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# -------------------------------------------------------------------------
# Copyright (C) 2005-2012 Martin Strohalm <www.mmass.org>
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 3 of the License, or
# (at your option) any later version.
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
# Complete text of GNU GPL can be found in the file LICENSE.TXT in the
# main directory of the program.
# -------------------------------------------------------------------------
# load stopper
from mod_stopper import CHECK_FORCE_QUIT
# load objects
import blocks
# load modules
import mod_basics
import mod_pattern
# COMPOUND OBJECT DEFINITION
# --------------------------
class compound:
"""Compound object definition."""
def __init__(self, expression, **attr):
# check formula
self._checkFormula(expression)
self.expression = expression
# buffers
self._composition = None
self._formula = None
self._mass = None
# get additional attributes
self.attributes = {}
for name, value in attr.items():
self.attributes[name] = value
# ----
def __iadd__(self, other):
"""Append formula."""
# check and append value
if isinstance(other, compound):
self.expression += other.expression
else:
self._checkFormula(other)
self.expression += other
# clear buffers
self.reset()
return self
# ----
def reset(self):
"""Clear formula buffers."""
self._composition = None
self._formula = None
self._mass = None
# ----
# GETTERS
def count(self, item, groupIsotopes=False):
"""Count atom in formula."""
# get composition
comp = self.composition()
# get atoms to count
atoms = [item]
if groupIsotopes and item in blocks.elements:
for massNo in blocks.elements[item].isotopes:
atom = '%s{%d}' % (item,massNo)
atoms.append(atom)
# count atom
atomsCount = 0
for atom in atoms:
if atom in comp:
atomsCount += comp[atom]
return atomsCount
# ----
def formula(self):
"""Get formula."""
# check formula buffer
if self._formula != None:
return self._formula
self._formula = ''
# get composition
comp = self.composition()
elements = sorted(comp.keys())
# add C and H first
for el in ('C', 'C{12}', 'C{13}', 'C{14}', 'H', 'H{1}', 'H{2}', 'H{3}'):
if el in elements:
if comp[el] == 1:
self._formula += el
else:
self._formula += '%s%d' % (el, comp[el])
del elements[elements.index(el)]
# add remaining atoms
for el in elements:
if comp[el] == 1:
self._formula += el
else:
self._formula += '%s%d' % (el, comp[el])
return self._formula
# ----
def composition(self):
"""Get elemental composition."""
# check composition buffer
if self._composition != None:
return self._composition
# unfold brackets
unfoldedFormula = self._unfoldBrackets(self.expression)
# group elements
self._composition = {}
for symbol, isotop, count in mod_basics.ELEMENT_PATTERN.findall(unfoldedFormula):
# make atom
if isotop:
atom = '%s{%s}' % (symbol, isotop)
else:
atom = symbol
# convert counting
if count:
count = int(count)
else:
count = 1
# add atom
if atom in self._composition:
self._composition[atom] += count
else:
self._composition[atom] = count
# remove zeros
for atom in self._composition.keys():
if self._composition[atom] == 0:
del self._composition[atom]
return self._composition
# ----
def mass(self, massType=None):
"""Get mass."""
# get mass
if self._mass == None:
massMo = 0
massAv = 0
# get composition
comp = self.composition()
# get mass for each atom
for atom in comp:
count = comp[atom]
# check specified isotope and mass
match = mod_basics.ELEMENT_PATTERN.match(atom)
symbol, massNumber, tmp = match.groups()
if massNumber:
isotope = blocks.elements[symbol].isotopes[int(massNumber)]
atomMass = (isotope[0], isotope[0])
else:
atomMass = blocks.elements[symbol].mass
# multiply atom mass
massMo += atomMass[0]*count
massAv += atomMass[1]*count
# store mass in buffer
self._mass = (massMo, massAv)
# return mass
if massType == 0:
return self._mass[0]
elif massType == 1:
return self._mass[1]
else:
return self._mass
# ----
def mz(self, charge, agentFormula='H', agentCharge=1):
"""Get ion m/z."""
return mod_basics.mz(self.mass(),
charge = charge,
agentFormula = agentFormula,
agentCharge = agentCharge
)
# ----
def pattern(self, fwhm=0.1, threshold=0.01, charge=0, agentFormula='H', agentCharge=1, real=True):
"""Get isotopic pattern."""
return mod_pattern.pattern(
compound = self,
fwhm = fwhm,
threshold = threshold,
charge = charge,
agentFormula = agentFormula,
agentCharge = agentCharge,
real = real
)
# ----
def rdbe(self):
"""Get RDBE (Range or Double Bonds Equivalents)."""
return mod_basics.rdbe(self)
# ----
def isvalid(self, charge=0, agentFormula='H', agentCharge=1):
"""Check ion composition."""
# check agent formula
if agentFormula != 'e' and not isinstance(agentFormula, compound):
agentFormula = compound(agentFormula)
# make ion compound
if charge and agentFormula != 'e':
ionFormula = self.expression
for atom, count in agentFormula.composition().items():
ionFormula += '%s%d' % (atom, count*(charge/agentCharge))
ion = compound(ionFormula)
else:
ion = compound(self.expression)
# get composition
for atom, count in ion.composition().items():
if count < 0:
return False
return True
# ----
def frules(self, rules=['HC','NOPSC','NOPS','RDBE'], HC=(0.1, 3.0), NOPSC=(4,3,2,3), RDBE=(-1,40)):
"""Check formula rules."""
return mod_basics.frules(
compound = self,
rules = rules,
HC = HC,
NOPSC = NOPSC,
RDBE = RDBE
)
# ----
# MODIFIERS
def negate(self):
"""Make all atom counts negative."""
# get composition
comp = self.composition()
# negate composition
formula = ''
for el in sorted(comp.keys()):
formula += '%s%d' % (el, -1*comp[el])
self.expression = formula
# clear buffers
self.reset()
# ----
# HELPERS
def _checkFormula(self, formula):
"""Check given formula."""
# check formula
if not mod_basics.FORMULA_PATTERN.match(formula):
raise ValueError, 'Wrong formula! --> ' + formula
# check elements and isotopes
for atom in mod_basics.ELEMENT_PATTERN.findall(formula):
if not atom[0] in blocks.elements:
raise ValueError, 'Unknown element in formula! --> ' + atom[0] + ' in ' + formula
elif atom[1] and not int(atom[1]) in blocks.elements[atom[0]].isotopes:
raise ValueError, 'Unknown isotope in formula! --> ' + atom[0] + atom[1] + ' in ' + formula
# check brackets
if formula.count(')') != formula.count('('):
raise ValueError, 'Wrong number of brackets in formula! --> ' + formula
# ----
def _unfoldBrackets(self, string):
"""Unfold formula and count each atom."""
unfoldedFormula = ''
brackets = [0,0]
enclosedFormula = ''
i = 0
while i < len(string):
# handle brackets
if string[i] == '(':
brackets[0] += 1
elif string[i] == ')':
brackets[1] += 1
# part outside brackets
if brackets == [0,0]:
unfoldedFormula += string[i]
# part within brackets
else:
enclosedFormula += string[i]
# unfold part within brackets
if brackets[0] == brackets[1]:
enclosedFormula = self._unfoldBrackets(enclosedFormula[1:-1])
# multiply part within brackets
count = ''
while len(string)>(i+1) and string[i+1].isdigit():
count += string[i+1]
i += 1
if count:
enclosedFormula = enclosedFormula * int(count)
# add and clear
unfoldedFormula += enclosedFormula
enclosedFormula = ''
brackets = [0,0]
i += 1
return unfoldedFormula
# ----
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