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make hydrophobicity scale user specific #2

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58 changes: 34 additions & 24 deletions src/metrics/metrics.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,29 +9,29 @@
from Bio.PDB.Polypeptide import three_to_one, standard_aa_names

GLYXGLY_ASA = { # from Miller, Janin et al (1987)
"A": 113,
"R": 241,
"N": 158,
"D": 151,
"C": 140,
"Q": 189,
"E": 183,
"G": 85,
"H": 194,
"I": 182,
"L": 180,
"K": 211,
"M": 204,
"F": 218,
"P": 143,
"S": 122,
"T": 146,
"W": 259,
"Y": 229,
"V": 160,
'A': 113,
'R': 241,
'N': 158,
'D': 151,
'C': 140,
'Q': 189,
'E': 183,
'G': 85,
'H': 194,
'I': 182,
'L': 180,
'K': 211,
'M': 204,
'F': 218,
'P': 143,
'S': 122,
'T': 146,
'W': 259,
'Y': 229,
'V': 160,
}

hydrophobicityscale = { # from Guy, H.R., Biophys J. 47:61-70(1985)
hydrophobicityscale = { # from Guy, H.R., Biophys J. 47:61-70(1985), table 4
'A': 0.100,
'R': 1.910,
'N': 0.480,
Expand Down Expand Up @@ -64,6 +64,7 @@ class ModStructure(Structure):

def __init__(self, id):
Structure.__init__(self, id)
self.hydrophobicityscale = hydrophobicityscale

def measure(self):
'''
Expand Down Expand Up @@ -227,7 +228,7 @@ def dipolevector(self):

def dipolemoment(self):
'''
Calculation of the dipole moment from the dipole vector.
Calculation of the dipole moment in Debye from the dipole vector.

:param self: Structure entity
:return: Dipole moment
Expand All @@ -236,6 +237,14 @@ def dipolemoment(self):
'''
return 4.803 * np.linalg.norm(self.dipolevector())

def sethydrophobicityscale(self, scale):
'''
Customize values of hydrophobicity scale.
:param scale: dictionary: {residue: energy required to transfer residue from surface of protein to its interior}
:rtype: None
'''
self.hydrophobicityscale = scale

def truehydrophobicity(self):
'''
Calculate total hydrophobicity for residues that are more than 25%
Expand All @@ -251,7 +260,7 @@ def truehydrophobicity(self):
# if residue.get_resname() in GLYXGLY_ASA:
sasaratio = residue.sasa / GLYXGLY_ASA[residue.resletter]
if sasaratio > 0.25:
truehydrophobicity += hydrophobicityscale[residue.resletter]
truehydrophobicity += self.hydrophobicityscale[residue.resletter]
return truehydrophobicity

def hydrophobicvector(self):
Expand All @@ -267,7 +276,7 @@ def hydrophobicvector(self):
for residue in self.get_residues():
#if residue.get_resname() in GLYXGLY_ASA:
hydrophobicvector += (
hydrophobicityscale[residue.resletter] * residue.sasa * (
self.hydrophobicityscale[residue.resletter] * residue.sasa * (
residue.center_of_mass() - self.center_of_mass()))
return hydrophobicvector

Expand Down Expand Up @@ -378,6 +387,7 @@ def init_residue(self, resname, field, resseq, icode):
parser = PDBParser(QUIET=1, structure_builder=Builder())
s = parser.get_structure("1ris", "data/data1/1ris.pdb")
# s.calculate_sasa()
s.sethydrophobicityscale({k: np.random.rand() for k in hydrophobicityscale})
s.measure()
com = s.center_of_mass()
dpv = s.dipolevector()
Expand Down