mirror of
https://github.com/PDB-REDO/dssp.git
synced 2026-06-04 13:44:21 +08:00
dssp werk
This commit is contained in:
Maarten L. Hekkelman
1
.gitignore
vendored
1
.gitignore
vendored
@@ -15,3 +15,4 @@ config.status
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config.log
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aclocal.m4
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dssp
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*.dssp
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232
src/dssp.cpp
232
src/dssp.cpp
@@ -39,116 +39,114 @@ void print_what (const std::exception& e)
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// --------------------------------------------------------------------
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#if 0
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std::string ResidueToDSSPLine(const MResidue& residue)
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std::string ResidueToDSSPLine(const mmcif::DSSP::ResidueInfo& info)
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{
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/*
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This is the header line for the residue lines in a DSSP file:
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# RESIDUE AA STRUCTURE BP1 BP2 ACC N-H-->O O-->H-N N-H-->O O-->H-N TCO KAPPA ALPHA PHI PSI X-CA Y-CA Z-CA CHAIN
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# RESIDUE AA STRUCTURE BP1 BP2 ACC N-H-->O O-->H-N N-H-->O O-->H-N TCO KAPPA ALPHA PHI PSI X-CA Y-CA Z-CA
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*/
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boost::format kDSSPResidueLine(
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"%5.5d%5.5d%1.1s%1.1s %c %c %c%c%c%c%c%c%c%4.4d%4.4d%c%4.4d %11s%11s%11s%11s %6.3f%6.1f%6.1f%6.1f%6.1f %6.1f %6.1f %6.1f %4.4s");
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"%5.5d%5.5d%1.1s%1.1s %c %c %c%c%c%c%c%c%c%4.4d%4.4d%c%4.4d %11s%11s%11s%11s %6.3f%6.1f%6.1f%6.1f%6.1f %6.1f %6.1f %6.1f");
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const MAtom& ca = residue.GetCAlpha();
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auto& residue = info.residue();
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char code = kResidueInfo[residue.GetType()].code;
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if (residue.GetType() == kCysteine and residue.GetSSBridgeNr() != 0)
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code = 'a' + ((residue.GetSSBridgeNr() - 1) % 26);
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if (residue.asymID().length() > 1)
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throw std::runtime_error("This file contains data that won't fit in the original DSSP format");
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char ss;
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switch (residue.GetSecondaryStructure())
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auto ca = residue.atomByID("CA");
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char code = 'X';
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if (mmcif::kAAMap.find(residue.compoundID()) != mmcif::kAAMap.end())
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code = mmcif::kAAMap.at(residue.compoundID());
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if (code == 'C') // a cysteine
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{
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case alphahelix: ss = 'H'; break;
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case betabridge: ss = 'B'; break;
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case strand: ss = 'E'; break;
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case helix_3: ss = 'G'; break;
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case helix_5: ss = 'I'; break;
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case turn: ss = 'T'; break;
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case bend: ss = 'S'; break;
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case loop: ss = ' '; break;
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auto ssbridgenr = info.ssBridgeNr();
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if (ssbridgenr)
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code = 'a' + ((ssbridgenr - 1) % 26);
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}
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char helix[3];
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for (uint32_t stride = 3; stride <= 5; ++stride)
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char ss;
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switch (info.ss())
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{
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switch (residue.GetHelixFlag(stride))
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case mmcif::ssAlphahelix: ss = 'H'; break;
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case mmcif::ssBetabridge: ss = 'B'; break;
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case mmcif::ssStrand: ss = 'E'; break;
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case mmcif::ssHelix_3: ss = 'G'; break;
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case mmcif::ssHelix_5: ss = 'I'; break;
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case mmcif::ssTurn: ss = 'T'; break;
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case mmcif::ssBend: ss = 'S'; break;
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case mmcif::ssLoop: ss = ' '; break;
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}
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char helix[3] = { ' ', ' ', ' ' };
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for (auto stride: { 3, 4, 5})
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{
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switch (info.helix(stride))
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{
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case helixNone: helix[stride - 3] = ' '; break;
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case helixStart: helix[stride - 3] = '>'; break;
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case helixEnd: helix[stride - 3] = '<'; break;
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case helixStartAndEnd: helix[stride - 3] = 'X'; break;
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case helixMiddle: helix[stride - 3] = '0' + stride; break;
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case mmcif::Helix::None: helix[stride - 3] = ' '; break;
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case mmcif::Helix::Start: helix[stride - 3] = '>'; break;
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case mmcif::Helix::End: helix[stride - 3] = '<'; break;
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case mmcif::Helix::StartAndEnd: helix[stride - 3] = 'X'; break;
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case mmcif::Helix::Middle: helix[stride - 3] = '0' + stride; break;
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}
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}
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char bend = ' ';
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if (residue.IsBend())
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if (info.bend())
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bend = 'S';
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double alpha;
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char chirality;
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std::tr1::tie(alpha,chirality) = residue.Alpha();
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double alpha = residue.alpha();
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char chirality = alpha == 360 ? ' ' : (alpha < 0 ? '-' : '+');
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uint32_t bp[2] = {};
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char bridgelabel[2] = { ' ', ' ' };
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for (uint32_t i = 0; i < 2; ++i)
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for (uint32_t i: { 0, 1 })
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{
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MBridgeParner p = residue.GetBetaPartner(i);
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if (p.residue != nullptr)
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{
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bp[i] = p.residue->GetNumber();
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bp[i] %= 10000; // won't fit otherwise...
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bridgelabel[i] = 'A' + p.ladder % 26;
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if (p.parallel)
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bridgelabel[i] = tolower(bridgelabel[i]);
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}
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const auto& [p, ladder, parallel] = info.bridgePartner(i);
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if (not p)
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continue;
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bp[i] = p.nr() % 10000; // won't fit otherwise...
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bridgelabel[i] = (parallel ? 'a' : 'A') + ladder % 26;
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}
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char sheet = ' ';
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if (residue.GetSheet() != 0)
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sheet = 'A' + (residue.GetSheet() - 1) % 26;
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if (info.sheet() != 0)
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sheet = 'A' + (info.sheet() - 1) % 26;
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std::string NHO[2], ONH[2];
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const HBond* acceptors = residue.Acceptor();
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const HBond* donors = residue.Donor();
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for (uint32_t i = 0; i < 2; ++i)
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for (int i: { 0, 1 })
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{
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const auto& [donor, donorE] = info.donor(i);
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const auto& [acceptor, acceptorE] = info.acceptor(i);
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NHO[i] = ONH[i] = "0, 0.0";
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if (acceptors[i].residue != nullptr)
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if (acceptor)
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{
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int32 d = acceptors[i].residue->GetNumber() - residue.GetNumber();
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NHO[i] = (boost::format("%d,%3.1f") % d % acceptors[i].energy).str();
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auto d = acceptor.nr() - info.nr();
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NHO[i] = (boost::format("%d,%3.1f") % d % acceptorE).str();
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}
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if (donors[i].residue != nullptr)
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if (donor)
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{
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int32 d = donors[i].residue->GetNumber() - residue.GetNumber();
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ONH[i] = (boost::format("%d,%3.1f") % d % donors[i].energy).str();
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auto d = donor.nr() - info.nr();
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ONH[i] = (boost::format("%d,%3.1f") % d % donorE).str();
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}
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}
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std::string chainChar = ca.mChainID,
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long_ChainID = "";
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if (ca.mChainID.length () > 1)
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{
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// For mmCIF compatibility
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auto const& [cax, cay, caz] = ca.location();
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chainChar = ">";
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long_ChainID = ca.mChainID;
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}
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return (kDSSPResidueLine % residue.GetNumber() % ca.mResSeq % ca.mICode % chainChar % code %
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return (kDSSPResidueLine % info.nr() % ca.authSeqId() % ca.pdbxAuthInsCode() % ca.authAsymId() % code %
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ss % helix[0] % helix[1] % helix[2] % bend % chirality % bridgelabel[0] % bridgelabel[1] %
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bp[0] % bp[1] % sheet % floor(residue.Accessibility() + 0.5) %
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bp[0] % bp[1] % sheet % floor(info.accessibility() + 0.5) %
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NHO[0] % ONH[0] % NHO[1] % ONH[1] %
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residue.TCO() % residue.Kappa() % alpha % residue.Phi() % residue.Psi() %
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ca.mLoc.mX % ca.mLoc.mY % ca.mLoc.mZ % long_ChainID).str();
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residue.tco() % residue.kappa() % alpha % residue.phi() % residue.psi() %
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cax % cay % caz).str();
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}
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#endif
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void writeDSSP(const mmcif::Structure& structure, const mmcif::DSSP& dssp, std::ostream& os)
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{
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const std::string kFirstLine("==== Secondary Structure Definition by the program DSSP, NKI version 3.0 ==== ");
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@@ -156,10 +154,7 @@ void writeDSSP(const mmcif::Structure& structure, const mmcif::DSSP& dssp, std::
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using namespace boost::gregorian;
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// uint32_t nrOfResidues, nrOfChains, nrOfSSBridges, nrOfIntraChainSSBridges, nrOfHBonds;
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// uint32_t nrOfHBondsPerDistance[11] = {};
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// dssp.GetStatistics(nrOfResidues, nrOfChains, nrOfSSBridges, nrOfIntraChainSSBridges, nrOfHBonds, nrOfHBondsPerDistance);
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auto stats = dssp.GetStatistics();
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date today = day_clock::local_day();
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@@ -172,69 +167,66 @@ void writeDSSP(const mmcif::Structure& structure, const mmcif::DSSP& dssp, std::
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<< GetPDBSOURCELine(cf, 127) << '.' << std::endl
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<< GetPDBAUTHORLine(cf, 127) << '.' << std::endl;
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// double accessibleSurface = 0; // calculate accessibility as
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// foreach (const MChain* chain, protein.GetChains())
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// {
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// foreach (const MResidue* residue, chain->GetResidues())
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// accessibleSurface += residue->Accessibility();
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// }
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os << boost::format("%5.5d%3.3d%3.3d%3.3d%3.3d TOTAL NUMBER OF RESIDUES, NUMBER OF CHAINS, NUMBER OF SS-BRIDGES(TOTAL,INTRACHAIN,INTERCHAIN) %|127t|%c") %
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stats.nrOfResidues % stats.nrOfChains % stats.nrOfSSBridges % stats.nrOfIntraChainSSBridges % (stats.nrOfSSBridges - stats.nrOfIntraChainSSBridges) % '.' << std::endl;
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os << kHeaderLine % (boost::format("%8.1f ACCESSIBLE SURFACE OF PROTEIN (ANGSTROM**2)") % stats.accessibleSurface) % '.' << std::endl;
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// os << boost::format("%5.5d%3.3d%3.3d%3.3d%3.3d TOTAL NUMBER OF RESIDUES, NUMBER OF CHAINS, NUMBER OF SS-BRIDGES(TOTAL,INTRACHAIN,INTERCHAIN) %|127t|%c") %
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// nrOfResidues % nrOfChains % nrOfSSBridges % nrOfIntraChainSSBridges % (nrOfSSBridges - nrOfIntraChainSSBridges) % '.' << std::endl;
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// os << kHeaderLine % (boost::format("%8.1f ACCESSIBLE SURFACE OF PROTEIN (ANGSTROM**2)") % accessibleSurface) % '.' << std::endl;
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// hydrogenbond summary
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// // hydrogenbond summary
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os << kHeaderLine % (
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boost::format("%5.5d%5.1f TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(J) , SAME NUMBER PER 100 RESIDUES")
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% stats.nrOfHBonds % (stats.nrOfHBonds * 100.0 / stats.nrOfResidues)) % '.' << std::endl;
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// os << kHeaderLine % (
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// boost::format("%5.5d%5.1f TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(J) , SAME NUMBER PER 100 RESIDUES")
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// % nrOfHBonds % (nrOfHBonds * 100.0 / nrOfResidues)) % '.' << std::endl;
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os << kHeaderLine % (
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boost::format("%5.5d%5.1f TOTAL NUMBER OF HYDROGEN BONDS IN PARALLEL BRIDGES, SAME NUMBER PER 100 RESIDUES")
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% stats.nrOfHBondsInParallelBridges % (stats.nrOfHBondsInParallelBridges * 100.0 / stats.nrOfResidues)) % '.' << std::endl;
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// uint32_t nrOfHBondsInParallelBridges = protein.GetNrOfHBondsInParallelBridges();
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// os << kHeaderLine % (
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// boost::format("%5.5d%5.1f TOTAL NUMBER OF HYDROGEN BONDS IN PARALLEL BRIDGES, SAME NUMBER PER 100 RESIDUES")
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// % nrOfHBondsInParallelBridges % (nrOfHBondsInParallelBridges * 100.0 / nrOfResidues)) % '.' << std::endl;
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os << kHeaderLine % (
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boost::format("%5.5d%5.1f TOTAL NUMBER OF HYDROGEN BONDS IN ANTIPARALLEL BRIDGES, SAME NUMBER PER 100 RESIDUES")
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% stats.nrOfHBondsInAntiparallelBridges % (stats.nrOfHBondsInAntiparallelBridges * 100.0 / stats.nrOfResidues)) % '.' << std::endl;
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// uint32_t nrOfHBondsInAntiparallelBridges = protein.GetNrOfHBondsInAntiparallelBridges();
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// os << kHeaderLine % (
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// boost::format("%5.5d%5.1f TOTAL NUMBER OF HYDROGEN BONDS IN ANTIPARALLEL BRIDGES, SAME NUMBER PER 100 RESIDUES")
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// % nrOfHBondsInAntiparallelBridges % (nrOfHBondsInAntiparallelBridges * 100.0 / nrOfResidues)) % '.' << std::endl;
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boost::format kHBondsLine("%5.5d%5.1f TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I%c%1.1d), SAME NUMBER PER 100 RESIDUES");
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for (int k = 0; k < 11; ++k)
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os << kHeaderLine % (kHBondsLine % stats.nrOfHBondsPerDistance[k] % (stats.nrOfHBondsPerDistance[k] * 100.0 / stats.nrOfResidues) % (k - 5 < 0 ? '-' : '+') % abs(k - 5)) % '.' << std::endl;
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// boost::format kHBondsLine("%5.5d%5.1f TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I%c%1.1d), SAME NUMBER PER 100 RESIDUES");
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// for (int32 k = 0; k < 11; ++k)
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// {
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// os << kHeaderLine % (kHBondsLine % nrOfHBondsPerDistance[k] % (nrOfHBondsPerDistance[k] * 100.0 / nrOfResidues) % (k - 5 < 0 ? '-' : '+') % abs(k - 5)) % '.' << std::endl;
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// }
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// histograms...
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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;
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// // histograms...
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for (auto hi: stats.residuesPerAlphaHelixHistogram)
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os << boost::format("%3.3d") % hi;
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os << " RESIDUES PER ALPHA HELIX ." << std::endl;
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// uint32_t histogram[kHistogramSize];
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// 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;
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for (auto hi: stats.parallelBridgesPerLadderHistogram)
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os << boost::format("%3.3d") % hi;
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os << " PARALLEL BRIDGES PER LADDER ." << std::endl;
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// protein.GetResiduesPerAlphaHelixHistogram(histogram);
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// for (uint32_t i = 0; i < kHistogramSize; ++i)
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// os << boost::format("%3.3d") % histogram[i];
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// os << " RESIDUES PER ALPHA HELIX ." << std::endl;
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for (auto hi: stats.antiparallelBridgesPerLadderHistogram)
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os << boost::format("%3.3d") % hi;
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os << " ANTIPARALLEL BRIDGES PER LADDER ." << std::endl;
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// protein.GetParallelBridgesPerLadderHistogram(histogram);
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// for (uint32_t i = 0; i < kHistogramSize; ++i)
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// os << boost::format("%3.3d") % histogram[i];
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// os << " PARALLEL BRIDGES PER LADDER ." << std::endl;
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for (auto hi: stats.laddersPerSheetHistogram)
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os << boost::format("%3.3d") % hi;
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os << " LADDERS PER SHEET ." << std::endl;
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// protein.GetAntiparallelBridgesPerLadderHistogram(histogram);
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// for (uint32_t i = 0; i < kHistogramSize; ++i)
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// os << boost::format("%3.3d") % histogram[i];
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// os << " ANTIPARALLEL BRIDGES PER LADDER ." << std::endl;
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// per residue information
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// protein.GetLaddersPerSheetHistogram(histogram);
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// for (uint32_t i = 0; i < kHistogramSize; ++i)
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// os << boost::format("%3.3d") % histogram[i];
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// os << " LADDERS PER SHEET ." << std::endl;
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os << " # RESIDUE AA STRUCTURE BP1 BP2 ACC N-H-->O O-->H-N N-H-->O O-->H-N TCO KAPPA ALPHA PHI PSI X-CA Y-CA Z-CA CHAIN" << std::endl;
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boost::format kDSSPResidueLine(
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"%5.5d !%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");
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// // per residue information
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int last = 0;
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for (auto ri: dssp)
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{
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// insert a break line whenever we detect missing residues
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// can be the transition to a different chain, or missing residues in the current chain
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// os << " # RESIDUE AA STRUCTURE BP1 BP2 ACC N-H-->O O-->H-N N-H-->O O-->H-N TCO KAPPA ALPHA PHI PSI X-CA Y-CA Z-CA CHAIN" << std::endl;
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// boost::format kDSSPResidueLine(
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// "%5.5d !%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");
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auto b = ri.chainBreak();
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if (b != mmcif::ChainBreak::None)
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os << (kDSSPResidueLine % (last + 1) % (b == mmcif::ChainBreak::Gap ? '*' : ' ')) << std::endl;
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os << ResidueToDSSPLine(ri) << std::endl;
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last = ri.nr();
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}
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// std::vector<const MResidue*> residues;
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