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dssp
Commit e802a8e1 by Maarten L. Hekkelman
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multi-threaded

parent 9cc2e4b1
Showing with 49 additions and 27 deletions
include/dssp.hpp
...@@ -97,8 +97,8 @@ class dssp ...@@ -97,8 +97,8 @@ class dssp
Gap Gap
}; };
dssp(const cif::datablock &db, 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, int max_thread_count);
dssp(const cif::mm::structure &s, int min_poly_proline_stretch_length, bool calculateSurfaceAccessibility); dssp(const cif::mm::structure &s, int min_poly_proline_stretch_length, bool calculateSurfaceAccessibility, int max_thread_count);
~dssp(); ~dssp();
......
src/dssp.cpp
...@@ -28,6 +28,7 @@ ...@@ -28,6 +28,7 @@
#include "dssp.hpp" #include "dssp.hpp"
#include <atomic>
#include <deque> #include <deque>
#include <iomanip> #include <iomanip>
#include <numeric> #include <numeric>
...@@ -765,36 +766,48 @@ double CalculateHBondEnergy(residue &inDonor, residue &inAcceptor) ...@@ -765,36 +766,48 @@ double CalculateHBondEnergy(residue &inDonor, residue &inAcceptor)
// -------------------------------------------------------------------- // --------------------------------------------------------------------
void CalculateHBondEnergies(std::vector<residue> &inResidues) void CalculateHBondEnergies(std::vector<residue> &inResidues, int max_thread_count)
{ {
if (cif::VERBOSE) if (cif::VERBOSE)
std::cerr << "calculating hbond energies" << std::endl; std::cerr << "calculating hbond energies" << std::endl;
// Calculate the HBond energies // Calculate the HBond energies
std::vector<std::thread> tg;
std::atomic<size_t> next(0);
std::unique_ptr<cif::progress_bar> progress; std::unique_ptr<cif::progress_bar> progress;
if (cif::VERBOSE == 0) if (cif::VERBOSE == 0 or cif::VERBOSE == 1)
progress.reset(new cif::progress_bar(inResidues.size() * (inResidues.size() - 1), "calculate hbond energies")); progress.reset(new cif::progress_bar((inResidues.size() * (inResidues.size() - 1) / 2), "calculate hbond energies"));
for (uint32_t i = 0; i + 1 < inResidues.size(); ++i) for (int t = 0; t < max_thread_count; ++t)
{ {
auto &ri = inResidues[i]; tg.emplace_back([&next,&inResidues,progress=progress.get()]()
for (uint32_t j = i + 1; j < inResidues.size(); ++j)
{ {
auto &rj = inResidues[j]; for (uint32_t i = next++; i < inResidues.size(); i = next++)
if (distance_sq(ri.mCAlpha, rj.mCAlpha) < kMinimalCADistance * kMinimalCADistance)
{ {
CalculateHBondEnergy(ri, rj); auto &ri = inResidues[i];
if (j != i + 1)
CalculateHBondEnergy(rj, ri);
}
if (progress) for (uint32_t j = i + 1; j < inResidues.size(); ++j)
progress->consumed(1); {
} auto &rj = inResidues[j];
if (distance_sq(ri.mCAlpha, rj.mCAlpha) < kMinimalCADistance * kMinimalCADistance)
{
CalculateHBondEnergy(ri, rj);
if (j != i + 1)
CalculateHBondEnergy(rj, ri);
}
if (progress)
progress->consumed(1);
}
}
});
} }
for (auto &t : tg)
t.join();
} }
// -------------------------------------------------------------------- // --------------------------------------------------------------------
...@@ -1365,7 +1378,8 @@ void CalculatePPHelices(std::vector<residue> &inResidues, statistics &stats, int ...@@ -1365,7 +1378,8 @@ void CalculatePPHelices(std::vector<residue> &inResidues, statistics &stats, int
struct DSSP_impl struct DSSP_impl
{ {
DSSP_impl(const cif::datablock &db, int model_nr, int min_poly_proline_stretch_length); DSSP_impl(const cif::datablock &db, int model_nr, int min_poly_proline_stretch_length,
int max_thread_count);
auto findRes(const std::string &asymID, int seqID) auto findRes(const std::string &asymID, int seqID)
{ {
...@@ -1386,16 +1400,22 @@ struct DSSP_impl ...@@ -1386,16 +1400,22 @@ struct DSSP_impl
std::vector<std::pair<residue *, residue *>> mSSBonds; std::vector<std::pair<residue *, residue *>> mSSBonds;
int m_min_poly_proline_stretch_length; int m_min_poly_proline_stretch_length;
statistics mStats = {}; statistics mStats = {};
int m_max_thread_count;
}; };
// -------------------------------------------------------------------- // --------------------------------------------------------------------
DSSP_impl::DSSP_impl(const cif::datablock &db, int model_nr, int min_poly_proline_stretch_length) DSSP_impl::DSSP_impl(const cif::datablock &db, int model_nr, int min_poly_proline_stretch_length, int max_thread_count)
: mDB(db) : mDB(db)
, m_min_poly_proline_stretch_length(min_poly_proline_stretch_length) , m_min_poly_proline_stretch_length(min_poly_proline_stretch_length)
, m_max_thread_count(max_thread_count)
{ {
using namespace cif::literals; using namespace cif::literals;
if (m_max_thread_count <= 0)
m_max_thread_count = std::thread::hardware_concurrency();
if (cif::VERBOSE) if (cif::VERBOSE)
std::cerr << "loading residues" << std::endl; std::cerr << "loading residues" << std::endl;
...@@ -1557,7 +1577,7 @@ void DSSP_impl::calculateSecondaryStructure() ...@@ -1557,7 +1577,7 @@ void DSSP_impl::calculateSecondaryStructure()
mSSBonds.emplace_back(&*r1, &*r2); mSSBonds.emplace_back(&*r1, &*r2);
} }
CalculateHBondEnergies(mResidues); CalculateHBondEnergies(mResidues, m_max_thread_count);
CalculateBetaSheets(mResidues, mStats); CalculateBetaSheets(mResidues, mStats);
CalculateAlphaHelices(mResidues, mStats); CalculateAlphaHelices(mResidues, mStats);
CalculatePPHelices(mResidues, mStats, m_min_poly_proline_stretch_length); CalculatePPHelices(mResidues, mStats, m_min_poly_proline_stretch_length);
...@@ -2136,13 +2156,13 @@ dssp::iterator &dssp::iterator::operator--() ...@@ -2136,13 +2156,13 @@ dssp::iterator &dssp::iterator::operator--()
// -------------------------------------------------------------------- // --------------------------------------------------------------------
dssp::dssp(const cif::mm::structure &s, int min_poly_proline_stretch_length, bool calculateSurfaceAccessibility) dssp::dssp(const cif::mm::structure &s, int min_poly_proline_stretch_length, bool calculateSurfaceAccessibility, int max_thread_count)
: dssp(s.get_datablock(), static_cast<int>(s.get_model_nr()), min_poly_proline_stretch_length, calculateSurfaceAccessibility) : dssp(s.get_datablock(), static_cast<int>(s.get_model_nr()), min_poly_proline_stretch_length, calculateSurfaceAccessibility, max_thread_count)
{ {
} }
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, int max_thread_count)
: m_impl(new DSSP_impl(db, model_nr, min_poly_proline_stretch)) : m_impl(new DSSP_impl(db, model_nr, min_poly_proline_stretch, max_thread_count))
{ {
if (calculateSurfaceAccessibility) if (calculateSurfaceAccessibility)
{ {
......
src/mkdssp.cpp
...@@ -81,6 +81,8 @@ int d_main(int argc, const char *argv[]) ...@@ -81,6 +81,8 @@ int d_main(int argc, const char *argv[])
mcfp::make_option("verbose,v", "verbose output"), mcfp::make_option("verbose,v", "verbose output"),
mcfp::make_option("quiet", "Reduce verbose output to a minimum"), mcfp::make_option("quiet", "Reduce verbose output to a minimum"),
mcfp::make_option<unsigned>("max-threads", 0, "Maximum number of threads to use, if zero the nummber of CPU's is the max"),
mcfp::make_hidden_option<int>("debug,d", "Debug level (for even more verbose output)")); mcfp::make_hidden_option<int>("debug,d", "Debug level (for even more verbose output)"));
config.parse(argc, argv); config.parse(argc, argv);
...@@ -162,7 +164,7 @@ int d_main(int argc, const char *argv[]) ...@@ -162,7 +164,7 @@ int d_main(int argc, const char *argv[])
fmt = "cif"; fmt = "cif";
} }
dssp dssp(f.front(), 1, pp_stretch, true); dssp dssp(f.front(), 1, pp_stretch, true, config.get<unsigned>("max-threads"));
if (not output.empty()) if (not output.empty())
{ {
......
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