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//
// $Id$
//
//
// Original author: Darren Kessner <darren@proteowizard.org>
//
// Copyright 2005 Louis Warschaw Prostate Cancer Center
// 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.
//
#ifndef _ION_HPP_
#define _ION_HPP_
#include "Chemistry.hpp"
#include <stdexcept>
namespace pwiz {
namespace chemistry {
namespace Ion
{
/*!
* Converts the m/z of an ion to a neutral mass.
* @param[in] mz The m/z to convert.
* @param[in] protonDelta The number of extra protons attached to the ion.
* @param[in] electronDelta The number of extra electrons attached to the ion.
* @param[in] neutronDelta The number of extra neutrons attached to the ion.
* \pre protonDelta != electronDelta
*/
inline double neutralMass(double mz, int protonDelta, int electronDelta = 0, int neutronDelta = 0)
{
int charge = protonDelta - electronDelta;
return charge == 0 ? throw std::invalid_argument("[Ion::neutralMass()] m/z with protonDelta=electronDelta is impossible")
: mz * charge - ((Proton * protonDelta) +
(Electron * electronDelta) +
(Neutron * neutronDelta));
}
/*!
* Converts a neutral mass to an ionized mass.
* @param[in] neutralMass The neutral mass to ionize.
* @param[in] protonDelta The number of extra protons to attach to the ion.
* @param[in] electronDelta The number of extra electrons to attach to the ion.
* @param[in] neutronDelta The number of extra neutrons to attach to the ion.
* \pre protonDelta != electronDelta
*/
inline double ionMass(double neutralMass, int protonDelta, int electronDelta = 0, int neutronDelta = 0)
{
return neutralMass + (Proton * protonDelta) +
(Electron * electronDelta) +
(Neutron * neutronDelta);
}
/*!
* Converts a neutral mass to an m/z.
* @param[in] neutralMass The neutral mass to ionize.
* @param[in] protonDelta The number of extra protons to attach to the ion.
* @param[in] electronDelta The number of extra electrons to attach to the ion.
* @param[in] neutronDelta The number of extra neutrons to attach to the ion.
* \pre protonDelta != electronDelta
*/
inline double mz(double neutralMass, int protonDelta, int electronDelta = 0, int neutronDelta = 0)
{
int z = protonDelta - electronDelta;
double m = ionMass(neutralMass, protonDelta, electronDelta, neutronDelta);
return z == 0 ? throw std::invalid_argument("[Ion::mz()] m/z with protonDelta=electronDelta is impossible")
: m / z;
}
}
} // namespace chemistry
} // namespace pwiz
#endif // _ION_HPP_
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