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dssp
Commit 6cebeaac by Maarten L. Hekkelman
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start renaming and reorganising

parent 32869b34
Showing with 82 additions and 81 deletions
CMakeLists.txt
......@@ -25,7 +25,7 @@
cmake_minimum_required(VERSION 3.15)
# set the project name
project(mkdssp VERSION 4.1.1 LANGUAGES CXX)
project(mkdssp VERSION 4.2.0 LANGUAGES CXX)
list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake")
......
src/DSSP.cpp
......@@ -34,9 +34,6 @@
// --------------------------------------------------------------------
namespace dssp
{
const double
kPI = 3.141592653589793238462643383279502884;
......@@ -803,7 +800,7 @@ bool TestBond(const residue *a, const residue *b)
(a->mHBondAcceptor[1].res == b and a->mHBondAcceptor[1].energy < kMaxHBondEnergy);
}
bool test_bond(DSSP::residue_info const &a, DSSP::residue_info const &b)
bool test_bond(dssp::residue_info const &a, dssp::residue_info const &b)
{
return a and b and TestBond(a.m_impl, b.m_impl);
}
......@@ -1833,92 +1830,92 @@ std::string DSSP_impl::GetPDBAUTHORLine()
// --------------------------------------------------------------------
std::string DSSP::residue_info::asym_id() const
std::string dssp::residue_info::asym_id() const
{
return m_impl->mAsymID;
}
std::string DSSP::residue_info::compound_id() const
std::string dssp::residue_info::compound_id() const
{
return m_impl->mCompoundID;
}
char DSSP::residue_info::compound_letter() const
char dssp::residue_info::compound_letter() const
{
return MapResidue(compound_id());
}
int DSSP::residue_info::seq_id() const
int dssp::residue_info::seq_id() const
{
return m_impl->mSeqID;
}
std::string DSSP::residue_info::alt_id() const
std::string dssp::residue_info::alt_id() const
{
return m_impl->mAltID;
}
std::string DSSP::residue_info::auth_asym_id() const
std::string dssp::residue_info::auth_asym_id() const
{
return m_impl->mAuthAsymID;
}
int DSSP::residue_info::auth_seq_id() const
int dssp::residue_info::auth_seq_id() const
{
return m_impl->mAuthSeqID;
}
std::string DSSP::residue_info::pdb_strand_id() const
std::string dssp::residue_info::pdb_strand_id() const
{
return m_impl->mPDBStrandID;
}
int DSSP::residue_info::pdb_seq_num() const
int dssp::residue_info::pdb_seq_num() const
{
return m_impl->mPDBSeqNum;
}
std::string DSSP::residue_info::pdb_ins_code() const
std::string dssp::residue_info::pdb_ins_code() const
{
return m_impl->mPDBInsCode;
}
float DSSP::residue_info::alpha() const
float dssp::residue_info::alpha() const
{
return m_impl->mAlpha;
}
float DSSP::residue_info::kappa() const
float dssp::residue_info::kappa() const
{
return m_impl->mKappa;
}
float DSSP::residue_info::omega() const
float dssp::residue_info::omega() const
{
return m_impl->mOmega;
}
float DSSP::residue_info::phi() const
float dssp::residue_info::phi() const
{
return m_impl->mPhi;
}
float DSSP::residue_info::psi() const
float dssp::residue_info::psi() const
{
return m_impl->mPsi;
}
float DSSP::residue_info::tco() const
float dssp::residue_info::tco() const
{
return m_impl->mTCO;
}
bool DSSP::residue_info::is_pre_pro() const
bool dssp::residue_info::is_pre_pro() const
{
return m_impl->mType != kProline and m_impl->mNext != nullptr and m_impl->mNext->mType == kProline;
}
float DSSP::residue_info::chiral_volume() const
float dssp::residue_info::chiral_volume() const
{
return m_impl->mChiralVolume;
}
......@@ -1945,14 +1942,14 @@ const std::map<residue_type, std::vector<std::string>> kChiAtomsMap = {
{ MapResidue("VAL"), { "CG1" } }
};
std::size_t DSSP::residue_info::nr_of_chis() const
std::size_t dssp::residue_info::nr_of_chis() const
{
auto i = kChiAtomsMap.find(m_impl->mType);
return i != kChiAtomsMap.end() ? i->second.size() : 0;
}
float DSSP::residue_info::chi(std::size_t index) const
float dssp::residue_info::chi(std::size_t index) const
{
float result = 0;
......@@ -1984,37 +1981,37 @@ float DSSP::residue_info::chi(std::size_t index) const
return result;
}
std::tuple<float, float, float> DSSP::residue_info::ca_location() const
std::tuple<float, float, float> dssp::residue_info::ca_location() const
{
return { m_impl->mCAlpha.mX, m_impl->mCAlpha.mY, m_impl->mCAlpha.mZ };
}
chain_break_type DSSP::residue_info::chain_break() const
chain_break_type dssp::residue_info::chain_break() const
{
return m_impl->mChainBreak;
}
int DSSP::residue_info::nr() const
int dssp::residue_info::nr() const
{
return m_impl->mNumber;
}
structure_type DSSP::residue_info::type() const
structure_type dssp::residue_info::type() const
{
return m_impl->mSecondaryStructure;
}
int DSSP::residue_info::ssBridgeNr() const
int dssp::residue_info::ssBridgeNr() const
{
return m_impl->mSSBridgeNr;
}
helix_position_type DSSP::residue_info::helix(helix_type helixType) const
helix_position_type dssp::residue_info::helix(helix_type helixType) const
{
return m_impl->GetHelixFlag(helixType);
}
bool DSSP::residue_info::is_alpha_helix_end_before_start() const
bool dssp::residue_info::is_alpha_helix_end_before_start() const
{
bool result = false;
......@@ -2024,17 +2021,17 @@ bool DSSP::residue_info::is_alpha_helix_end_before_start() const
return result;
}
bool DSSP::residue_info::bend() const
bool dssp::residue_info::bend() const
{
return m_impl->IsBend();
}
double DSSP::residue_info::accessibility() const
double dssp::residue_info::accessibility() const
{
return m_impl->mAccessibility;
}
std::tuple<DSSP::residue_info, int, bool> DSSP::residue_info::bridge_partner(int i) const
std::tuple<dssp::residue_info, int, bool> dssp::residue_info::bridge_partner(int i) const
{
auto bp = m_impl->GetBetaPartner(i);
......@@ -2043,18 +2040,18 @@ std::tuple<DSSP::residue_info, int, bool> DSSP::residue_info::bridge_partner(int
return std::make_tuple(std::move(ri), bp.ladder, bp.parallel);
}
int DSSP::residue_info::sheet() const
int dssp::residue_info::sheet() const
{
return m_impl->GetSheet();
}
std::tuple<DSSP::residue_info, double> DSSP::residue_info::acceptor(int i) const
std::tuple<dssp::residue_info, double> dssp::residue_info::acceptor(int i) const
{
auto &a = m_impl->mHBondAcceptor[i];
return { residue_info(a.res), a.energy };
}
std::tuple<DSSP::residue_info, double> DSSP::residue_info::donor(int i) const
std::tuple<dssp::residue_info, double> dssp::residue_info::donor(int i) const
{
auto &d = m_impl->mHBondDonor[i];
return { residue_info(d.res), d.energy };
......@@ -2062,18 +2059,18 @@ std::tuple<DSSP::residue_info, double> DSSP::residue_info::donor(int i) const
// --------------------------------------------------------------------
DSSP::iterator::iterator(residue *res)
dssp::iterator::iterator(residue *res)
: m_current(res)
{
}
DSSP::iterator &DSSP::iterator::operator++()
dssp::iterator &dssp::iterator::operator++()
{
++m_current.m_impl;
return *this;
}
DSSP::iterator &DSSP::iterator::operator--()
dssp::iterator &dssp::iterator::operator--()
{
--m_current.m_impl;
return *this;
......@@ -2081,7 +2078,7 @@ DSSP::iterator &DSSP::iterator::operator--()
// --------------------------------------------------------------------
DSSP::DSSP(const cif::datablock &db, int model_nr, int min_poly_proline_stretch, bool calculateSurfaceAccessibility)
dssp::dssp(const cif::datablock &db, int model_nr, int min_poly_proline_stretch, bool calculateSurfaceAccessibility)
: m_impl(new DSSP_impl(db, model_nr, min_poly_proline_stretch))
{
if (calculateSurfaceAccessibility)
......@@ -2094,17 +2091,17 @@ DSSP::DSSP(const cif::datablock &db, int model_nr, int min_poly_proline_stretch,
m_impl->calculateSecondaryStructure();
}
DSSP::~DSSP()
dssp::~dssp()
{
delete m_impl;
}
DSSP::iterator DSSP::begin() const
dssp::iterator dssp::begin() const
{
return iterator(m_impl->mResidues.empty() ? nullptr : m_impl->mResidues.data());
}
DSSP::iterator DSSP::end() const
dssp::iterator dssp::end() const
{
// careful now, MSVC is picky when it comes to dereferencing iterators that are at the end.
residue *res = nullptr;
......@@ -2117,7 +2114,7 @@ DSSP::iterator DSSP::end() const
return iterator(res);
}
DSSP::residue_info DSSP::operator[](const key_type &key) const
dssp::residue_info dssp::operator[](const key_type &key) const
{
auto i = std::find_if(begin(), end(),
[key](const residue_info &res) { return res.asym_id() == std::get<0>(key) and res.seq_id() == std::get<1>(key); });
......@@ -2128,12 +2125,12 @@ DSSP::residue_info DSSP::operator[](const key_type &key) const
return *i;
}
statistics DSSP::get_statistics() const
dssp::statistics dssp::get_statistics() const
{
return m_impl->mStats;
}
std::string DSSP::get_pdb_header_line(pdb_record_type pdb_record) const
std::string dssp::get_pdb_header_line(pdb_record_type pdb_record) const
{
switch (pdb_record)
{
......@@ -2149,5 +2146,3 @@ std::string DSSP::get_pdb_header_line(pdb_record_type pdb_record) const
return {};
}
}
} // namespace dssp
src/DSSP.hpp
......@@ -24,20 +24,22 @@
* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*/
#pragma once
/// \file DSSP.hpp
/// Calculate DSSP-like secondary structure information.
#pragma once
#include <filesystem>
#include <cif++.hpp>
namespace dssp
class dssp
{
public:
struct residue;
struct residue;
enum class structure_type : char
{
enum class structure_type : char
{
Loop = ' ',
Alphahelix = 'H',
Betabridge = 'B',
......@@ -47,30 +49,29 @@ enum class structure_type : char
Helix_PPII = 'P',
Turn = 'T',
Bend = 'S'
};
};
enum class helix_type
{
enum class helix_type
{
_3_10,
alpha,
pi,
pp
};
};
enum class helix_position_type
{
enum class helix_position_type
{
None,
Start,
End,
StartAndEnd,
Middle
};
};
const size_t
kHistogramSize = 30;
static constexpr size_t kHistogramSize = 30;
struct statistics
{
struct statistics
{
struct
{
uint32_t residues, chains, SS_bridges, intra_chain_SS_bridges, H_bonds;
......@@ -87,23 +88,23 @@ struct statistics
uint32_t antiparallel_bridges_per_ladder[kHistogramSize];
uint32_t ladders_per_sheet[kHistogramSize];
} histogram;
};
};
enum class chain_break_type
{
enum class chain_break_type
{
None,
NewChain,
Gap
};
};
class DSSP
{
public:
DSSP(const cif::datablock &db, int model_nr, int min_poly_proline_stretch_length, bool calculateSurfaceAccessibility);
~DSSP();
dssp(const std::filesystem::path &file, int model_nr, int min_poly_proline_stretch_length, bool calculateSurfaceAccessibility);
dssp(const cif::datablock &db, int model_nr, int min_poly_proline_stretch_length, bool calculateSurfaceAccessibility);
dssp(const cif::mm::structure &s, int min_poly_proline_stretch_length, bool calculateSurfaceAccessibility);
DSSP(const DSSP &) = delete;
DSSP &operator=(const DSSP &) = delete;
~dssp();
dssp(const dssp &) = delete;
dssp &operator=(const dssp &) = delete;
statistics get_statistics() const;
......@@ -237,7 +238,7 @@ class DSSP
using value_type = residue_info;
// To access residue info by key, i.e. LabelAsymID and LabelSeqID
using key_type = std::tuple<std::string,int>;
using key_type = std::tuple<std::string, int>;
iterator begin() const;
iterator end() const;
......@@ -248,7 +249,13 @@ class DSSP
// convenience method, when creating old style DSSP files
enum class pdb_record_type { HEADER, COMPND, SOURCE, AUTHOR };
enum class pdb_record_type
{
HEADER,
COMPND,
SOURCE,
AUTHOR
};
std::string get_pdb_header_line(pdb_record_type pdb_record) const;
......@@ -256,4 +263,3 @@ class DSSP
struct DSSP_impl *m_impl;
};
} // namespace dssp
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