leonarski_f
90bbba33bc
The placed-model END block lost everything but the atoms, so the writer's _model.cif had no sequence references, authors, software or secondary structure, and gemmi relabelled the subchains. The block now also carries label_asym_id, label_entity_id and label_seq_id per atom and the input model's metadata as the mmCIF categories gemmi writes without coordinates (metadata_mmcif), which the writer parses with gemmi and puts back. The writer's _model.cif is now the same text as the one rugnux writes itself and as /rugnux/model.cif serves. Older blocks without the new fields are read as before. Test: a predicted myoglobin model through END -> CBOR -> writer gives byte-identical _model.cif/_model.pdb to WritePlacedModel and to PlacedModelMmcif, with its _struct_ref, _entity_poly_seq, _audit_author, _software and _struct_conf. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu (cherry picked from commit 29d752e6a107e3b8bc71ad6e9af0d81064966537)
58 lines
2.8 KiB
C++
58 lines
2.8 KiB
C++
// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
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// SPDX-License-Identifier: GPL-3.0-only
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#include "RugnuxResultBlocks.h"
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#include <sstream>
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#include <gemmi/to_cif.hpp> // write_cif_block_to_stream
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#include <gemmi/to_mmcif.hpp> // make_mmcif_block
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PlacedModelMessage PlacedModelFromStructure(const gemmi::Structure &st, const UnitCell &cell,
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const std::string &data_space_group_name) {
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PlacedModelMessage p;
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p.name = st.name;
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p.unit_cell = cell;
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p.space_group_name = data_space_group_name;
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p.model_space_group_name = st.spacegroup_hm;
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bool has_aniso = false;
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for (const gemmi::Model &m : st.models)
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for (const gemmi::Chain &ch : m.chains)
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for (const gemmi::Residue &r : ch.residues)
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for (const gemmi::Atom &a : r.atoms) {
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p.model_number.push_back(m.num);
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p.chain.push_back(ch.name);
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p.residue_name.push_back(r.name);
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p.seq_num.push_back(*r.seqid.num);
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p.icode.push_back(static_cast<uint8_t>(r.seqid.icode));
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p.het_flag.push_back(static_cast<uint8_t>(r.het_flag));
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p.subchain.push_back(r.subchain);
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p.entity_id.push_back(r.entity_id);
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p.label_seq.push_back(r.label_seq.value);
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p.atom_name.push_back(a.name);
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p.element.push_back(a.element.name());
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p.altloc.push_back(static_cast<uint8_t>(a.altloc));
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p.charge.push_back(a.charge);
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p.x.push_back(a.pos.x);
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p.y.push_back(a.pos.y);
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p.z.push_back(a.pos.z);
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p.b_iso.push_back(a.b_iso);
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p.occupancy.push_back(a.occ);
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p.aniso.insert(p.aniso.end(), {a.aniso.u11, a.aniso.u22, a.aniso.u33,
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a.aniso.u12, a.aniso.u13, a.aniso.u23});
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has_aniso = has_aniso || a.aniso.nonzero();
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}
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if (!has_aniso)
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p.aniso.clear();
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// Everything of the model but its coordinates (and what goes with them: cell, symmetry, scale), as the mmCIF
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// categories gemmi writes, for the writer to put back on _model.cif.
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gemmi::MmcifOutputGroups groups(true);
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groups.atoms = groups.cell = groups.symmetry = groups.scale = groups.atom_type = groups.origx = false;
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// _entry.id would otherwise be made up from the name, which the block carries anyway.
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groups.entry = st.info.count("_entry.id") > 0;
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std::ostringstream os;
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gemmi::cif::write_cif_block_to_stream(os, gemmi::make_mmcif_block(st, groups));
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p.metadata_mmcif = os.str();
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return p;
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}
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