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dssp
Commit d62d4eca by Maarten L. Hekkelman
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new DSSP output, dssp as shared lib

parent b862723c
Showing with 98 additions and 134 deletions
CMakeLists.txt
...@@ -195,7 +195,6 @@ file(GENERATE OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/libdssp.pc ...@@ -195,7 +195,6 @@ file(GENERATE OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/libdssp.pc
INPUT ${CMAKE_CURRENT_BINARY_DIR}/libdssp.pc.in) INPUT ${CMAKE_CURRENT_BINARY_DIR}/libdssp.pc.in)
install(FILES ${CMAKE_CURRENT_BINARY_DIR}/libdssp.pc DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig) install(FILES ${CMAKE_CURRENT_BINARY_DIR}/libdssp.pc DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
install(TARGETS ${PROJECT_NAME} install(TARGETS ${PROJECT_NAME}
RUNTIME DESTINATION ${BIN_INSTALL_DIR} RUNTIME DESTINATION ${BIN_INSTALL_DIR}
) )
...@@ -248,8 +247,8 @@ set(CPACK_SOURCE_TBZ2 OFF) ...@@ -248,8 +247,8 @@ set(CPACK_SOURCE_TBZ2 OFF)
set(CPACK_SOURCE_TXZ OFF) set(CPACK_SOURCE_TXZ OFF)
set(CPACK_SOURCE_TZ OFF) set(CPACK_SOURCE_TZ OFF)
set(CPACK_SOURCE_IGNORE_FILES "/data/components.cif;/build;/.vscode;/.git") set(CPACK_SOURCE_IGNORE_FILES "/data/components.cif;/build;/.vscode;/.git")
set (CPACK_PACKAGE_FILE_NAME "${PROJECT_NAME}-${PROJECT_VERSION}") set(CPACK_PACKAGE_FILE_NAME "${PROJECT_NAME}-${PROJECT_VERSION}")
set (CPACK_SOURCE_PACKAGE_FILE_NAME ${CPACK_PACKAGE_FILE_NAME}) set(CPACK_SOURCE_PACKAGE_FILE_NAME ${CPACK_PACKAGE_FILE_NAME})
# NSIS options # NSIS options
set(CPACK_NSIS_MODIFY_PATH ON) set(CPACK_NSIS_MODIFY_PATH ON)
......
changelog
Version 4.2 Version 4.2.0
- Changes for packaging - Changes for packaging
- New mmCIF DSSP output, added several categories - New mmCIF DSSP output, added several categories
......
include/dssp.hpp
...@@ -97,7 +97,6 @@ class dssp ...@@ -97,7 +97,6 @@ class dssp
Gap Gap
}; };
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::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 cif::mm::structure &s, int min_poly_proline_stretch_length, bool calculateSurfaceAccessibility);
......
src/dssp-io.cpp
...@@ -77,8 +77,8 @@ std::string ResidueToDSSPLine(const dssp::residue_info &info) ...@@ -77,8 +77,8 @@ std::string ResidueToDSSPLine(const dssp::residue_info &info)
case dssp::structure_type::Loop: ss = ' '; break; case dssp::structure_type::Loop: ss = ' '; break;
} }
char helix[4] = {' ', ' ', ' ', ' '}; char helix[4] = { ' ', ' ', ' ', ' ' };
for (dssp::helix_type helixType : {dssp::helix_type::_3_10, dssp::helix_type::alpha, dssp::helix_type::pi, dssp::helix_type::pp}) for (dssp::helix_type helixType : { dssp::helix_type::_3_10, dssp::helix_type::alpha, dssp::helix_type::pi, dssp::helix_type::pp })
{ {
switch (info.helix(helixType)) switch (info.helix(helixType))
{ {
...@@ -98,8 +98,8 @@ std::string ResidueToDSSPLine(const dssp::residue_info &info) ...@@ -98,8 +98,8 @@ std::string ResidueToDSSPLine(const dssp::residue_info &info)
char chirality = alpha == 360 ? ' ' : (alpha < 0 ? '-' : '+'); char chirality = alpha == 360 ? ' ' : (alpha < 0 ? '-' : '+');
uint32_t bp[2] = {}; uint32_t bp[2] = {};
char bridgelabel[2] = {' ', ' '}; char bridgelabel[2] = { ' ', ' ' };
for (uint32_t i : {0, 1}) for (uint32_t i : { 0, 1 })
{ {
const auto &[p, ladder, parallel] = info.bridge_partner(i); const auto &[p, ladder, parallel] = info.bridge_partner(i);
if (not p) if (not p)
...@@ -114,7 +114,7 @@ std::string ResidueToDSSPLine(const dssp::residue_info &info) ...@@ -114,7 +114,7 @@ std::string ResidueToDSSPLine(const dssp::residue_info &info)
sheet = 'A' + (info.sheet() - 1) % 26; sheet = 'A' + (info.sheet() - 1) % 26;
std::string NHO[2], ONH[2]; std::string NHO[2], ONH[2];
for (int i : {0, 1}) for (int i : { 0, 1 })
{ {
const auto &[donor, donorE] = info.donor(i); const auto &[donor, donorE] = info.donor(i);
const auto &[acceptor, acceptorE] = info.acceptor(i); const auto &[acceptor, acceptorE] = info.acceptor(i);
...@@ -211,7 +211,8 @@ void writeDSSP(const dssp &dssp, std::ostream &os) ...@@ -211,7 +211,8 @@ void writeDSSP(const dssp &dssp, std::ostream &os)
if (ri.nr() != last + 1) if (ri.nr() != last + 1)
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", 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;
last = ri.nr(); last = ri.nr();
...@@ -234,9 +235,8 @@ void writeBridgePairs(cif::datablock &db, const dssp &dssp) ...@@ -234,9 +235,8 @@ void writeBridgePairs(cif::datablock &db, const dssp &dssp)
hb.add_column("auth_asym_id"); hb.add_column("auth_asym_id");
hb.add_column("pdbx_PDB_ins_code"); hb.add_column("pdbx_PDB_ins_code");
// force right order // force right order
for (std::string da : { "acceptor_", "donor_"}) for (std::string da : { "acceptor_", "donor_" })
{ {
for (std::string i : { "1_", "2_" }) for (std::string i : { "1_", "2_" })
{ {
...@@ -249,32 +249,26 @@ void writeBridgePairs(cif::datablock &db, const dssp &dssp) ...@@ -249,32 +249,26 @@ void writeBridgePairs(cif::datablock &db, const dssp &dssp)
{ {
auto write_res = [&](const std::string &prefix, ResidueInfo const &r, double energy) auto write_res = [&](const std::string &prefix, ResidueInfo const &r, double energy)
{ {
hb.back().assign({ hb.back().assign({ { prefix + "label_comp_id", r.compound_id() },
{ prefix + "label_comp_id", r.compound_id() },
{ prefix + "label_seq_id", r.seq_id() }, { prefix + "label_seq_id", r.seq_id() },
{ prefix + "label_asym_id", r.asym_id() }, { prefix + "label_asym_id", r.asym_id() },
// { prefix + "auth_comp_id", r.compound_id() }, // { prefix + "auth_comp_id", r.compound_id() },
{ prefix + "auth_seq_id", r.auth_seq_id() }, { prefix + "auth_seq_id", r.auth_seq_id() },
{ prefix + "auth_asym_id", r.auth_asym_id() }, { prefix + "auth_asym_id", r.auth_asym_id() },
{ prefix + "pdbx_PDB_ins_code", r.pdb_ins_code() } { prefix + "pdbx_PDB_ins_code", r.pdb_ins_code() } });
});
if (not prefix.empty()) if (not prefix.empty())
hb.back().assign({ hb.back().assign({ { prefix + "energy", energy, 1 } });
{ prefix + "energy", energy, 1 }
});
}; };
hb.emplace({ hb.emplace({ { "id", hb.get_unique_id("") } });
{ "id", hb.get_unique_id("") }
});
write_res("", res, 0); write_res("", res, 0);
for (int i : {0, 1}) for (int i : { 0, 1 })
{ {
const auto &&[ acceptor, acceptorEnergy ] = res.acceptor(i); const auto &&[acceptor, acceptorEnergy] = res.acceptor(i);
const auto &&[ donor, donorEnergy ] = res.donor(i); const auto &&[donor, donorEnergy] = res.donor(i);
if (acceptor) if (acceptor)
write_res(i ? "acceptor_2_" : "acceptor_1_", acceptor, acceptorEnergy); write_res(i ? "acceptor_2_" : "acceptor_1_", acceptor, acceptorEnergy);
...@@ -293,18 +287,20 @@ void writeSheets(cif::datablock &db, const dssp &dssp) ...@@ -293,18 +287,20 @@ void writeSheets(cif::datablock &db, const dssp &dssp)
// clean up old info first // clean up old info first
for (auto sheet_cat : { "struct_sheet", "struct_sheet_order", "struct_sheet_range", "struct_sheet_hbond", "pdbx_struct_sheet_hbond" }) for (auto sheet_cat : { "struct_sheet", "struct_sheet_order", "struct_sheet_range", "struct_sheet_hbond", "pdbx_struct_sheet_hbond" })
db.erase(remove_if(db.begin(), db.end(), [sheet_cat](const cif::category &cat) { return cat.name() == sheet_cat; }), db.end()); db.erase(remove_if(db.begin(), db.end(), [sheet_cat](const cif::category &cat)
{ return cat.name() == sheet_cat; }),
db.end());
// create a list of strands, based on the SS info in DSSP. Store sheet number along with the strand. // create a list of strands, based on the SS info in DSSP. Store sheet number along with the strand.
std::vector<std::tuple<int,res_list>> strands; std::vector<std::tuple<int, res_list>> strands;
std::map<std::tuple<std::string,int>,int> sheetMap; // mapping from bridge number (=info.sheet()) in DSSP to sheet ID std::map<std::tuple<std::string, int>, int> sheetMap; // mapping from bridge number (=info.sheet()) in DSSP to sheet ID
ss_type ss = ss_type::Loop; ss_type ss = ss_type::Loop;
for (auto &res : dssp) for (auto &res : dssp)
{ {
std::tuple<std::string,int> sheetID{ res.asym_id(), res.sheet() }; std::tuple<std::string, int> sheetID{ res.asym_id(), res.sheet() };
ss_type iss = res.type(); ss_type iss = res.type();
if (iss == ss and ss == ss_type::Strand and sheetMap[sheetID] == std::get<0>(strands.back())) if (iss == ss and ss == ss_type::Strand and sheetMap[sheetID] == std::get<0>(strands.back()))
...@@ -333,21 +329,19 @@ void writeSheets(cif::datablock &db, const dssp &dssp) ...@@ -333,21 +329,19 @@ void writeSheets(cif::datablock &db, const dssp &dssp)
int d = sheetA - sheetB; int d = sheetA - sheetB;
if (d == 0) if (d == 0)
d = strandsA.front().nr() - strandsB.front().nr(); d = strandsA.front().nr() - strandsB.front().nr();
return d < 0; return d < 0; });
});
// write out the struct_sheet, since all info is available now // write out the struct_sheet, since all info is available now
auto &struct_sheet = db["struct_sheet"]; auto &struct_sheet = db["struct_sheet"];
int lastSheet = -1; int lastSheet = -1;
for (const auto &[ sheetNr, strand ] : strands) for (const auto &[sheetNr, strand] : strands)
{ {
if (sheetNr != lastSheet) if (sheetNr != lastSheet)
{ {
struct_sheet.emplace({ struct_sheet.emplace({ { "id", cif::cif_id_for_number(sheetNr) },
{ "id", cif::cif_id_for_number(sheetNr) }, { "number_strands", std::count_if(strands.begin(), strands.end(), [nr = sheetNr](std::tuple<int, res_list> const &s)
{ "number_strands", std::count_if(strands.begin(), strands.end(), [nr=sheetNr](std::tuple<int,res_list> const &s) { return std::get<0>(s) == nr; }) } { return std::get<0>(s) == nr; }) } });
});
lastSheet = sheetNr; lastSheet = sheetNr;
} }
...@@ -356,7 +350,7 @@ void writeSheets(cif::datablock &db, const dssp &dssp) ...@@ -356,7 +350,7 @@ void writeSheets(cif::datablock &db, const dssp &dssp)
// Each residue resides in a single strand which is part of a single sheet // Each residue resides in a single strand which is part of a single sheet
// this function returns the sequence number inside the sheet for the strand // this function returns the sequence number inside the sheet for the strand
// containing res // containing res
auto strandNrForResidue = [&strands,&sheetMap](dssp::residue_info const &res) auto strandNrForResidue = [&strands, &sheetMap](dssp::residue_info const &res)
{ {
for (const auto &[k, iSheet] : sheetMap) for (const auto &[k, iSheet] : sheetMap)
{ {
...@@ -379,7 +373,7 @@ void writeSheets(cif::datablock &db, const dssp &dssp) ...@@ -379,7 +373,7 @@ void writeSheets(cif::datablock &db, const dssp &dssp)
// This map is used to record the sense of a ladder, and can be used // This map is used to record the sense of a ladder, and can be used
// to detect ladders already seen. // to detect ladders already seen.
std::map<std::tuple<int,int,int>, std::tuple<int,bool>> ladderSense; std::map<std::tuple<int, int, int>, std::tuple<int, bool>> ladderSense;
for (auto &res : dssp) for (auto &res : dssp)
{ {
...@@ -399,7 +393,7 @@ void writeSheets(cif::datablock &db, const dssp &dssp) ...@@ -399,7 +393,7 @@ void writeSheets(cif::datablock &db, const dssp &dssp)
if (s2 == s1) if (s2 == s1)
continue; continue;
std::tuple<std::string,int> sheetID{res.asym_id(), res.sheet() }; std::tuple<std::string, int> sheetID{ res.asym_id(), res.sheet() };
int sheet = sheetMap[sheetID]; int sheet = sheetMap[sheetID];
auto k = s1 > s2 ? std::make_tuple(sheet, s2, s1) : std::make_tuple(sheet, s1, s2); auto k = s1 > s2 ? std::make_tuple(sheet, s2, s1) : std::make_tuple(sheet, s1, s2);
...@@ -419,18 +413,16 @@ void writeSheets(cif::datablock &db, const dssp &dssp) ...@@ -419,18 +413,16 @@ void writeSheets(cif::datablock &db, const dssp &dssp)
auto &pdbx_struct_sheet_hbond = db["pdbx_struct_sheet_hbond"]; auto &pdbx_struct_sheet_hbond = db["pdbx_struct_sheet_hbond"];
auto &pdbx_poly_seq_scheme = db["pdbx_poly_seq_scheme"]; auto &pdbx_poly_seq_scheme = db["pdbx_poly_seq_scheme"];
for (const auto&[key, value] : ladderSense) for (const auto &[key, value] : ladderSense)
{ {
const auto &[sheet, s1, s2] = key; const auto &[sheet, s1, s2] = key;
const auto &[ladder, parallel] = value; const auto &[ladder, parallel] = value;
struct_sheet_order.emplace({ struct_sheet_order.emplace({ { "sheet_id", cif::cif_id_for_number(sheet) },
{ "sheet_id", cif::cif_id_for_number(sheet) },
// { "dssp_struct_ladder_id", cif::cifIdForNumber(ladder) }, // { "dssp_struct_ladder_id", cif::cifIdForNumber(ladder) },
{ "range_id_1", s1 + 1 }, { "range_id_1", s1 + 1 },
{ "range_id_2", s2 + 1 }, { "range_id_2", s2 + 1 },
{ "sense", parallel ? "parallel" : "anti-parallel" } { "sense", parallel ? "parallel" : "anti-parallel" } });
});
res_list strand1, strand2; res_list strand1, strand2;
...@@ -452,7 +444,7 @@ void writeSheets(cif::datablock &db, const dssp &dssp) ...@@ -452,7 +444,7 @@ void writeSheets(cif::datablock &db, const dssp &dssp)
++strandIx; ++strandIx;
} }
assert(not (strand1.empty() or strand2.empty())); assert(not(strand1.empty() or strand2.empty()));
int beg1SeqID = 0, beg2SeqID = 0, end1SeqID = 0, end2SeqID = 0; int beg1SeqID = 0, beg2SeqID = 0, end1SeqID = 0, end2SeqID = 0;
std::string beg1AtomID, beg2AtomID, end1AtomID, end2AtomID; std::string beg1AtomID, beg2AtomID, end1AtomID, end2AtomID;
...@@ -662,8 +654,7 @@ void writeSheets(cif::datablock &db, const dssp &dssp) ...@@ -662,8 +654,7 @@ void writeSheets(cif::datablock &db, const dssp &dssp)
} }
} }
struct_sheet_hbond.emplace({ struct_sheet_hbond.emplace({ { "sheet_id", cif::cif_id_for_number(sheet) },
{ "sheet_id", cif::cif_id_for_number(sheet) },
{ "range_id_1", s1 + 1 }, { "range_id_1", s1 + 1 },
{ "range_id_2", s2 + 1 }, { "range_id_2", s2 + 1 },
{ "range_1_beg_label_seq_id", beg1SeqID }, { "range_1_beg_label_seq_id", beg1SeqID },
...@@ -673,8 +664,7 @@ void writeSheets(cif::datablock &db, const dssp &dssp) ...@@ -673,8 +664,7 @@ void writeSheets(cif::datablock &db, const dssp &dssp)
{ "range_1_end_label_seq_id", end1SeqID }, { "range_1_end_label_seq_id", end1SeqID },
{ "range_1_end_label_atom_id", end1AtomID }, { "range_1_end_label_atom_id", end1AtomID },
{ "range_2_end_label_seq_id", end2SeqID }, { "range_2_end_label_seq_id", end2SeqID },
{ "range_2_end_label_atom_id", end2AtomID } { "range_2_end_label_atom_id", end2AtomID } });
});
using namespace cif::literals; using namespace cif::literals;
...@@ -683,7 +673,7 @@ void writeSheets(cif::datablock &db, const dssp &dssp) ...@@ -683,7 +673,7 @@ void writeSheets(cif::datablock &db, const dssp &dssp)
auto b2 = pdbx_poly_seq_scheme.find1("asym_id"_key == strand2.front().asym_id() and "seq_id"_key == beg2SeqID); auto b2 = pdbx_poly_seq_scheme.find1("asym_id"_key == strand2.front().asym_id() and "seq_id"_key == beg2SeqID);
auto e2 = pdbx_poly_seq_scheme.find1("asym_id"_key == strand2.front().asym_id() and "seq_id"_key == end2SeqID); auto e2 = pdbx_poly_seq_scheme.find1("asym_id"_key == strand2.front().asym_id() and "seq_id"_key == end2SeqID);
if (not (b1 and e1 and b2 and e2)) if (not(b1 and e1 and b2 and e2))
{ {
if (cif::VERBOSE > 0) if (cif::VERBOSE > 0)
std::cerr << "error looking up strand ends" << std::endl; std::cerr << "error looking up strand ends" << std::endl;
...@@ -726,15 +716,12 @@ void writeSheets(cif::datablock &db, const dssp &dssp) ...@@ -726,15 +716,12 @@ void writeSheets(cif::datablock &db, const dssp &dssp)
continue; continue;
std::sort(strand.begin(), strand.end(), [](dssp::residue_info const &a, dssp::residue_info const &b) std::sort(strand.begin(), strand.end(), [](dssp::residue_info const &a, dssp::residue_info const &b)
{ { return a.nr() < b.nr(); });
return a.nr() < b.nr();
});
auto &beg = strand.front(); auto &beg = strand.front();
auto &end = strand.back(); auto &end = strand.back();
struct_sheet_range.emplace({ struct_sheet_range.emplace({ { "sheet_id", cif::cif_id_for_number(sheet) },
{ "sheet_id", cif::cif_id_for_number(sheet) },
{ "id", strandNrForResidue(strand.front()) + 1 }, { "id", strandNrForResidue(strand.front()) + 1 },
{ "beg_label_comp_id", beg.compound_id() }, { "beg_label_comp_id", beg.compound_id() },
{ "beg_label_asym_id", beg.asym_id() }, { "beg_label_asym_id", beg.asym_id() },
...@@ -749,8 +736,7 @@ void writeSheets(cif::datablock &db, const dssp &dssp) ...@@ -749,8 +736,7 @@ void writeSheets(cif::datablock &db, const dssp &dssp)
{ "beg_auth_seq_id", beg.auth_seq_id() }, { "beg_auth_seq_id", beg.auth_seq_id() },
{ "end_auth_comp_id", end.compound_id() }, { "end_auth_comp_id", end.compound_id() },
{ "end_auth_asym_id", end.auth_asym_id() }, { "end_auth_asym_id", end.auth_asym_id() },
{ "end_auth_seq_id", end.auth_seq_id() } { "end_auth_seq_id", end.auth_seq_id() } });
});
} }
} }
} }
...@@ -763,20 +749,20 @@ void writeLadders(cif::datablock &db, const dssp &dssp) ...@@ -763,20 +749,20 @@ void writeLadders(cif::datablock &db, const dssp &dssp)
ladder_info(const std::string &label, bool parallel, const dssp::residue_info &a, const dssp::residue_info &b) ladder_info(const std::string &label, bool parallel, const dssp::residue_info &a, const dssp::residue_info &b)
: label(label) : label(label)
, parallel(parallel) , parallel(parallel)
, pairs({{a, b}}) , pairs({ { a, b } })
{ {
} }
std::string label; std::string label;
bool parallel; bool parallel;
std::vector<std::pair<dssp::residue_info,dssp::residue_info>> pairs; std::vector<std::pair<dssp::residue_info, dssp::residue_info>> pairs;
}; };
std::vector<ladder_info> ladders; std::vector<ladder_info> ladders;
for (auto res : dssp) for (auto res : dssp)
{ {
for (int i : { 0, 1}) for (int i : { 0, 1 })
{ {
const auto &[p, ladder, parallel] = res.bridge_partner(i); const auto &[p, ladder, parallel] = res.bridge_partner(i);
...@@ -793,7 +779,8 @@ void writeLadders(cif::datablock &db, const dssp &dssp) ...@@ -793,7 +779,8 @@ void writeLadders(cif::datablock &db, const dssp &dssp)
assert(l.parallel == parallel); assert(l.parallel == parallel);
if (find_if(l.pairs.begin(), l.pairs.end(), [na=p.nr(), nb=res.nr()] (const auto &p) { return p.first.nr() == na and p.second.nr() == nb; }) != l.pairs.end()) if (find_if(l.pairs.begin(), l.pairs.end(), [na = p.nr(), nb = res.nr()](const auto &p)
{ return p.first.nr() == na and p.second.nr() == nb; }) != l.pairs.end())
{ {
is_new = false; is_new = false;
break; break;
...@@ -818,8 +805,7 @@ void writeLadders(cif::datablock &db, const dssp &dssp) ...@@ -818,8 +805,7 @@ void writeLadders(cif::datablock &db, const dssp &dssp)
const auto &[beg1, beg2] = l.pairs.front(); const auto &[beg1, beg2] = l.pairs.front();
const auto &[end1, end2] = l.pairs.back(); const auto &[end1, end2] = l.pairs.back();
dssp_struct_ladder.emplace({ dssp_struct_ladder.emplace({ { "id", l.label },
{ "id", l.label },
{ "type", l.parallel ? "parallel" : "anti-parallel" }, { "type", l.parallel ? "parallel" : "anti-parallel" },
{ "beg_1_label_comp_id", beg1.compound_id() }, { "beg_1_label_comp_id", beg1.compound_id() },
...@@ -850,71 +836,49 @@ void writeLadders(cif::datablock &db, const dssp &dssp) ...@@ -850,71 +836,49 @@ void writeLadders(cif::datablock &db, const dssp &dssp)
{ "beg_2_auth_seq_id", beg2.auth_seq_id() }, { "beg_2_auth_seq_id", beg2.auth_seq_id() },
{ "end_2_auth_comp_id", end2.compound_id() }, { "end_2_auth_comp_id", end2.compound_id() },
{ "end_2_auth_asym_id", end2.auth_asym_id() }, { "end_2_auth_asym_id", end2.auth_asym_id() },
{ "end_2_auth_seq_id", end2.auth_seq_id() } { "end_2_auth_seq_id", end2.auth_seq_id() } });
});
} }
} }
void annotateDSSP(cif::datablock &db, const dssp &dssp, bool writeOther, std::ostream &os) void writeStatistics(cif::datablock &db, const dssp &dssp)
{ {
using namespace std::literals; using namespace std::literals;
if (dssp.empty())
{
if (cif::VERBOSE > 0)
std::cout << "No secondary structure information found" << std::endl;
}
else
{
writeBridgePairs(db, dssp);
writeSheets(db, dssp);
writeLadders(db, dssp);
auto stats = dssp.get_statistics(); auto stats = dssp.get_statistics();
auto &dssp_statistics = db["dssp_statistics"]; auto &dssp_statistics = db["dssp_statistics"];
dssp_statistics.emplace({ dssp_statistics.emplace({ { "entry_id", db.name() },
{ "entry_id", db.name() },
{ "nr_of_residues", stats.count.residues }, { "nr_of_residues", stats.count.residues },
{ "nr_of_chains", stats.count.chains }, { "nr_of_chains", stats.count.chains },
{ "nr_of_ss_bridges_total", stats.count.SS_bridges }, { "nr_of_ss_bridges_total", stats.count.SS_bridges },
{ "nr_of_ss_bridges_intra_chain", stats.count.intra_chain_SS_bridges }, { "nr_of_ss_bridges_intra_chain", stats.count.intra_chain_SS_bridges },
{ "nr_of_ss_bridges_inter_chain", stats.count.SS_bridges - stats.count.intra_chain_SS_bridges }, { "nr_of_ss_bridges_inter_chain", stats.count.SS_bridges - stats.count.intra_chain_SS_bridges },
{ "accessible_surface_of_protein", stats.accessible_surface } { "accessible_surface_of_protein", stats.accessible_surface } });
});
auto &dssp_struct_hbonds = db["dssp_statistics_hbond"]; auto &dssp_struct_hbonds = db["dssp_statistics_hbond"];
dssp_struct_hbonds.emplace({ dssp_struct_hbonds.emplace({ { "entry_id", db.name() },
{ "entry_id", db.name() },
{ "type", "O(I)-->H-N(J)" }, { "type", "O(I)-->H-N(J)" },
{ "count", stats.count.H_bonds }, { "count", stats.count.H_bonds },
{ "count_per_100", stats.count.H_bonds * 100.0 / stats.count.residues, 1 } { "count_per_100", stats.count.H_bonds * 100.0 / stats.count.residues, 1 } });
});
dssp_struct_hbonds.emplace({ dssp_struct_hbonds.emplace({ { "entry_id", db.name() },
{ "entry_id", db.name() },
{ "type", "PARALLEL BRIDGES" }, { "type", "PARALLEL BRIDGES" },
{ "count", stats.count.H_bonds_in_parallel_bridges }, { "count", stats.count.H_bonds_in_parallel_bridges },
{ "count_per_100", stats.count.H_bonds_in_parallel_bridges * 100.0 / stats.count.residues, 1 } { "count_per_100", stats.count.H_bonds_in_parallel_bridges * 100.0 / stats.count.residues, 1 } });
});
dssp_struct_hbonds.emplace({ dssp_struct_hbonds.emplace({ { "entry_id", db.name() },
{ "entry_id", db.name() },
{ "type", "ANTIPARALLEL BRIDGES" }, { "type", "ANTIPARALLEL BRIDGES" },
{ "count", stats.count.H_bonds_in_antiparallel_bridges }, { "count", stats.count.H_bonds_in_antiparallel_bridges },
{ "count_per_100", stats.count.H_bonds_in_antiparallel_bridges * 100.0 / stats.count.residues, 1 } { "count_per_100", stats.count.H_bonds_in_antiparallel_bridges * 100.0 / stats.count.residues, 1 } });
});
for (int k = 0; k < 11; ++k) for (int k = 0; k < 11; ++k)
dssp_struct_hbonds.emplace({ dssp_struct_hbonds.emplace({ { "entry_id", db.name() },
{ "entry_id", db.name() },
{ "type", "O(I)-->H-N(I"s + char(k - 5 < 0 ? '-' : '+') + std::to_string(abs(k - 5)) + ")" }, { "type", "O(I)-->H-N(I"s + char(k - 5 < 0 ? '-' : '+') + std::to_string(abs(k - 5)) + ")" },
{ "count", stats.count.H_Bonds_per_distance[k] }, { "count", stats.count.H_Bonds_per_distance[k] },
{ "count_per_100", stats.count.H_Bonds_per_distance[k] * 100.0 / stats.count.residues, 1 } { "count_per_100", stats.count.H_Bonds_per_distance[k] * 100.0 / stats.count.residues, 1 } });
});
auto &dssp_statistics_histogram = db["dssp_statistics_histogram"]; auto &dssp_statistics_histogram = db["dssp_statistics_histogram"];
...@@ -923,8 +887,7 @@ void annotateDSSP(cif::datablock &db, const dssp &dssp, bool writeOther, std::os ...@@ -923,8 +887,7 @@ void annotateDSSP(cif::datablock &db, const dssp &dssp, bool writeOther, std::os
{ "parallel_bridges_per_ladder", stats.histogram.residues_per_alpha_helix }, { "parallel_bridges_per_ladder", stats.histogram.residues_per_alpha_helix },
{ "parallel_bridges_per_ladder", stats.histogram.parallel_bridges_per_ladder }, { "parallel_bridges_per_ladder", stats.histogram.parallel_bridges_per_ladder },
{ "antiparallel_bridges_per_ladder", stats.histogram.antiparallel_bridges_per_ladder }, { "antiparallel_bridges_per_ladder", stats.histogram.antiparallel_bridges_per_ladder },
{ "ladders_per_sheet", stats.histogram.ladders_per_sheet } { "ladders_per_sheet", stats.histogram.ladders_per_sheet } })
})
{ {
auto hi = dssp_statistics_histogram.emplace({ auto hi = dssp_statistics_histogram.emplace({
{ "entry_id", db.name() }, { "entry_id", db.name() },
...@@ -961,7 +924,10 @@ void annotateDSSP(cif::datablock &db, const dssp &dssp, bool writeOther, std::os ...@@ -961,7 +924,10 @@ void annotateDSSP(cif::datablock &db, const dssp &dssp, bool writeOther, std::os
{ "30", values[29] }, { "30", values[29] },
}); });
} }
}
void writeSummary(cif::datablock &db, const dssp &dssp)
{
// A approximation of the old format // A approximation of the old format
auto &dssp_struct_summary = db["dssp_struct_summary"]; auto &dssp_struct_summary = db["dssp_struct_summary"];
...@@ -981,8 +947,8 @@ void annotateDSSP(cif::datablock &db, const dssp &dssp, bool writeOther, std::os ...@@ -981,8 +947,8 @@ void annotateDSSP(cif::datablock &db, const dssp &dssp, bool writeOther, std::os
std::string ss = { res.type() == dssp::structure_type::Loop ? '.' : static_cast<char>(res.type()) }; std::string ss = { res.type() == dssp::structure_type::Loop ? '.' : static_cast<char>(res.type()) };
std::string helix[4] = { ".", ".", ".", "."}; std::string helix[4] = { ".", ".", ".", "." };
for (dssp::helix_type helixType : {dssp::helix_type::_3_10, dssp::helix_type::alpha, dssp::helix_type::pi, dssp::helix_type::pp}) for (dssp::helix_type helixType : { dssp::helix_type::_3_10, dssp::helix_type::alpha, dssp::helix_type::pi, dssp::helix_type::pp })
{ {
switch (res.helix(helixType)) switch (res.helix(helixType))
{ {
...@@ -1022,7 +988,7 @@ void annotateDSSP(cif::datablock &db, const dssp &dssp, bool writeOther, std::os ...@@ -1022,7 +988,7 @@ void annotateDSSP(cif::datablock &db, const dssp &dssp, bool writeOther, std::os
std::string ladders[2] = { ".", "." }; std::string ladders[2] = { ".", "." };
for (uint32_t i : {0, 1}) for (uint32_t i : { 0, 1 })
{ {
const auto &[p, ladder, parallel] = res.bridge_partner(i); const auto &[p, ladder, parallel] = res.bridge_partner(i);
if (not p) if (not p)
...@@ -1069,6 +1035,27 @@ void annotateDSSP(cif::datablock &db, const dssp &dssp, bool writeOther, std::os ...@@ -1069,6 +1035,27 @@ void annotateDSSP(cif::datablock &db, const dssp &dssp, bool writeOther, std::os
{ "z_ca", caz, 1 }, { "z_ca", caz, 1 },
}); });
} }
}
void annotateDSSP(cif::datablock &db, const dssp &dssp, bool writeOther, bool writeExperimental, std::ostream &os)
{
using namespace std::literals;
if (dssp.empty())
{
if (cif::VERBOSE > 0)
std::cout << "No secondary structure information found" << std::endl;
}
else
{
if (writeExperimental)
{
writeBridgePairs(db, dssp);
writeSheets(db, dssp);
writeLadders(db, dssp);
writeStatistics(db, dssp);
writeSummary(db, dssp);
}
// replace all struct_conf and struct_conf_type records // replace all struct_conf and struct_conf_type records
auto &structConfType = db["struct_conf_type"]; auto &structConfType = db["struct_conf_type"];
...@@ -1177,8 +1164,7 @@ void annotateDSSP(cif::datablock &db, const dssp &dssp, bool writeOther, std::os ...@@ -1177,8 +1164,7 @@ void annotateDSSP(cif::datablock &db, const dssp &dssp, bool writeOther, std::os
} }
auto &software = db["software"]; auto &software = db["software"];
software.emplace({ software.emplace({ { "pdbx_ordinal", software.get_unique_id("") },
{ "pdbx_ordinal", software.get_unique_id("") },
{ "name", "dssp" }, { "name", "dssp" },
{ "version", kVersionNumber }, { "version", kVersionNumber },
{ "date", kBuildDate }, { "date", kBuildDate },
......
src/dssp-io.hpp
...@@ -29,5 +29,5 @@ ...@@ -29,5 +29,5 @@
#include "dssp.hpp" #include "dssp.hpp"
void writeDSSP(const dssp& dssp, std::ostream& os); void writeDSSP(const dssp& dssp, std::ostream& os);
void annotateDSSP(cif::datablock &db, const dssp& dssp, bool writeOther, std::ostream& os); void annotateDSSP(cif::datablock &db, const dssp& dssp, bool writeOther, bool writeExperimental, std::ostream& os);
src/dssp.cpp
...@@ -2085,6 +2085,11 @@ dssp::iterator &dssp::iterator::operator--() ...@@ -2085,6 +2085,11 @@ dssp::iterator &dssp::iterator::operator--()
// -------------------------------------------------------------------- // --------------------------------------------------------------------
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::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)) : m_impl(new DSSP_impl(db, model_nr, min_poly_proline_stretch))
{ {
......
src/mkdssp.cpp
...@@ -72,6 +72,7 @@ int d_main(int argc, const char *argv[]) ...@@ -72,6 +72,7 @@ int d_main(int argc, const char *argv[])
mcfp::make_option<std::string>("output-format", "Output format, can be either 'dssp' for classic DSSP or 'mmcif' for annotated mmCIF. The default is chosen based on the extension of the output file, if any."), mcfp::make_option<std::string>("output-format", "Output format, can be either 'dssp' for classic DSSP or 'mmcif' for annotated mmCIF. The default is chosen based on the extension of the output file, if any."),
mcfp::make_option<short>("min-pp-stretch", 3, "Minimal number of residues having PSI/PHI in range for a PP helix, default is 3"), mcfp::make_option<short>("min-pp-stretch", 3, "Minimal number of residues having PSI/PHI in range for a PP helix, default is 3"),
mcfp::make_option("write-other", "If set, write the type OTHER for loops, default is to leave this out"), mcfp::make_option("write-other", "If set, write the type OTHER for loops, default is to leave this out"),
mcfp::make_option("write-experimental", "If set, write the new, experimental DSSP output in mmCIF format, default is to leave this out"),
// mcfp::make_option("components", po::value<std::string, "Location of the components.cif file from CCD") // mcfp::make_option("components", po::value<std::string, "Location of the components.cif file from CCD")
// mcfp::make_option("extra-compounds", po::value<std::string, "File containing residue information for extra compounds in this specific target, should be either in CCD format or a CCP4 restraints file") // mcfp::make_option("extra-compounds", po::value<std::string, "File containing residue information for extra compounds in this specific target, should be either in CCD format or a CCP4 restraints file")
...@@ -185,14 +186,14 @@ int d_main(int argc, const char *argv[]) ...@@ -185,14 +186,14 @@ int d_main(int argc, const char *argv[])
if (fmt == "dssp") if (fmt == "dssp")
writeDSSP(dssp, out); writeDSSP(dssp, out);
else else
annotateDSSP(f.front(), dssp, writeOther, out); annotateDSSP(f.front(), dssp, writeOther, config.has("write-experimental"), out);
} }
else else
{ {
if (fmt == "dssp") if (fmt == "dssp")
writeDSSP(dssp, std::cout); writeDSSP(dssp, std::cout);
else else
annotateDSSP(f.front(), dssp, writeOther, std::cout); annotateDSSP(f.front(), dssp, writeOther, config.has("write-experimental"), std::cout);
} }
return 0; return 0;
......
src/mkdssp.hpp deleted 100644 → 0
/*-
* SPDX-License-Identifier: BSD-2-Clause
*
* Copyright (c) 2020 NKI/AVL, Netherlands Cancer Institute
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the above copyright notice, this
* list of conditions and the following disclaimer
* 2. Redistributions in binary form must reproduce the above copyright notice,
* this list of conditions and the following disclaimer in the documentation
* and/or other materials provided with the distribution.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
* ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
* WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
* DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
* ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
* (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
* LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
* ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*/
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