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//
// $Id$
//
//
// Original author: Darren Kessner <darren@proteowizard.org>
//
// Copyright 2007 Spielberg Family Center for Applied Proteomics
// Cedars Sinai Medical Center, Los Angeles, California 90048
//
// Licensed under the Apache License, Version 2.0 (the "License");
// you may not use this file except in compliance with the License.
// You may obtain a copy of the License at
//
// http://www.apache.org/licenses/LICENSE-2.0
//
// Unless required by applicable law or agreed to in writing, software
// distributed under the License is distributed on an "AS IS" BASIS,
// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
// See the License for the specific language governing permissions and
// limitations under the License.
//
#define PWIZ_SOURCE
#include "IsotopeEnvelopeEstimator.hpp"
#include "IsotopeCalculator.hpp"
#include "pwiz/utility/math/round.hpp"
#include "pwiz/utility/misc/Std.hpp"
#include <cmath>
namespace pwiz {
namespace chemistry {
class IsotopeEnvelopeEstimator::Impl
{
public:
Impl(const Config& config);
MassDistribution isotopeEnvelope(double mass) const;
private:
Config config_;
vector<MassDistribution> cache_;
unsigned int massToIndex(double mass) const;
double indexToMass(unsigned int index) const;
void initializeCache();
};
IsotopeEnvelopeEstimator::Impl::Impl(const Config& config)
: config_(config)
{
initializeCache();
}
unsigned int IsotopeEnvelopeEstimator::Impl::massToIndex(double mass) const
{
unsigned int index = (unsigned int)round(config_.cacheSize * mass / config_.cacheMaxMass);
if (index >= config_.cacheSize)
throw runtime_error("IsotopeEnvelopeEstimator::massToIndex()] Index out of bounds.");
return index;
}
double IsotopeEnvelopeEstimator::Impl::indexToMass(unsigned int index) const
{
double mass = config_.cacheMaxMass * index / config_.cacheSize;
return mass;
}
namespace {
Formula estimateFormula(double mass)
{
// estimate formula assuming it's a peptide, using average elemental composition
// of amino acid residues
using namespace Element;
const double averageResidueMass = 111.10524;
const double averageC = 4.944;
const double averageH = 7.763;
const double averageN = 1.357;
const double averageO = 1.476;
const double averageS = 0.042;
Formula water("H2O1");
double residueCount = (mass - water.monoisotopicMass())/averageResidueMass;
if (residueCount < 0) residueCount = 0;
Formula result;
result[C] = (int)round(residueCount * averageC);
result[H] = (int)round(residueCount * averageH);
result[N] = (int)round(residueCount * averageN);
result[O] = (int)round(residueCount * averageO);
result[S] = (int)round(residueCount * averageS);
result += water;
return result;
}
} // namespace
void IsotopeEnvelopeEstimator::Impl::initializeCache()
{
if (!config_.isotopeCalculator)
throw runtime_error("[IsotopeEnvelopeEstimator::initializeCache()] Initialization with null IsotopeCalculator*.");
cache_.reserve(config_.cacheSize);
for (unsigned int index=0; index<config_.cacheSize; ++index)
{
// estimate the peptide formula and cache the normalized distribution
Formula formula = estimateFormula(indexToMass(index));
MassDistribution md =
config_.isotopeCalculator->distribution(formula,
0, // charge state
config_.normalization);
cache_.push_back(md);
}
}
MassDistribution IsotopeEnvelopeEstimator::Impl::isotopeEnvelope(double mass) const
{
return cache_[massToIndex(mass)];
}
//
// forwarding to impl
//
PWIZ_API_DECL IsotopeEnvelopeEstimator::IsotopeEnvelopeEstimator(const Config& config)
: impl_(new Impl(config))
{}
PWIZ_API_DECL IsotopeEnvelopeEstimator::~IsotopeEnvelopeEstimator() {} // auto destruction of impl_
PWIZ_API_DECL MassDistribution IsotopeEnvelopeEstimator::isotopeEnvelope(double mass) const
{
return impl_->isotopeEnvelope(mass);
}
} // namespace chemistry
} // namespace pwiz
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