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libcifpp
Commit 557a1c2d by Maarten L. Hekkelman
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Reactivated several structure methods

parent f77bbfed
Showing with 698 additions and 498 deletions
.gitignore
......@@ -12,5 +12,3 @@ CMakeSettings.json
msvc/
Testing/
rsrc/feature-request.txt
test/*.cif*
test/*.ent*
include/cif++/compound.hpp
......@@ -114,9 +114,6 @@ class compound
compound_atom get_atom_by_atom_id(const std::string &atom_id) const;
bool atoms_bonded(const std::string &atomId_1, const std::string &atomId_2) const;
// float atomBondValue(const std::string &atomId_1, const std::string &atomId_2) const;
// float bondAngle(const std::string &atomId_1, const std::string &atomId_2, const std::string &atomId_3) const;
// float chiralVolume(const std::string &centreID) const;
bool is_water() const
{
......
include/cif++/model.hpp
......@@ -303,7 +303,7 @@ class atom
// std::string symmetry() const { return impl().mSymmetryOperator; }
// const compound &compound() const;
// bool isWater() const { return impl().mCompID == "HOH" or impl().mCompID == "H2O" or impl().mCompID == "WAT"; }
// bool is_water() const { return impl().mCompID == "HOH" or impl().mCompID == "H2O" or impl().mCompID == "WAT"; }
int get_charge() const;
// float uIso() const;
......@@ -473,6 +473,10 @@ class residue
virtual ~residue() = default;
std::string get_entity_id() const;
EntityType entity_type() const;
const std::string &get_asym_id() const { return m_asym_id; }
int get_seq_id() const { return m_seq_id; }
......@@ -509,47 +513,29 @@ class residue
/// \brief Unique atoms returns only the atoms without alternates and the first of each alternate atom id.
std::vector<atom> unique_atoms() const;
// /// \brief The alt ID used for the unique atoms
// std::string unique_alt_id() const;
/// \brief The alt ID used for the unique atoms
std::string unique_alt_id() const;
atom get_atom_by_atom_id(const std::string &atomID) const;
// const std::string &asymID() const { return m_asym_id; }
// int seqID() const { return m_seq_id; }
std::string get_entity_id() const;
EntityType entity_type() const;
// std::string authAsymID() const;
// std::string authSeqID() const;
// std::string authInsCode() const;
// // return a human readable PDB-like auth id (chain+seqnr+iCode)
// std::string authID() const;
// // similar for mmCIF space
// std::string labelID() const;
// Is this residue a single entity?
bool is_entity() const;
// bool isWater() const { return m_compound_id == "HOH"; }
bool is_water() const { return m_compound_id == "HOH"; }
// bool empty() const { return m_structure == nullptr; }
// bool hasAlternateAtoms() const;
bool has_alternate_atoms() const;
// /// \brief Return the list of unique alt ID's present in this residue
// std::set<std::string> getAlternateIDs() const;
/// \brief Return the list of unique alt ID's present in this residue
std::set<std::string> get_alternate_ids() const;
// /// \brief Return the list of unique atom ID's
// std::set<std::string> getAtomIDs() const;
/// \brief Return the list of unique atom ID's
std::set<std::string> get_atom_ids() const;
// /// \brief Return the list of atoms having ID \a atomID
// std::vector<atom> getAtomsByID(const std::string &atomID) const;
/// \brief Return the list of atoms having ID \a atomID
std::vector<atom> get_atoms_by_id(const std::string &atomID) const;
// // some routines for 3d work
// std::tuple<point, float> centerAndRadius() const;
// some routines for 3d work
std::tuple<point, float> center_and_radius() const;
friend std::ostream &operator<<(std::ostream &os, const residue &res);
......@@ -588,51 +574,51 @@ class monomer : public residue
monomer(const polymer &polymer, size_t index, int seqID, const std::string &authSeqID,
const std::string &compoundID);
// bool is_first_in_chain() const;
// bool is_last_in_chain() const;
bool is_first_in_chain() const;
bool is_last_in_chain() const;
// // convenience
// bool has_alpha() const;
// bool has_kappa() const;
// convenience
bool has_alpha() const;
bool has_kappa() const;
// // Assuming this is really an amino acid...
// Assuming this is really an amino acid...
// float phi() const;
// float psi() const;
// float alpha() const;
// float kappa() const;
// float tco() const;
// float omega() const;
float phi() const;
float psi() const;
float alpha() const;
float kappa() const;
float tco() const;
float omega() const;
// // torsion angles
// size_t nrOfChis() const;
// float chi(size_t i) const;
// torsion angles
size_t nr_of_chis() const;
float chi(size_t i) const;
// bool isCis() const;
bool is_cis() const;
// /// \brief Returns true if the four atoms C, CA, N and O are present
// bool isComplete() const;
/// \brief Returns true if the four atoms C, CA, N and O are present
bool is_complete() const;
// /// \brief Returns true if any of the backbone atoms has an alternate
// bool hasAlternateBackboneAtoms() const;
/// \brief Returns true if any of the backbone atoms has an alternate
bool has_alternate_backbone_atoms() const;
// atom CAlpha() const { return get_atom_by_atom_id("CA"); }
// atom C() const { return get_atom_by_atom_id("C"); }
// atom N() const { return get_atom_by_atom_id("N"); }
// atom O() const { return get_atom_by_atom_id("O"); }
// atom H() const { return get_atom_by_atom_id("H"); }
atom CAlpha() const { return get_atom_by_atom_id("CA"); }
atom C() const { return get_atom_by_atom_id("C"); }
atom N() const { return get_atom_by_atom_id("N"); }
atom O() const { return get_atom_by_atom_id("O"); }
atom H() const { return get_atom_by_atom_id("H"); }
// bool isBondedTo(const monomer &rhs) const
// {
// return this != &rhs and areBonded(*this, rhs);
// }
bool is_bonded_to(const monomer &rhs) const
{
return this != &rhs and are_bonded(*this, rhs);
}
// static bool areBonded(const monomer &a, const monomer &b, float errorMargin = 0.5f);
// static bool isCis(const monomer &a, const monomer &b);
// static float omega(const monomer &a, const monomer &b);
static bool are_bonded(const monomer &a, const monomer &b, float errorMargin = 0.5f);
static bool is_cis(const monomer &a, const monomer &b);
static float omega(const monomer &a, const monomer &b);
// // for LEU and VAL
// float chiralVolume() const;
// for LEU and VAL
float chiral_volume() const;
bool operator==(const monomer &rhs) const
{
......@@ -821,11 +807,11 @@ class structure
atom get_atom_by_id(const std::string &id) const;
// atom getAtomByLocation(point pt, float maxDistance) const;
// atom getAtomByLabel(const std::string &atomID, const std::string &asymID,
// const std::string &compID, int seqID, const std::string &altID = "");
atom get_atom_by_label(const std::string &atomID, const std::string &asymID,
const std::string &compID, int seqID, const std::string &altID = "");
// /// \brief Return the atom closest to point \a p
// atom getAtomByPosition(point p) const;
atom get_atom_by_position(point p) const;
/// \brief Return the atom closest to point \a p with atom type \a type in a residue of type \a res_type
atom get_atom_by_position_and_type(point p, std::string_view type, std::string_view res_type) const;
......@@ -968,7 +954,7 @@ class structure
std::string create_entity_for_branch(branch &branch);
void loadData();
void load_data();
void load_atoms_for_model(StructureOpenOptions options);
......
src/model.cpp
......@@ -425,19 +425,19 @@ std::vector<atom> residue::unique_atoms() const
return result;
}
// std::set<std::string> residue::getAlternateIDs() const
// {
// std::set<std::string> result;
std::set<std::string> residue::get_alternate_ids() const
{
std::set<std::string> result;
// for (auto a : m_atoms)
// {
// auto alt = a.get_label_alt_id();
// if (not alt.empty())
// result.insert(alt);
// }
for (auto a : m_atoms)
{
auto alt = a.get_label_alt_id();
if (not alt.empty())
result.insert(alt);
}
// return result;
// }
return result;
}
atom residue::get_atom_by_atom_id(const std::string &atom_id) const
{
......@@ -471,63 +471,50 @@ bool residue::is_entity() const
return a1.size() == a2.size();
}
// std::string residue::authID() const
// {
// return get_auth_asym_id() + authSeqID() + authInsCode();
// }
// std::string residue::labelID() const
// {
// if (m_compound_id == "HOH")
// return m_asym_id + m_auth_seq_id;
// else
// return m_asym_id + std::to_string(m_seq_id);
// }
// std::tuple<point, float> residue::centerAndRadius() const
// {
// std::vector<point> pts;
// for (auto &a : m_atoms)
// pts.push_back(a.location());
std::tuple<point, float> residue::center_and_radius() const
{
std::vector<point> pts;
for (auto &a : m_atoms)
pts.push_back(a.get_location());
// auto center = Centroid(pts);
// float radius = 0;
auto center = centroid(pts);
float radius = 0;
// for (auto &pt : pts)
// {
// float d = static_cast<float>(Distance(pt, center));
// if (radius < d)
// radius = d;
// }
for (auto &pt : pts)
{
float d = static_cast<float>(distance(pt, center));
if (radius < d)
radius = d;
}
// return std::make_tuple(center, radius);
// }
return std::make_tuple(center, radius);
}
// bool residue::hasAlternateAtoms() const
// {
// return std::find_if(m_atoms.begin(), m_atoms.end(), [](const atom &atom)
// { return atom.is_alternate(); }) != m_atoms.end();
// }
bool residue::has_alternate_atoms() const
{
return std::find_if(m_atoms.begin(), m_atoms.end(), [](const atom &atom)
{ return atom.is_alternate(); }) != m_atoms.end();
}
// std::set<std::string> residue::getAtom_ids() const
// {
// std::set<std::string> ids;
// for (auto a : m_atoms)
// ids.insert(a.get_label_atom_id());
std::set<std::string> residue::get_atom_ids() const
{
std::set<std::string> ids;
for (auto a : m_atoms)
ids.insert(a.get_label_atom_id());
// return ids;
// }
return ids;
}
// std::vector<atom> residue::getAtomsByID(const std::string &atom_id) const
// {
// std::vector<atom> atoms;
// for (auto a : m_atoms)
// {
// if (a.get_label_atom_id() == atom_id)
// atoms.push_back(a);
// }
// return atoms;
// }
std::vector<atom> residue::get_atoms_by_id(const std::string &atom_id) const
{
std::vector<atom> atoms;
for (auto a : m_atoms)
{
if (a.get_label_atom_id() == atom_id)
atoms.push_back(a);
}
return atoms;
}
std::ostream &operator<<(std::ostream &os, const residue &res)
{
......@@ -567,366 +554,366 @@ monomer &monomer::operator=(monomer &&rhs)
return *this;
}
// bool monomer::is_first_in_chain() const
// {
// return m_index == 0;
// }
bool monomer::is_first_in_chain() const
{
return m_index == 0;
}
// bool monomer::is_last_in_chain() const
// {
// return m_index + 1 == m_polymer->size();
// }
bool monomer::is_last_in_chain() const
{
return m_index + 1 == m_polymer->size();
}
// bool monomer::has_alpha() const
// {
// return m_index >= 1 and m_index + 2 < m_polymer->size();
// }
bool monomer::has_alpha() const
{
return m_index >= 1 and m_index + 2 < m_polymer->size();
}
// bool monomer::has_kappa() const
// {
// return m_index >= 2 and m_index + 2 < m_polymer->size();
// }
bool monomer::has_kappa() const
{
return m_index >= 2 and m_index + 2 < m_polymer->size();
}
// float monomer::phi() const
// {
// float result = 360;
float monomer::phi() const
{
float result = 360;
// try
// {
// if (m_index > 0)
// {
// auto &prev = m_polymer->operator[](m_index - 1);
// if (prev.m_seq_id + 1 == m_seq_id)
// result = static_cast<float>(DihedralAngle(prev.C().location(), N().location(), CAlpha().location(), C().location()));
// }
// }
// catch (const std::exception &ex)
// {
// if (VERBOSE > 0)
// std::cerr << ex.what() << std::endl;
// }
try
{
if (m_index > 0)
{
auto &prev = m_polymer->operator[](m_index - 1);
if (prev.m_seq_id + 1 == m_seq_id)
result = static_cast<float>(dihedral_angle(prev.C().get_location(), N().get_location(), CAlpha().get_location(), C().get_location()));
}
}
catch (const std::exception &ex)
{
if (VERBOSE > 0)
std::cerr << ex.what() << std::endl;
}
// return result;
// }
return result;
}
// float monomer::psi() const
// {
// float result = 360;
float monomer::psi() const
{
float result = 360;
// try
// {
// if (m_index + 1 < m_polymer->size())
// {
// auto &next = m_polymer->operator[](m_index + 1);
// if (m_seq_id + 1 == next.m_seq_id)
// result = static_cast<float>(DihedralAngle(N().location(), CAlpha().location(), C().location(), next.N().location()));
// }
// }
// catch (const std::exception &ex)
// {
// if (VERBOSE > 0)
// std::cerr << ex.what() << std::endl;
// }
try
{
if (m_index + 1 < m_polymer->size())
{
auto &next = m_polymer->operator[](m_index + 1);
if (m_seq_id + 1 == next.m_seq_id)
result = static_cast<float>(dihedral_angle(N().get_location(), CAlpha().get_location(), C().get_location(), next.N().get_location()));
}
}
catch (const std::exception &ex)
{
if (VERBOSE > 0)
std::cerr << ex.what() << std::endl;
}
// return result;
// }
return result;
}
// float monomer::alpha() const
// {
// float result = 360;
float monomer::alpha() const
{
float result = 360;
// try
// {
// if (m_index >= 1 and m_index + 2 < m_polymer->size())
// {
// auto &prev = m_polymer->operator[](m_index - 1);
// auto &next = m_polymer->operator[](m_index + 1);
// auto &nextNext = m_polymer->operator[](m_index + 2);
try
{
if (m_index >= 1 and m_index + 2 < m_polymer->size())
{
auto &prev = m_polymer->operator[](m_index - 1);
auto &next = m_polymer->operator[](m_index + 1);
auto &nextNext = m_polymer->operator[](m_index + 2);
// result = static_cast<float>(DihedralAngle(prev.CAlpha().location(), CAlpha().location(), next.CAlpha().location(), nextNext.CAlpha().location()));
// }
// }
// catch (const std::exception &ex)
// {
// if (VERBOSE > 0)
// std::cerr << ex.what() << std::endl;
// }
result = static_cast<float>(dihedral_angle(prev.CAlpha().get_location(), CAlpha().get_location(), next.CAlpha().get_location(), nextNext.CAlpha().get_location()));
}
}
catch (const std::exception &ex)
{
if (VERBOSE > 0)
std::cerr << ex.what() << std::endl;
}
// return result;
// }
return result;
}
// float monomer::kappa() const
// {
// float result = 360;
float monomer::kappa() const
{
float result = 360;
// try
// {
// if (m_index >= 2 and m_index + 2 < m_polymer->size())
// {
// auto &prevPrev = m_polymer->operator[](m_index - 2);
// auto &nextNext = m_polymer->operator[](m_index + 2);
try
{
if (m_index >= 2 and m_index + 2 < m_polymer->size())
{
auto &prevPrev = m_polymer->operator[](m_index - 2);
auto &nextNext = m_polymer->operator[](m_index + 2);
// if (prevPrev.m_seq_id + 4 == nextNext.m_seq_id)
// {
// double ckap = CosinusAngle(CAlpha().location(), prevPrev.CAlpha().location(), nextNext.CAlpha().location(), CAlpha().location());
// double skap = std::sqrt(1 - ckap * ckap);
// result = static_cast<float>(std::atan2(skap, ckap) * 180 / kPI);
// }
// }
// }
// catch (const std::exception &ex)
// {
// if (VERBOSE > 0)
// std::cerr << "When trying to calculate kappa for " << asym_id() << ':' << seqID() << ": "
// << ex.what() << std::endl;
// }
if (prevPrev.m_seq_id + 4 == nextNext.m_seq_id)
{
double ckap = cosinus_angle(CAlpha().get_location(), prevPrev.CAlpha().get_location(), nextNext.CAlpha().get_location(), CAlpha().get_location());
double skap = std::sqrt(1 - ckap * ckap);
result = static_cast<float>(std::atan2(skap, ckap) * 180 / kPI);
}
}
}
catch (const std::exception &ex)
{
if (VERBOSE > 0)
std::cerr << "When trying to calculate kappa for " << m_asym_id << ':' << m_seq_id << ": "
<< ex.what() << std::endl;
}
// return result;
// }
return result;
}
// float monomer::tco() const
// {
// float result = 0.0;
float monomer::tco() const
{
float result = 0.0;
// try
// {
// if (m_index > 0)
// {
// auto &prev = m_polymer->operator[](m_index - 1);
// if (prev.m_seq_id + 1 == m_seq_id)
// result = static_cast<float>(CosinusAngle(C().location(), O().location(), prev.C().location(), prev.O().location()));
// }
// }
// catch (const std::exception &ex)
// {
// if (VERBOSE > 0)
// std::cerr << "When trying to calculate tco for " << asym_id() << ':' << seqID() << ": "
// << ex.what() << std::endl;
// }
try
{
if (m_index > 0)
{
auto &prev = m_polymer->operator[](m_index - 1);
if (prev.m_seq_id + 1 == m_seq_id)
result = static_cast<float>(cosinus_angle(C().get_location(), O().get_location(), prev.C().get_location(), prev.O().get_location()));
}
}
catch (const std::exception &ex)
{
if (VERBOSE > 0)
std::cerr << "When trying to calculate tco for " << get_asym_id() << ':' << get_seq_id() << ": "
<< ex.what() << std::endl;
}
// return result;
// }
return result;
}
// float monomer::omega() const
// {
// float result = 360;
float monomer::omega() const
{
float result = 360;
// try
// {
// if (not is_last_in_chain())
// result = omega(*this, m_polymer->operator[](m_index + 1));
// }
// catch (const std::exception &ex)
// {
// if (VERBOSE > 0)
// std::cerr << "When trying to calculate omega for " << asym_id() << ':' << seqID() << ": "
// << ex.what() << std::endl;
// }
try
{
if (not is_last_in_chain())
result = omega(*this, m_polymer->operator[](m_index + 1));
}
catch (const std::exception &ex)
{
if (VERBOSE > 0)
std::cerr << "When trying to calculate omega for " << get_asym_id() << ':' << get_seq_id() << ": "
<< ex.what() << std::endl;
}
// return result;
// }
return result;
}
// const std::map<std::string, std::vector<std::string>> kChiAtomsMap = {
// {"ASP", {"CG", "OD1"}},
// {"ASN", {"CG", "OD1"}},
// {"ARG", {"CG", "CD", "NE", "CZ"}},
// {"HIS", {"CG", "ND1"}},
// {"GLN", {"CG", "CD", "OE1"}},
// {"GLU", {"CG", "CD", "OE1"}},
// {"SER", {"OG"}},
// {"THR", {"OG1"}},
// {"LYS", {"CG", "CD", "CE", "NZ"}},
// {"TYR", {"CG", "CD1"}},
// {"PHE", {"CG", "CD1"}},
// {"LEU", {"CG", "CD1"}},
// {"TRP", {"CG", "CD1"}},
// {"CYS", {"SG"}},
// {"ILE", {"CG1", "CD1"}},
// {"MET", {"CG", "SD", "CE"}},
// {"MSE", {"CG", "SE", "CE"}},
// {"PRO", {"CG", "CD"}},
// {"VAL", {"CG1"}}};
// size_t monomer::nrOfChis() const
// {
// size_t result = 0;
const std::map<std::string, std::vector<std::string>> kChiAtomsMap = {
{"ASP", {"CG", "OD1"}},
{"ASN", {"CG", "OD1"}},
{"ARG", {"CG", "CD", "NE", "CZ"}},
{"HIS", {"CG", "ND1"}},
{"GLN", {"CG", "CD", "OE1"}},
{"GLU", {"CG", "CD", "OE1"}},
{"SER", {"OG"}},
{"THR", {"OG1"}},
{"LYS", {"CG", "CD", "CE", "NZ"}},
{"TYR", {"CG", "CD1"}},
{"PHE", {"CG", "CD1"}},
{"LEU", {"CG", "CD1"}},
{"TRP", {"CG", "CD1"}},
{"CYS", {"SG"}},
{"ILE", {"CG1", "CD1"}},
{"MET", {"CG", "SD", "CE"}},
{"MSE", {"CG", "SE", "CE"}},
{"PRO", {"CG", "CD"}},
{"VAL", {"CG1"}}};
size_t monomer::nr_of_chis() const
{
size_t result = 0;
// auto i = kChiAtomsMap.find(m_compound_id);
// if (i != kChiAtomsMap.end())
// result = i->second.size();
auto i = kChiAtomsMap.find(m_compound_id);
if (i != kChiAtomsMap.end())
result = i->second.size();
// return result;
// }
return result;
}
// float monomer::chi(size_t nr) const
// {
// float result = 0;
float monomer::chi(size_t nr) const
{
float result = 0;
// try
// {
// auto i = kChiAtomsMap.find(m_compound_id);
// if (i != kChiAtomsMap.end() and nr < i->second.size())
// {
// std::vector<std::string> atoms{"N", "CA", "CB"};
try
{
auto i = kChiAtomsMap.find(m_compound_id);
if (i != kChiAtomsMap.end() and nr < i->second.size())
{
std::vector<std::string> atoms{"N", "CA", "CB"};
// atoms.insert(atoms.end(), i->second.begin(), i->second.end());
atoms.insert(atoms.end(), i->second.begin(), i->second.end());
// // in case we have a positive chiral volume we need to swap atoms
// if (chiralVolume() > 0)
// {
// if (m_compound_id == "LEU")
// atoms.back() = "CD2";
// if (m_compound_id == "VAL")
// atoms.back() = "CG2";
// }
// in case we have a positive chiral volume we need to swap atoms
if (chiral_volume() > 0)
{
if (m_compound_id == "LEU")
atoms.back() = "CD2";
if (m_compound_id == "VAL")
atoms.back() = "CG2";
}
// result = static_cast<float>(DihedralAngle(
// get_atom_by_id(atoms[nr + 0]).location(),
// get_atom_by_id(atoms[nr + 1]).location(),
// get_atom_by_id(atoms[nr + 2]).location(),
// get_atom_by_id(atoms[nr + 3]).location()));
// }
// }
// catch (const std::exception &e)
// {
// if (VERBOSE > 0)
// std::cerr << e.what() << std::endl;
// result = 0;
// }
result = static_cast<float>(dihedral_angle(
get_atom_by_atom_id(atoms[nr + 0]).get_location(),
get_atom_by_atom_id(atoms[nr + 1]).get_location(),
get_atom_by_atom_id(atoms[nr + 2]).get_location(),
get_atom_by_atom_id(atoms[nr + 3]).get_location()));
}
}
catch (const std::exception &e)
{
if (VERBOSE > 0)
std::cerr << e.what() << std::endl;
result = 0;
}
// return result;
// }
return result;
}
// bool monomer::isCis() const
// {
// bool result = false;
bool monomer::is_cis() const
{
bool result = false;
// if (m_index + 1 < m_polymer->size())
// {
// auto &next = m_polymer->operator[](m_index + 1);
if (m_index + 1 < m_polymer->size())
{
auto &next = m_polymer->operator[](m_index + 1);
// result = monomer::isCis(*this, next);
// }
result = monomer::is_cis(*this, next);
}
// return result;
// }
return result;
}
// bool monomer::isComplete() const
// {
// int seen = 0;
// for (auto &a : m_atoms)
// {
// if (a.get_label_atom_id() == "CA")
// seen |= 1;
// else if (a.get_label_atom_id() == "C")
// seen |= 2;
// else if (a.get_label_atom_id() == "N")
// seen |= 4;
// else if (a.get_label_atom_id() == "O")
// seen |= 8;
// // else if (a.get_label_atom_id() == "OXT") seen |= 16;
// }
// return seen == 15;
// }
bool monomer::is_complete() const
{
int seen = 0;
for (auto &a : m_atoms)
{
if (a.get_label_atom_id() == "CA")
seen |= 1;
else if (a.get_label_atom_id() == "C")
seen |= 2;
else if (a.get_label_atom_id() == "N")
seen |= 4;
else if (a.get_label_atom_id() == "O")
seen |= 8;
// else if (a.get_label_atom_id() == "OXT") seen |= 16;
}
return seen == 15;
}
// bool monomer::hasAlternateBackboneAtoms() const
// {
// bool result = false;
bool monomer::has_alternate_backbone_atoms() const
{
bool result = false;
// for (auto &a : m_atoms)
// {
// if (not a.is_alternate())
// continue;
for (auto &a : m_atoms)
{
if (not a.is_alternate())
continue;
// auto atom_id = a.get_label_atom_id();
// if (atom_id == "CA" or atom_id == "C" or atom_id == "N" or atom_id == "O")
// {
// result = true;
// break;
// }
// }
auto atom_id = a.get_label_atom_id();
if (atom_id == "CA" or atom_id == "C" or atom_id == "N" or atom_id == "O")
{
result = true;
break;
}
}
// return result;
// }
return result;
}
// float monomer::chiralVolume() const
// {
// float result = 0;
float monomer::chiral_volume() const
{
float result = 0;
// if (m_compound_id == "LEU")
// {
// auto centre = get_atom_by_id("CG");
// auto atom1 = get_atom_by_id("CB");
// auto atom2 = get_atom_by_id("CD1");
// auto atom3 = get_atom_by_id("CD2");
if (m_compound_id == "LEU")
{
auto centre = get_atom_by_atom_id("CG");
auto atom1 = get_atom_by_atom_id("CB");
auto atom2 = get_atom_by_atom_id("CD1");
auto atom3 = get_atom_by_atom_id("CD2");
// result = DotProduct(atom1.location() - centre.location(),
// CrossProduct(atom2.location() - centre.location(), atom3.location() - centre.location()));
// }
// else if (m_compound_id == "VAL")
// {
// auto centre = get_atom_by_id("CB");
// auto atom1 = get_atom_by_id("CA");
// auto atom2 = get_atom_by_id("CG1");
// auto atom3 = get_atom_by_id("CG2");
result = dot_product(atom1.get_location() - centre.get_location(),
cross_product(atom2.get_location() - centre.get_location(), atom3.get_location() - centre.get_location()));
}
else if (m_compound_id == "VAL")
{
auto centre = get_atom_by_atom_id("CB");
auto atom1 = get_atom_by_atom_id("CA");
auto atom2 = get_atom_by_atom_id("CG1");
auto atom3 = get_atom_by_atom_id("CG2");
// result = DotProduct(atom1.location() - centre.location(),
// CrossProduct(atom2.location() - centre.location(), atom3.location() - centre.location()));
// }
result = dot_product(atom1.get_location() - centre.get_location(),
cross_product(atom2.get_location() - centre.get_location(), atom3.get_location() - centre.get_location()));
}
// return result;
// }
return result;
}
// bool monomer::areBonded(const monomer &a, const monomer &b, float errorMargin)
// {
// bool result = false;
bool monomer::are_bonded(const monomer &a, const monomer &b, float errorMargin)
{
bool result = false;
// try
// {
// point atoms[4] = {
// a.get_atom_by_id("CA").location(),
// a.get_atom_by_id("C").location(),
// b.get_atom_by_id("N").location(),
// b.get_atom_by_id("CA").location()};
try
{
point atoms[4] = {
a.get_atom_by_atom_id("CA").get_location(),
a.get_atom_by_atom_id("C").get_location(),
b.get_atom_by_atom_id("N").get_location(),
b.get_atom_by_atom_id("CA").get_location()};
// auto distanceCACA = Distance(atoms[0], atoms[3]);
// double omega = DihedralAngle(atoms[0], atoms[1], atoms[2], atoms[3]);
auto distanceCACA = distance(atoms[0], atoms[3]);
double omega = dihedral_angle(atoms[0], atoms[1], atoms[2], atoms[3]);
// bool cis = std::abs(omega) <= 30.0;
// float maxCACADistance = cis ? 3.0f : 3.8f;
bool cis = std::abs(omega) <= 30.0;
float maxCACADistance = cis ? 3.0f : 3.8f;
// result = std::abs(distanceCACA - maxCACADistance) < errorMargin;
// }
// catch (...)
// {
// }
result = std::abs(distanceCACA - maxCACADistance) < errorMargin;
}
catch (...)
{
}
// return result;
// }
return result;
}
// float monomer::omega(const mmmonomer &a, const mmmonomer &b)
// {
// float result = 360;
float monomer::omega(const monomer &a, const monomer &b)
{
float result = 360;
// try
// {
// result = static_cast<float>(DihedralAngle(
// a.get_atom_by_id("CA").location(),
// a.get_atom_by_id("C").location(),
// b.get_atom_by_id("N").location(),
// b.get_atom_by_id("CA").location()));
// }
// catch (...)
// {
// }
try
{
result = static_cast<float>(dihedral_angle(
a.get_atom_by_atom_id("CA").get_location(),
a.get_atom_by_atom_id("C").get_location(),
b.get_atom_by_atom_id("N").get_location(),
b.get_atom_by_atom_id("CA").get_location()));
}
catch (...)
{
}
// return result;
// }
return result;
}
// bool monomer::isCis(const mmmonomer &a, const mmmonomer &b)
// {
// return omega(a, b) < 30.0f;
// }
bool monomer::is_cis(const monomer &a, const monomer &b)
{
return omega(a, b) < 30.0f;
}
// --------------------------------------------------------------------
// polymer
......@@ -1249,7 +1236,7 @@ structure::structure(datablock &db, size_t modelNr, StructureOpenOptions options
std::cerr << "Warning: no atoms loaded" << std::endl;
}
else
loadData();
load_data();
}
void structure::load_atoms_for_model(StructureOpenOptions options)
......@@ -1281,14 +1268,14 @@ void structure::load_atoms_for_model(StructureOpenOptions options)
// for (auto &atom : s.m_atoms)
// emplace_atom(atom.clone());
// loadData();
// load_data();
// }
// structure::~structure()
// {
// }
void structure::loadData()
void structure::load_data()
{
auto &polySeqScheme = m_db["pdbx_poly_seq_scheme"];
......@@ -1449,45 +1436,45 @@ atom structure::get_atom_by_id(const std::string &id) const
throw std::out_of_range("Could not find atom with id " + id);
}
// atom structure::getAtomByLabel(const std::string &atom_id, const std::string &asym_id, const std::string &compID, int seqID, const std::string &altID)
// {
// for (auto &a : m_atoms)
// {
// if (a.get_label_atom_id() == atom_id and
// a.get_label_asym_id() == asym_id and
// a.labelCompID() == compID and
// a.get_label_seq_id() == seqID and
// a.get_label_alt_id() == altID)
// {
// return a;
// }
// }
atom structure::get_atom_by_label(const std::string &atom_id, const std::string &asym_id, const std::string &compID, int seqID, const std::string &altID)
{
for (auto &a : m_atoms)
{
if (a.get_label_atom_id() == atom_id and
a.get_label_asym_id() == asym_id and
a.get_label_comp_id() == compID and
a.get_label_seq_id() == seqID and
a.get_label_alt_id() == altID)
{
return a;
}
}
// throw std::out_of_range("Could not find atom with specified label");
// }
throw std::out_of_range("Could not find atom with specified label");
}
// atom structure::getAtomByPosition(point p) const
// {
// double distance = std::numeric_limits<double>::max();
// size_t index = std::numeric_limits<size_t>::max();
atom structure::get_atom_by_position(point p) const
{
double dist = std::numeric_limits<double>::max();
size_t index = std::numeric_limits<size_t>::max();
// for (size_t i = 0; i < m_atoms.size(); ++i)
// {
// auto &a = m_atoms.at(i);
for (size_t i = 0; i < m_atoms.size(); ++i)
{
auto &a = m_atoms.at(i);
// auto d = Distance(a.location(), p);
// if (d < distance)
// {
// distance = d;
// index = i;
// }
// }
auto d = distance(a.get_location(), p);
if (d < dist)
{
dist = d;
index = i;
}
}
// if (index < m_atoms.size())
// return m_atoms.at(index);
if (index < m_atoms.size())
return m_atoms.at(index);
// return {};
// }
return {};
}
atom structure::get_atom_by_position_and_type(point p, std::string_view type, std::string_view res_type) const
{
......
test/HEM.cif 0 → 100644
data_HEM
#
_chem_comp.id HEM
_chem_comp.name "PROTOPORPHYRIN IX CONTAINING FE"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C34 H32 Fe N4 O4"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms HEME
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 1999-07-08
_chem_comp.pdbx_modified_date 2020-06-17
_chem_comp.pdbx_ambiguous_flag Y
_chem_comp.pdbx_release_status REL
_chem_comp.pdbx_replaced_by ?
_chem_comp.pdbx_replaces MHM
_chem_comp.formula_weight 616.487
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code HEM
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details Corina
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 3IA3
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
# #
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.alt_atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.charge
_chem_comp_atom.pdbx_align
_chem_comp_atom.pdbx_aromatic_flag
_chem_comp_atom.pdbx_leaving_atom_flag
_chem_comp_atom.pdbx_stereo_config
_chem_comp_atom.model_Cartn_x
_chem_comp_atom.model_Cartn_y
_chem_comp_atom.model_Cartn_z
_chem_comp_atom.pdbx_model_Cartn_x_ideal
_chem_comp_atom.pdbx_model_Cartn_y_ideal
_chem_comp_atom.pdbx_model_Cartn_z_ideal
_chem_comp_atom.pdbx_component_atom_id
_chem_comp_atom.pdbx_component_comp_id
_chem_comp_atom.pdbx_ordinal
HEM CHA CHA C 0 1 N N N 2.748 -19.531 39.896 -2.161 -0.125 0.490 CHA HEM 1
HEM CHB CHB C 0 1 N N N 3.258 -17.744 35.477 1.458 -3.419 0.306 CHB HEM 2
HEM CHC CHC C 0 1 N N N 1.703 -21.900 33.637 4.701 0.169 -0.069 CHC HEM 3
HEM CHD CHD C 0 1 N N N 1.149 -23.677 38.059 1.075 3.460 0.018 CHD HEM 4
HEM C1A C1A C 0 1 Y N N 3.031 -18.673 38.872 -1.436 -1.305 0.380 C1A HEM 5
HEM C2A C2A C 0 1 Y N N 3.578 -17.325 39.013 -2.015 -2.587 0.320 C2A HEM 6
HEM C3A C3A C 0 1 Y N N 3.705 -16.820 37.785 -1.009 -3.500 0.270 C3A HEM 7
HEM C4A C4A C 0 1 Y N N 3.256 -17.863 36.862 0.216 -2.803 0.298 C4A HEM 8
HEM CMA CMA C 0 1 N N N 4.227 -15.469 37.393 -1.175 -4.996 0.197 CMA HEM 9
HEM CAA CAA C 0 1 N N N 3.945 -16.670 40.296 -3.490 -2.893 0.314 CAA HEM 10
HEM CBA CBA C 0 1 N N N 5.391 -17.138 40.581 -3.998 -2.926 -1.129 CBA HEM 11
HEM CGA CGA C 0 1 N N N 6.095 -16.663 41.825 -5.473 -3.232 -1.136 CGA HEM 12
HEM O1A O1A O 0 1 N N N 7.098 -15.928 41.683 -6.059 -3.405 -0.094 O1A HEM 13
HEM O2A O2A O 0 1 N N N 5.657 -17.040 42.940 -6.137 -3.311 -2.300 O2A HEM 14
HEM C1B C1B C 0 1 N N N 2.888 -18.698 34.579 2.664 -2.707 0.308 C1B HEM 15
HEM C2B C2B C 0 1 N N N 2.933 -18.535 33.146 3.937 -3.328 0.418 C2B HEM 16
HEM C3B C3B C 0 1 N N N 2.499 -19.716 32.632 4.874 -2.341 0.314 C3B HEM 17
HEM C4B C4B C 0 1 N N N 2.187 -20.580 33.743 4.117 -1.079 0.139 C4B HEM 18
HEM CMB CMB C 0 1 N N N 3.391 -17.290 32.422 4.203 -4.798 0.613 CMB HEM 19
HEM CAB CAB C 0 1 N N N 2.345 -20.140 31.217 6.339 -2.497 0.365 CAB HEM 20
HEM CBB CBB C 0 1 N N N 1.755 -19.492 30.233 6.935 -3.419 -0.385 CBB HEM 21
HEM C1C C1C C 0 1 Y N N 1.395 -22.786 34.659 3.964 1.345 -0.174 C1C HEM 22
HEM C2C C2C C 0 1 Y N N 0.854 -24.130 34.500 4.531 2.601 -0.445 C2C HEM 23
HEM C3C C3C C 0 1 Y N N 0.689 -24.626 35.757 3.510 3.536 -0.437 C3C HEM 24
HEM C4C C4C C 0 1 Y N N 1.139 -23.583 36.674 2.304 2.846 -0.139 C4C HEM 25
HEM CMC CMC C 0 1 N N N 0.550 -24.782 33.175 5.991 2.880 -0.697 CMC HEM 26
HEM CAC CAC C 0 1 N N N 0.164 -25.943 36.196 3.649 4.981 -0.692 CAC HEM 27
HEM CBC CBC C 0 1 N N N 0.498 -27.158 35.750 4.201 5.407 -1.823 CBC HEM 28
HEM C1D C1D C 0 1 N N N 1.550 -22.718 38.980 -0.102 2.753 0.298 C1D HEM 29
HEM C2D C2D C 0 1 N N N 1.513 -22.879 40.415 -1.382 3.388 0.641 C2D HEM 30
HEM C3D C3D C 0 1 N N N 1.951 -21.691 40.929 -2.283 2.389 0.774 C3D HEM 31
HEM C4D C4D C 0 1 N N N 2.277 -20.826 39.811 -1.561 1.137 0.511 C4D HEM 32
HEM CMD CMD C 0 1 N N N 1.055 -24.094 41.156 -1.639 4.863 0.811 CMD HEM 33
HEM CAD CAD C 0 1 N N N 2.048 -21.326 42.352 -3.741 2.532 1.123 CAD HEM 34
HEM CBD CBD C 0 1 N N N 0.741 -20.498 42.530 -4.573 2.563 -0.160 CBD HEM 35
HEM CGD CGD C 0 1 N N N 0.578 -19.987 43.892 -6.032 2.706 0.189 CGD HEM 36
HEM O1D O1D O 0 1 N N N 1.387 -19.103 44.303 -6.372 2.776 1.347 O1D HEM 37
HEM O2D O2D O 0 1 N N N -0.401 -20.468 44.537 -6.954 2.755 -0.785 O2D HEM 38
HEM NA NA N 0 1 Y N N 2.863 -18.969 37.554 -0.068 -1.456 0.321 NA HEM 39
HEM NB NB N 0 1 N N N 2.439 -19.944 34.911 2.820 -1.386 0.207 NB HEM 40
HEM NC NC N 0 1 Y N N 1.537 -22.509 35.976 2.604 1.506 -0.033 NC HEM 41
HEM ND ND N 0 1 N N N 2.008 -21.465 38.663 -0.276 1.431 0.298 ND HEM 42
HEM FE FE FE 0 0 N N N 2.196 -20.749 36.814 1.010 0.157 -0.060 FE HEM 43
HEM HHB HHB H 0 1 N N N 3.587 -16.798 35.072 1.498 -4.508 0.309 HHB HEM 44
HEM HHC HHC H 0 1 N N N 1.553 -22.268 32.633 5.786 0.229 -0.153 HHC HEM 45
HEM HHD HHD H 0 1 N N N 0.802 -24.613 38.472 1.018 4.543 -0.083 HHD HEM 46
HEM HMA HMA H 0 1 N N N 5.316 -15.524 37.249 -1.220 -5.306 -0.847 HMA HEM 47
HEM HMAA HMAA H 0 0 N N N 3.749 -15.149 36.455 -0.328 -5.480 0.683 HMAA HEM 48
HEM HMAB HMAB H 0 0 N N N 3.998 -14.743 38.187 -2.097 -5.285 0.702 HMAB HEM 49
HEM HAA HAA H 0 1 N N N 3.905 -15.575 40.197 -3.662 -3.862 0.782 HAA HEM 50
HEM HAAA HAAA H 0 0 N N N 3.268 -16.991 41.102 -4.024 -2.121 0.869 HAAA HEM 51
HEM HBA HBA H 0 1 N N N 5.368 -18.237 40.627 -3.825 -1.956 -1.597 HBA HEM 52
HEM HBAA HBAA H 0 0 N N N 6.004 -16.819 39.725 -3.464 -3.697 -1.684 HBAA HEM 53
HEM HMB HMB H 0 1 N N N 3.319 -17.449 31.336 3.256 -5.336 0.660 HMB HEM 54
HEM HMBA HMBA H 0 0 N N N 2.753 -16.442 32.711 4.794 -5.175 -0.222 HMBA HEM 55
HEM HMBB HMBB H 0 0 N N N 4.435 -17.072 32.692 4.752 -4.948 1.543 HMBB HEM 56
HEM HAB HAB H 0 1 N N N 2.770 -21.100 30.963 6.927 -1.863 1.011 HAB HEM 57
HEM HBB HBB H 0 1 N N N 1.719 -19.927 29.245 7.994 -3.600 -0.277 HBB HEM 58
HEM HBBA HBBA H 0 0 N N N 1.308 -18.526 30.414 6.360 -3.987 -1.102 HBBA HEM 59
HEM HMC HMC H 0 1 N N N 0.153 -25.793 33.346 6.554 1.949 -0.639 HMC HEM 60
HEM HMCA HMCA H 0 0 N N N -0.196 -24.182 32.634 6.110 3.316 -1.689 HMCA HEM 61
HEM HMCB HMCB H 0 0 N N N 1.472 -24.846 32.578 6.362 3.578 0.053 HMCB HEM 62
HEM HAC HAC H 0 1 N N N -0.583 -25.916 36.975 3.303 5.694 0.042 HAC HEM 63
HEM HBC HBC H 0 1 N N N 0.027 -28.035 36.169 4.614 4.696 -2.523 HBC HEM 64
HEM HBCA HBCA H 0 0 N N N 1.239 -27.263 34.971 4.235 6.464 -2.043 HBCA HEM 65
HEM HMD HMD H 0 1 N N N 1.142 -23.919 42.238 -0.715 5.415 0.639 HMD HEM 66
HEM HMDA HMDA H 0 0 N N N 0.006 -24.304 40.902 -2.394 5.185 0.094 HMDA HEM 67
HEM HMDB HMDB H 0 0 N N N 1.680 -24.954 40.872 -1.994 5.055 1.824 HMDB HEM 68
HEM HAD HAD H 0 1 N N N 2.055 -22.216 42.999 -4.052 1.687 1.738 HAD HEM 69
HEM HADA HADA H 0 0 N N N 2.943 -20.719 42.554 -3.893 3.459 1.677 HADA HEM 70
HEM HBD HBD H 0 1 N N N 0.767 -19.646 41.835 -4.262 3.408 -0.775 HBD HEM 71
HEM HBDA HBDA H 0 0 N N N -0.119 -21.141 42.290 -4.421 1.636 -0.714 HBDA HEM 72
HEM H2A H2A H 0 1 N N N 6.201 -16.682 43.632 -7.082 -3.510 -2.254 H2A HEM 73
HEM H2D H2D H 0 1 N N N -0.445 -20.063 45.395 -7.877 2.847 -0.512 H2D HEM 74
HEM HHA HHA H 0 1 N N N 2.913 -19.150 40.893 -3.246 -0.188 0.567 HHA HEM 75
# #
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_aromatic_flag
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_ordinal
HEM CHA C1A SING N N 1
HEM CHA C4D DOUB N N 2
HEM CHA HHA SING N N 3
HEM CHB C4A SING N N 4
HEM CHB C1B DOUB N N 5
HEM CHB HHB SING N N 6
HEM CHC C4B SING N N 7
HEM CHC C1C DOUB N N 8
HEM CHC HHC SING N N 9
HEM CHD C4C DOUB N N 10
HEM CHD C1D SING N N 11
HEM CHD HHD SING N N 12
HEM C1A C2A DOUB Y N 13
HEM C1A NA SING Y N 14
HEM C2A C3A SING Y N 15
HEM C2A CAA SING N N 16
HEM C3A C4A DOUB Y N 17
HEM C3A CMA SING N N 18
HEM C4A NA SING Y N 19
HEM CMA HMA SING N N 20
HEM CMA HMAA SING N N 21
HEM CMA HMAB SING N N 22
HEM CAA CBA SING N N 23
HEM CAA HAA SING N N 24
HEM CAA HAAA SING N N 25
HEM CBA CGA SING N N 26
HEM CBA HBA SING N N 27
HEM CBA HBAA SING N N 28
HEM CGA O1A DOUB N N 29
HEM CGA O2A SING N N 30
HEM C1B C2B SING N N 31
HEM C1B NB SING N N 32
HEM C2B C3B DOUB N N 33
HEM C2B CMB SING N N 34
HEM C3B C4B SING N N 35
HEM C3B CAB SING N N 36
HEM C4B NB DOUB N N 37
HEM CMB HMB SING N N 38
HEM CMB HMBA SING N N 39
HEM CMB HMBB SING N N 40
HEM CAB CBB DOUB N N 41
HEM CAB HAB SING N N 42
HEM CBB HBB SING N N 43
HEM CBB HBBA SING N N 44
HEM C1C C2C SING Y N 45
HEM C1C NC SING Y N 46
HEM C2C C3C DOUB Y N 47
HEM C2C CMC SING N N 48
HEM C3C C4C SING Y N 49
HEM C3C CAC SING N N 50
HEM C4C NC SING Y N 51
HEM CMC HMC SING N N 52
HEM CMC HMCA SING N N 53
HEM CMC HMCB SING N N 54
HEM CAC CBC DOUB N N 55
HEM CAC HAC SING N N 56
HEM CBC HBC SING N N 57
HEM CBC HBCA SING N N 58
HEM C1D C2D SING N N 59
HEM C1D ND DOUB N N 60
HEM C2D C3D DOUB N N 61
HEM C2D CMD SING N N 62
HEM C3D C4D SING N N 63
HEM C3D CAD SING N N 64
HEM C4D ND SING N N 65
HEM CMD HMD SING N N 66
HEM CMD HMDA SING N N 67
HEM CMD HMDB SING N N 68
HEM CAD CBD SING N N 69
HEM CAD HAD SING N N 70
HEM CAD HADA SING N N 71
HEM CBD CGD SING N N 72
HEM CBD HBD SING N N 73
HEM CBD HBDA SING N N 74
HEM CGD O1D DOUB N N 75
HEM CGD O2D SING N N 76
HEM O2A H2A SING N N 77
HEM O2D H2D SING N N 78
HEM FE NA SING N N 79
HEM FE NB SING N N 80
HEM FE NC SING N N 81
HEM FE ND SING N N 82
# #
loop_
_pdbx_chem_comp_descriptor.comp_id
_pdbx_chem_comp_descriptor.type
_pdbx_chem_comp_descriptor.program
_pdbx_chem_comp_descriptor.program_version
_pdbx_chem_comp_descriptor.descriptor
HEM SMILES ACDLabs 12.01 "C=1c3c(c(c4C=C5C(=C(C=6C=C7C(=C(C8=CC=2C(=C(C=1N=2[Fe](n34)(N5=6)N78)CCC(=O)O)C)\C=C)C)\C=C)C)C)CCC(=O)O"
HEM InChI InChI 1.03 "InChI=1S/C34H34N4O4.Fe/c1-7-21-17(3)25-13-26-19(5)23(9-11-33(39)40)31(37-26)16-32-24(10-12-34(41)42)20(6)28(38-32)15-30-22(8-2)18(4)27(36-30)14-29(21)35-25;/h7-8,13-16H,1-2,9-12H2,3-6H3,(H4,35,36,37,38,39,40,41,42);/q;+2/p-2/b25-13-,26-13-,27-14-,28-15-,29-14-,30-15-,31-16-,32-16-;"
HEM InChIKey InChI 1.03 KABFMIBPWCXCRK-RGGAHWMASA-L
HEM SMILES_CANONICAL CACTVS 3.385 "CC1=C(CCC(O)=O)C2=Cc3n4[Fe]5|6|N2=C1C=c7n5c(=CC8=N|6C(=Cc4c(C)c3CCC(O)=O)C(=C8C=C)C)c(C)c7C=C"
HEM SMILES CACTVS 3.385 "CC1=C(CCC(O)=O)C2=Cc3n4[Fe]5|6|N2=C1C=c7n5c(=CC8=N|6C(=Cc4c(C)c3CCC(O)=O)C(=C8C=C)C)c(C)c7C=C"
HEM SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "Cc1c2n3c(c1CCC(=O)O)C=C4C(=C(C5=[N]4[Fe]36[N]7=C(C=C8N6C(=C5)C(=C8C)C=C)C(=C(C7=C2)C)C=C)C)CCC(=O)O"
HEM SMILES "OpenEye OEToolkits" 1.7.6 "Cc1c2n3c(c1CCC(=O)O)C=C4C(=C(C5=[N]4[Fe]36[N]7=C(C=C8N6C(=C5)C(=C8C)C=C)C(=C(C7=C2)C)C=C)C)CCC(=O)O"
# #
loop_
_pdbx_chem_comp_identifier.comp_id
_pdbx_chem_comp_identifier.type
_pdbx_chem_comp_identifier.program
_pdbx_chem_comp_identifier.program_version
_pdbx_chem_comp_identifier.identifier
HEM "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.6.1 "3-[(5Z,10Z,14Z,19Z)-18-(2-carboxyethyl)-8,13-bis(ethenyl)-3,7,12,17-tetramethyl-21,23-dihydroporphyrin-2-yl]propanoic acid"
HEM "SYSTEMATIC NAME" ACDLabs 12.01 "[3,3'-(7,12-diethenyl-3,8,13,17-tetramethylporphyrin-2,18-diyl-kappa~4~N~21~,N~22~,N~23~,N~24~)dipropanoato(2-)]iron"
# #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
HEM "Create component" 1999-07-08 RCSB
HEM "Other modification" 2016-01-20 RCSB
HEM "Modify synonyms" 2020-06-05 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id HEM
_pdbx_chem_comp_synonyms.name HEME
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
##
test/model-test.cpp
......@@ -190,27 +190,6 @@ _struct_asym.details ?
}
}
// // --------------------------------------------------------------------
// BOOST_AUTO_TEST_CASE(test_load_1)
// {
// cif::file cf(gTestDir / "5v3g.cif.gz");
// cif::mm::structure s(cf);
// for (auto &poly : s.polymers())
// {
// std::cout << std::string(80, '=') << std::endl;
// for (auto &res : poly)
// {
// std::cout << res << std::endl;
// for (auto &atom : res.atoms())
// std::cout << " " << atom << std::endl;
// }
// }
// }
// --------------------------------------------------------------------
BOOST_AUTO_TEST_CASE(test_atom_id)
......@@ -323,7 +302,7 @@ BOOST_AUTO_TEST_CASE(atom_numbers_1)
}
// --------------------------------------------------------------------
BOOST_AUTO_TEST_CASE(test_load_1)
BOOST_AUTO_TEST_CASE(test_load_2)
{
using namespace cif::literals;
......
test/unit-v2-test.cpp
......@@ -1672,7 +1672,7 @@ _cat_2.parent_id_2
BOOST_CHECK( cat2.has_parents(cat2.find1("id"_key == 2)));
BOOST_CHECK(not cat2.has_parents(cat2.find1("id"_key == 3)));
BOOST_CHECK( cat2.has_parents(cat2.find1("id"_key == 4)));
BOOST_CHECK( cat2.has_parents(cat2.find1("id"_key == 5)));
BOOST_CHECK(not cat2.has_parents(cat2.find1("id"_key == 5)));
BOOST_CHECK( cat2.has_parents(cat2.find1("id"_key == 6)));
}
......
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