Create non poly from described atoms

cmake/VersionString.cmake

+# SPDX-License-Identifier: BSD-2-Clause
+
+# Copyright (c) 2021 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.
+
+cmake_minimum_required(VERSION 3.15)
+
+# Create a revision file, containing the current git version info, if any
+function(write_version_header)
+	include(GetGitRevisionDescription)
+	if(NOT(GIT-NOTFOUND OR HEAD-HASH-NOTFOUND))
+		git_describe_working_tree(BUILD_VERSION_STRING --match=build --dirty)
+
+		if(BUILD_VERSION_STRING MATCHES "build-([0-9]+)-g([0-9a-f]+)(-dirty)?")
+			set(BUILD_GIT_TAGREF "${CMAKE_MATCH_2}")
+			if(CMAKE_MATCH_3)
+				set(BUILD_VERSION_STRING "${CMAKE_MATCH_1}*")
+			else()
+				set(BUILD_VERSION_STRING "${CMAKE_MATCH_1}")
+			endif()
+		endif()
+	else()
+		set(BUILD_VERSION_STRING "no git info available")
+	endif()
+
+	include_directories(${CMAKE_BINARY_DIR} PRIVATE)
+	string(TIMESTAMP BUILD_DATE_TIME "%Y-%m-%dT%H:%M:%SZ" UTC)
+
+	if(ARGC GREATER 0)
+		set(VAR_PREFIX "${ARGV0}")
+	endif()
+
+	file(WRITE "${CMAKE_BINARY_DIR}/revision.hpp.in" [[// Generated revision file
+
+#pragma once
+
+#include <ostream>
+
+const char k@VAR_PREFIX@ProjectName[] = "@PROJECT_NAME@";
+const char k@VAR_PREFIX@VersionNumber[] = "@PROJECT_VERSION@";
+const char k@VAR_PREFIX@VersionGitTag[] = "@BUILD_GIT_TAGREF@";
+const char k@VAR_PREFIX@BuildInfo[] = "@BUILD_VERSION_STRING@";
+const char k@VAR_PREFIX@BuildDate[] = "@BUILD_DATE_TIME@";
+
+inline void write_version_string(std::ostream &os, bool verbose)
+{
+	os << k@VAR_PREFIX@ProjectName << " version " << k@VAR_PREFIX@VersionNumber << std::endl;
+	if (verbose)
+	{
+		os << "build: " << k@VAR_PREFIX@BuildInfo << ' ' << k@VAR_PREFIX@BuildDate << std::endl;
+		if (k@VAR_PREFIX@VersionGitTag[0] != 0)
+			os << "git tag: " << k@VAR_PREFIX@VersionGitTag << std::endl;
+	}
+}
+]])
+	configure_file("${CMAKE_BINARY_DIR}/revision.hpp.in" "${CMAKE_BINARY_DIR}/revision.hpp" @ONLY)
+endfunction()
+

include/cif++/Structure.hpp

@@ -605,6 +605,14 @@ class Structure
 	/// \return				The newly create asym ID
 	std::string createNonpoly(const std::string &entity_id, const std::vector<mmcif::Atom> &atoms);
 
+	/// \brief Create a new NonPolymer struct_asym with atoms constructed from info in \a atom_info, returns asym_id.
+	/// This method creates new atom records filled with info from the info.
+	///
+	/// \param entity_id	The entity ID of the new nonpoly
+	/// \param atoms		The array of sets of cif::item data containing the data for the atoms.
+	/// \return				The newly create asym ID
+	std::string createNonpoly(const std::string &entity_id, std::vector<std::vector<cif::Item>> &atom_info);
+
 	/// \brief To sort the atoms in order of model > asym-id > res-id > atom-id
 	/// Will asssign new atom_id's to all atoms. Be carefull
 	void sortAtoms();

src/Structure.cpp

@@ -2088,7 +2088,8 @@ std::string Structure::createNonpoly(const std::string &entity_id, const std::ve
 	{
 		auto atom_id = atom_site.getUniqueID("");
 
-		auto &&[row, inserted] = atom_site.emplace({{"group_PDB", atom.get_property<std::string>("group_PDB")},
+		auto &&[row, inserted] = atom_site.emplace({
+			{"group_PDB", atom.get_property<std::string>("group_PDB")},
 			{"id", atom_id},
 			{"type_symbol", atom.get_property<std::string>("type_symbol")},
 			{"label_atom_id", atom.get_property<std::string>("label_atom_id")},
@@ -2117,6 +2118,53 @@ std::string Structure::createNonpoly(const std::string &entity_id, const std::ve
 	return asym_id;
 }
 
+std::string Structure::createNonpoly(const std::string &entity_id, std::vector<std::vector<cif::Item>> &atom_info)
+{
+	using namespace cif::literals;
+
+	cif::Datablock &db = *mFile.impl().mDb;
+	auto &struct_asym = db["struct_asym"];
+	std::string asym_id = struct_asym.getUniqueID();
+
+	struct_asym.emplace({{"id", asym_id},
+		{"pdbx_blank_PDB_chainid_flag", "N"},
+		{"pdbx_modified", "N"},
+		{"entity_id", entity_id},
+		{"details", "?"}});
+
+	std::string comp_id = db["pdbx_entity_nonpoly"].find1<std::string>("entity_id"_key == entity_id, "comp_id");
+
+	auto &atom_site = db["atom_site"];
+
+	auto &res = mNonPolymers.emplace_back(*this, comp_id, asym_id);
+
+	for (auto &atom : atom_info)
+	{
+		auto atom_id = atom_site.getUniqueID("");
+
+		atom.insert(atom.end(), {
+			{"group_PDB", "HETATM"},
+			{"id", atom_id},
+			{"label_comp_id", comp_id},
+			{"label_asym_id", asym_id},
+			{"label_seq_id", ""},
+			{"label_entity_id", entity_id},
+			{"auth_comp_id", comp_id},
+			{"auth_asym_id", asym_id},
+			{"auth_seq_id", ""},
+			{"pdbx_PDB_model_num", 1},
+			{"label_alt_id", ""}
+		});
+
+		auto &&[row, inserted] = atom_site.emplace(atom.begin(), atom.end());
+
+		auto &newAtom = mAtoms.emplace_back(std::make_shared<Atom::AtomImpl>(db, atom_id, row));
+		res.addAtom(newAtom);
+	}
+
+	return asym_id;
+}
+
 void Structure::cleanupEmptyCategories()
 {
 	using namespace cif::literals;

src/revision.hpp.in

-const char kRevision[] = R"(
-lib@PROJECT_NAME@-version: @PROJECT_VERSION@
-@BUILD_VERSION_STRING@
-Date: @BUILD_DATE_TIME@
-)";