Refinement restraints: the CCP4 Monomer Library subset embedded in rugnux, read through gemmi's MonLib

A restraint dictionary carried in the binary, so refinement reads nothing from disk and needs no
CLIBD_MON: the 20 amino acids and MSE, the DNA/RNA nucleotides, ATP/ADP/AMP/GTP/GDP/GMP, DMSO, PEG
fragments (PEG, PGE, PG4, 1PE), GOL, EDO, SO4, PO4, ACT, MPD, water and common ions - copied verbatim
from the CCP4 Monomer Library (LGPL-3.0) - plus links_and_mods.cif cut down to the links and
modifications those compounds can take (peptide, cis-peptide, proline, N-methyl, disulfide,
nucleic-acid backbone, termini, metal-Cys/His) and ener_lib.cif cut to its atom-type table.
monomers/update_monomers.py holds the compound list and regenerates the subset; CMake embeds every
.cif of the directory as string pieces under MSVC's literal limit; EmbeddedMonomerLibrary() parses
them from memory into a gemmi::MonLib once per process. About 0.7 MB of text in the binary.

gemmi v0.7.5's monlib.cpp, topo.cpp and riding_h.cpp vendored verbatim (prepare_topology). Licence
text in licenses/, rows and a note in THIRD_PARTY_NOTICES.md.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu
(cherry picked from commit 38034718052c4a300691393b5b817f476c83dfc2)

image_analysis/structure_refinement/MonomerLibrary.cpp

@@ -0,0 +1,41 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#include "MonomerLibrary.h"
+
+#include <cstring>
+
+#include "gemmi/read_cif.hpp"   // read_cif_from_memory
+
+// Generated by CMakeLists.txt from monomers/*.cif (MonomerLibraryData.cpp in the build tree).
+extern const EmbeddedMonomerFile embedded_monomer_files[];
+extern const size_t embedded_monomer_file_count;
+
+namespace {
+
+gemmi::MonLib ReadEmbeddedMonomerLibrary() {
+    gemmi::MonLib monlib;
+    for (size_t i = 0; i < embedded_monomer_file_count; i++) {
+        const EmbeddedMonomerFile &f = embedded_monomer_files[i];
+        std::string text;
+        for (size_t k = 0; k < f.n_pieces; k++)
+            text += f.pieces[k];
+        const gemmi::cif::Document doc = gemmi::read_cif_from_memory(text.data(), text.size(), f.name);
+        if (std::strcmp(f.name, "ener_lib.cif") == 0)
+            monlib.ener_lib.read(doc);
+        else
+            monlib.read_monomer_doc(doc);
+    }
+    return monlib;
+}
+
+}  // namespace
+
+const gemmi::MonLib &EmbeddedMonomerLibrary() {
+    static const gemmi::MonLib monlib = ReadEmbeddedMonomerLibrary();
+    return monlib;
+}
+
+bool InEmbeddedMonomerLibrary(const std::string &code) {
+    return EmbeddedMonomerLibrary().monomers.count(code) > 0;
+}