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libcifpp
Commit 78dd9a3c by Maarten L. Hekkelman
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for PPII helices

parent 52d6b2ea
Showing with 171 additions and 32 deletions
include/cif++/Secondary.hpp
...@@ -26,7 +26,7 @@ enum SecondaryStructureType : char ...@@ -26,7 +26,7 @@ enum SecondaryStructureType : char
ssStrand = 'E', ssStrand = 'E',
ssHelix_3 = 'G', ssHelix_3 = 'G',
ssHelix_5 = 'I', ssHelix_5 = 'I',
ssHelix_PP = 'P', ssHelix_PPII = 'P',
ssTurn = 'T', ssTurn = 'T',
ssBend = 'S' ssBend = 'S'
}; };
......
src/Secondary.cpp
...@@ -332,7 +332,7 @@ struct Res ...@@ -332,7 +332,7 @@ struct Res
HBond mHBondDonor[2] = {}, mHBondAcceptor[2] = {}; HBond mHBondDonor[2] = {}, mHBondAcceptor[2] = {};
BridgeParner mBetaPartner[2] = {}; BridgeParner mBetaPartner[2] = {};
uint32_t mSheet = 0; uint32_t mSheet = 0;
Helix mHelixFlags[3] = { Helix::None, Helix::None, Helix::None }; // Helix mHelixFlags[4] = { Helix::None, Helix::None, Helix::None, Helix::None }; //
bool mBend = false; bool mBend = false;
ChainBreak mChainBreak = ChainBreak::None; ChainBreak mChainBreak = ChainBreak::None;
}; };
...@@ -1002,49 +1002,45 @@ void CalculateAlphaHelices(std::vector<Res>& inResidues, DSSP_Statistics& stats, ...@@ -1002,49 +1002,45 @@ void CalculateAlphaHelices(std::vector<Res>& inResidues, DSSP_Statistics& stats,
void CalculatePPHelices(std::vector<Res>& inResidues, DSSP_Statistics& stats) void CalculatePPHelices(std::vector<Res>& inResidues, DSSP_Statistics& stats)
{ {
// less strict variant: three residues instead of four
size_t N = inResidues.size(); size_t N = inResidues.size();
const float epsilon = 29;
const float phi_min = -75 - epsilon;
const float phi_max = -75 + epsilon;
const float psi_min = 145 - epsilon;
const float psi_max = 145 + epsilon;
std::vector<float> phi(N), psi(N); std::vector<float> phi(N), psi(N);
for (uint32_t i = 1; i + 1 < inResidues.size(); ++i) for (uint32_t i = 1; i + 1 < inResidues.size(); ++i)
{ {
// if (not NoChainBreak(inResidues[i], inResidues[i]))
// continue;
phi[i] = inResidues[i].mM.phi(); phi[i] = inResidues[i].mM.phi();
psi[i] = inResidues[i].mM.psi(); psi[i] = inResidues[i].mM.psi();
} }
for (uint32_t i = 1; i + 3 < inResidues.size(); ++i) for (uint32_t i = 1; i + 3 < inResidues.size(); ++i)
{ {
if (-95 > phi[i - 1] or phi[i - 1] > -55 or if (phi_min > phi[i - 1] or phi[i - 1] > phi_max or
-95 > phi[i + 0] or phi[i + 0] > -55 or phi_min > phi[i + 0] or phi[i + 0] > phi_max)
-95 > phi[i + 1] or phi[i + 1] > -55 or
-95 > phi[i + 2] or phi[i + 2] > -55)
continue; continue;
if (125 > psi[i - 1] or psi[i - 1] > 165 or if (psi_min > psi[i - 1] or psi[i - 1] > psi_max or
125 > psi[i + 0] or psi[i + 0] > 165 or psi_min > psi[i + 0] or psi[i + 0] > psi_max)
125 > psi[i + 1] or psi[i + 1] > 165 or
125 > psi[i + 2] or psi[i + 2] > 165)
continue; continue;
auto phi_avg = (phi[i - 1] + phi[i] + phi[i + 1] + phi[i + 2]) / 4; auto phi_avg = (phi[i - 1] + phi[i]) / 2;
auto phi_sq = (phi[i - 1] - phi_avg) * (phi[i - 1] - phi_avg) + auto phi_sq = (phi[i - 1] - phi_avg) * (phi[i - 1] - phi_avg) +
(phi[i + 0] - phi_avg) * (phi[i + 0] - phi_avg) + (phi[i + 0] - phi_avg) * (phi[i + 0] - phi_avg);
(phi[i + 1] - phi_avg) * (phi[i + 1] - phi_avg) +
(phi[i + 2] - phi_avg) * (phi[i + 2] - phi_avg);
if (phi_sq >= 400) if (phi_sq >= 200)
continue; continue;
auto psi_avg = (psi[i - 1] + psi[i] + psi[i + 1] + psi[i + 2]) / 4; auto psi_avg = (psi[i - 1] + psi[i]) / 2;
auto psi_sq = (psi[i - 1] - psi_avg) * (psi[i - 1] - psi_avg) + auto psi_sq = (psi[i - 1] - psi_avg) * (psi[i - 1] - psi_avg) +
(psi[i + 0] - psi_avg) * (psi[i + 0] - psi_avg) + (psi[i + 0] - psi_avg) * (psi[i + 0] - psi_avg);
(psi[i + 1] - psi_avg) * (psi[i + 1] - psi_avg) +
(psi[i + 2] - psi_avg) * (psi[i + 2] - psi_avg);
if (psi_sq >= 400) if (psi_sq >= 200)
continue; continue;
switch (inResidues[i - 1].GetHelixFlag(HelixType::rh_pp)) switch (inResidues[i - 1].GetHelixFlag(HelixType::rh_pp))
...@@ -1062,20 +1058,163 @@ void CalculatePPHelices(std::vector<Res>& inResidues, DSSP_Statistics& stats) ...@@ -1062,20 +1058,163 @@ void CalculatePPHelices(std::vector<Res>& inResidues, DSSP_Statistics& stats)
} }
inResidues[i].SetHelixFlag(HelixType::rh_pp, Helix::Middle); inResidues[i].SetHelixFlag(HelixType::rh_pp, Helix::Middle);
inResidues[i + 1].SetHelixFlag(HelixType::rh_pp, Helix::Middle); inResidues[i + 1].SetHelixFlag(HelixType::rh_pp, Helix::End);
inResidues[i + 2].SetHelixFlag(HelixType::rh_pp, Helix::End);
if (inResidues[i - 1].GetSecondaryStructure() == SecondaryStructureType::ssLoop and if (inResidues[i - 1].GetSecondaryStructure() == SecondaryStructureType::ssLoop and
inResidues[i + 0].GetSecondaryStructure() == SecondaryStructureType::ssLoop and inResidues[i + 0].GetSecondaryStructure() == SecondaryStructureType::ssLoop and
inResidues[i + 1].GetSecondaryStructure() == SecondaryStructureType::ssLoop and inResidues[i + 1].GetSecondaryStructure() == SecondaryStructureType::ssLoop)
inResidues[i + 2].GetSecondaryStructure() == SecondaryStructureType::ssLoop)
{ {
inResidues[i - 1].SetSecondaryStructure(SecondaryStructureType::ssHelix_PP); inResidues[i - 1].SetSecondaryStructure(SecondaryStructureType::ssHelix_PPII);
inResidues[i + 0].SetSecondaryStructure(SecondaryStructureType::ssHelix_PP); inResidues[i + 0].SetSecondaryStructure(SecondaryStructureType::ssHelix_PPII);
inResidues[i + 1].SetSecondaryStructure(SecondaryStructureType::ssHelix_PP); inResidues[i + 1].SetSecondaryStructure(SecondaryStructureType::ssHelix_PPII);
inResidues[i + 2].SetSecondaryStructure(SecondaryStructureType::ssHelix_PP);
} }
} }
// // less strict variant: three residues instead of four
// size_t N = inResidues.size();
// std::vector<float> phi(N), psi(N);
// for (uint32_t i = 1; i + 1 < inResidues.size(); ++i)
// {
// // if (not NoChainBreak(inResidues[i], inResidues[i]))
// // continue;
// phi[i] = inResidues[i].mM.phi();
// psi[i] = inResidues[i].mM.psi();
// }
// for (uint32_t i = 1; i + 3 < inResidues.size(); ++i)
// {
// if (phi_min > phi[i - 1] or phi[i - 1] > phi_max or
// phi_min > phi[i + 0] or phi[i + 0] > phi_max or
// phi_min > phi[i + 1] or phi[i + 1] > phi_max)
// continue;
// if (psi_min > psi[i - 1] or psi[i - 1] > psi_max or
// psi_min > psi[i + 0] or psi[i + 0] > psi_max or
// psi_min > psi[i + 1] or psi[i + 1] > psi_max)
// continue;
// // auto phi_avg = (phi[i - 1] + phi[i] + phi[i + 1]) / 3;
// // auto phi_sq = (phi[i - 1] - phi_avg) * (phi[i - 1] - phi_avg) +
// // (phi[i + 0] - phi_avg) * (phi[i + 0] - phi_avg) +
// // (phi[i + 1] - phi_avg) * (phi[i + 1] - phi_avg);
// // if (phi_sq >= 300)
// // continue;
// // auto psi_avg = (psi[i - 1] + psi[i] + psi[i + 1]) / 3;
// // auto psi_sq = (psi[i - 1] - psi_avg) * (psi[i - 1] - psi_avg) +
// // (psi[i + 0] - psi_avg) * (psi[i + 0] - psi_avg) +
// // (psi[i + 1] - psi_avg) * (psi[i + 1] - psi_avg);
// // if (psi_sq >= 300)
// // continue;
// switch (inResidues[i - 1].GetHelixFlag(HelixType::rh_pp))
// {
// case Helix::None:
// inResidues[i - 1].SetHelixFlag(HelixType::rh_pp, Helix::Start);
// break;
// case Helix::End:
// inResidues[i - 1].SetHelixFlag(HelixType::rh_pp, Helix::StartAndEnd);
// break;
// default:
// break;
// }
// inResidues[i].SetHelixFlag(HelixType::rh_pp, Helix::Middle);
// inResidues[i + 1].SetHelixFlag(HelixType::rh_pp, Helix::End);
// if (inResidues[i - 1].GetSecondaryStructure() == SecondaryStructureType::ssLoop and
// inResidues[i + 0].GetSecondaryStructure() == SecondaryStructureType::ssLoop and
// inResidues[i + 1].GetSecondaryStructure() == SecondaryStructureType::ssLoop)
// {
// inResidues[i - 1].SetSecondaryStructure(SecondaryStructureType::ssHelix_PPII);
// inResidues[i + 0].SetSecondaryStructure(SecondaryStructureType::ssHelix_PPII);
// inResidues[i + 1].SetSecondaryStructure(SecondaryStructureType::ssHelix_PPII);
// }
// }
// size_t N = inResidues.size();
// std::vector<float> phi(N), psi(N);
// for (uint32_t i = 1; i + 1 < inResidues.size(); ++i)
// {
// // if (not NoChainBreak(inResidues[i], inResidues[i]))
// // continue;
// phi[i] = inResidues[i].mM.phi();
// psi[i] = inResidues[i].mM.psi();
// }
// for (uint32_t i = 1; i + 3 < inResidues.size(); ++i)
// {
// if (phi_min > phi[i - 1] or phi[i - 1] > phi_max or
// phi_min > phi[i + 0] or phi[i + 0] > phi_max or
// phi_min > phi[i + 1] or phi[i + 1] > phi_max or
// phi_min > phi[i + 2] or phi[i + 2] > phi_max)
// continue;
// if (psi_min > psi[i - 1] or psi[i - 1] > psi_max or
// psi_min > psi[i + 0] or psi[i + 0] > psi_max or
// psi_min > psi[i + 1] or psi[i + 1] > psi_max or
// psi_min > psi[i + 2] or psi[i + 2] > psi_max)
// continue;
// auto phi_avg = (phi[i - 1] + phi[i] + phi[i + 1] + phi[i + 2]) / 4;
// auto phi_sq = (phi[i - 1] - phi_avg) * (phi[i - 1] - phi_avg) +
// (phi[i + 0] - phi_avg) * (phi[i + 0] - phi_avg) +
// (phi[i + 1] - phi_avg) * (phi[i + 1] - phi_avg) +
// (phi[i + 2] - phi_avg) * (phi[i + 2] - phi_avg);
// if (phi_sq >= 400)
// continue;
// auto psi_avg = (psi[i - 1] + psi[i] + psi[i + 1] + psi[i + 2]) / 4;
// auto psi_sq = (psi[i - 1] - psi_avg) * (psi[i - 1] - psi_avg) +
// (psi[i + 0] - psi_avg) * (psi[i + 0] - psi_avg) +
// (psi[i + 1] - psi_avg) * (psi[i + 1] - psi_avg) +
// (psi[i + 2] - psi_avg) * (psi[i + 2] - psi_avg);
// if (psi_sq >= 400)
// continue;
// switch (inResidues[i - 1].GetHelixFlag(HelixType::rh_pp))
// {
// case Helix::None:
// inResidues[i - 1].SetHelixFlag(HelixType::rh_pp, Helix::Start);
// break;
// case Helix::End:
// inResidues[i - 1].SetHelixFlag(HelixType::rh_pp, Helix::StartAndEnd);
// break;
// default:
// break;
// }
// inResidues[i].SetHelixFlag(HelixType::rh_pp, Helix::Middle);
// inResidues[i + 1].SetHelixFlag(HelixType::rh_pp, Helix::Middle);
// inResidues[i + 2].SetHelixFlag(HelixType::rh_pp, Helix::End);
// if (inResidues[i - 1].GetSecondaryStructure() == SecondaryStructureType::ssLoop and
// inResidues[i + 0].GetSecondaryStructure() == SecondaryStructureType::ssLoop and
// inResidues[i + 1].GetSecondaryStructure() == SecondaryStructureType::ssLoop and
// inResidues[i + 2].GetSecondaryStructure() == SecondaryStructureType::ssLoop)
// {
// inResidues[i - 1].SetSecondaryStructure(SecondaryStructureType::ssHelix_PPII);
// inResidues[i + 0].SetSecondaryStructure(SecondaryStructureType::ssHelix_PPII);
// inResidues[i + 1].SetSecondaryStructure(SecondaryStructureType::ssHelix_PPII);
// inResidues[i + 2].SetSecondaryStructure(SecondaryStructureType::ssHelix_PPII);
// }
// }
} }
// -------------------------------------------------------------------- // --------------------------------------------------------------------
...@@ -1198,7 +1337,7 @@ DSSPImpl::DSSPImpl(const Structure& s) ...@@ -1198,7 +1337,7 @@ DSSPImpl::DSSPImpl(const Structure& s)
switch (r.GetHelixFlag(helixType)) switch (r.GetHelixFlag(helixType))
{ {
case Helix::Start: helix[static_cast<int>(helixType)] = '>'; break; case Helix::Start: helix[static_cast<int>(helixType)] = '>'; break;
case Helix::Middle: helix[static_cast<int>(helixType)] = helixType == HelixType::rh_pp ? 'P' : '0' + static_cast<int>(helixType); break; case Helix::Middle: helix[static_cast<int>(helixType)] = helixType == HelixType::rh_pp ? 'P' : '3' + static_cast<int>(helixType); break;
case Helix::StartAndEnd: helix[static_cast<int>(helixType)] = 'X'; break; case Helix::StartAndEnd: helix[static_cast<int>(helixType)] = 'X'; break;
case Helix::End: helix[static_cast<int>(helixType)] = '<'; break; case Helix::End: helix[static_cast<int>(helixType)] = '<'; break;
case Helix::None: helix[static_cast<int>(helixType)] = ' '; break; case Helix::None: helix[static_cast<int>(helixType)] = ' '; break;
......
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