/usr/include/libpwiz/pwiz/data/common/Unimod.hpp is in libpwiz-dev 3.0.9393-1+b2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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// $Id: Unimod.hpp 4922 2013-09-05 22:33:08Z pcbrefugee $
//
//
// Original author: Matt Chambers <matt.chambers .@. vanderbilt.edu>
//
// Copyright 2011 Vanderbilt University - Nashville, TN 37232
//
// 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 _UNIMOD_HPP_
#define _UNIMOD_HPP_
#include "pwiz/utility/misc/Export.hpp"
#include "pwiz/utility/chemistry/Chemistry.hpp"
#include "pwiz/utility/chemistry/MZTolerance.hpp"
#include "cv.hpp"
#include <boost/enum.hpp>
#include <boost/logic/tribool.hpp>
namespace pwiz {
namespace data {
namespace unimod {
using namespace cv;
using namespace chemistry;
using namespace boost::logic;
BOOST_BITFIELD_EX(Site, PWIZ_API_DECL,
(Any)(1<<0)
(NTerminus)(1<<1)
(CTerminus)(1<<2)
(Alanine)(1<<3)
(Cysteine)(1<<4)
(AsparticAcid)(1<<5)
(GlutamicAcid)(1<<6)
(Phenylalanine)(1<<7)
(Glycine)(1<<8)
(Histidine)(1<<9)
(Isoleucine)(1<<10)
(Lysine)(1<<11)
(Leucine)(1<<12)
(Methionine)(1<<13)
(Asparagine)(1<<14)
(Proline)(1<<15)
(Glutamine)(1<<16)
(Arginine)(1<<17)
(Serine)(1<<18)
(Threonine)(1<<19)
(Selenocysteine)(1<<20)
(Valine)(1<<21)
(Tryptophan)(1<<22)
(Tyrosine)(1<<23)
)
BOOST_BITFIELD_DOMAIN_OPERATORS(Site)
BOOST_ENUM_EX(Position, PWIZ_API_DECL,
(Anywhere)
(AnyNTerminus)
(AnyCTerminus)
(ProteinNTerminus)
(ProteinCTerminus)
)
BOOST_ENUM_DOMAIN_OPERATORS(Position)
BOOST_BITFIELD_EX(Classification, PWIZ_API_DECL,
(Any)(1<<0)
(Artifact)(1<<1)
(ChemicalDerivative)(1<<2)
(CoTranslational)(1<<3)
(IsotopicLabel)(1<<4)
(Multiple)(1<<5)
(NLinkedGlycosylation)(1<<6)
(NonStandardResidue)(1<<7)
(OLinkedGlycosylation)(1<<8)
(OtherGlycosylation)(1<<9)
(Other)(1<<10)
(PostTranslational)(1<<11)
(PreTranslational)(1<<12)
(Substitution)(1<<13)
)
BOOST_BITFIELD_DOMAIN_OPERATORS(Classification)
/// a modification from Unimod
struct PWIZ_API_DECL Modification
{
struct PWIZ_API_DECL Specificity
{
Site site;
Position position;
bool hidden;
Classification classification;
};
CVID cvid;
std::string name;
Formula deltaComposition;
double deltaMonoisotopicMass() const;
double deltaAverageMass() const;
bool approved;
std::vector<Specificity> specificities;
};
/// returns the Site given a one-letter residue code, or:
/// 'x' for Site::Any, 'n' for Site::NTerminus, 'c' for Site::CTerminus
PWIZ_API_DECL Site site(char symbol);
/// returns a Position corresponding to one of the following CVIDs:
/// CVID_Unknown: Position::Anywhere
/// MS_modification_specificity_peptide_N_term: Position::AnyNTerminus
/// MS_modification_specificity_peptide_C_term: Position::AnyCTerminus
/// Else: invalid_argument exception
PWIZ_API_DECL Position position(CVID cvid = CVID_Unknown);
/// the entire list of Unimod modifications
PWIZ_API_DECL const std::vector<Modification>& modifications();
/// get a list of modifications by mass and tolerance;
/// - mass is treated as monoisotopic if monoisotopic=true; if indeterminate, both average and monoisotopic lookups are done
/// - if approved is not indeterminate, only approved/unapproved modifications are considered
/// - the site, position, and classification parameters filter the resulting modifications such that
/// every modification must have at least one specificity matching all three criteria;
/// - if hidden is not indeterminate, matching site/position/classification specificities must be hidden (or not)
PWIZ_API_DECL std::vector<Modification> modifications(double mass,
double tolerance,
tribool monoisotopic = true,
tribool approved = true,
Site site = Site::Any,
Position position = Position::Anywhere,
Classification classification = Classification::Any,
tribool hidden = indeterminate);
/// find a modification by CVID
PWIZ_API_DECL const Modification& modification(CVID cvid);
/// find a modification by title, e.g. "Phospho" not "Phosphorylation"
PWIZ_API_DECL const Modification& modification(const std::string& title);
} // namespace unimod
} // namespace data
} // namespace pwiz
#endif // _UNIMOD_HPP_
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