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dssp
Commit 3c3a2118 by Maarten L. Hekkelman
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update for new libcifpp

parent d1c6fdf6
Showing with 21 additions and 30 deletions
.gitmodules
...@@ -4,9 +4,6 @@ ...@@ -4,9 +4,6 @@
[submodule "date"] [submodule "date"]
path = date path = date
url = https://github.com/HowardHinnant/date.git url = https://github.com/HowardHinnant/date.git
[submodule "libpdbxpp"]
path = libpdbxpp
url = https://github.com/PDB-REDO/libpdbxpp.git
[submodule "libcifpp"] [submodule "libcifpp"]
path = libcifpp path = libcifpp
url = https://github.com/PDB-REDO/libcifpp.git url = https://github.com/PDB-REDO/libcifpp.git
CMakeLists.txt
...@@ -125,17 +125,12 @@ if(NOT cifpp_FOUND) ...@@ -125,17 +125,12 @@ if(NOT cifpp_FOUND)
add_git_submodule(libcifpp EXCLUDE_FROM_ALL) add_git_submodule(libcifpp EXCLUDE_FROM_ALL)
endif() endif()
find_package(pdbxpp 5.0.0 QUIET)
if(NOT pdbxpp_FOUND)
add_git_submodule(libpdbxpp EXCLUDE_FROM_ALL)
endif()
add_git_submodule(date EXCLUDE_FROM_ALL) add_git_submodule(date EXCLUDE_FROM_ALL)
add_git_submodule(libconfig EXCLUDE_FROM_ALL) add_git_submodule(libconfig EXCLUDE_FROM_ALL)
# The DSSP code is in a separate library, optionally to be used by others # The DSSP code is in a separate library, optionally to be used by others
add_library(dssp_library OBJECT ${PROJECT_SOURCE_DIR}/src/DSSP.cpp) add_library(dssp_library OBJECT ${PROJECT_SOURCE_DIR}/src/DSSP.cpp)
target_link_libraries(dssp_library cifpp::cifpp pdbxpp::pdbxpp) target_link_libraries(dssp_library cifpp::cifpp)
add_executable(mkdssp add_executable(mkdssp
${PROJECT_SOURCE_DIR}/src/dssp_wrapper.cpp ${PROJECT_SOURCE_DIR}/src/dssp_wrapper.cpp
...@@ -144,7 +139,7 @@ add_executable(mkdssp ...@@ -144,7 +139,7 @@ add_executable(mkdssp
$<TARGET_OBJECTS:dssp_library>) $<TARGET_OBJECTS:dssp_library>)
target_include_directories(mkdssp PRIVATE ${CMAKE_BINARY_DIR}) target_include_directories(mkdssp PRIVATE ${CMAKE_BINARY_DIR})
target_link_libraries(mkdssp PRIVATE dssp_library cifpp::cifpp pdbxpp::pdbxpp date::date libconfig::libconfig) target_link_libraries(mkdssp PRIVATE dssp_library cifpp::cifpp date::date libconfig::libconfig)
if(USE_RSRC) if(USE_RSRC)
mrc_target_resources(mkdssp ${CIFPP_SHARE_DIR}/mmcif_pdbx.dic) mrc_target_resources(mkdssp ${CIFPP_SHARE_DIR}/mmcif_pdbx.dic)
...@@ -181,7 +176,7 @@ if(ENABLE_TESTING) ...@@ -181,7 +176,7 @@ if(ENABLE_TESTING)
${CMAKE_CURRENT_SOURCE_DIR}/include ${CMAKE_CURRENT_SOURCE_DIR}/include
) )
target_link_libraries(dssp-unit-test dssp_library cifpp::cifpp pdbxpp::pdbxpp date::date Boost::boost) target_link_libraries(dssp-unit-test dssp_library cifpp::cifpp date::date Boost::boost)
if(MSVC) if(MSVC)
# Specify unwind semantics so that MSVC knowns how to handle exceptions # Specify unwind semantics so that MSVC knowns how to handle exceptions
......
libpdbxpp @ 8a2dd325
Subproject commit 8a2dd3255c077cc6d51c5e118e997c3ab234c3f1
src/dssp_wrapper.cpp
...@@ -33,9 +33,8 @@ ...@@ -33,9 +33,8 @@
#include <fstream> #include <fstream>
#include <iostream> #include <iostream>
#include <cif++.hpp> #include <cif++/pdb/io.hpp>
#include <date/date.h> #include <date/date.h>
#include <pdbx++.hpp>
#include "dssp_wrapper.hpp" #include "dssp_wrapper.hpp"
#include "revision.hpp" #include "revision.hpp"
...@@ -126,20 +125,20 @@ std::string ResidueToDSSPLine(const dssp::DSSP::residue_info &info) ...@@ -126,20 +125,20 @@ std::string ResidueToDSSPLine(const dssp::DSSP::residue_info &info)
if (acceptor) if (acceptor)
{ {
auto d = acceptor.nr() - info.nr(); auto d = acceptor.nr() - info.nr();
NHO[i] = pdbx::format("%d,%3.1f", d, acceptorE).str(); NHO[i] = cif::format("%d,%3.1f", d, acceptorE).str();
} }
if (donor) if (donor)
{ {
auto d = donor.nr() - info.nr(); auto d = donor.nr() - info.nr();
ONH[i] = pdbx::format("%d,%3.1f", d, donorE).str(); ONH[i] = cif::format("%d,%3.1f", d, donorE).str();
} }
} }
// auto ca = residue.atomByID("CA"); // auto ca = residue.atomByID("CA");
auto const &[cax, cay, caz] = residue.ca_location(); auto const &[cax, cay, caz] = residue.ca_location();
return pdbx::format("%5d%5d%1.1s%1.1s %c %c%c%c%c%c%c%c%c%c%4d%4d%c%4.0f %11s%11s%11s%11s %6.3f%6.1f%6.1f%6.1f%6.1f %6.1f %6.1f %6.1f", return cif::format("%5d%5d%1.1s%1.1s %c %c%c%c%c%c%c%c%c%c%4d%4d%c%4.0f %11s%11s%11s%11s %6.3f%6.1f%6.1f%6.1f%6.1f %6.1f %6.1f %6.1f",
info.nr(), residue.pdb_seq_num(), residue.pdb_ins_code(), residue.pdb_strand_id(), code, info.nr(), residue.pdb_seq_num(), residue.pdb_ins_code(), residue.pdb_strand_id(), code,
ss, helix[3], helix[0], helix[1], helix[2], bend, chirality, bridgelabel[0], bridgelabel[1], ss, helix[3], helix[0], helix[1], helix[2], bend, chirality, bridgelabel[0], bridgelabel[1],
bp[0], bp[1], sheet, floor(info.accessibility() + 0.5), bp[0], bp[1], sheet, floor(info.accessibility() + 0.5),
...@@ -165,40 +164,40 @@ void writeDSSP(const dssp::DSSP &dssp, std::ostream &os) ...@@ -165,40 +164,40 @@ void writeDSSP(const dssp::DSSP &dssp, std::ostream &os)
<< dssp.get_pdb_header_line(dssp::DSSP::pdb_record_type::SOURCE) << '.' << std::endl << dssp.get_pdb_header_line(dssp::DSSP::pdb_record_type::SOURCE) << '.' << std::endl
<< dssp.get_pdb_header_line(dssp::DSSP::pdb_record_type::AUTHOR) << '.' << std::endl; << dssp.get_pdb_header_line(dssp::DSSP::pdb_record_type::AUTHOR) << '.' << std::endl;
os << pdbx::format("%5d%3d%3d%3d%3d TOTAL NUMBER OF RESIDUES, NUMBER OF CHAINS, NUMBER OF SS-BRIDGES(TOTAL,INTRACHAIN,INTERCHAIN) .", os << cif::format("%5d%3d%3d%3d%3d TOTAL NUMBER OF RESIDUES, NUMBER OF CHAINS, NUMBER OF SS-BRIDGES(TOTAL,INTRACHAIN,INTERCHAIN) .",
stats.count.residues, stats.count.chains, stats.count.SS_bridges, stats.count.intra_chain_SS_bridges, (stats.count.SS_bridges - stats.count.intra_chain_SS_bridges)) stats.count.residues, stats.count.chains, stats.count.SS_bridges, stats.count.intra_chain_SS_bridges, (stats.count.SS_bridges - stats.count.intra_chain_SS_bridges))
<< std::endl; << std::endl;
os << pdbx::format("%8.1f ACCESSIBLE SURFACE OF PROTEIN (ANGSTROM**2) .", stats.accessible_surface) << std::endl; os << cif::format("%8.1f ACCESSIBLE SURFACE OF PROTEIN (ANGSTROM**2) .", stats.accessible_surface) << std::endl;
// hydrogenbond summary // hydrogenbond summary
os << pdbx::format("%5d%5.1f TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(J) , SAME NUMBER PER 100 RESIDUES .", stats.count.H_bonds, (stats.count.H_bonds * 100.0 / stats.count.residues)) << std::endl; os << cif::format("%5d%5.1f TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(J) , SAME NUMBER PER 100 RESIDUES .", stats.count.H_bonds, (stats.count.H_bonds * 100.0 / stats.count.residues)) << std::endl;
os << pdbx::format("%5d%5.1f TOTAL NUMBER OF HYDROGEN BONDS IN PARALLEL BRIDGES, SAME NUMBER PER 100 RESIDUES .", stats.count.H_bonds_in_parallel_bridges, (stats.count.H_bonds_in_parallel_bridges * 100.0 / stats.count.residues)) << std::endl; os << cif::format("%5d%5.1f TOTAL NUMBER OF HYDROGEN BONDS IN PARALLEL BRIDGES, SAME NUMBER PER 100 RESIDUES .", stats.count.H_bonds_in_parallel_bridges, (stats.count.H_bonds_in_parallel_bridges * 100.0 / stats.count.residues)) << std::endl;
os << pdbx::format("%5d%5.1f TOTAL NUMBER OF HYDROGEN BONDS IN ANTIPARALLEL BRIDGES, SAME NUMBER PER 100 RESIDUES .", stats.count.H_bonds_in_antiparallel_bridges, (stats.count.H_bonds_in_antiparallel_bridges * 100.0 / stats.count.residues)) << std::endl; os << cif::format("%5d%5.1f TOTAL NUMBER OF HYDROGEN BONDS IN ANTIPARALLEL BRIDGES, SAME NUMBER PER 100 RESIDUES .", stats.count.H_bonds_in_antiparallel_bridges, (stats.count.H_bonds_in_antiparallel_bridges * 100.0 / stats.count.residues)) << std::endl;
for (int k = 0; k < 11; ++k) for (int k = 0; k < 11; ++k)
os << pdbx::format("%5d%5.1f TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I%c%1d), SAME NUMBER PER 100 RESIDUES .", stats.count.H_Bonds_per_distance[k], (stats.count.H_Bonds_per_distance[k] * 100.0 / stats.count.residues), (k - 5 < 0 ? '-' : '+'), abs(k - 5)) << std::endl; os << cif::format("%5d%5.1f TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I%c%1d), SAME NUMBER PER 100 RESIDUES .", stats.count.H_Bonds_per_distance[k], (stats.count.H_Bonds_per_distance[k] * 100.0 / stats.count.residues), (k - 5 < 0 ? '-' : '+'), abs(k - 5)) << std::endl;
// histograms... // histograms...
os << " 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 *** HISTOGRAMS OF *** ." << std::endl; os << " 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 *** HISTOGRAMS OF *** ." << std::endl;
for (auto hi : stats.histogram.residues_per_alpha_helix) for (auto hi : stats.histogram.residues_per_alpha_helix)
os << pdbx::format("%3d", hi); os << cif::format("%3d", hi);
os << " RESIDUES PER ALPHA HELIX ." << std::endl; os << " RESIDUES PER ALPHA HELIX ." << std::endl;
for (auto hi : stats.histogram.parallel_bridges_per_ladder) for (auto hi : stats.histogram.parallel_bridges_per_ladder)
os << pdbx::format("%3d", hi); os << cif::format("%3d", hi);
os << " PARALLEL BRIDGES PER LADDER ." << std::endl; os << " PARALLEL BRIDGES PER LADDER ." << std::endl;
for (auto hi : stats.histogram.antiparallel_bridges_per_ladder) for (auto hi : stats.histogram.antiparallel_bridges_per_ladder)
os << pdbx::format("%3d", hi); os << cif::format("%3d", hi);
os << " ANTIPARALLEL BRIDGES PER LADDER ." << std::endl; os << " ANTIPARALLEL BRIDGES PER LADDER ." << std::endl;
for (auto hi : stats.histogram.ladders_per_sheet) for (auto hi : stats.histogram.ladders_per_sheet)
os << pdbx::format("%3d", hi); os << cif::format("%3d", hi);
os << " LADDERS PER SHEET ." << std::endl; os << " LADDERS PER SHEET ." << std::endl;
// per residue information // per residue information
...@@ -212,7 +211,7 @@ void writeDSSP(const dssp::DSSP &dssp, std::ostream &os) ...@@ -212,7 +211,7 @@ void writeDSSP(const dssp::DSSP &dssp, std::ostream &os)
// can be the transition to a different chain, or missing residues in the current chain // can be the transition to a different chain, or missing residues in the current chain
if (ri.nr() != last + 1) if (ri.nr() != last + 1)
os << pdbx::format("%5d !%c 0 0 0 0, 0.0 0, 0.0 0, 0.0 0, 0.0 0.000 360.0 360.0 360.0 360.0 0.0 0.0 0.0", os << cif::format("%5d !%c 0 0 0 0, 0.0 0, 0.0 0, 0.0 0, 0.0 0.000 360.0 360.0 360.0 360.0 0.0 0.0 0.0",
(last + 1), (ri.chain_break() == dssp::chain_break_type::NewChain ? '*' : ' ')) << std::endl; (last + 1), (ri.chain_break() == dssp::chain_break_type::NewChain ? '*' : ' ')) << std::endl;
os << ResidueToDSSPLine(ri) << std::endl; os << ResidueToDSSPLine(ri) << std::endl;
......
src/mkdssp.cpp
...@@ -35,7 +35,8 @@ ...@@ -35,7 +35,8 @@
#include <cfg.hpp> #include <cfg.hpp>
#include <gxrio.hpp> #include <gxrio.hpp>
#include <pdbx++.hpp>
#include <cif++/pdb/io.hpp>
#include "DSSP.hpp" #include "DSSP.hpp"
...@@ -141,7 +142,7 @@ int d_main(int argc, const char *argv[]) ...@@ -141,7 +142,7 @@ int d_main(int argc, const char *argv[])
exit(1); exit(1);
} }
cif::file f = pdbx::load_pdb_file(in); cif::file f = cif::pdb::read(in);
if (not f.is_valid()) if (not f.is_valid())
{ {
std::cerr << "Could not validate file" << std::endl; std::cerr << "Could not validate file" << std::endl;
......
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