositionPolarity(ProteinSequence: str):
-    return CalculateComposition(ProteinSequence, _Polarity, "_Polarity")
-
-
-def CalculateCompositionCharge(ProteinSequence: str) -> Dict[Any, Any]:
-    return CalculateComposition(ProteinSequence, _Charge, "_Charge")
-
-
-def CalculateCompositionSecondaryStr(ProteinSequence: str) -> Dict[Any, Any]:
-    return CalculateComposition(ProteinSequence, _SecondaryStr, "_SecondaryStr")
-
-
-def CalculateCompositionSolventAccessibility(ProteinSequence: str) -> Dict[Any, Any]:
-    return CalculateComposition(
-        ProteinSequence, _SolventAccessibility, "_SolventAccessibility"
-    )
-
-
-def CalculateCompositionPolarizability(ProteinSequence: str) -> Dict[Any, Any]:
-    return CalculateComposition(ProteinSequence, _Polarizability, "_Polarizability")
-
-
-def CalculateTransitionHydrophobicity(ProteinSequence: str) -> Dict[Any, Any]:
-    result = CalculateTransition(ProteinSequence, _Hydrophobicity, "_Hydrophobicity")
-    return result
-
-
-def CalculateTransitionNormalizedVDWV(ProteinSequence: str) -> Dict[Any, Any]:
-    result = CalculateTransition(ProteinSequence, _NormalizedVDWV, "_NormalizedVDWV")
-    return result
-
-
-def CalculateTransitionPolarity(ProteinSequence: str) -> Dict[Any, Any]:
-    result = CalculateTransition(ProteinSequence, _Polarity, "_Polarity")
-    return result
-
-
-def CalculateTransitionCharge(ProteinSequence: str) -> Dict[Any, Any]:
-    result = CalculateTransition(ProteinSequence, _Charge, "_Charge")
-    return result
-
-
-def CalculateTransitionSecondaryStr(ProteinSequence: str) -> Dict[Any, Any]:
-    result = CalculateTransition(ProteinSequence, _SecondaryStr, "_SecondaryStr")
-    return result
-
-
-def CalculateTransitionSolventAccessibility(ProteinSequence: str) -> Dict[Any, Any]:
-    result = CalculateTransition(
-        ProteinSequence, _SolventAccessibility, "_SolventAccessibility"
-    )
-    return result
-
-
-def CalculateTransitionPolarizability(ProteinSequence: str) -> Dict[Any, Any]:
-    result = CalculateTransition(ProteinSequence, _Polarizability, "_Polarizability")
-    return result
-
-
-def CalculateDistributionHydrophobicity(ProteinSequence: str) -> Dict[Any, Any]:
-    result = CalculateDistribution(ProteinSequence, _Hydrophobicity, "_Hydrophobicity")
-    return result
-
-
-def CalculateDistributionNormalizedVDWV(ProteinSequence: str) -> Dict[Any, Any]:
-    result = CalculateDistribution(ProteinSequence, _NormalizedVDWV, "_NormalizedVDWV")
-    return result
-
-
-def CalculateDistributionPolarity(ProteinSequence: str) -> Dict[Any, Any]:
-    result = CalculateDistribution(ProteinSequence, _Polarity, "_Polarity")
-    return result
-
-
-def CalculateDistributionCharge(ProteinSequence: str) -> Dict[Any, Any]:
-    result = CalculateDistribution(ProteinSequence, _Charge, "_Charge")
-    return result
-
-
-def CalculateDistributionSecondaryStr(ProteinSequence: str) -> Dict[Any, Any]:
-    result = CalculateDistribution(ProteinSequence, _SecondaryStr, "_SecondaryStr")
-    return result
-
-
-def CalculateDistributionSolventAccessibility(ProteinSequence: str) -> Dict[Any, Any]:
-    result = CalculateDistribution(
-        ProteinSequence, _SolventAccessibility, "_SolventAccessibility"
-    )
-    return result
-
-
-def CalculateDistributionPolarizability(ProteinSequence: str) -> Dict[Any, Any]:
-    result = CalculateDistribution(ProteinSequence, _Polarizability, "_Polarizability")
-    return result
-
-
-def CalculateC(ProteinSequence: str) -> Dict[Any, Any]:
-    result: Dict[Any, Any] = {}
-    result.update(CalculateCompositionPolarizability(ProteinSequence))
-    result.update(CalculateCompositionSolventAccessibility(ProteinSequence))
-    result.update(CalculateCompositionSecondaryStr(ProteinSequence))
-    result.update(CalculateCompositionCharge(ProteinSequence))
-    result.update(CalculateCompositionPolarity(ProteinSequence))
-    result.update(CalculateCompositionNormalizedVDWV(ProteinSequence))
-    result.update(CalculateCompositionHydrophobicity(ProteinSequence))
-    return result
-
-
-def CalculateT(ProteinSequence: str) -> Dict[Any, Any]:
-    result: Dict[Any, Any] = {}
-    result.update(CalculateTransitionPolarizability(ProteinSequence))
-    result.update(CalculateTransitionSolventAccessibility(ProteinSequence))
-    result.update(CalculateTransitionSecondaryStr(ProteinSequence))
-    result.update(CalculateTransitionCharge(ProteinSequence))
-    result.update(CalculateTransitionPolarity(ProteinSequence))
-    result.update(CalculateTransitionNormalizedVDWV(ProteinSequence))
-    result.update(CalculateTransitionHydrophobicity(ProteinSequence))
-    return result
-
-
-def CalculateD(ProteinSequence: str) -> Dict[Any, Any]:
-    result: Dict[Any, Any] = {}
-    result.update(CalculateDistributionPolarizability(ProteinSequence))
-    result.update(CalculateDistributionSolventAccessibility(ProteinSequence))
-    result.update(CalculateDistributionSecondaryStr(ProteinSequence))
-    result.update(CalculateDistributionCharge(ProteinSequence))
-    result.update(CalculateDistributionPolarity(ProteinSequence))
-    result.update(CalculateDistributionNormalizedVDWV(ProteinSequence))
-    result.update(CalculateDistributionHydrophobicity(ProteinSequence))
-    return result
-
-
-def CalculateCTD(ProteinSequence: str) -> Dict[Any, Any]:
-    result: Dict[Any, Any] = {}
-    result.update(CalculateCompositionPolarizability(ProteinSequence))
-    result.update(CalculateCompositionSolventAccessibility(ProteinSequence))
-    result.update(CalculateCompositionSecondaryStr(ProteinSequence))
-    result.update(CalculateCompositionCharge(ProteinSequence))
-    result.update(CalculateCompositionPolarity(ProteinSequence))
-    result.update(CalculateCompositionNormalizedVDWV(ProteinSequence))
-    result.update(CalculateCompositionHydrophobicity(ProteinSequence))
-    result.update(CalculateTransitionPolarizability(ProteinSequence))
-    result.update(CalculateTransitionSolventAccessibility(ProteinSequence))
-    result.update(CalculateTransitionSecondaryStr(ProteinSequence))
-    result.update(CalculateTransitionCharge(ProteinSequence))
-    result.update(CalculateTransitionPolarity(ProteinSequence))
-    result.update(CalculateTransitionNormalizedVDWV(ProteinSequence))
-    result.update(CalculateTransitionHydrophobicity(ProteinSequence))
-    result.update(CalculateDistributionPolarizability(ProteinSequence))
-    result.update(CalculateDistributionSolventAccessibility(ProteinSequence))
-    result.update(CalculateDistributionSecondaryStr(ProteinSequence))
-    result.update(CalculateDistributionCharge(ProteinSequence))
-    result.update(CalculateDistributionPolarity(ProteinSequence))
-    result.update(CalculateDistributionNormalizedVDWV(ProteinSequence))
-    result.update(CalculateDistributionHydrophobicity(ProteinSequence))
-    return result
-
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