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libcifpp
Commit 545aca88 by Maarten L. Hekkelman
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parent ac272487
Showing with 122 additions and 9 deletions
include/cif++/structure/DSSP.hpp
...@@ -163,6 +163,21 @@ class DSSP ...@@ -163,6 +163,21 @@ class DSSP
std::string asym_id() const; std::string asym_id() const;
int seq_id() const; int seq_id() const;
std::string alt_id() const; std::string alt_id() const;
std::string compound_id() const;
std::string auth_asym_id() const;
int auth_seq_id() const;
std::string pdb_strand_id() const;
int pdb_seq_num() const;
std::string pdb_ins_code() const;
float alpha() const;
float kappa() const;
float phi() const;
float psi() const;
float tco() const;
std::tuple<float,float,float> ca_location() const;
/// \brief return 0 if not a break, ' ' in case of a new chain and '*' in case of a broken chain /// \brief return 0 if not a break, ' ' in case of a new chain and '*' in case of a broken chain
ChainBreak chainBreak() const; ChainBreak chainBreak() const;
......
src/structure/DSSP.cpp
...@@ -167,8 +167,13 @@ const float ...@@ -167,8 +167,13 @@ const float
struct Res struct Res
{ {
Res(int model_nr, const std::vector<cif::row_handle> &atoms) Res(int model_nr,
: mChainBreak(ChainBreak::None) std::string_view pdb_strand_id, int pdb_seq_num, std::string_view pdb_ins_code,
const std::vector<cif::row_handle> &atoms)
: mPDBStrandID(pdb_strand_id)
, mPDBSeqNum(pdb_seq_num)
, mPDBInsCode(pdb_ins_code)
, mChainBreak(ChainBreak::None)
{ {
// update the box containing all atoms // update the box containing all atoms
mBox[0].mX = mBox[0].mY = mBox[0].mZ = std::numeric_limits<float>::max(); mBox[0].mX = mBox[0].mY = mBox[0].mZ = std::numeric_limits<float>::max();
...@@ -180,15 +185,16 @@ struct Res ...@@ -180,15 +185,16 @@ struct Res
for (auto atom : atoms) for (auto atom : atoms)
{ {
std::string asymID, compID, atomID, type; std::string asymID, compID, atomID, type, authAsymID;
std::optional<std::string> altID; std::optional<std::string> altID;
int seqID; int seqID, authSeqID;
std::optional<int> model; std::optional<int> model;
float x, y, z; float x, y, z;
cif::tie(asymID, compID, atomID, altID, type, seqID, model, x, y, z) = cif::tie(asymID, compID, atomID, altID, type, seqID, model, x, y, z, authAsymID, authSeqID) =
atom.get("label_asym_id", "label_comp_id", "label_atom_id", "label_alt_id", "type_symbol", "label_seq_id", atom.get("label_asym_id", "label_comp_id", "label_atom_id", "label_alt_id", "type_symbol", "label_seq_id",
"pdbx_PDB_model_num", "Cartn_x", "Cartn_y", "Cartn_z"); "pdbx_PDB_model_num", "Cartn_x", "Cartn_y", "Cartn_z",
"auth_asym_id", "auth_seq_id");
if (model and model != model_nr) if (model and model != model_nr)
continue; continue;
...@@ -198,6 +204,10 @@ struct Res ...@@ -198,6 +204,10 @@ struct Res
mAsymID = asymID; mAsymID = asymID;
mCompoundID = compID; mCompoundID = compID;
mSeqID = seqID; mSeqID = seqID;
mAuthSeqID = authSeqID;
mAuthAsymID = authAsymID;
if (altID) if (altID)
mAltID = *altID; mAltID = *altID;
} }
...@@ -217,7 +227,7 @@ struct Res ...@@ -217,7 +227,7 @@ struct Res
else if (atomID == "N") else if (atomID == "N")
{ {
seen |= 4; seen |= 4;
mN = {x, y, z}; mH = mN = {x, y, z};
ExtendBox(mN, kRadiusN + 2 * kRadiusWater); ExtendBox(mN, kRadiusN + 2 * kRadiusWater);
} }
else if (atomID == "O") else if (atomID == "O")
...@@ -364,6 +374,13 @@ struct Res ...@@ -364,6 +374,13 @@ struct Res
int mNumber; int mNumber;
bool mComplete = false; bool mComplete = false;
std::string mAuthAsymID;
int mAuthSeqID;
std::string mPDBStrandID;
int mPDBSeqNum;
std::string mPDBInsCode;
Point mCAlpha, mC, mN, mO, mH; Point mCAlpha, mC, mN, mO, mH;
Point mBox[2] = {}; Point mBox[2] = {};
float mRadius; float mRadius;
...@@ -371,7 +388,7 @@ struct Res ...@@ -371,7 +388,7 @@ struct Res
std::vector<Point> mSideChain; std::vector<Point> mSideChain;
double mAccessibility = 0; double mAccessibility = 0;
double mKappa = 360, mPhi = 360, mPsi = 360; double mAlpha = 360, mKappa = 360, mPhi = 360, mPsi = 360, mTCO = 0;
ResidueType mType; ResidueType mType;
uint8_t mSSBridgeNr = 0; uint8_t mSSBridgeNr = 0;
...@@ -1211,9 +1228,14 @@ DSSPImpl::DSSPImpl(const cif::datablock &db, int model_nr, int min_poly_proline_ ...@@ -1211,9 +1228,14 @@ DSSPImpl::DSSPImpl(const cif::datablock &db, int model_nr, int min_poly_proline_
for (auto r : pdbx_poly_seq_scheme) for (auto r : pdbx_poly_seq_scheme)
{ {
std::string pdb_strand_id, pdb_ins_code;
int pdb_seq_num;
cif::tie(pdb_strand_id, pdb_seq_num, pdb_ins_code) = r.get("pdb_strand_id", "pdb_seq_num", "pdb_ins_code");
ChainBreak brk = ChainBreak::NewChain; ChainBreak brk = ChainBreak::NewChain;
Res residue(model_nr, pdbx_poly_seq_scheme.get_children(r, atom_site)); Res residue(model_nr, pdb_strand_id, pdb_seq_num, pdb_ins_code, pdbx_poly_seq_scheme.get_children(r, atom_site));
if (not residue.mComplete) if (not residue.mComplete)
continue; continue;
...@@ -1284,6 +1306,22 @@ DSSPImpl::DSSPImpl(const cif::datablock &db, int model_nr, int min_poly_proline_ ...@@ -1284,6 +1306,22 @@ DSSPImpl::DSSPImpl(const cif::datablock &db, int model_nr, int min_poly_proline_
if (cur.mSeqID + 1 == next.mSeqID) if (cur.mSeqID + 1 == next.mSeqID)
cur.mPsi = DihedralAngle(cur.mN, cur.mCAlpha, cur.mC, next.mN); cur.mPsi = DihedralAngle(cur.mN, cur.mCAlpha, cur.mC, next.mN);
} }
if (i >= 1 and i + 2 < mResidues.size())
{
auto &prev = mResidues[i - 1];
auto &next = mResidues[i + 1];
auto &nextNext = mResidues[i + 2];
cur.mAlpha = DihedralAngle(prev.mCAlpha, cur.mCAlpha, next.mCAlpha, nextNext.mCAlpha);
}
if (i > 0)
{
auto &prev = mResidues[i - 1];
if (prev.mSeqID + 1 == cur.mSeqID)
cur.mTCO = CosinusAngle(cur.mC, cur.mO, prev.mC, prev.mO);
}
} }
} }
...@@ -1396,6 +1434,11 @@ std::string DSSP::ResidueInfo::asym_id() const ...@@ -1396,6 +1434,11 @@ std::string DSSP::ResidueInfo::asym_id() const
return mImpl->mAsymID; return mImpl->mAsymID;
} }
std::string DSSP::ResidueInfo::compound_id() const
{
return mImpl->mCompoundID;
}
int DSSP::ResidueInfo::seq_id() const int DSSP::ResidueInfo::seq_id() const
{ {
return mImpl->mSeqID; return mImpl->mSeqID;
...@@ -1406,6 +1449,61 @@ std::string DSSP::ResidueInfo::alt_id() const ...@@ -1406,6 +1449,61 @@ std::string DSSP::ResidueInfo::alt_id() const
return mImpl->mAltID; return mImpl->mAltID;
} }
std::string DSSP::ResidueInfo::auth_asym_id() const
{
return mImpl->mAuthAsymID;
}
int DSSP::ResidueInfo::auth_seq_id() const
{
return mImpl->mAuthSeqID;
}
std::string DSSP::ResidueInfo::pdb_strand_id() const
{
return mImpl->mPDBStrandID;
}
int DSSP::ResidueInfo::pdb_seq_num() const
{
return mImpl->mPDBSeqNum;
}
std::string DSSP::ResidueInfo::pdb_ins_code() const
{
return mImpl->mPDBInsCode;
}
float DSSP::ResidueInfo::alpha() const
{
return mImpl->mAlpha;
}
float DSSP::ResidueInfo::kappa() const
{
return mImpl->mKappa;
}
float DSSP::ResidueInfo::phi() const
{
return mImpl->mPhi;
}
float DSSP::ResidueInfo::psi() const
{
return mImpl->mPsi;
}
float DSSP::ResidueInfo::tco() const
{
return mImpl->mTCO;
}
std::tuple<float,float,float> DSSP::ResidueInfo::ca_location() const
{
return { mImpl->mCAlpha.mX, mImpl->mCAlpha.mY, mImpl->mCAlpha.mZ };
}
ChainBreak DSSP::ResidueInfo::chainBreak() const ChainBreak DSSP::ResidueInfo::chainBreak() const
{ {
return mImpl->mChainBreak; return mImpl->mChainBreak;
......
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