weight/_dep/libcifpp/src/model.cpp

/*-
 * 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++.hpp"

#include <filesystem>
#include <fstream>
#include <iomanip>
#include <numeric>
#include <stack>

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();

#if __cpp_lib_format
	r.assign("Cartn_x", std::format("{:.3f}", p.m_x), false, false);
	r.assign("Cartn_y", std::format("{:.3f}", p.m_y), false, false);
	r.assign("Cartn_z", std::format("{:.3f}", p.m_z), false, false);
#else
	r.assign("Cartn_x", cif::format("%.3f", p.m_x).str(), false, false);
	r.assign("Cartn_y", cif::format("%.3f", p.m_y).str(), false, false);
	r.assign("Cartn_z", cif::format("%.3f", p.m_z).str(), false, false);
#endif
	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 = m_asym_id.compare(b.m_asym_id);
// 	if (d == 0)
// 		d = m_seq_id - b.m_seq_id;
// 	if (d == 0)
// 		d = m_auth_seq_id.compare(b.m_auth_seq_id);
// 	if (d == 0)
// 		d = mAtom_id.compare(b.mAtom_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);
}

// const Compound *atom::atom_impl::compound() const
// {
// 	if (mCompound == nullptr)
// 	{
// 		std::string compID = get_property("label_comp_id");

// 		mCompound = compound_factory::instance().create(compID);
// 	}

// 	return mCompound;
// }

// const std::string atom::atom_impl::get_property(const std::string_view name) const
// {
// 	for (auto &&[item_name, ref] : mCachedRefs)
// 	{
// 		if (item_name == name)
// 			return ref.as<std::string>();
// 	}

// 	mCachedRefs.emplace_back(name, const_cast<Row &>(mRow)[name]);
// 	return std::get<1>(mCachedRefs.back()).as<std::string>();
// }

// void atom::atom_impl::set_property(const std::string_view name, const std::string &value)
// {
// 	for (auto &&[item_name, ref] : mCachedRefs)
// 	{
// 		if (item_name != name)
// 			continue;

// 		ref = value;
// 		return;
// 	}

// 	mCachedRefs.emplace_back(name, mRow[name]);
// 	std::get<1>(mCachedRefs.back()) = value;
// }

// const Row atom::getRowAniso() const
// {
// 	auto &db = m_impl->m_db;
// 	auto cat = db.get("atom_site_anisotrop");
// 	if (not cat)
// 		return {};
// 	else
// 		return cat->find1(key("id") == m_impl->m_id);
// }

// float atom::uIso() const
// {
// 	float result;

// 	if (not get_property<std::string>("U_iso_or_equiv").empty())
// 		result = get_property<float>("U_iso_or_equiv");
// 	else if (not get_property<std::string>("B_iso_or_equiv").empty())
// 		result = get_property<float>("B_iso_or_equiv") / static_cast<float>(8 * kPI * kPI);
// 	else
// 		throw std::runtime_error("Missing B_iso or U_iso");

// 	return result;
// }

// const Compound &atom::compound() const
// {
// 	auto result = impl().compound();

// 	if (result == nullptr)
// 	{
// 		if (VERBOSE > 0)
// 			std::cerr << "Compound not found: '" << get_property<std::string>("label_comp_id") << '\'' << '\n';

// 		throw std::runtime_error("no compound");
// 	}

// 	return *result;
// }

// std::string atom::labelEntityID() const
// {
// 	return get_property<std::string>("label_entity_id");
// }

// std::string atom::authAtom_id() const
// {
// 	return get_property<std::string>("auth_atom_id");
// }

// std::string atom::authCompID() const
// {
// 	return get_property<std::string>("auth_comp_id");
// }

// std::string atom::get_auth_asym_id() const
// {
// 	return get_property<std::string>("auth_asym_id");
// }

// std::string atom::get_pdb_ins_code() const
// {
// 	return get_property<std::string>("pdbx_PDB_ins_code");
// }

// std::string atom::pdbxAuthAltID() const
// {
// 	return get_property<std::string>("pdbx_auth_alt_id");
// }

// void atom::translate(point t)
// {
// 	auto loc = location();
// 	loc += t;
// 	location(loc);
// }

// void atom::rotate(quaternion q)
// {
// 	auto loc = location();
// 	loc.rotate(q);
// 	location(loc);
// }

// void atom::translate_and_rotate(point t, quaternion q)
// {
// 	auto loc = location();
// 	loc += t;
// 	loc.rotate(q);
// 	location(loc);
// }

// void atom::translate_rotate_and_translate(point t1, quaternion q, point t2)
// {
// 	auto loc = location();
// 	loc += t1;
// 	loc.rotate(q);
// 	loc += t2;
// 	location(loc);
// }

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_auth_asym_id = a.get_auth_asym_id();
	m_auth_seq_id = 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)
{
	m_atoms.push_back(atom);
}

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;
}

// 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());

	auto center = centroid(pts);
	float radius = 0;

	for (auto &pt : pts)
	{
		float d = static_cast<float>(distance(pt, center));
		if (radius < d)
			radius = d;
	}

	return std::make_tuple(center, radius);
}

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::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_auth_asym_id() != res.get_asym_id() or res.get_auth_seq_id() != std::to_string(res.get_seq_id()))
		os << " [" << res.get_auth_asym_id() << ':' << res.get_auth_seq_id() << ']';

	return os;
}

// --------------------------------------------------------------------
// monomer

monomer::monomer(const polymer &polymer, 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_auth_asym_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();
}

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->operator[](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->operator[](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->operator[](m_index - 1);
			auto &next = m_polymer->operator[](m_index + 1);
			auto &nextNext = m_polymer->operator[](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->operator[](m_index - 2);
			auto &nextNext = m_polymer->operator[](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->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() << '\n';
	}

	return result;
}

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 " << 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"}}};

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();

	return result;
}

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"};

			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->operator[](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;
}

// --------------------------------------------------------------------
// 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_auth_asym_id(auth_asym_id)
{
	using namespace cif::literals;

	std::map<size_t, 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::optional<int> pdbSeqNum;
		std::string compoundID, authSeqID, pdbInsCode;
		cif::tie(seqID, authSeqID, compoundID, pdbInsCode, pdbSeqNum) = r.get("seq_id", "auth_seq_num", "mon_id", "pdb_ins_code", "pdb_seq_num");

		if (authSeqID.empty() and pdbSeqNum.has_value())
			authSeqID = std::to_string(*pdbSeqNum);

		size_t index = size();

		// store only the first
		if (not ix.count(seqID))
		{
			ix[seqID] = index;
			emplace_back(*this, index, seqID, authSeqID, pdbInsCode, compoundID);
		}
		else if (VERBOSE > 0)
		{
			monomer m{*this, index, seqID, authSeqID, 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_auth_seq_id});
	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<size_t, 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<size_t, 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.num()},
		{"pdb_mon_id", result.get_compound_id()},

		{"auth_asym_id", result.get_auth_asym_id()},
		{"auth_mon_id", result.get_compound_id()},
		{"auth_seq_num", result.get_auth_seq_id()},

		{"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_auth_seq_id())
			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, size_t modelNr, StructureOpenOptions options)
	: structure(p.front(), modelNr, options)
{
}

structure::structure(datablock &db, size_t modelNr, StructureOpenOptions options)
	: m_db(db)
	, m_model_nr(modelNr)
{
	auto &atomCat = 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<size_t> model_nr;
		cif::tie(model_nr) = atomCat.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(StructureOpenOptions options)
{
	using namespace literals;

	auto &atomCat = m_db["atom_site"];

	condition c = "pdbx_PDB_model_num"_key == null or "pdbx_PDB_model_num"_key == m_model_nr;
	if (options bitand StructureOpenOptions::SkipHydrogen)
		c = std::move(c) and ("type_symbol"_key != "H" and "type_symbol"_key != "D");

	for (auto id : atomCat.find<std::string>(std::move(c), "id"))
		emplace_atom(std::make_shared<atom::atom_impl>(m_db, id));
}

// structure::structure(const structure &s)
// 	: m_db(s.m_db)
// 	, m_model_nr(s.m_model_nr)
// {
// 	m_atoms.reserve(s.m_atoms.size());
// 	for (auto &atom : s.m_atoms)
// 		emplace_atom(atom.clone());

// 	load_data();
// }

// structure::~structure()
// {
// }

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 or m_polymers.back().get_entity_id() != entityID)
			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_auth_seq_id()}] = &res;
	}

	for (auto &res : m_non_polymers)
		resMap[{res.get_asym_id(), res.get_seq_id(), res.get_auth_seq_id()}] = &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_auth_seq_id()}] = &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);
}

// std::vector<atom> structure::waters() const
// {
// 	using namespace literals;

// 	std::vector<atom> result;

// 	auto &db = datablock();

// 	// Get the entity id for water. Watch out, structure may not have water at all
// 	auto &entityCat = db["entity"];
// 	for (const auto &[waterEntityID] : entityCat.find<std::string>("type"_key == "water", "id"))
// 	{
// 		for (auto &a : m_atoms)
// 		{
// 			if (a.get_property("label_entity_id") == waterEntityID)
// 				result.push_back(a);
// 		}

// 		break;
// 	}

// 	return result;
// }

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();
	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);

		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();
	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);

		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_auth_seq_id() == 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_auth_seq_id() == 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_auth_seq_id() == 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_auth_seq_id() == 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());

		auto l1 = r1["label_atom_id"];
		auto l2 = r2["label_atom_id"];
		l1.swap(l2);

		auto l3 = r1["auth_atom_id"];
		auto l4 = r2["auth_atom_id"];
		l3.swap(l4);
	}
	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_auth_seq_id() == 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_auth_seq_id() == 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");
	size_t six = si - branch.begin();

	if (six == 0)	// first sugar, means the death of this branch
		remove_branch(branch);
	else
	{
		std::set<size_t> dix;
		std::stack<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_auth_seq_id()},

				{"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"];
	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_auth_seq_id()},
		{"auth_seq_num", res.get_auth_seq_id()},
		{"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"];
	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_auth_seq_id()},
		{"auth_seq_num", res.get_auth_seq_id()},
		{"pdb_mon_id", comp_id},
		{"auth_mon_id", comp_id},
		{"pdb_strand_id", asym_id},
		{"pdb_ins_code", "."},
	});

	return asym_id;
}

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", "."},
	});
}

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_auth_seq_id()},
				{"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_auth_seq_id()},
				{"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"];

	// 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))
			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);
	}

	for (auto entity : obsoleteEntities)
		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<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 (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());
}

} // namespace pdbx