diff --git a/rpg/core.py b/rpg/core.py
index 37c63b178371ba7fa1c36594159de4d9ef794f47..124e34864efbaa268ed1338a4684269fb329cc4d 100644
--- a/rpg/core.py
+++ b/rpg/core.py
@@ -23,6 +23,7 @@
########################################################################
"""Contains generic functions and global variables used by RPG"""
+import decimal
import sys
import gzip
@@ -31,71 +32,71 @@ AMINOACIDS = ["A", "C", "D", "E", "F", "G", "H", "I", "J", "K", "L", "M", "N",
"#", "*"]
"""All character accepted in a peptide."""
-AA_MASS_AVERAGE = {"*" : 0.0,
- "A" : 71.0788,
- "C" : 103.1388,
- "D" : 115.0886,
- "E" : 129.1155,
- "F" : 147.1766,
- "G" : 57.0519,
- "H" : 137.1411,
- "I" : 113.1594,
- "J" : 113.1594,
- "K" : 128.1741,
- "L" : 113.1594,
- "M" : 131.1926,
- "N" : 114.1038,
- "O" : 237.3018,
- "P" : 97.1167,
- "Q" : 128.1307,
- "R" : 156.1875,
- "S" : 87.0782,
- "T" : 101.1051,
- "U" : 150.0388,
- "V" : 99.1326,
- "W" : 186.2132,
- "Y" : 163.1760,
- "B" : 0.0,
- "X" : 0.0,
- "Z" : 0.0,
- "#" : 0.0}
+AA_MASS_AVERAGE = {"*" : decimal.Decimal("0.0"),
+ "A" : decimal.Decimal("71.0788"),
+ "C" : decimal.Decimal("103.1388"),
+ "D" : decimal.Decimal("115.0886"),
+ "E" : decimal.Decimal("129.1155"),
+ "F" : decimal.Decimal("147.1766"),
+ "G" : decimal.Decimal("57.0519"),
+ "H" : decimal.Decimal("137.1411"),
+ "I" : decimal.Decimal("113.1594"),
+ "J" : decimal.Decimal("113.1594"),
+ "K" : decimal.Decimal("128.1741"),
+ "L" : decimal.Decimal("113.1594"),
+ "M" : decimal.Decimal("131.1926"),
+ "N" : decimal.Decimal("114.1038"),
+ "O" : decimal.Decimal("237.3018"),
+ "P" : decimal.Decimal("97.1167"),
+ "Q" : decimal.Decimal("128.1307"),
+ "R" : decimal.Decimal("156.1875"),
+ "S" : decimal.Decimal("87.0782"),
+ "T" : decimal.Decimal("101.1051"),
+ "U" : decimal.Decimal("150.0388"),
+ "V" : decimal.Decimal("99.1326"),
+ "W" : decimal.Decimal("186.2132"),
+ "Y" : decimal.Decimal("163.1760"),
+ "B" : decimal.Decimal("0.0"),
+ "X" : decimal.Decimal("0.0"),
+ "Z" : decimal.Decimal("0.0"),
+ "#" : decimal.Decimal("0.0")}
""" Average mass of all amino acids."""
-AA_MASS_MONO = {"*" : 0.0,
- "A" : 71.037113805,
- "C" : 103.009184505,
- "D" : 115.026943065,
- "E" : 129.042593135,
- "F" : 147.068413945,
- "G" : 57.021463735,
- "H" : 137.058911875,
- "I" : 113.084064015,
- "J" : 113.084064015,
- "K" : 128.09496305,
- "L" : 113.084064015,
- "M" : 131.040484645,
- "N" : 114.04292747,
- "O" : 237.147726925,
- "P" : 97.052763875,
- "Q" : 128.05857754,
- "R" : 156.10111105,
- "S" : 87.032028435,
- "T" : 101.047678505,
- "U" : 150.953633405,
- "V" : 99.068413945,
- "W" : 186.07931298,
- "Y" : 163.063328575,
- "B" : 0.0,
- "X" : 0.0,
- "Z" : 0.0,
- "#" : 0.0}
+AA_MASS_MONO = {"*" : decimal.Decimal("0.0"),
+ "A" : decimal.Decimal("71.037113805"),
+ "C" : decimal.Decimal("103.009184505"),
+ "D" : decimal.Decimal("115.026943065"),
+ "E" : decimal.Decimal("129.042593135"),
+ "F" : decimal.Decimal("147.068413945"),
+ "G" : decimal.Decimal("57.021463735"),
+ "H" : decimal.Decimal("137.058911875"),
+ "I" : decimal.Decimal("113.084064015"),
+ "J" : decimal.Decimal("113.084064015"),
+ "K" : decimal.Decimal("128.09496305"),
+ "L" : decimal.Decimal("113.084064015"),
+ "M" : decimal.Decimal("131.040484645"),
+ "N" : decimal.Decimal("114.04292747"),
+ "O" : decimal.Decimal("237.147726925"),
+ "P" : decimal.Decimal("97.052763875"),
+ "Q" : decimal.Decimal("128.05857754"),
+ "R" : decimal.Decimal("156.10111105"),
+ "S" : decimal.Decimal("87.032028435"),
+ "T" : decimal.Decimal("101.047678505"),
+ "U" : decimal.Decimal("150.953633405"),
+ "V" : decimal.Decimal("99.068413945"),
+ "W" : decimal.Decimal("186.07931298"),
+ "Y" : decimal.Decimal("163.063328575"),
+ "B" : decimal.Decimal("0.0"),
+ "X" : decimal.Decimal("0.0"),
+ "Z" : decimal.Decimal("0.0"),
+ "#" : decimal.Decimal("0.0")}
""" Monoisotopic mass of all amino acids.
From https://proteomicsresource.washington.edu/protocols06/masses.php
"""
-WATER_MASS = 18.01528
+WATER_MASS = decimal.Decimal("18.01528")
"""Mass of a water molecule."""
-WATER_MASS_MONO = 18.0105647
+WATER_MASS_MONO = decimal.Decimal("18.0105647")
"""Monoisotopic mass of a water molecule."""
# Biochemistry Stryer 7th
diff --git a/rpg/sequence.py b/rpg/sequence.py
index 374445c41da526f3303d8be5f5a11b1108ac98a1..efea0abe631b5aae5d769fcc2c3286fc75bf1d16 100644
--- a/rpg/sequence.py
+++ b/rpg/sequence.py
@@ -23,6 +23,7 @@
########################################################################
"""Contains classes and function related to sequences"""
+import decimal
from rpg import core
class Peptide:
@@ -66,10 +67,9 @@ class Peptide:
self.position = position # position of cleavage
self.size = len(sequence) # size of the peptide
# Mass of the peptide
- tmp_mass = water_mass
+ self.mass = water_mass
for i in sequence:
- tmp_mass += aa_mass[i]
- self.mass = round(tmp_mass, len(str(aa_mass["A"]).split(".")[1])) # mass of the peptide
+ self.mass += aa_mass[i]
self.p_i = self.get_isoelectric_point()
# self representation for print
diff --git a/tests/test_core.py b/tests/test_core.py
index 54542eaa17ee41be9bdb9b980e3570d0a21fca51..2239df7bb80e35134514616728f378ec20aa4ba5 100644
--- a/tests/test_core.py
+++ b/tests/test_core.py
@@ -91,12 +91,12 @@ def test_output_results(capsys, tmp_path):
assert out == outf.read()
assert out == "Original_header,No_peptide,Enzyme,Cleaving_"\
"pos,Peptide_size,Peptide_mass,pI,Sequence\n"\
- "Input,0,fake_enzyme1,4,4,534.20743,3.14,WQS"\
- "D\nInput,1,fake_enzyme1,7,3,349.11213,3.04,"\
- "ESD\nInput,2,fake_enzyme1,12,5,495.19653,3."\
- "14,FZQSD\nInput,3,fake_enzyme1,15,3,349.112"\
- "13,3.04,ESD\nInput,4,fake_enzyme1,16,1,165."\
- "07898,5.97,F\n"
+ "Input,0,fake_enzyme1,4,4,534.207426720,3.14,WQS"\
+ "D\nInput,1,fake_enzyme1,7,3,349.112129335,3.04,"\
+ "ESD\nInput,2,fake_enzyme1,12,5,495.196527685,3."\
+ "14,FZQSD\nInput,3,fake_enzyme1,15,3,349.112129335"\
+ ",3.04,ESD\nInput,4,fake_enzyme1,16,1,165."\
+ "078978645,5.97,F\n"
# CSV output
seq = "WQSDESDFZQSDESDF"