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dssp
Commit 20c95733 by Maarten L. Hekkelman
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Merge branch 'trunk' of github.com:PDB-REDO/dssp into trunk

parents b6ce7ae6 57494d98
Showing with 59 additions and 53 deletions
.gitignore
...@@ -7,3 +7,4 @@ build ...@@ -7,3 +7,4 @@ build
.gdb_history .gdb_history
**/*.dssp **/*.dssp
src/revision.hpp src/revision.hpp
out/
CMakeLists.txt
...@@ -50,13 +50,20 @@ elseif(MSVC) ...@@ -50,13 +50,20 @@ elseif(MSVC)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /W4") set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /W4")
endif() endif()
if(NOT "$ENV{CCP4}" STREQUAL "") # Optionally build a version to be installed inside CCP4
set(CCP4 $ENV{CCP4}) option(BUILD_FOR_CCP4 "Build a version to be installed in CCP4" OFF)
list(PREPEND CMAKE_MODULE_PATH "${CCP4}/Lib")
list(APPEND CMAKE_PREFIX_PATH ${CCP4}) if(BUILD_FOR_CCP4)
if("$ENV{CCP4}" STREQUAL "" OR NOT EXISTS $ENV{CCP4})
if(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT) message(FATAL_ERROR "A CCP4 built was requested but CCP4 was not sourced")
set(CMAKE_INSTALL_PREFIX ${CCP4}) else()
list(APPEND CMAKE_MODULE_PATH "$ENV{CCP4}")
list(APPEND CMAKE_PREFIX_PATH "$ENV{CCP4}")
set(CMAKE_INSTALL_PREFIX "$ENV{CCP4}")
if(WIN32)
set(BUILD_SHARED_LIBS ON)
endif()
endif() endif()
endif() endif()
......
include/dssp.hpp
...@@ -29,10 +29,10 @@ ...@@ -29,10 +29,10 @@
/// \file DSSP.hpp /// \file DSSP.hpp
/// Calculate DSSP-like secondary structure information. /// Calculate DSSP-like secondary structure information.
#include <filesystem>
#include <cif++.hpp> #include <cif++.hpp>
#include <filesystem>
class dssp class dssp
{ {
public: public:
......
src/dssp-io.cpp
...@@ -24,19 +24,16 @@ ...@@ -24,19 +24,16 @@
* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*/ */
#if __has_include("config.hpp") #include "dssp-io.hpp"
#include "config.hpp" #include "revision.hpp"
#endif
#include <cif++/pdb/io.hpp>
#include <exception> #include <exception>
#include <filesystem> #include <filesystem>
#include <fstream> #include <fstream>
#include <iostream> #include <iostream>
#include <cif++/pdb/io.hpp>
#include "dssp-io.hpp"
#include "revision.hpp"
// -------------------------------------------------------------------- // --------------------------------------------------------------------
...@@ -315,7 +312,7 @@ void writeSheets(cif::datablock &db, const dssp &dssp) ...@@ -315,7 +312,7 @@ void writeSheets(cif::datablock &db, const dssp &dssp)
continue; continue;
if (not sheetMap.count(sheetID)) if (not sheetMap.count(sheetID))
sheetMap[sheetID] = sheetMap.size(); sheetMap[sheetID] = static_cast<int>(sheetMap.size());
strands.emplace_back(std::make_tuple(sheetMap[sheetID], res_list{ res })); strands.emplace_back(std::make_tuple(sheetMap[sheetID], res_list{ res }));
} }
......
src/dssp.cpp
...@@ -26,12 +26,13 @@ ...@@ -26,12 +26,13 @@
// Calculate DSSP-like secondary structure information // Calculate DSSP-like secondary structure information
#include "dssp.hpp"
#include <deque>
#include <iomanip> #include <iomanip>
#include <numeric> #include <numeric>
#include <thread> #include <thread>
#include "dssp.hpp"
using residue = dssp::residue; using residue = dssp::residue;
using statistics = dssp::statistics; using statistics = dssp::statistics;
using structure_type = dssp::structure_type; using structure_type = dssp::structure_type;
...@@ -96,16 +97,16 @@ float dihedral_angle(const point &p1, const point &p2, const point &p3, const po ...@@ -96,16 +97,16 @@ float dihedral_angle(const point &p1, const point &p2, const point &p3, const po
point x = cross_product(z, v43); point x = cross_product(z, v43);
point y = cross_product(z, x); point y = cross_product(z, x);
double u = dot_product(x, x); float u = dot_product(x, x);
double v = dot_product(y, y); float v = dot_product(y, y);
double result = 360; float result = 360;
if (u > 0 and v > 0) if (u > 0 and v > 0)
{ {
u = dot_product(p, x) / std::sqrt(u); u = dot_product(p, x) / std::sqrt(u);
v = dot_product(p, y) / std::sqrt(v); v = dot_product(p, y) / std::sqrt(v);
if (u != 0 or v != 0) if (u != 0 or v != 0)
result = std::atan2(v, u) * 180 / kPI; result = std::atan2(v, u) * 180.f / static_cast<float>(kPI);
} }
return result; return result;
...@@ -116,9 +117,9 @@ float cosinus_angle(const point &p1, const point &p2, const point &p3, const poi ...@@ -116,9 +117,9 @@ float cosinus_angle(const point &p1, const point &p2, const point &p3, const poi
point v12 = p1 - p2; point v12 = p1 - p2;
point v34 = p3 - p4; point v34 = p3 - p4;
double result = 0; float result = 0;
double x = dot_product(v12, v12) * dot_product(v34, v34); float x = dot_product(v12, v12) * dot_product(v34, v34);
if (x > 0) if (x > 0)
result = dot_product(v12, v34) / std::sqrt(x); result = dot_product(v12, v34) / std::sqrt(x);
...@@ -450,8 +451,8 @@ struct dssp::residue ...@@ -450,8 +451,8 @@ struct dssp::residue
return mSSBridgeNr; return mSSBridgeNr;
} }
double CalculateSurface(const std::vector<residue> &inResidues); float CalculateSurface(const std::vector<residue> &inResidues);
double CalculateSurface(const point &inAtom, float inRadius, const std::vector<residue *> &inNeighbours); float CalculateSurface(const point &inAtom, float inRadius, const std::vector<residue *> &inNeighbours);
bool AtomIntersectsBox(const point &atom, float inRadius) const bool AtomIntersectsBox(const point &atom, float inRadius) const
{ {
...@@ -527,10 +528,10 @@ struct dssp::residue ...@@ -527,10 +528,10 @@ struct dssp::residue
float mRadius; float mRadius;
point mCenter; point mCenter;
std::vector<std::tuple<std::string, point>> mSideChain; std::vector<std::tuple<std::string, point>> mSideChain;
double mAccessibility = 0; float mAccessibility = 0;
double mChiralVolume = 0; float mChiralVolume = 0;
double mAlpha = 360, mKappa = 360, mPhi = 360, mPsi = 360, mTCO = 0, mOmega = 360; float mAlpha = 360, mKappa = 360, mPhi = 360, mPsi = 360, mTCO = 0, mOmega = 360;
residue_type mType; residue_type mType;
uint8_t mSSBridgeNr = 0; uint8_t mSSBridgeNr = 0;
...@@ -629,7 +630,7 @@ MSurfaceDots::MSurfaceDots(int32_t N) ...@@ -629,7 +630,7 @@ MSurfaceDots::MSurfaceDots(int32_t N)
} }
} }
double residue::CalculateSurface(const point &inAtom, float inRadius, const std::vector<residue *> &inNeighbours) float residue::CalculateSurface(const point &inAtom, float inRadius, const std::vector<residue *> &inNeighbours)
{ {
accumulator accumulate; accumulator accumulate;
...@@ -650,7 +651,7 @@ double residue::CalculateSurface(const point &inAtom, float inRadius, const std: ...@@ -650,7 +651,7 @@ double residue::CalculateSurface(const point &inAtom, float inRadius, const std:
accumulate.sort(); accumulate.sort();
float radius = inRadius + kRadiusWater; float radius = inRadius + kRadiusWater;
double surface = 0; float surface = 0;
MSurfaceDots &surfaceDots = MSurfaceDots::Instance(); MSurfaceDots &surfaceDots = MSurfaceDots::Instance();
...@@ -663,20 +664,20 @@ double residue::CalculateSurface(const point &inAtom, float inRadius, const std: ...@@ -663,20 +664,20 @@ double residue::CalculateSurface(const point &inAtom, float inRadius, const std:
free = accumulate.m_x[k].radius < distance_sq(xx, accumulate.m_x[k].location); free = accumulate.m_x[k].radius < distance_sq(xx, accumulate.m_x[k].location);
if (free) if (free)
surface += surfaceDots.weight(); surface += static_cast<float>(surfaceDots.weight());
} }
return surface * radius * radius; return surface * radius * radius;
} }
double residue::CalculateSurface(const std::vector<residue> &inResidues) float residue::CalculateSurface(const std::vector<residue> &inResidues)
{ {
std::vector<residue *> neighbours; std::vector<residue *> neighbours;
for (auto &r : inResidues) for (auto &r : inResidues)
{ {
point center = r.mCenter; point center = r.mCenter;
double radius = r.mRadius; float radius = r.mRadius;
if (distance(mCenter, center) < mRadius + radius) if (distance(mCenter, center) < mRadius + radius)
neighbours.push_back(const_cast<residue *>(&r)); neighbours.push_back(const_cast<residue *>(&r));
...@@ -1215,8 +1216,8 @@ void CalculatePPHelices(std::vector<residue> &inResidues, statistics &stats, int ...@@ -1215,8 +1216,8 @@ void CalculatePPHelices(std::vector<residue> &inResidues, statistics &stats, int
for (uint32_t i = 1; i + 1 < inResidues.size(); ++i) for (uint32_t i = 1; i + 1 < inResidues.size(); ++i)
{ {
phi[i] = inResidues[i].mPhi; phi[i] = static_cast<float>(inResidues[i].mPhi);
psi[i] = inResidues[i].mPsi; psi[i] = static_cast<float>(inResidues[i].mPsi);
} }
for (uint32_t i = 1; i + 3 < inResidues.size(); ++i) for (uint32_t i = 1; i + 3 < inResidues.size(); ++i)
...@@ -1435,13 +1436,13 @@ DSSP_impl::DSSP_impl(const cif::datablock &db, int model_nr, int min_poly_prolin ...@@ -1435,13 +1436,13 @@ DSSP_impl::DSSP_impl(const cif::datablock &db, int model_nr, int min_poly_prolin
if (NoChainBreak(prevPrev, nextNext) and prevPrev.mSeqID + 4 == nextNext.mSeqID) if (NoChainBreak(prevPrev, nextNext) and prevPrev.mSeqID + 4 == nextNext.mSeqID)
{ {
double ckap = cosinus_angle( float ckap = cosinus_angle(
cur.mCAlpha, cur.mCAlpha,
prevPrev.mCAlpha, prevPrev.mCAlpha,
nextNext.mCAlpha, nextNext.mCAlpha,
cur.mCAlpha); cur.mCAlpha);
double skap = std::sqrt(1 - ckap * ckap); float skap = std::sqrt(1 - ckap * ckap);
cur.mKappa = std::atan2(skap, ckap) * 180 / kPI; cur.mKappa = std::atan2(skap, ckap) * static_cast<float>(180 / kPI);
} }
} }
...@@ -2086,7 +2087,7 @@ dssp::iterator &dssp::iterator::operator--() ...@@ -2086,7 +2087,7 @@ 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)
: dssp(s.get_datablock(), 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)
{ {
} }
......
test/unit-test-dssp.cpp
...@@ -166,16 +166,16 @@ BOOST_AUTO_TEST_CASE(dssp_1) ...@@ -166,16 +166,16 @@ BOOST_AUTO_TEST_CASE(dssp_1)
std::cout << line << std::endl; std::cout << line << std::endl;
auto f = cif::split(line, "\t"); auto fld = cif::split(line, "\t");
BOOST_CHECK_EQUAL(f.size(), 3); BOOST_CHECK_EQUAL(fld.size(), 3);
if (f.size() != 3) if (fld.size() != 3)
continue; continue;
int seqID; int seqID;
std::from_chars(f[0].begin(), f[0].end(), seqID); std::from_chars(fld[0].data(), fld[0].data() + fld[0].length(), seqID);
std::string asymID{ f[1] }; std::string asymID{ fld[1] };
std::string secstr{ f[2] }; std::string secstr{ fld[2] };
if (secstr == "_") if (secstr == "_")
secstr = " "; secstr = " ";
...@@ -200,16 +200,16 @@ BOOST_AUTO_TEST_CASE(dssp_2) ...@@ -200,16 +200,16 @@ BOOST_AUTO_TEST_CASE(dssp_2)
while (getline(t, line)) while (getline(t, line))
{ {
auto f = cif::split(line, "\t"); auto fld = cif::split(line, "\t");
BOOST_CHECK_EQUAL(f.size(), 3); BOOST_CHECK_EQUAL(fld.size(), 3);
if (f.size() != 3) if (fld.size() != 3)
continue; continue;
int seqID; int seqID;
std::from_chars(f[0].begin(), f[0].end(), seqID); std::from_chars(fld[0].data(), fld[0].data() + fld[0].length(), seqID);
std::string asymID{ f[1] }; std::string asymID{ fld[1] };
std::string secstr{ f[2] }; std::string secstr{ fld[2] };
if (secstr == "_") if (secstr == "_")
secstr = " "; secstr = " ";
......
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