Skip to content

D
dssp
Commit 0cedf7b1 by Maarten L. Hekkelman
Options

Alternate sheet writing, again

parent 7460007b
Showing with 122 additions and 90 deletions
src/dssp-io.cpp
......@@ -340,7 +340,7 @@ void writeSheets(cif::datablock &db, const dssp &dssp)
for (auto &res : dssp)
{
if (res.type() != dssp::structure_type::Strand)
if (res.type() != dssp::structure_type::Strand and res.type() != dssp::structure_type::Betabridge)
continue;
strands[{res.sheet(), res.strand()}].emplace_back(res);
......@@ -377,7 +377,7 @@ void writeSheets(cif::datablock &db, const dssp &dssp)
if (strand.front().sheet() != sheetNr)
continue;
std::string strandID = "strand_" + cif::cif_id_for_number(strand.front().strand() - 1);
std::string strandID = cif::cif_id_for_number(strand.front().strand() - 1);
std::sort(strand.begin(), strand.end(), [](dssp::residue_info const &a, dssp::residue_info const &b)
{ return a.nr() < b.nr(); });
......@@ -409,7 +409,8 @@ void writeSheets(cif::datablock &db, const dssp &dssp)
for (int i : { 0, 1 })
{
const auto &[bp, ladder, parallel] = res.bridge_partner(i);
if (not bp or bp.type() != dssp::structure_type::Strand)
// if (not bp or bp.type() != dssp::structure_type::Strand)
if (not bp)
continue;
auto s1 = res.strand();
......@@ -431,13 +432,13 @@ void writeSheets(cif::datablock &db, const dssp &dssp)
bool parallel = parallel_test > 0;
std::string strandID_1 = "strand_" + cif::cif_id_for_number(s1 - 1);
std::string strandID_2 = "strand_" + cif::cif_id_for_number(s2 - 1);
std::string strandID_1 = cif::cif_id_for_number(s1 - 1);
std::string strandID_2 = cif::cif_id_for_number(s2 - 1);
struct_sheet_order.emplace({
{ "sheet_id", sheetID },
{ "range_id_1", "strand_" + strandID_1 },
{ "range_id_2", "strand_" + strandID_2 },
{ "range_id_1", strandID_1 },
{ "range_id_2", strandID_2 },
{ "sense", parallel > 0 ? "parallel" : "anti-parallel" }
});
......@@ -748,14 +749,21 @@ void writeLadders(cif::datablock &db, const dssp &dssp)
// Write out the DSSP ladders
struct ladder_info
{
ladder_info(const std::string &label, bool parallel, const dssp::residue_info &a, const dssp::residue_info &b)
: label(label)
ladder_info(int label, int sheet, bool parallel, const dssp::residue_info &a, const dssp::residue_info &b)
: ladder(label)
, sheet(sheet)
, parallel(parallel)
, pairs({ { a, b } })
{
}
std::string label;
bool operator<(const ladder_info &rhs) const
{
return ladder < rhs.ladder;
}
int ladder;
int sheet;
bool parallel;
std::vector<std::pair<dssp::residue_info, dssp::residue_info>> pairs;
};
......@@ -771,12 +779,10 @@ void writeLadders(cif::datablock &db, const dssp &dssp)
if (not p)
continue;
auto label = cif::cif_id_for_number(ladder);
bool is_new = true;
for (auto &l : ladders)
{
if (l.label != label)
if (l.ladder != ladder)
continue;
assert(l.parallel == parallel);
......@@ -796,10 +802,12 @@ void writeLadders(cif::datablock &db, const dssp &dssp)
if (not is_new)
continue;
ladders.emplace_back(label, parallel, res, p);
ladders.emplace_back(ladder, res.sheet() - 1, parallel, res, p);
}
}
std::sort(ladders.begin(), ladders.end());
auto &dssp_struct_ladder = db["dssp_struct_ladder"];
for (const auto &l : ladders)
......@@ -807,7 +815,11 @@ void writeLadders(cif::datablock &db, const dssp &dssp)
const auto &[beg1, beg2] = l.pairs.front();
const auto &[end1, end2] = l.pairs.back();
dssp_struct_ladder.emplace({ { "id", l.label },
dssp_struct_ladder.emplace({
{ "id", cif::cif_id_for_number(l.ladder) },
{ "sheet_id", cif::cif_id_for_number(l.sheet) },
{ "range_1", cif::cif_id_for_number(beg1.strand() - 1) },
{ "range_2", cif::cif_id_for_number(beg2.strand() - 1) },
{ "type", l.parallel ? "parallel" : "anti-parallel" },
{ "beg_1_label_comp_id", beg1.compound_id() },
......@@ -939,7 +951,7 @@ void writeSummary(cif::datablock &db, const dssp &dssp)
// prime the category with the field labels we need, this is to ensure proper order in writing out the data.
for (auto label : { "entry_id", "label_comp_id", "label_asym_id", "label_seq_id", "secondary_structure", "ss_bridge", "helix_3_10", "helix_alpha", "helix_pi", "helix_pp", "bend", "chirality", "ladder_1", "ladder_2", "sheet", "accessibility", "TCO", "kappa", "alpha", "phi", "psi", "x_ca", "y_ca", "z_ca"})
for (auto label : { "entry_id", "label_comp_id", "label_asym_id", "label_seq_id", "secondary_structure", "ss_bridge", "helix_3_10", "helix_alpha", "helix_pi", "helix_pp", "bend", "chirality", "sheet", "strand", "ladder_1", "ladder_2", "accessibility", "TCO", "kappa", "alpha", "phi", "psi", "x_ca", "y_ca", "z_ca"})
dssp_struct_summary.add_column(label);
for (auto res : dssp)
......@@ -1026,11 +1038,11 @@ void writeSummary(cif::datablock &db, const dssp &dssp)
{ "bend", bend },
{ "chirality", chirality },
{ "sheet", res.sheet() ? cif::cif_id_for_number(res.sheet() - 1) : "." },
{ "strand", res.strand() ? cif::cif_id_for_number(res.strand() - 1) : "." },
{ "ladder_1", ladders[0] },
{ "ladder_2", ladders[1] },
{ "sheet", res.sheet() ? cif::cif_id_for_number(res.sheet() - 1) : "." },
{ "x_ca", cax, 1 },
{ "y_ca", cay, 1 },
{ "z_ca", caz, 1 },
......
src/dssp.cpp
......@@ -1104,85 +1104,105 @@ void CalculateBetaSheets(std::vector<residue> &inResidues, statistics &stats, st
}
}
// Construct the 'strands'
// For mmCIF output, this is needed and since we now have the information available
// it is best to do the calculation here.
// strands are ranges of residues of length > 1 that form beta bridges in a sheet.
// Second attempt to create 'strands'. A strand is a range of residues
// without a gap in between in the same chain that belong to the same sheet.
int strand = 0;
for (uint32_t iSheet = 1; iSheet < sheet; ++iSheet)
{
std::vector<std::tuple<uint32_t,uint32_t>> strands;
for (auto &bridge : bridges)
int lastNr = -1;
for (auto &res : inResidues)
{
if (bridge.sheet != iSheet)
if (res.mSheet != iSheet)
continue;
for (auto &range : { bridge.i, bridge.j})
{
auto imin = range.front();
auto imax = range.back();
if (imin == imax)
continue;
if (imin > imax)
std::swap(imin, imax);
auto ii = find_if(strands.begin(), strands.end(), [a = imin, b = imax] (std::tuple<uint32_t,uint32_t> &t)
{
auto &&[start, end] = t;
bool result = false;
if (start <= b and end >= a)
{
result = true;
if (start > a)
start = a;
if (end < b)
end = b;
}
return result;
});
if (ii == strands.end())
strands.emplace_back(imin, imax);
}
}
std::sort(strands.begin(), strands.end());
// collapse ranges that overlap
if (strands.size() > 1)
{
auto si = strands.begin();
while (std::next(si) != strands.end())
{
auto &&[afirst, alast] = *si;
auto &&[bfirst, blast] = *(std::next(si));
if (alast >= bfirst)
{
bfirst = afirst;
si = strands.erase(si);
continue;
}
++si;
}
}
for (size_t i = 0; i < strands.size(); ++i)
{
const auto &[first, last] = strands[i];
for (auto nr = first; nr <= last; ++nr)
{
assert(inResidues[nr].mStrand == 0);
inResidues[nr].SetStrand(i + 1);
}
if (lastNr + 1 < res.mNumber)
++strand;
res.mStrand = strand;
lastNr = res.mNumber;
}
}
// // Construct the 'strands'
// // For mmCIF output, this is needed and since we now have the information available
// // it is best to do the calculation here.
// // strands are ranges of residues of length > 1 that form beta bridges in a sheet.
// for (uint32_t iSheet = 1; iSheet < sheet; ++iSheet)
// {
// std::vector<std::tuple<uint32_t,uint32_t>> strands;
// for (auto &bridge : bridges)
// {
// if (bridge.sheet != iSheet)
// continue;
// for (auto &range : { bridge.i, bridge.j})
// {
// auto imin = range.front();
// auto imax = range.back();
// // if (imin == imax)
// // continue;
// if (imin > imax)
// std::swap(imin, imax);
// auto ii = find_if(strands.begin(), strands.end(), [a = imin, b = imax] (std::tuple<uint32_t,uint32_t> &t)
// {
// auto &&[start, end] = t;
// bool result = false;
// if (start <= b and end >= a)
// {
// result = true;
// if (start > a)
// start = a;
// if (end < b)
// end = b;
// }
// return result;
// });
// if (ii == strands.end())
// strands.emplace_back(imin, imax);
// }
// }
// std::sort(strands.begin(), strands.end());
// // collapse ranges that overlap
// if (strands.size() > 1)
// {
// auto si = strands.begin();
// while (std::next(si) != strands.end())
// {
// auto &&[afirst, alast] = *si;
// auto &&[bfirst, blast] = *(std::next(si));
// if (alast >= bfirst)
// {
// bfirst = afirst;
// si = strands.erase(si);
// continue;
// }
// ++si;
// }
// }
// for (size_t i = 0; i < strands.size(); ++i)
// {
// const auto &[first, last] = strands[i];
// for (auto nr = first; nr <= last; ++nr)
// {
// assert(inResidues[nr].mStrand == 0);
// inResidues[nr].SetStrand(i + 1);
// }
// }
// }
}
// --------------------------------------------------------------------
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment