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changeset 31:3d94608aea7a draft

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Uploaded
author jose_duarte
date Mon, 13 Dec 2021 11:19:23 +0000
parents 921004017f3c
children 5a0afb1578ea
files local_ctd.py
diffstat 1 files changed, 324 insertions(+), 0 deletions(-) [+]
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line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/local_ctd.py	Mon Dec 13 11:19:23 2021 +0000
@@ -0,0 +1,324 @@
+# -*- 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": "GASTPD", "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": "CPNVEQIL", "3": "KMHFRYW"}
+# '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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+