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cql
libcifpp/src/model.cpp
Maarten L. Hekkelman 6eda9aaf36 better center_and_radius for residue
2025-11-18 16:44:53 +01:00

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/*-
* SPDX-License-Identifier: BSD-2-Clause
*
* Copyright (c) 2020 NKI/AVL, Netherlands Cancer Institute
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the above copyright notice, this
* list of conditions and the following disclaimer
* 2. Redistributions in binary form must reproduce the above copyright notice,
* this list of conditions and the following disclaimer in the documentation
* and/or other materials provided with the distribution.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
* ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
* WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
* DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
* ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
* (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
* LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
* ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*/
#include "cif++/model.hpp"
#include "cif++.hpp"
#include "cif++/point.hpp"
#include <filesystem>
#include <fstream>
#include <initializer_list>
#include <iomanip>
#include <numeric>
#include <stack>
#include <stdexcept>
namespace fs = std::filesystem;
namespace cif::mm
{
// --------------------------------------------------------------------
// atom
void atom::atom_impl::moveTo(const point &p)
{
if (m_symop != "1_555")
throw std::runtime_error("Moving symmetry copy");
auto r = row();
r.assign("Cartn_x", cif::format("{:.3f}", p.m_x), false, false);
r.assign("Cartn_y", cif::format("{:.3f}", p.m_y), false, false);
r.assign("Cartn_z", cif::format("{:.3f}", p.m_z), false, false);
m_location = p;
}
// const compound *compound() const;
std::string atom::atom_impl::get_property(std::string_view name) const
{
return row()[name].as<std::string>();
}
int atom::atom_impl::get_property_int(std::string_view name) const
{
int result = 0;
if (not row()[name].empty())
{
auto s = get_property(name);
std::from_chars_result r = std::from_chars(s.data(), s.data() + s.length(), result);
if ((bool)r.ec and VERBOSE > 0)
std::cerr << "Error converting " << s << " to number for property " << name << '\n';
}
return result;
}
float atom::atom_impl::get_property_float(std::string_view name) const
{
float result = 0;
if (not row()[name].empty())
{
auto s = get_property(name);
std::from_chars_result r = cif::from_chars(s.data(), s.data() + s.length(), result);
if ((bool)r.ec and VERBOSE > 0)
std::cerr << "Error converting " << s << " to number for property " << name << '\n';
}
return result;
}
void atom::atom_impl::set_property(const std::string_view name, const std::string &value)
{
auto r = row();
if (not r)
throw std::runtime_error("Trying to modify a row that does not exist");
r.assign(name, value, true, true);
}
int atom::atom_impl::compare(const atom_impl &b) const
{
int d = get_property("label_asym_id").compare(b.get_property("label_asym_id"));
if (d == 0)
d = get_property_int("label_seq_id") - b.get_property_int("label_seq_id");
if (d == 0)
d = get_property_int("auth_seq_id") - b.get_property_int("auth_seq_id");
if (d == 0)
d = get_property("label_atom_id").compare(b.get_property("label_atom_id"));
return d;
}
// bool atom::atom_impl::getAnisoU(float anisou[6]) const
// {
// bool result = false;
// auto cat = m_db.get("atom_site_anisotrop");
// if (cat)
// {
// for (auto r : cat->find(key("id") == m_id))
// {
// tie(anisou[0], anisou[1], anisou[2], anisou[3], anisou[4], anisou[5]) =
// r.get("U[1][1]", "U[1][2]", "U[1][3]", "U[2][2]", "U[2][3]", "U[3][3]");
// result = true;
// break;
// }
// }
// return result;
// }
int atom::atom_impl::get_charge() const
{
auto formalCharge = row()["pdbx_formal_charge"].as<std::optional<int>>();
if (not formalCharge.has_value())
{
auto c = cif::compound_factory::instance().create(get_property("label_comp_id"));
if (c != nullptr and c->atoms().size() == 1)
formalCharge = c->atoms().front().charge;
}
return formalCharge.value_or(0);
}
std::ostream &operator<<(std::ostream &os, const atom &atom)
{
if (atom.is_water())
os << atom.get_label_comp_id() << ' ' << atom.get_label_asym_id() << ':' << atom.get_auth_seq_id() << ' ' << atom.get_label_atom_id();
else
{
os << atom.get_label_comp_id() << ' ' << atom.get_label_asym_id() << ':' << atom.get_label_seq_id() << ' ' << atom.get_label_atom_id();
if (atom.is_alternate())
os << '(' << atom.get_label_alt_id() << ')';
if (atom.get_auth_asym_id() != atom.get_label_asym_id() or atom.get_auth_seq_id() != std::to_string(atom.get_label_seq_id()) or atom.get_pdb_ins_code().empty() == false)
os << " [" << atom.get_auth_asym_id() << ':' << atom.get_auth_seq_id() << atom.get_pdb_ins_code() << ']';
}
return os;
}
// --------------------------------------------------------------------
// residue
residue::residue(structure &structure, const std::vector<atom> &atoms)
: m_structure(&structure)
{
if (atoms.empty())
throw std::runtime_error("Empty list of atoms");
auto &a = atoms.front();
m_compound_id = a.get_label_comp_id();
m_asym_id = a.get_label_asym_id();
m_seq_id = a.get_label_seq_id();
m_pdb_strand_id = a.get_auth_asym_id();
m_pdb_seq_num = a.get_auth_seq_id();
m_pdb_ins_code = a.get_pdb_ins_code();
for (auto atom : atoms)
m_atoms.push_back(atom);
}
std::string residue::get_entity_id() const
{
std::string result;
if (not m_atoms.empty())
result = m_atoms.front().get_label_entity_id();
else if (m_structure != nullptr and not m_asym_id.empty())
{
using namespace literals;
auto &db = m_structure->get_datablock();
result = db["struct_asym"].find1<std::string>("id"_key == m_asym_id, "entity_id");
}
return result;
}
EntityType residue::entity_type() const
{
assert(m_structure);
return m_structure->get_entity_type_for_entity_id(get_entity_id());
}
void residue::add_atom(atom &atom)
{
// update atom since it is now part of this residue
m_atoms.push_back(atom);
}
atom residue::create_new_atom(atom_type inType, const std::string &inAtomID, point inLocation)
{
auto &db = m_structure->get_datablock();
auto &atom_site = db["atom_site"];
auto ai = atom_site.emplace({
{ "group_PDB", "HETATM" },
{ "id", atom_site.get_unique_id("") },
{ "type_symbol", atom_type_traits(inType).symbol() },
{ "label_entity_id", get_entity_id() },
{ "label_atom_id", inAtomID },
{ "label_asym_id", m_asym_id },
{ "label_alt_id", "." },
{ "label_comp_id", m_compound_id },
{ "label_seq_id", m_seq_id },
{ "auth_asym_id", m_pdb_strand_id },
{ "auth_atom_id", inAtomID },
{ "auth_comp_id", m_compound_id },
{ "auth_seq_id", m_pdb_seq_num },
{ "occupancy", 1.0f, 2 },
{ "B_iso_or_equiv", 20.0f },
{ "pdbx_PDB_model_num", m_structure->get_model_nr() },
});
atom a(db, *ai);
m_atoms.push_back(a);
a.set_location(inLocation);
return a;
}
std::vector<atom> residue::unique_atoms() const
{
std::vector<atom> result;
std::string firstAlt;
for (auto &atom : m_atoms)
{
auto alt = atom.get_label_alt_id();
if (alt.empty())
{
result.push_back(atom);
continue;
}
if (firstAlt.empty())
firstAlt = alt;
else if (alt != firstAlt)
{
if (VERBOSE > 0)
std::cerr << "skipping alternate atom " << atom << '\n';
continue;
}
result.push_back(atom);
}
return 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);
}
return result;
}
atom residue::get_atom_by_atom_id(const std::string &atom_id) const
{
atom result;
for (auto &a : m_atoms)
{
if (a.get_label_atom_id() == atom_id)
{
result = a;
break;
}
}
if (not result and VERBOSE > 1)
std::cerr << "atom with atom_id " << atom_id << " not found in residue " << m_asym_id << ':' << m_seq_id << '\n';
return result;
}
atom residue::get_atom_by_atom_id(const std::string &atomID, const std::string &altID) const
{
if (altID.empty())
return get_atom_by_atom_id(atomID);
atom result;
for (auto &a : m_atoms)
{
if (auto a_alt_id = a.get_label_alt_id(); a.get_label_atom_id() == atomID and (a_alt_id.empty() or a_alt_id == altID))
{
result = a;
break;
}
}
if (not result and VERBOSE > 1)
std::cerr << "atom with atom_id " << atomID << " and alt_id " << altID << " not found in residue " << m_asym_id << ':' << m_seq_id << '\n';
return result;
}
// residue is a single entity if the atoms for the asym with m_asym_id is equal
// to the number of atoms in this residue... hope this is correct....
bool residue::is_entity() const
{
auto &db = m_structure->get_datablock();
auto a1 = db["atom_site"].find(key("label_asym_id") == m_asym_id);
// auto a2 = atoms();
auto &a2 = m_atoms;
return a1.size() == a2.size();
}
std::tuple<point, float> residue::center_and_radius() const
{
std::vector<point> pts;
for (auto &a : m_atoms)
pts.push_back(a.get_location());
return smallest_sphere_around_points(pts);
}
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();
}
bool residue::has_alternate_atoms_for(const std::string &atomID) const
{
return std::find_if(m_atoms.begin(), m_atoms.end(), [atomID](const atom &atom)
{ return atom.get_label_atom_id() == atomID and atom.is_alternate(); }) != m_atoms.end();
}
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;
}
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)
{
os << res.get_compound_id() << ' ' << res.get_asym_id() << ':' << res.get_seq_id();
if (res.get_pdb_strand_id() != res.get_asym_id() or res.get_pdb_seq_num() != std::to_string(res.get_seq_id()))
os << " [" << res.get_pdb_strand_id() << ':' << res.get_pdb_seq_num() << ']';
return os;
}
// --------------------------------------------------------------------
// monomer
monomer::monomer(const polymer &polymer, std::size_t index, int seqID, const std::string &authSeqID, const std::string &pdbInsCode, const std::string &compoundID)
: residue(*polymer.get_structure(), compoundID, polymer.get_asym_id(), seqID, polymer.get_pdb_strand_id(), authSeqID, pdbInsCode)
, m_polymer(&polymer)
, m_index(index)
{
}
monomer::monomer(monomer &&rhs)
: residue(std::move(rhs))
, m_polymer(rhs.m_polymer)
, m_index(rhs.m_index)
{
rhs.m_polymer = nullptr;
}
monomer &monomer::operator=(monomer &&rhs)
{
residue::operator=(std::move(rhs));
m_polymer = rhs.m_polymer;
rhs.m_polymer = nullptr;
m_index = rhs.m_index;
return *this;
}
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();
}
const monomer &monomer::prev() const
{
return m_polymer->at(m_index - 1);
}
const monomer &monomer::next() const
{
return m_polymer->at(m_index + 1);
}
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();
}
float monomer::phi() const
{
float result = 360;
if (m_index > 0)
{
auto &prev = m_polymer->at(m_index - 1);
if (prev.m_seq_id + 1 == m_seq_id)
{
auto a1 = prev.C();
auto a2 = N();
auto a3 = CAlpha();
auto a4 = C();
if (a1 and a2 and a3 and a4)
result = dihedral_angle(a1.get_location(), a2.get_location(), a3.get_location(), a4.get_location());
}
}
return result;
}
float monomer::psi() const
{
float result = 360;
if (m_index + 1 < m_polymer->size())
{
auto &next = m_polymer->at(m_index + 1);
if (m_seq_id + 1 == next.m_seq_id)
{
auto a1 = N();
auto a2 = CAlpha();
auto a3 = C();
auto a4 = next.N();
if (a1 and a2 and a3 and a4)
result = dihedral_angle(a1.get_location(), a2.get_location(), a3.get_location(), a4.get_location());
}
}
return result;
}
float monomer::alpha() const
{
float result = 360;
try
{
if (m_index >= 1 and m_index + 2 < m_polymer->size())
{
auto &prev = m_polymer->at(m_index - 1);
auto &next = m_polymer->at(m_index + 1);
auto &nextNext = m_polymer->at(m_index + 2);
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() << '\n';
}
return result;
}
float monomer::kappa() const
{
float result = 360;
try
{
if (m_index >= 2 and m_index + 2 < m_polymer->size())
{
auto &prevPrev = m_polymer->at(m_index - 2);
auto &nextNext = m_polymer->at(m_index + 2);
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() << '\n';
}
return result;
}
float monomer::tco() const
{
float result = 0.0;
try
{
if (m_index > 0)
{
auto &prev = m_polymer->at(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() << '\n';
}
return result;
}
float monomer::omega() const
{
float result = 360;
try
{
if (not is_last_in_chain())
result = omega(*this, m_polymer->at(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() << '\n';
}
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" } }
};
std::size_t monomer::nr_of_chis() const
{
std::size_t result = 0;
auto i = kChiAtomsMap.find(m_compound_id);
if (i != kChiAtomsMap.end())
result = i->second.size();
return result;
}
float monomer::chi(std::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" };
atoms.insert(atoms.end(), i->second.begin(), i->second.end());
// 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";
}
auto atom_0 = get_atom_by_atom_id(atoms[nr + 0]);
auto atom_1 = get_atom_by_atom_id(atoms[nr + 1]);
auto atom_2 = get_atom_by_atom_id(atoms[nr + 2]);
auto atom_3 = get_atom_by_atom_id(atoms[nr + 3]);
if (atom_0 and atom_1 and atom_2 and atom_3)
result = static_cast<float>(dihedral_angle(
atom_0.get_location(),
atom_1.get_location(),
atom_2.get_location(),
atom_3.get_location()));
}
}
catch (const std::exception &e)
{
if (VERBOSE > 0)
std::cerr << e.what() << '\n';
result = 0;
}
return result;
}
bool monomer::is_cis() const
{
bool result = false;
if (m_index + 1 < m_polymer->size())
{
auto &next = m_polymer->at(m_index + 1);
result = monomer::is_cis(*this, next);
}
return result;
}
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::has_alternate_backbone_atoms() const
{
bool result = false;
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;
}
}
return result;
}
float monomer::chiral_volume() const
{
float result = 0;
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 = 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 = dot_product(atom1.get_location() - centre.get_location(),
cross_product(atom2.get_location() - centre.get_location(), atom3.get_location() - centre.get_location()));
}
return result;
}
bool monomer::are_bonded(const monomer &a, const monomer &b, float errorMargin)
{
bool result = false;
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 = dihedral_angle(atoms[0], atoms[1], atoms[2], atoms[3]);
bool cis = std::abs(omega) <= 30.0;
float maxCACADistance = cis ? 3.0f : 3.8f;
result = std::abs(distanceCACA - maxCACADistance) < errorMargin;
}
catch (...)
{
}
return result;
}
float monomer::omega(const monomer &a, const monomer &b)
{
float result = 360;
auto a1 = a.get_atom_by_atom_id("CA");
auto a2 = a.get_atom_by_atom_id("C");
auto a3 = b.get_atom_by_atom_id("N");
auto a4 = b.get_atom_by_atom_id("CA");
if (a1 and a2 and a3 and a4)
result = static_cast<float>(dihedral_angle(
a1.get_location(),
a2.get_location(),
a3.get_location(),
a4.get_location()));
return result;
}
bool monomer::is_cis(const monomer &a, const monomer &b)
{
return std::abs(omega(a, b)) < 30.0f;
}
atom monomer::create_new_atom(atom_type inType, const std::string &inAtomID, point inLocation)
{
atom a = residue::create_new_atom(inType, inAtomID, inLocation);
a.set_property("group_PDB", "ATOM");
return a;
}
// --------------------------------------------------------------------
// polymer
polymer::polymer(structure &s, const std::string &entityID, const std::string &asym_id, const std::string &auth_asym_id)
: m_structure(const_cast<structure *>(&s))
, m_entity_id(entityID)
, m_asym_id(asym_id)
, m_pdb_strand_id(auth_asym_id)
{
using namespace cif::literals;
std::map<std::size_t, std::size_t> ix;
auto &poly_seq_scheme = s.get_datablock()["pdbx_poly_seq_scheme"];
reserve(poly_seq_scheme.size());
for (auto r : poly_seq_scheme.find("asym_id"_key == asym_id))
{
int seqID;
std::string compoundID, pdbSeqNum, pdbInsCode;
cif::tie(seqID, pdbSeqNum, compoundID, pdbInsCode) = r.get("seq_id", "pdb_seq_num", "mon_id", "pdb_ins_code");
std::size_t index = size();
// store only the first
if (not ix.count(seqID))
{
ix[seqID] = index;
emplace_back(*this, index, seqID, pdbSeqNum, pdbInsCode, compoundID);
}
else if (VERBOSE > 0)
{
monomer m{ *this, index, seqID, pdbSeqNum, pdbInsCode, compoundID };
std::cerr << "Dropping alternate residue " << m << '\n';
}
}
}
// std::string polymer::chainID() const
// {
// return mPolySeq.front()["pdb_strand_id"].as<std::string>();
// }
// monomer &polymer::getBySeqID(int seqID)
// {
// for (auto &m : *this)
// if (m.get_seq_id() == seqID)
// return m;
// throw std::runtime_error("monomer with seqID " + std::to_string(seqID) + " not found in polymer " + m_asym_id);
// }
// const monomer &polymer::getBySeqID(int seqID) const
// {
// for (auto &m : *this)
// if (m.get_seq_id() == seqID)
// return m;
// throw std::runtime_error("monomer with seqID " + std::to_string(seqID) + " not found in polymer " + m_asym_id);
// }
// int polymer::Distance(const monomer &a, const monomer &b) const
// {
// int result = std::numeric_limits<int>::max();
// if (a.get_asym_id() == b.get_asym_id())
// {
// int ixa = std::numeric_limits<int>::max(), ixb = std::numeric_limits<int>::max();
// int ix = 0, f = 0;
// for (auto &m : *this)
// {
// if (m.get_seq_id() == a.get_seq_id())
// ixa = ix, ++f;
// if (m.get_seq_id() == b.get_seq_id())
// ixb = ix, ++f;
// if (f == 2)
// {
// result = std::abs(ixa - ixb);
// break;
// }
// }
// }
// return result;
// }
// --------------------------------------------------------------------
sugar::sugar(branch &branch, const std::string &compoundID,
const std::string &asym_id, int authSeqID)
: residue(branch.get_structure(), compoundID, asym_id, 0, asym_id, std::to_string(authSeqID), "")
, m_branch(&branch)
{
}
sugar::sugar(sugar &&rhs)
: residue(std::forward<residue>(rhs))
, m_branch(rhs.m_branch)
{
}
sugar &sugar::operator=(sugar &&rhs)
{
if (this != &rhs)
{
residue::operator=(std::forward<residue>(rhs));
m_branch = rhs.m_branch;
}
return *this;
}
// bool sugar::hasLinkedSugarAtLeavingO(int leavingO) const
// {
// return false;
// }
// sugar &sugar::operator[](int leavingO)
// {
// throw std::logic_error("not implemented");
// }
// const sugar &sugar::operator[](int leavingO) const
// {
// throw std::logic_error("not implemented");
// }
std::string sugar::name() const
{
std::string result;
if (m_compound_id == "MAN")
result += "alpha-D-mannopyranose";
else if (m_compound_id == "BMA")
result += "beta-D-mannopyranose";
else if (m_compound_id == "NAG")
result += "2-acetamido-2-deoxy-beta-D-glucopyranose";
else if (m_compound_id == "NDG")
result += "2-acetamido-2-deoxy-alpha-D-glucopyranose";
else if (m_compound_id == "FUC")
result += "alpha-L-fucopyranose";
else if (m_compound_id == "FUL")
result += "beta-L-fucopyranose";
else
{
auto compound = compound_factory::instance().create(m_compound_id);
if (compound)
result += compound->name();
else
result += m_compound_id;
}
return result;
}
cif::mm::atom sugar::add_atom(row_initializer atom_info)
{
auto &db = m_structure->get_datablock();
auto &atom_site = db["atom_site"];
auto atom_id = atom_site.get_unique_id("");
atom_info.set_value({ "group_PDB", "HETATM" });
atom_info.set_value({ "id", atom_id });
atom_info.set_value({ "label_entity_id", m_branch->get_entity_id() });
atom_info.set_value({ "label_asym_id", m_branch->get_asym_id() });
atom_info.set_value({ "label_comp_id", m_compound_id });
atom_info.set_value({ "label_seq_id", "." });
atom_info.set_value({ "label_alt_id", "." });
atom_info.set_value({ "auth_asym_id", m_branch->get_asym_id() });
atom_info.set_value({ "auth_comp_id", m_compound_id });
atom_info.set_value({ "auth_seq_id", m_pdb_seq_num });
atom_info.set_value({ "occupancy", 1.0, 2 });
atom_info.set_value({ "B_iso_or_equiv", 30.0, 2 });
atom_info.set_value({ "pdbx_PDB_model_num", 1 });
auto row = atom_site.emplace(std::move(atom_info));
auto result = m_structure->emplace_atom(db, row);
residue::add_atom(result);
return result;
}
branch::branch(structure &structure, const std::string &asym_id, const std::string &entity_id)
: m_structure(&structure)
, m_asym_id(asym_id)
, m_entity_id(entity_id)
{
using namespace literals;
auto &db = structure.get_datablock();
auto &struct_asym = db["struct_asym"];
auto &branch_scheme = db["pdbx_branch_scheme"];
auto &branch_link = db["pdbx_entity_branch_link"];
for (const auto &asym_entity_id : struct_asym.find<std::string>("id"_key == asym_id, "entity_id"))
{
for (const auto &[comp_id, num] : branch_scheme.find<std::string, int>(
"asym_id"_key == asym_id, "mon_id", "pdb_seq_num"))
{
emplace_back(*this, comp_id, asym_id, num);
}
for (const auto &[num1, num2, atom1, atom2] : branch_link.find<std::size_t, std::size_t, std::string, std::string>(
"entity_id"_key == asym_entity_id, "entity_branch_list_num_1", "entity_branch_list_num_2", "atom_id_1", "atom_id_2"))
{
// if (not iequals(atom1, "c1"))
// throw std::runtime_error("invalid pdbx_entity_branch_link");
auto &s1 = at(num1 - 1);
auto &s2 = at(num2 - 1);
s1.set_link(s2.get_atom_by_atom_id(atom2));
}
break;
}
}
void branch::link_atoms()
{
if (not empty())
{
using namespace literals;
auto &db = m_structure->get_datablock();
auto &branch_link = db["pdbx_entity_branch_link"];
auto entity_id = front().get_entity_id();
for (const auto &[num1, num2, atom1, atom2] : branch_link.find<std::size_t, std::size_t, std::string, std::string>(
"entity_id"_key == entity_id, "entity_branch_list_num_1", "entity_branch_list_num_2", "atom_id_1", "atom_id_2"))
{
// if (not iequals(atom1, "c1"))
// throw std::runtime_error("invalid pdbx_entity_branch_link");
auto &s1 = at(num1 - 1);
auto &s2 = at(num2 - 1);
s1.set_link(s2.get_atom_by_atom_id(atom2));
}
}
}
sugar &branch::get_sugar_by_num(int nr)
{
auto i = find_if(begin(), end(), [nr](const sugar &s)
{ return s.num() == nr; });
if (i == end())
throw std::out_of_range("Sugar with num " + std::to_string(nr) + " not found in branch " + m_asym_id);
return *i;
}
std::string branch::name() const
{
return empty() ? "" : name(front());
}
sugar &branch::construct_sugar(const std::string &compound_id)
{
auto &db = m_structure->get_datablock();
auto compound = compound_factory::instance().create(compound_id);
if (compound == nullptr)
throw std::runtime_error("Trying to insert unknown compound " + compound_id + " (not found in CCD)");
auto &chemComp = db["chem_comp"];
auto r = chemComp.find(key("id") == compound_id);
if (r.empty())
{
chemComp.emplace({ { "id", compound_id },
{ "name", compound->name() },
{ "formula", compound->formula() },
{ "formula_weight", compound->formula_weight() },
{ "type", compound->type() } });
}
sugar &result = emplace_back(*this, compound_id, m_asym_id, static_cast<int>(size() + 1));
db["pdbx_branch_scheme"].emplace({ { "asym_id", result.get_asym_id() },
{ "entity_id", result.get_entity_id() },
{ "num", result.num() },
{ "mon_id", result.get_compound_id() },
{ "pdb_asym_id", result.get_asym_id() },
{ "pdb_seq_num", result.get_pdb_seq_num() },
{ "pdb_mon_id", result.get_compound_id() },
{ "auth_asym_id", result.get_pdb_strand_id() },
{ "auth_mon_id", result.get_compound_id() },
{ "auth_seq_num", result.get_pdb_seq_num() },
{ "hetero", "n" } });
return result;
}
sugar &branch::construct_sugar(const std::string &compound_id, const std::string &atom_id,
int linked_sugar_nr, const std::string &linked_atom_id)
{
auto &result = construct_sugar(compound_id);
auto &linked = get_sugar_by_num(linked_sugar_nr);
result.set_link(linked.get_atom_by_atom_id(linked_atom_id));
auto &db = m_structure->get_datablock();
auto &pdbx_entity_branch_link = db["pdbx_entity_branch_link"];
auto linkID = pdbx_entity_branch_link.get_unique_id("");
db["pdbx_entity_branch_link"].emplace({ { "link_id", linkID },
{ "entity_id", get_entity_id() },
{ "entity_branch_list_num_1", result.num() },
{ "comp_id_1", compound_id },
{ "atom_id_1", atom_id },
{ "leaving_atom_id_1", "O1" }, /// TODO: Need to fix this!
{ "entity_branch_list_num_2", linked.num() },
{ "comp_id_2", linked.get_compound_id() },
{ "atom_id_2", linked_atom_id },
{ "leaving_atom_id_2", "." },
{ "value_order", "sing" } });
return result;
}
std::string branch::name(const sugar &s) const
{
using namespace literals;
std::string result;
for (auto &sn : *this)
{
if (not sn.get_link() or sn.get_link().get_auth_seq_id() != s.get_pdb_seq_num())
continue;
auto n = name(sn) + "-(1-" + sn.get_link().get_label_atom_id().substr(1) + ')';
result = result.empty() ? n : result + "-[" + n + ']';
}
if (not result.empty() and result.back() != ']')
result += '-';
return result + s.name();
}
float branch::weight() const
{
return std::accumulate(begin(), end(), 0.f, [](float sum, const sugar &s)
{
auto compound = compound_factory::instance().create(s.get_compound_id());
if (compound)
sum += compound->formula_weight();
return sum; });
}
// --------------------------------------------------------------------
// structure
structure::structure(file &p, std::size_t modelNr, structure_open_options options)
: structure(p.front(), modelNr, options)
{
}
structure::structure(datablock &db, std::size_t modelNr, structure_open_options options)
: m_db(db)
, m_model_nr(modelNr)
{
if (db.get_validator() == nullptr)
db.load_dictionary();
auto &atom_site = db["atom_site"];
load_atoms_for_model(options);
// Check to see if we should actually load another model?
if (m_atoms.empty() and m_model_nr == 1)
{
std::optional<std::size_t> model_nr;
cif::tie(model_nr) = atom_site.front().get("pdbx_PDB_model_num");
if (model_nr and *model_nr != m_model_nr)
{
if (VERBOSE > 0)
std::cerr << "No atoms loaded for model 1, trying model " << *model_nr << '\n';
m_model_nr = *model_nr;
load_atoms_for_model(options);
}
}
if (m_atoms.empty())
{
if (VERBOSE >= 0)
std::cerr << "Warning: no atoms loaded\n";
}
else
load_data();
}
void structure::load_atoms_for_model(structure_open_options options)
{
using namespace literals;
auto &atom_site = m_db["atom_site"];
condition c = "pdbx_PDB_model_num"_key == null or "pdbx_PDB_model_num"_key == m_model_nr;
if (options.skip_hydrogen)
c = std::move(c) and (cif::key("type_symbol") != "H" and cif::key("type_symbol") != "D");
if (options.skip_water)
c = std::move(c) and (cif::key("auth_comp_id") != "HOH" and cif::key("auth_comp_id") != "H20" and cif::key("auth_comp_id") != "WAT");
if (options.skip_hetatom)
{
if (options.skip_water)
c = std::move(c) and cif::key("group_PDB") != "HETATM";
else
c = std::move(c) and (cif::key("group_PDB") != "HETATM" or (cif::key("auth_comp_id") == "HOH" or cif::key("auth_comp_id") == "H20" or cif::key("auth_comp_id") == "WAT"));
}
if (options.min_b_factor.has_value())
c = std::move(c) and cif::key("B_iso_or_equiv") >= *options.min_b_factor;
if (options.max_b_factor.has_value())
c = std::move(c) and cif::key("B_iso_or_equiv") <= *options.max_b_factor;
if (not options.asyms.empty())
{
condition tmp_c;
for (auto asym_id : options.asyms)
tmp_c = std::move(tmp_c) or cif::key("label_asym_id") == asym_id;
c = std::move(c) and std::move(tmp_c);
}
if (options.occupancy_mode == occupancy_policy::ALL)
{
for (auto id : atom_site.find<std::string>(std::move(c), "id"))
emplace_atom(std::make_shared<atom::atom_impl>(m_db, id));
}
else if (options.occupancy_mode == occupancy_policy::UNOCCUPIED)
{
for (auto id : atom_site.find<std::string>(std::move(c), "id"))
{
auto a = std::make_shared<atom::atom_impl>(m_db, id);
if (a->get_property_float("occupancy") > 0)
continue;
emplace_atom(a);
}
}
else
{
std::vector<cif::mm::atom> atoms;
std::map<std::tuple<std::string, int>, std::map<std::string, float>> alts;
for (auto id : atom_site.find<std::string>(std::move(c), "id"))
{
auto a = atoms.emplace_back(std::make_shared<atom::atom_impl>(m_db, id));
if (a.is_alternate())
{
auto key = std::make_tuple(a.get_label_asym_id(), a.get_label_seq_id());
auto alt_id = a.get_label_alt_id();
if (auto i = alts.find(key); i != alts.end())
i->second[alt_id] += a.get_occupancy();
else
alts[key][alt_id] = a.get_occupancy();
}
}
for (auto &&[key, value] : alts)
{
// const auto &[asym_id, seq_id] = key;
// select highest occupancy for this residue's alternates
std::string alt_id;
float occupancy = options.occupancy_mode == occupancy_policy::MAX ? 0.f : std::numeric_limits<float>::max();
for (const auto &[alt_key, alt_value] : value)
{
if (options.occupancy_mode == occupancy_policy::MAX)
{
if (occupancy < alt_value)
{
alt_id = alt_key;
occupancy = alt_value;
}
}
else
{
if (occupancy > alt_value)
{
alt_id = alt_key;
occupancy = alt_value;
}
}
}
value.clear();
value.emplace(alt_id, occupancy);
}
for (auto a : atoms)
{
if (a.is_alternate())
{
auto key = std::make_tuple(a.get_label_asym_id(), a.get_label_seq_id());
if (alts[key].contains(a.get_label_alt_id()))
emplace_atom(a);
}
else
emplace_atom(a);
}
}
}
void structure::load_data()
{
auto &polySeqScheme = m_db["pdbx_poly_seq_scheme"];
for (const auto &[asym_id, auth_asym_id, entityID] : polySeqScheme.rows<std::string, std::string, std::string>("asym_id", "pdb_strand_id", "entity_id"))
{
if (m_polymers.empty() or m_polymers.back().get_asym_id() != asym_id)
m_polymers.emplace_back(*this, entityID, asym_id, auth_asym_id);
}
auto &branchScheme = m_db["pdbx_branch_scheme"];
for (const auto &[asym_id, entity_id] : branchScheme.rows<std::string, std::string>("asym_id", "entity_id"))
{
if (m_branches.empty() or m_branches.back().get_asym_id() != asym_id)
m_branches.emplace_back(*this, asym_id, entity_id);
}
auto &nonPolyScheme = m_db["pdbx_nonpoly_scheme"];
for (const auto &[asym_id, monID, pdbStrandID, pdbSeqNum, pdbInsCode] :
nonPolyScheme.rows<std::string, std::string, std::string, std::string, std::string>("asym_id", "mon_id", "pdb_strand_id", "pdb_seq_num", "pdb_ins_code"))
m_non_polymers.emplace_back(*this, monID, asym_id, 0, pdbStrandID, pdbSeqNum, pdbInsCode);
// place atoms in residues
using key_type = std::tuple<std::string, int, std::string>;
std::map<key_type, residue *> resMap;
for (auto &poly : m_polymers)
{
for (auto &res : poly)
resMap[{ res.get_asym_id(), res.get_seq_id(), res.get_pdb_seq_num() }] = &res;
}
for (auto &res : m_non_polymers)
resMap[{ res.get_asym_id(), res.get_seq_id(), res.get_pdb_seq_num() }] = &res;
std::set<std::string> sugars;
for (auto &branch : m_branches)
{
for (auto &sugar : branch)
{
resMap[{ sugar.get_asym_id(), sugar.get_seq_id(), sugar.get_pdb_seq_num() }] = &sugar;
sugars.insert(sugar.get_compound_id());
}
}
for (auto &atom : m_atoms)
{
key_type k(atom.get_label_asym_id(), atom.get_label_seq_id(), atom.get_auth_seq_id());
auto ri = resMap.find(k);
if (ri == resMap.end())
{
if (VERBOSE > 0)
std::cerr << "Missing residue for atom " << atom << '\n';
// see if it might match a non poly
for (auto &res : m_non_polymers)
{
if (res.get_asym_id() != atom.get_label_asym_id())
continue;
res.add_atom(atom);
break;
}
continue;
}
ri->second->add_atom(atom);
}
// what the ...
m_branches.erase(std::remove_if(m_branches.begin(), m_branches.end(), [](const branch &b)
{ return b.empty(); }),
m_branches.end());
for (auto &branch : m_branches)
branch.link_atoms();
}
EntityType structure::get_entity_type_for_entity_id(const std::string entityID) const
{
using namespace literals;
auto &entity = m_db["entity"];
auto entity_type = entity.find1<std::string>("id"_key == entityID, "type");
EntityType result;
if (iequals(entity_type, "polymer"))
result = EntityType::Polymer;
else if (iequals(entity_type, "non-polymer"))
result = EntityType::NonPolymer;
else if (iequals(entity_type, "macrolide"))
result = EntityType::Macrolide;
else if (iequals(entity_type, "water"))
result = EntityType::Water;
else if (iequals(entity_type, "branched"))
result = EntityType::Branched;
else
throw std::runtime_error("Unknown entity type " + entity_type);
return result;
}
EntityType structure::get_entity_type_for_asym_id(const std::string asym_id) const
{
using namespace literals;
auto &struct_asym = m_db["struct_asym"];
auto entityID = struct_asym.find1<std::string>("id"_key == asym_id, "entity_id");
return get_entity_type_for_entity_id(entityID);
}
bool structure::has_atom_id(const std::string &id) const
{
assert(m_atoms.size() == m_atom_index.size());
bool result = false;
int L = 0, R = static_cast<int>(m_atoms.size() - 1);
while (L <= R)
{
int i = (L + R) / 2;
const atom &atom = m_atoms[m_atom_index[i]];
int d = atom.id().compare(id);
if (d == 0)
{
result = true;
break;
}
if (d < 0)
L = i + 1;
else
R = i - 1;
}
return result;
}
atom structure::get_atom_by_id(const std::string &id) const
{
assert(m_atoms.size() == m_atom_index.size());
int L = 0, R = static_cast<int>(m_atoms.size() - 1);
while (L <= R)
{
int i = (L + R) / 2;
const atom &atom = m_atoms[m_atom_index[i]];
int d = atom.id().compare(id);
if (d == 0)
return atom;
if (d < 0)
L = i + 1;
else
R = i - 1;
}
throw std::out_of_range("Could not find atom with id " + id);
}
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");
}
atom structure::get_atom_by_position(point p) const
{
double dist = std::numeric_limits<double>::max();
std::size_t index = std::numeric_limits<std::size_t>::max();
for (std::size_t i = 0; i < m_atoms.size(); ++i)
{
auto &a = m_atoms.at(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);
return {};
}
atom structure::get_atom_by_position_and_type(point p, std::string_view type, std::string_view res_type) const
{
double dist = std::numeric_limits<double>::max();
std::size_t index = std::numeric_limits<std::size_t>::max();
for (std::size_t i = 0; i < m_atoms.size(); ++i)
{
auto &a = m_atoms.at(i);
if (a.get_label_comp_id() != res_type)
continue;
if (a.get_label_atom_id() != type)
continue;
auto d = distance(a.get_location(), p);
if (dist > d)
{
dist = d;
index = i;
}
}
if (index < m_atoms.size())
return m_atoms.at(index);
return {};
}
polymer &structure::get_polymer_by_asym_id(const std::string &asym_id)
{
for (auto &poly : m_polymers)
{
if (poly.get_asym_id() != asym_id)
continue;
return poly;
}
throw std::runtime_error("polymer with asym id " + asym_id + " not found");
}
residue &structure::create_residue(const std::vector<atom> &atoms)
{
return m_non_polymers.emplace_back(*this, atoms);
}
residue &structure::get_residue(const std::string &asym_id, int seqID, const std::string &authSeqID)
{
if (seqID == 0)
{
for (auto &res : m_non_polymers)
{
if (res.get_asym_id() == asym_id and (authSeqID.empty() or res.get_pdb_seq_num() == authSeqID))
return res;
}
}
for (auto &poly : m_polymers)
{
if (poly.get_asym_id() != asym_id)
continue;
for (auto &res : poly)
{
if (res.get_seq_id() == seqID)
return res;
}
}
for (auto &branch : m_branches)
{
if (branch.get_asym_id() != asym_id)
continue;
for (auto &sugar : branch)
{
if (sugar.get_asym_id() == asym_id and sugar.get_pdb_seq_num() == authSeqID)
return sugar;
}
}
std::string desc = asym_id;
if (seqID != 0)
desc += "/" + std::to_string(seqID);
if (not authSeqID.empty())
desc += "-" + authSeqID;
throw std::out_of_range("Could not find residue " + desc);
}
residue &structure::get_residue(const std::string &asym_id, const std::string &compID, int seqID, const std::string &authSeqID)
{
if (seqID == 0)
{
for (auto &res : m_non_polymers)
{
if (res.get_asym_id() == asym_id and res.get_pdb_seq_num() == authSeqID and res.get_compound_id() == compID)
return res;
}
}
for (auto &poly : m_polymers)
{
if (poly.get_asym_id() != asym_id)
continue;
for (auto &res : poly)
{
if (res.get_seq_id() == seqID and res.get_compound_id() == compID)
return res;
}
}
for (auto &branch : m_branches)
{
if (branch.get_asym_id() != asym_id)
continue;
for (auto &sugar : branch)
{
if (sugar.get_asym_id() == asym_id and sugar.get_pdb_seq_num() == authSeqID and sugar.get_compound_id() == compID)
return sugar;
}
}
std::string desc = asym_id;
if (seqID != 0)
desc += "/" + std::to_string(seqID);
if (not authSeqID.empty())
desc += "-" + authSeqID;
throw std::out_of_range("Could not find residue " + desc + " of type " + compID);
}
branch &structure::get_branch_by_asym_id(const std::string &asym_id)
{
for (auto &branch : m_branches)
{
if (branch.get_asym_id() == asym_id)
return branch;
}
throw std::runtime_error("branch not found for asym id " + asym_id);
}
std::string structure::insert_compound(const std::string &compoundID, bool is_entity)
{
using namespace literals;
auto compound = compound_factory::instance().create(compoundID);
if (compound == nullptr)
throw std::runtime_error("Trying to insert unknown compound " + compoundID + " (not found in CCD)");
auto &chemComp = m_db["chem_comp"];
auto r = chemComp.find(key("id") == compoundID);
if (r.empty())
{
chemComp.emplace({ { "id", compoundID },
{ "name", compound->name() },
{ "formula", compound->formula() },
{ "formula_weight", compound->formula_weight() },
{ "type", compound->type() } });
}
std::string entity_id;
if (is_entity)
{
auto &pdbxEntityNonpoly = m_db["pdbx_entity_nonpoly"];
entity_id = pdbxEntityNonpoly.find_first<std::string>("comp_id"_key == compoundID, "entity_id");
if (entity_id.empty())
{
auto &entity = m_db["entity"];
entity_id = entity.get_unique_id("");
entity.emplace({ { "id", entity_id },
{ "type", "non-polymer" },
{ "pdbx_description", compound->name() },
{ "formula_weight", compound->formula_weight() } });
pdbxEntityNonpoly.emplace({ { "entity_id", entity_id },
{ "name", compound->name() },
{ "comp_id", compoundID } });
}
}
return entity_id;
}
// --------------------------------------------------------------------
atom &structure::emplace_atom(atom &&atom)
{
int L = 0, R = static_cast<int>(m_atom_index.size() - 1);
while (L <= R)
{
int i = (L + R) / 2;
auto &ai = m_atoms[m_atom_index[i]];
int d = ai.id().compare(atom.id());
if (d == 0)
throw std::runtime_error("Duplicate atom ID " + atom.id());
if (d < 0)
L = i + 1;
else
R = i - 1;
}
if (R == -1) // msvc...
m_atom_index.insert(m_atom_index.begin(), m_atoms.size());
else
m_atom_index.insert(m_atom_index.begin() + R + 1, m_atoms.size());
// make sure the atom_type is known
auto &atom_type = m_db["atom_type"];
std::string symbol = atom.get_property("type_symbol");
using namespace cif::literals;
if (not atom_type.contains("symbol"_key == symbol))
atom_type.emplace({ { "symbol", symbol } });
return m_atoms.emplace_back(std::move(atom));
}
void structure::remove_atom(atom &a, bool removeFromResidue)
{
using namespace literals;
auto &atomSite = m_db["atom_site"];
if (a.is_water())
{
auto ra = atomSite.find1("id"_key == a.id());
if (ra)
{
auto &nps = m_db["pdbx_nonpoly_scheme"];
for (auto rnp : atomSite.get_children(ra, nps))
nps.erase(rnp);
}
}
else if (removeFromResidue)
{
try
{
auto &res = get_residue(a);
res.m_atoms.erase(std::remove(res.m_atoms.begin(), res.m_atoms.end(), a), res.m_atoms.end());
}
catch (const std::exception &ex)
{
if (VERBOSE > 0)
std::cerr << "Error removing atom from residue: " << ex.what() << '\n';
}
}
for (auto ri : atomSite.find("id"_key == a.id()))
{
// also remove struct_conn records for this atom
auto &structConn = m_db["struct_conn"];
condition cond;
for (std::string prefix : { "ptnr1_", "ptnr2_", "pdbx_ptnr3_" })
{
if (a.get_label_seq_id() == 0)
cond = std::move(cond) or (cif::key(prefix + "label_asym_id") == a.get_label_asym_id() and
cif::key(prefix + "label_seq_id") == null and
cif::key(prefix + "auth_seq_id") == a.get_auth_seq_id() and
cif::key(prefix + "label_atom_id") == a.get_label_atom_id());
else
cond = std::move(cond) or (cif::key(prefix + "label_asym_id") == a.get_label_asym_id() and
cif::key(prefix + "label_seq_id") == a.get_label_seq_id() and
cif::key(prefix + "auth_seq_id") == a.get_auth_seq_id() and
cif::key(prefix + "label_atom_id") == a.get_label_atom_id());
}
if (cond)
structConn.erase(std::move(cond));
atomSite.erase(ri);
break;
}
assert(m_atom_index.size() == m_atoms.size());
#ifndef NDEBUG
bool removed = false;
#endif
int L = 0, R = static_cast<int>(m_atom_index.size() - 1);
while (L <= R)
{
int i = (L + R) / 2;
const atom &atom = m_atoms[m_atom_index[i]];
int d = atom.id().compare(a.id());
if (d == 0)
{
m_atoms.erase(m_atoms.begin() + m_atom_index[i]);
auto ai = m_atom_index[i];
m_atom_index.erase(m_atom_index.begin() + i);
for (auto &j : m_atom_index)
{
if (j > ai)
--j;
}
#ifndef NDEBUG
removed = true;
#endif
break;
}
if (d < 0)
L = i + 1;
else
R = i - 1;
}
#ifndef NDEBUG
assert(removed);
#endif
}
void structure::swap_atoms(atom a1, atom a2)
{
auto &atomSites = m_db["atom_site"];
try
{
auto r1 = atomSites.find1(key("id") == a1.id());
auto r2 = atomSites.find1(key("id") == a2.id());
for (std::string fld : std::initializer_list<std::string>{ "label_atom_id", "auth_atom_id", "type_symbol" })
{
auto l1 = r1[fld];
auto l2 = r2[fld];
l1.swap(l2);
}
}
catch (const std::exception &ex)
{
std::throw_with_nested(std::runtime_error("Failed to swap atoms"));
}
}
void structure::move_atom(atom a, point p)
{
a.set_location(p);
}
void structure::change_residue(residue &res, const std::string &newCompound,
const std::vector<std::tuple<std::string, std::string>> &remappedAtoms)
{
using namespace literals;
std::string asym_id = res.get_asym_id();
const auto compound = compound_factory::instance().create(newCompound);
if (not compound)
throw std::runtime_error("Unknown compound " + newCompound);
// First make sure the compound is already known or insert it.
// And if the residue is an entity, we must make sure it exists
std::string entityID;
if (res.is_entity())
{
// create a copy of the entity first
auto &entity = m_db["entity"];
entityID = entity.find_first<std::string>("type"_key == "non-polymer" and "pdbx_description"_key == compound->name(), "id");
if (entityID.empty())
{
entityID = entity.get_unique_id("");
entity.emplace({ { "id", entityID },
{ "type", "non-polymer" },
{ "pdbx_description", compound->name() },
{ "formula_weight", compound->formula_weight() } });
auto &pdbxEntityNonpoly = m_db["pdbx_entity_nonpoly"];
pdbxEntityNonpoly.emplace({ { "entity_id", entityID },
{ "name", compound->name() },
{ "comp_id", newCompound } });
}
auto &pdbxNonPolyScheme = m_db["pdbx_nonpoly_scheme"];
for (auto nps : pdbxNonPolyScheme.find("asym_id"_key == asym_id))
{
nps.assign("mon_id", newCompound, true);
nps.assign("pdb_mon_id", newCompound, true);
nps.assign("auth_mon_id", newCompound, true);
nps.assign("entity_id", entityID, true);
}
// create rest
auto &chemComp = m_db["chem_comp"];
if (not chemComp.contains(key("id") == newCompound))
{
chemComp.emplace({ { "id", newCompound },
{ "name", compound->name() },
{ "formula", compound->formula() },
{ "formula_weight", compound->formula_weight() },
{ "type", compound->type() } });
}
// update the struct_asym for the new entity
m_db["struct_asym"].update_value("id"_key == asym_id, "entity_id", entityID);
}
else
insert_compound(newCompound, false);
res.set_compound_id(newCompound);
auto &atomSites = m_db["atom_site"];
auto atoms = res.atoms();
for (const auto &[a1, a2] : remappedAtoms)
{
auto i = find_if(atoms.begin(), atoms.end(), [id = a1](const atom &a)
{ return a.get_label_atom_id() == id; });
if (i == atoms.end())
{
if (VERBOSE >= 0)
std::cerr << "Missing atom for atom ID " << a1 << '\n';
continue;
}
auto r = atomSites.find(key("id") == i->id());
if (r.size() != 1)
continue;
if (a2.empty() or a2 == ".")
{
i->set_property("label_comp_id", newCompound);
remove_atom(*i);
}
else if (a1 != a2)
{
auto ra = r.front();
ra["label_atom_id"] = a2;
ra["auth_atom_id"] = a2;
ra["type_symbol"] = atom_type_traits(compound->get_atom_by_atom_id(a2).type_symbol).symbol();
}
}
for (auto a : atoms)
{
atomSites.update_value(key("id") == a.id(), "label_comp_id", newCompound);
atomSites.update_value(key("id") == a.id(), "auth_comp_id", newCompound);
}
}
void structure::remove_residue(const std::string &asym_id, int seq_id, const std::string &auth_seq_id)
{
if (seq_id == 0)
{
for (auto &res : m_non_polymers)
{
if (res.get_asym_id() == asym_id and (auth_seq_id.empty() or res.get_pdb_seq_num() == auth_seq_id))
{
remove_residue(res);
return;
}
}
}
for (auto &poly : m_polymers)
{
if (poly.get_asym_id() != asym_id)
continue;
for (auto &res : poly)
{
if (res.get_seq_id() == seq_id)
{
remove_residue(res);
return;
}
}
}
for (auto &branch : m_branches)
{
if (branch.get_asym_id() != asym_id)
continue;
for (auto &sugar : branch)
{
if (sugar.get_asym_id() == asym_id and sugar.get_pdb_seq_num() == auth_seq_id)
{
remove_residue(sugar);
return;
}
}
}
}
void structure::remove_residue(residue &res)
{
using namespace literals;
auto atoms = res.atoms();
switch (res.entity_type())
{
case EntityType::Polymer:
{
auto &m = dynamic_cast<monomer &>(res);
m_db["pdbx_poly_seq_scheme"].erase(
"asym_id"_key == res.get_asym_id() and
"seq_id"_key == res.get_seq_id());
for (auto &poly : m_polymers)
poly.erase(std::remove(poly.begin(), poly.end(), m), poly.end());
break;
}
case EntityType::NonPolymer:
m_db["pdbx_nonpoly_scheme"].erase("asym_id"_key == res.get_asym_id());
m_db["struct_asym"].erase("id"_key == res.get_asym_id());
m_non_polymers.erase(std::remove(m_non_polymers.begin(), m_non_polymers.end(), res), m_non_polymers.end());
break;
case EntityType::Water:
m_db["pdbx_nonpoly_scheme"].erase("asym_id"_key == res.get_asym_id());
m_non_polymers.erase(std::remove(m_non_polymers.begin(), m_non_polymers.end(), res), m_non_polymers.end());
break;
case EntityType::Branched:
{
auto &s = dynamic_cast<sugar &>(res);
remove_sugar(s);
atoms.clear();
break;
}
case EntityType::Macrolide:
// TODO: Fix this?
throw std::runtime_error("no support for macrolides yet");
}
for (auto atom : atoms)
remove_atom(atom, false);
}
void structure::remove_sugar(sugar &s)
{
using namespace literals;
std::string asym_id = s.get_asym_id();
branch &branch = get_branch_by_asym_id(asym_id);
auto si = std::find(branch.begin(), branch.end(), s);
if (si == branch.end())
throw std::runtime_error("sugar not part of branch");
std::size_t six = si - branch.begin();
if (six == 0) // first sugar, means the death of this branch
remove_branch(branch);
else
{
std::set<std::size_t> dix;
std::stack<std::size_t> test;
test.push(s.num());
while (not test.empty())
{
auto tix = test.top();
test.pop();
if (dix.count(tix))
continue;
dix.insert(tix);
for (auto &s2 : branch)
{
if (s2.get_link_nr() == tix)
test.push(s2.num());
}
for (auto atom : branch[tix - 1].atoms())
remove_atom(atom, false);
}
branch.erase(remove_if(branch.begin(), branch.end(), [dix](const sugar &s)
{ return dix.count(s.num()); }),
branch.end());
auto entity_id = create_entity_for_branch(branch);
// Update the entity id of the asym
auto &struct_asym = m_db["struct_asym"];
auto r = struct_asym.find1("id"_key == asym_id);
r["entity_id"] = entity_id;
for (auto &sugar : branch)
{
for (auto atom : sugar.atoms())
atom.set_property("label_entity_id", entity_id);
}
auto &pdbx_branch_scheme = m_db["pdbx_branch_scheme"];
pdbx_branch_scheme.erase("asym_id"_key == asym_id);
for (auto &sugar : branch)
{
pdbx_branch_scheme.emplace({ { "asym_id", asym_id },
{ "entity_id", entity_id },
{ "num", sugar.num() },
{ "mon_id", sugar.get_compound_id() },
{ "pdb_asym_id", asym_id },
{ "pdb_seq_num", sugar.num() },
{ "pdb_mon_id", sugar.get_compound_id() },
// TODO: need fix, collect from nag_atoms?
{ "auth_asym_id", asym_id },
{ "auth_mon_id", sugar.get_compound_id() },
{ "auth_seq_num", sugar.get_pdb_seq_num() },
{ "hetero", "n" } });
}
}
}
void structure::remove_branch(branch &branch)
{
using namespace literals;
for (auto &sugar : branch)
{
auto atoms = sugar.atoms();
for (auto atom : atoms)
remove_atom(atom);
}
m_db["pdbx_branch_scheme"].erase("asym_id"_key == branch.get_asym_id());
m_db["struct_asym"].erase("id"_key == branch.get_asym_id());
m_db["struct_conn"].erase("ptnr1_label_asym_id"_key == branch.get_asym_id() or "ptnr2_label_asym_id"_key == branch.get_asym_id());
m_branches.erase(remove(m_branches.begin(), m_branches.end(), branch), m_branches.end());
}
std::string structure::create_non_poly_entity(const std::string &comp_id)
{
return insert_compound(comp_id, true);
}
std::string structure::create_non_poly(const std::string &entity_id, const std::vector<atom> &atoms)
{
using namespace cif::literals;
auto &struct_asym = m_db["struct_asym"];
std::string asym_id = struct_asym.get_unique_id();
struct_asym.emplace({ { "id", asym_id },
{ "pdbx_blank_PDB_chainid_flag", "N" },
{ "pdbx_modified", "N" },
{ "entity_id", entity_id },
{ "details", "?" } });
std::string comp_id = m_db["pdbx_entity_nonpoly"].find1<std::string>("entity_id"_key == entity_id, "comp_id");
auto &atom_site = m_db["atom_site"];
auto &res = m_non_polymers.emplace_back(*this, comp_id, asym_id, 0, asym_id, "1", "");
for (auto &atom : atoms)
{
auto atom_id = atom_site.get_unique_id("");
auto row = atom_site.emplace({ { "group_PDB", atom.get_property("group_PDB") },
{ "id", atom_id },
{ "type_symbol", atom.get_property("type_symbol") },
{ "label_atom_id", atom.get_property("label_atom_id") },
{ "label_alt_id", atom.get_property("label_alt_id") },
{ "label_comp_id", comp_id },
{ "label_asym_id", asym_id },
{ "label_entity_id", entity_id },
{ "label_seq_id", "." },
{ "pdbx_PDB_ins_code", "" },
{ "Cartn_x", atom.get_property("Cartn_x") },
{ "Cartn_y", atom.get_property("Cartn_y") },
{ "Cartn_z", atom.get_property("Cartn_z") },
{ "occupancy", atom.get_property("occupancy") },
{ "B_iso_or_equiv", atom.get_property("B_iso_or_equiv") },
{ "pdbx_formal_charge", atom.get_property("pdbx_formal_charge") },
{ "auth_seq_id", 1 },
{ "auth_comp_id", comp_id },
{ "auth_asym_id", asym_id },
{ "auth_atom_id", atom.get_property("label_atom_id") },
{ "pdbx_PDB_model_num", 1 } });
auto &newAtom = emplace_atom(std::make_shared<atom::atom_impl>(m_db, atom_id));
res.add_atom(newAtom);
}
auto &pdbx_nonpoly_scheme = m_db["pdbx_nonpoly_scheme"];
std::size_t ndb_nr = pdbx_nonpoly_scheme.find("asym_id"_key == asym_id and "entity_id"_key == entity_id).size() + 1;
pdbx_nonpoly_scheme.emplace({
{ "asym_id", asym_id },
{ "entity_id", entity_id },
{ "mon_id", comp_id },
{ "ndb_seq_num", ndb_nr },
{ "pdb_seq_num", res.get_pdb_seq_num() },
{ "auth_seq_num", res.get_pdb_seq_num() },
{ "pdb_mon_id", comp_id },
{ "auth_mon_id", comp_id },
{ "pdb_strand_id", asym_id },
{ "pdb_ins_code", "." },
});
return asym_id;
}
std::string structure::create_non_poly(const std::string &entity_id, std::vector<row_initializer> atoms)
{
using namespace literals;
auto &struct_asym = m_db["struct_asym"];
std::string asym_id = struct_asym.get_unique_id();
struct_asym.emplace({ { "id", asym_id },
{ "pdbx_blank_PDB_chainid_flag", "N" },
{ "pdbx_modified", "N" },
{ "entity_id", entity_id },
{ "details", "?" } });
std::string comp_id = m_db["pdbx_entity_nonpoly"].find1<std::string>("entity_id"_key == entity_id, "comp_id");
auto &atom_site = m_db["atom_site"];
auto &res = m_non_polymers.emplace_back(*this, comp_id, asym_id, 0, asym_id, "1", "");
for (auto &atom : atoms)
{
auto atom_id = atom_site.get_unique_id("");
atom.set_value("id", atom_id);
atom.set_value("label_asym_id", asym_id);
atom.set_value("auth_asym_id", asym_id);
atom.set_value("label_entity_id", entity_id);
atom.set_value_if_empty({ "group_PDB", "HETATM" });
atom.set_value_if_empty({ "label_comp_id", comp_id });
atom.set_value_if_empty({ "label_seq_id", "." });
atom.set_value_if_empty({ "auth_comp_id", comp_id });
atom.set_value_if_empty({ "auth_seq_id", 1 });
atom.set_value_if_empty({ "pdbx_PDB_model_num", 1 });
atom.set_value_if_empty({ "label_alt_id", "" });
atom.set_value_if_empty({ "occupancy", 1.0, 2 });
auto row = atom_site.emplace(atom.begin(), atom.end());
auto &newAtom = emplace_atom(std::make_shared<atom::atom_impl>(m_db, atom_id));
res.add_atom(newAtom);
}
auto &pdbx_nonpoly_scheme = m_db["pdbx_nonpoly_scheme"];
std::size_t ndb_nr = pdbx_nonpoly_scheme.find("asym_id"_key == asym_id and "entity_id"_key == entity_id).size() + 1;
pdbx_nonpoly_scheme.emplace({
{ "asym_id", asym_id },
{ "entity_id", entity_id },
{ "mon_id", comp_id },
{ "ndb_seq_num", ndb_nr },
{ "pdb_seq_num", res.get_pdb_seq_num() },
{ "auth_seq_num", res.get_pdb_seq_num() },
{ "pdb_mon_id", comp_id },
{ "auth_mon_id", comp_id },
{ "pdb_strand_id", asym_id },
{ "pdb_ins_code", "." },
});
return asym_id;
}
std::string structure::create_non_poly(const std::string &compound_id, bool skip_hydrogen)
{
auto compound = cif::compound_factory::instance().create(compound_id);
if (compound == nullptr)
throw std::runtime_error(std::format("{} is not a known compound", compound_id));
std::vector<cif::row_initializer> atoms;
for (auto a : compound->atoms())
{
// We skip H-atoms, as fitting without H-atoms works better and we avoid conflicts in protonation states between CCD and MONLIB
if (skip_hydrogen and cif::atom_type_traits(a.type_symbol).symbol() == "H")
continue;
auto ax = a.get_location().get_x();
auto ay = a.get_location().get_y();
auto az = a.get_location().get_z();
atoms.emplace_back(cif::row_initializer{
{ "type_symbol", cif::atom_type_traits(a.type_symbol).symbol() },
{ "label_atom_id", a.id },
{ "auth_atom_id", a.id },
{ "Cartn_x", ax },
{ "Cartn_y", ay },
{ "Cartn_z", az },
{ "B_iso_or_equiv", 30.00 } });
}
return create_non_poly(create_non_poly_entity(compound_id), atoms);
}
void structure::create_water(row_initializer atom)
{
using namespace literals;
auto entity_id = insert_compound("HOH", true);
auto &struct_asym = m_db["struct_asym"];
std::string asym_id;
try
{
asym_id = struct_asym.find1<std::string>("entity_id"_key == entity_id, "id");
}
catch (const std::exception &)
{
asym_id = struct_asym.get_unique_id();
struct_asym.emplace({ { "id", asym_id },
{ "pdbx_blank_PDB_chainid_flag", "N" },
{ "pdbx_modified", "N" },
{ "entity_id", entity_id },
{ "details", "?" } });
}
auto &atom_site = m_db["atom_site"];
auto auth_seq_id = atom_site.find_max<int>("auth_seq_id", "label_entity_id"_key == entity_id) + 1;
if (auth_seq_id < 0)
auth_seq_id = 1;
auto atom_id = atom_site.get_unique_id("");
atom.set_value("id", atom_id);
atom.set_value("label_asym_id", asym_id);
atom.set_value("auth_asym_id", asym_id);
atom.set_value("label_entity_id", entity_id);
atom.set_value("auth_seq_id", std::to_string(auth_seq_id));
atom.set_value_if_empty({ "group_PDB", "HETATM" });
atom.set_value_if_empty({ "label_comp_id", "HOH" });
atom.set_value_if_empty({ "label_seq_id", "." });
atom.set_value_if_empty({ "auth_comp_id", "HOH" });
atom.set_value_if_empty({ "pdbx_PDB_model_num", 1 });
atom.set_value_if_empty({ "label_alt_id", "" });
atom.set_value_if_empty({ "occupancy", 1.0, 2 });
auto row = atom_site.emplace(atom.begin(), atom.end());
emplace_atom(std::make_shared<atom::atom_impl>(m_db, atom_id));
auto &pdbx_nonpoly_scheme = m_db["pdbx_nonpoly_scheme"];
int ndb_nr = pdbx_nonpoly_scheme.find_max<int>("ndb_seq_num") + 1;
pdbx_nonpoly_scheme.emplace({
{ "asym_id", asym_id },
{ "entity_id", entity_id },
{ "mon_id", "HOH" },
{ "ndb_seq_num", ndb_nr },
{ "pdb_seq_num", auth_seq_id },
{ "auth_seq_num", auth_seq_id },
{ "pdb_mon_id", "HOH" },
{ "auth_mon_id", "HOH" },
{ "pdb_strand_id", asym_id },
{ "pdb_ins_code", "." },
});
}
std::string structure::create_link(atom a1, atom a2, const std::string &link_type, const std::string &role)
{
using namespace literals;
auto &struct_conn = m_db["struct_conn"];
auto &struct_conn_type = m_db["struct_conn_type"];
// This will validate link_type :-)
if (not struct_conn_type.contains("id"_key == link_type))
struct_conn_type.emplace({ { "id", link_type } });
std::string link_id = struct_conn.get_unique_id(link_type + '_');
item label_seq_id_1("ptnr1_label_seq_id");
if (int nr = a1.get_label_seq_id(); nr != 0)
label_seq_id_1.value(std::to_string(nr));
item label_seq_id_2("ptnr2_label_seq_id");
if (int nr = a2.get_label_seq_id(); nr != 0)
label_seq_id_2.value(std::to_string(nr));
struct_conn.emplace(
{ //
{ "id", link_id },
{ "conn_type_id", link_type },
{ "pdbx_leaving_atom_flag", "one" },
{ "ptnr1_label_asym_id", a1.get_label_asym_id() },
{ "ptnr1_label_comp_id", a1.get_label_comp_id() },
label_seq_id_1,
{ "ptnr1_label_atom_id", a1.get_label_atom_id() },
{ "pdbx_ptnr1_label_alt_id", a1.get_label_alt_id() },
{ "pdbx_ptnr1_PDB_ins_code", a1.get_pdb_ins_code() },
{ "ptnr1_auth_asym_id", a1.get_auth_asym_id() },
{ "ptnr1_auth_comp_id", a1.get_auth_comp_id() },
{ "ptnr1_auth_seq_id", a1.get_auth_seq_id() },
{ "ptnr1_symmetry", a1.symmetry() },
{ "ptnr2_label_asym_id", a2.get_label_asym_id() },
{ "ptnr2_label_comp_id", a2.get_label_comp_id() },
label_seq_id_2,
{ "ptnr2_label_atom_id", a2.get_label_atom_id() },
{ "pdbx_ptnr2_label_alt_id", a2.get_label_alt_id() },
{ "pdbx_ptnr2_PDB_ins_code", a2.get_pdb_ins_code() },
{ "ptnr2_auth_asym_id", a2.get_auth_asym_id() },
{ "ptnr2_auth_comp_id", a2.get_auth_comp_id() },
{ "ptnr2_auth_seq_id", a2.get_auth_seq_id() },
{ "ptnr2_symmetry", a2.symmetry() },
{ "pdbx_dist_value", distance(a1.get_location(), a2.get_location()), 3 },
{ "pdbx_role", role } });
return link_id;
}
branch &structure::create_branch()
{
auto &entity = m_db["entity"];
auto &struct_asym = m_db["struct_asym"];
auto entity_id = entity.get_unique_id("");
auto asym_id = struct_asym.get_unique_id();
entity.emplace({ { "id", entity_id },
{ "type", "branched" } });
struct_asym.emplace({ { "id", asym_id },
{ "pdbx_blank_PDB_chainid_flag", "N" },
{ "pdbx_modified", "N" },
{ "entity_id", entity_id },
{ "details", "?" } });
return m_branches.emplace_back(*this, asym_id, entity_id);
}
// branch &structure::create_branch(std::vector<row_initializer> atoms)
// {
// // // sanity check
// // for (auto &nag_atom : atoms)
// // {
// // for (const auto &[name, value] : nag_atom)
// // {
// // if (name == "label_comp_id" and value != "NAG")
// // throw std::logic_error("The first sugar in a branch should be a NAG");
// // }
// // }
// // using namespace literals;
// // auto &branch = create_branch();
// // auto asym_id = branch.get_asym_id();
// // auto entity_id = branch.get_entity_id();
// // auto &sugar = branch.emplace_back(branch, "NAG", asym_id, 1);
// // auto &atom_site = m_db["atom_site"];
// // for (auto &atom : atoms)
// // {
// // auto atom_id = atom_site.get_unique_id("");
// // atom.set_value("id", atom_id);
// // atom.set_value("label_asym_id", asym_id);
// // atom.set_value("auth_asym_id", asym_id);
// // atom.set_value("label_entity_id", entity_id);
// // atom.set_value({ "auth_seq_id", 1 });
// // atom.set_value_if_empty({"group_PDB", "HETATM"});
// // atom.set_value_if_empty({"label_comp_id", "NAG"});
// // atom.set_value_if_empty({"label_seq_id", "."});
// // atom.set_value_if_empty({"auth_comp_id", "NAG"});
// // atom.set_value_if_empty({"pdbx_PDB_model_num", 1});
// // atom.set_value_if_empty({"label_alt_id", ""});
// // auto row = atom_site.emplace(atom.begin(), atom.end());
// // auto &newAtom = emplace_atom(std::make_shared<atom::atom_impl>(m_db, atom_id));
// // sugar.add_atom(newAtom);
// // }
// // // // now we can create the entity and get the real ID
// // // auto entity_id = create_entity_for_branch(branch);
// // // assert(not entity_id.empty());
// // for (auto &a : sugar.atoms())
// // a.set_property("label_entity_id", entity_id);
// // m_db["pdbx_branch_scheme"].emplace({
// // {"asym_id", asym_id},
// // {"entity_id", entity_id},
// // {"num", 1},
// // {"mon_id", "NAG"},
// // {"pdb_asym_id", asym_id},
// // {"pdb_seq_num", 1},
// // {"pdb_mon_id", "NAG"},
// // // TODO: need fix, collect from nag_atoms?
// // {"auth_asym_id", asym_id},
// // {"auth_mon_id", "NAG"},
// // {"auth_seq_num", 1},
// // {"hetero", "n"}
// // });
// // return branch;
// }
// branch &structure::extend_branch(const std::string &asym_id, std::vector<row_initializer> atom_info,
// int link_sugar, const std::string &link_atom)
// {
// // // sanity check
// // std::string compoundID;
// // for (auto &atom : atom_info)
// // {
// // for (const auto &[name, value] : atom)
// // {
// // if (name != "label_comp_id")
// // continue;
// // if (compoundID.empty())
// // compoundID = value;
// // else if (value != compoundID)
// // throw std::logic_error("All atoms should be of the same type");
// // }
// // }
// // using namespace literals;
// // // auto &branch = m_branches.emplace_back(*this, asym_id);
// // auto tmp_entity_id = m_db["entity"].get_unique_id("");
// // auto &atom_site = m_db["atom_site"];
// // auto bi = std::find_if(m_branches.begin(), m_branches.end(), [asym_id](branch &b)
// // { return b.get_asym_id() == asym_id; });
// // if (bi == m_branches.end())
// // throw std::logic_error("Create a branch first!");
// // branch &branch = *bi;
// // int sugarNum = static_cast<int>(branch.size() + 1);
// // auto &sugar = branch.emplace_back(branch, compoundID, asym_id, sugarNum);
// // for (auto &atom : atom_info)
// // {
// // auto atom_id = atom_site.get_unique_id("");
// // atom.set_value("id", atom_id);
// // atom.set_value("label_asym_id", asym_id);
// // atom.set_value("auth_asym_id", asym_id);
// // atom.set_value("label_entity_id", tmp_entity_id);
// // atom.set_value({"auth_seq_id", sugarNum });
// // atom.set_value_if_empty({"group_PDB", "HETATM"});
// // atom.set_value_if_empty({"label_comp_id", compoundID});
// // atom.set_value_if_empty({"auth_comp_id", compoundID});
// // atom.set_value_if_empty({"pdbx_PDB_model_num", 1});
// // atom.set_value_if_empty({"label_alt_id", ""});
// // auto row = atom_site.emplace(atom.begin(), atom.end());
// // auto &newAtom = emplace_atom(std::make_shared<atom::atom_impl>(m_db, atom_id));
// // sugar.add_atom(newAtom);
// // }
// // sugar.set_link(branch.at(link_sugar - 1).get_atom_by_atom_id(link_atom));
// // auto entity_id = create_entity_for_branch(branch);
// // // Update the entity id of the asym
// // auto &struct_asym = m_db["struct_asym"];
// // auto r = struct_asym.find1("id"_key == asym_id);
// // r["entity_id"] = entity_id;
// // for (auto &s2 : branch)
// // {
// // for (auto atom : s2.atoms())
// // atom.set_property("label_entity_id", entity_id);
// // }
// // auto &pdbx_branch_scheme = m_db["pdbx_branch_scheme"];
// // pdbx_branch_scheme.erase("asym_id"_key == asym_id);
// // for (auto &s2 : branch)
// // {
// // pdbx_branch_scheme.emplace({
// // {"asym_id", asym_id},
// // {"entity_id", entity_id},
// // {"num", s2.num()},
// // {"mon_id", s2.get_compound_id()},
// // {"pdb_asym_id", asym_id},
// // {"pdb_seq_num", s2.num()},
// // {"pdb_mon_id", s2.get_compound_id()},
// // // TODO: need fix, collect from nag_atoms?
// // {"auth_asym_id", asym_id},
// // {"auth_mon_id", s2.get_compound_id()},
// // {"auth_seq_num", s2.get_auth_seq_id()},
// // {"hetero", "n"}
// // });
// // }
// // return branch;
// }
std::string structure::create_entity_for_branch(branch &branch)
{
using namespace literals;
std::string entityName = branch.name();
auto &entity = m_db["entity"];
std::string entityID = entity.find_first<std::string>("type"_key == "branched" and "pdbx_description"_key == entityName, "id");
if (entityID.empty())
{
entityID = entity.get_unique_id("");
if (VERBOSE)
std::cout << "Creating new entity " << entityID << " for branched sugar " << entityName << '\n';
entity.emplace({ { "id", entityID },
{ "type", "branched" },
{ "src_method", "man" },
{ "pdbx_description", entityName },
{ "formula_weight", branch.weight() } });
auto &pdbx_entity_branch_list = m_db["pdbx_entity_branch_list"];
for (auto &sugar : branch)
{
pdbx_entity_branch_list.emplace({ { "entity_id", entityID },
{ "comp_id", sugar.get_compound_id() },
{ "num", sugar.num() },
{ "hetero", "n" } });
}
auto &pdbx_entity_branch_link = m_db["pdbx_entity_branch_link"];
for (auto &s1 : branch)
{
auto l2 = s1.get_link();
if (not l2 or l2.get_auth_seq_id().empty())
continue;
auto &s2 = branch.at(stoi(l2.get_auth_seq_id()) - 1);
auto l1 = s2.get_atom_by_atom_id("C1");
pdbx_entity_branch_link.emplace({ { "link_id", pdbx_entity_branch_link.get_unique_id("") },
{ "entity_id", entityID },
{ "entity_branch_list_num_1", s1.get_pdb_seq_num() },
{ "comp_id_1", s1.get_compound_id() },
{ "atom_id_1", l1.get_label_atom_id() },
{ "leaving_atom_id_1", "O1" },
{ "entity_branch_list_num_2", s2.get_pdb_seq_num() },
{ "comp_id_2", s2.get_compound_id() },
{ "atom_id_2", l2.get_label_atom_id() },
{ "leaving_atom_id_2", "H" + l2.get_label_atom_id() },
{ "value_order", "sing" } });
}
}
return entityID;
}
void structure::cleanup_empty_categories()
{
using namespace literals;
auto &atomSite = m_db["atom_site"];
auto &pdbxPolySeqScheme = m_db["pdbx_poly_seq_scheme"];
auto &entityPolySeq = m_db["entity_poly_seq"];
// Remove chem_comp's for which there are no atoms at all
auto &chem_comp = m_db["chem_comp"];
std::vector<row_handle> obsoleteChemComps;
for (auto chemComp : chem_comp)
{
std::string compID = chemComp["id"].as<std::string>();
if (atomSite.contains("label_comp_id"_key == compID or "auth_comp_id"_key == compID) or
pdbxPolySeqScheme.contains("mon_id"_key == compID or "auth_mon_id"_key == compID or "pdb_mon_id"_key == compID) or
entityPolySeq.contains("mon_id"_key == compID))
{
continue;
}
obsoleteChemComps.push_back(chemComp);
}
for (auto chemComp : obsoleteChemComps)
chem_comp.erase(chemComp);
// similarly, remove entities not referenced by any atom
auto &entities = m_db["entity"];
std::vector<row_handle> obsoleteEntities;
for (auto entity : entities)
{
std::string entityID = entity["id"].as<std::string>();
if (atomSite.contains("label_entity_id"_key == entityID))
continue;
obsoleteEntities.push_back(entity);
}
auto validator = m_db.get_validator();
for (auto entity : obsoleteEntities)
{
std::string entityID = entity["id"].as<std::string>();
if (validator)
{
for (auto linked : validator->get_links_for_parent("entity"))
{
if (auto cat = m_db.get(linked->m_child_category))
cat->erase(cif::key(linked->m_child_keys.front()) == entityID);
}
}
entities.erase(entity);
}
// the rest?
for (const char *cat : { "pdbx_entity_nonpoly" })
{
auto &category = m_db[cat];
std::vector<row_handle> empty;
for (auto row : category)
{
if (not category.has_children(row) and not category.has_parents(row))
empty.push_back(row);
}
for (auto row : empty)
category.erase(row);
}
// count molecules
for (auto entity : entities)
{
std::string type, id;
cif::tie(type, id) = entity.get("type", "id");
std::optional<std::size_t> count;
if (type == "polymer")
count = m_db["struct_asym"].find("entity_id"_key == id).size();
else if (type == "non-polymer" or type == "water")
count = m_db["pdbx_nonpoly_scheme"].find("entity_id"_key == id).size();
else if (type == "branched")
{
// is this correct?
std::set<std::string> asym_ids;
for (const auto &asym_id : m_db["pdbx_branch_scheme"].find<std::string>("entity_id"_key == id, "asym_id"))
asym_ids.insert(asym_id);
count = asym_ids.size();
}
entity["pdbx_number_of_molecules"] = count.value_or(0);
}
}
void structure::translate(point t)
{
for (auto &a : m_atoms)
a.translate(t);
}
void structure::rotate(quaternion q)
{
for (auto &a : m_atoms)
a.rotate(q);
}
void structure::translate_and_rotate(point t, quaternion q)
{
for (auto &a : m_atoms)
a.translate_and_rotate(t, q);
}
void structure::translate_rotate_and_translate(point t1, quaternion q, point t2)
{
for (auto &a : m_atoms)
a.translate_rotate_and_translate(t1, q, t2);
}
void structure::validate_atoms() const
{
// validate order
assert(m_atoms.size() == m_atom_index.size());
for (std::size_t i = 0; i + i < m_atoms.size(); ++i)
assert(m_atoms[m_atom_index[i]].id().compare(m_atoms[m_atom_index[i + 1]].id()) < 0);
std::vector<atom> atoms = m_atoms;
auto removeAtomFromList = [&atoms](const atom &a)
{
auto i = std::find(atoms.begin(), atoms.end(), a);
assert(i != atoms.end());
atoms.erase(i);
};
for (auto &poly : m_polymers)
{
for (auto &monomer : poly)
{
for (auto &atom : monomer.atoms())
removeAtomFromList(atom);
}
}
for (auto &branch : m_branches)
{
for (auto &sugar : branch)
{
for (auto &atom : sugar.atoms())
removeAtomFromList(atom);
}
}
for (auto &res : m_non_polymers)
{
for (auto &atom : res.atoms())
removeAtomFromList(atom);
}
assert(atoms.empty());
}
static int compare_numbers(std::string_view a, std::string_view b)
{
int result = 0;
double da, db;
using namespace cif;
using namespace std;
std::from_chars_result ra, rb;
ra = from_chars(a.data(), a.data() + a.length(), da);
rb = from_chars(b.data(), b.data() + b.length(), db);
if (not(bool) ra.ec and not(bool) rb.ec)
{
auto d = da - db;
if (std::abs(d) > std::numeric_limits<double>::epsilon())
{
if (d > 0)
result = 1;
else if (d < 0)
result = -1;
}
}
else if ((bool)ra.ec)
result = 1;
else
result = -1;
return result;
}
int compare_cif_id(const std::string &a, const std::string &b)
{
int d = static_cast<int>(a.length() - b.length());
if (d == 0)
d = a.compare(b);
return d;
}
void structure::reorder_atoms()
{
auto &atom_site = m_db["atom_site"];
atom_site.sort([](row_handle a, row_handle b)
{
int d;
// First by model number
d = a.get<int>("pdbx_PDB_model_num") - b.get<int>("pdbx_PDB_model_num");
if (d == 0)
d = compare_cif_id(a.get<std::string>("label_asym_id"), b.get<std::string>("label_asym_id"));
if (d == 0)
{
auto na = a.get<std::optional<int>>("label_seq_id");
auto nb = b.get<std::optional<int>>("label_seq_id");
if (na.has_value() and nb.has_value())
d = *na - *nb;
else if (na.has_value())
d = 1;
else if (nb.has_value())
d = -1;
}
if (d == 0)
{
auto na = a.get<std::optional<int>>("auth_seq_id");
auto nb = b.get<std::optional<int>>("auth_seq_id");
if (na.has_value() and nb.has_value())
d = *na - *nb;
else if (na.has_value())
d = 1;
else if (nb.has_value())
d = -1;
}
if (d == 0)
d = compare_numbers(a.get<std::string>("id"), b.get<std::string>("id"));
return d;
//
});
// atom_site.set_validator(nullptr, m_db);
// for (int nr = 1; auto r : atom_site)
// r["id"] = nr++;
// atom_site.set_validator(m_db.get_validator(), m_db);
}
} // namespace cif::mm
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