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Marco Biasini authoredMarco Biasini authored
sec_structure_segments.cc 4.14 KiB
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
// Copyright (C) 2008-2011 by the OpenStructure authors
//
// This library is free software; you can redistribute it and/or modify it under
// the terms of the GNU Lesser General Public License as published by the Free
// Software Foundation; either version 3.0 of the License, or (at your option)
// any later version.
// This library 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 Lesser General Public License for more
// details.
//
// You should have received a copy of the GNU Lesser General Public License
// along with this library; if not, write to the Free Software Foundation, Inc.,
// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
//------------------------------------------------------------------------------
#include <ost/mol/mol.hh>
#include "sec_structure_segments.hh"
/*
Author: Marco Biasini
*/
namespace ost { namespace mol { namespace alg {
namespace {
class SecStrExtractor : public EntityVisitor {
public:
SecStrExtractor(): index_(0) {}
virtual bool VisitResidue(const ResidueHandle& r)
{
if (sec_.empty()) {
sec_.push_back(SecStructureSegment(index_, index_, r.GetSecStructure()));
} else if (sec_.back().ss_type!=r.GetSecStructure()) {
sec_.push_back(SecStructureSegment(index_, index_, r.GetSecStructure()));
} else {
sec_.back().last+=1;
}
index_+=1;
return false;
}
const SecStructureSegments& GetList() const { return sec_; }
protected:
SecStructureSegments sec_;
int index_;
};
// pretty bad case of code duplication.
class HelicalExtractor : public SecStrExtractor {
public:
HelicalExtractor(): SecStrExtractor(), extend_(false)
{ }
virtual bool VisitResidue(const ResidueHandle& r)
{
mol::SecStructure helical(mol::SecStructure::ALPHA_HELIX);
if (r.GetSecStructure().IsHelical()) {
if (sec_.empty()) {
sec_.push_back(SecStructureSegment(index_, index_, helical));
extend_=true;
} else if (extend_) {
sec_.back().last+=1;
} else {
sec_.push_back(SecStructureSegment(index_, index_, helical));
extend_=true;
}
} else {
extend_=false;
}
index_+=1;
return false;
}
private:
bool extend_;
};
class ExtendedExtractor : public SecStrExtractor {
public:
ExtendedExtractor(): SecStrExtractor(), extend_(false)
{ }
virtual bool VisitResidue(const ResidueHandle& r)
{
mol::SecStructure extended(mol::SecStructure::EXTENDED);
if (r.GetSecStructure().IsExtended()) {
if (sec_.empty()) {
sec_.push_back(SecStructureSegment(index_, index_, extended));
extend_=true;
} else if (extend_) {
sec_.back().last+=1;
} else {
sec_.push_back(SecStructureSegment(index_, index_, extended));
extend_=true;
}
} else {
extend_=false;
}
index_+=1;
return false;
}
private:
bool extend_;
};
template <typename E, typename C>
inline SecStructureSegments extract_ss(C c)
{
E extractor;
c.Apply(extractor);
return extractor.GetList();
}
}
SecStructureSegments ExtractSecStructureSegments(const ChainHandle& chain)
{
return extract_ss<SecStrExtractor, ChainHandle>(chain);
}
SecStructureSegments ExtractSecStructureSegments(const ChainView& chain)
{
return extract_ss<SecStrExtractor, ChainView>(chain);
}
SecStructureSegments ExtractHelicalSegments(const ChainHandle& chain)
{
return extract_ss<HelicalExtractor, ChainHandle>(chain);
}
SecStructureSegments ExtractHelicalSegments(const ChainView& chain)
{
return extract_ss<HelicalExtractor, ChainView>(chain);
}
SecStructureSegments ExtractExtendedSegments(const ChainHandle& chain)
{
return extract_ss<ExtendedExtractor, ChainHandle>(chain);
}
SecStructureSegments ExtractExtendedSegments(const ChainView& chain)
{
return extract_ss<ExtendedExtractor, ChainView>(chain);
}
}}}