leonarski_f
15ca4b329f
A rugnux live run that placed a model keeps it, with a copy of its map coefficients, beside the live status (RugnuxStructure), for as long as /rugnux/status keeps the run. Made in memory on the first request and cached, never written to disk: - GET /rugnux/model.cif: the placed model as mmCIF, labelled as WritePlacedModel labels _model.cif (PlacedModelMmcif, the labelling factored out of WritePlacedModel; the file output is unchanged). - GET /rugnux/map.ccp4?type=2fofc|fofc: the 2mFo-DFc / mFo-DFc map as a CCP4 map, FFT of the FWT/PHWT or DELFWT/PHDELWT coefficients (get_f_phi_on_grid + MapFromFPhi, sampled as ModelValidation samples), cut to the box around the model plus 5 A, with the whole cell's mean and RMS in the header. - 404 without a placed model or maps, 400 for an unknown map type; both routes protected by the dataset bearer token like /rugnux/status. rugnux_live_status gets placed_model. C++ model, python client docs, TypeScript client and redoc regenerated. Tests: a point's coefficients give a map peaking at the atom in a cropped box; the mmCIF; the structure is cleared at the next start; the auth test covers the new routes. End to end (myoglobin 2M replay with an AlphaFold model): the maps equal gemmi's FFT of the written _maps.mtz to 2.5e-6 rms. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu (cherry picked from commit 33124c3288ba112def3f51c0d91f5206886f3495)
35 lines
1.8 KiB
C++
35 lines
1.8 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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#pragma once
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#include <string>
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#include "gemmi/model.hpp"
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#include "gemmi/symmetry.hpp"
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#include "../common/UnitCell.h"
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class Logger;
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// Write `placed` - the atomic model as ValidateAgainstModel left it, re-fractionalized into the data
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// cell and moved by the rigid-body step - to `output_prefix`_model.cif, and to `_model.pdb` as well where a PDB can express the cell. Everything the input carried
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// comes with it: chains, residues, ligands, waters, B-factors, occupancies, anisotropic Us.
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//
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// `cell` and `space_group` must be the ones the reflection files beside it are written in, i.e. the
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// unit cell and DiffractionExperiment::GetSpaceGroupOrP1() that WriteReflections is given after
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// AdoptModelFrame has settled the enantiomorph. The cell is always taken; the group is taken wherever
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// the model's coordinates obey it, which is the ordinary case. Where they do not - data merged in a
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// supergroup of the model's group, or in the other hand - the model keeps its own group and a warning
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// says the two files disagree, because a label whose operations the coordinates contradict makes a
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// refinement program build a different structure and say nothing.
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void WritePlacedModel(const gemmi::Structure &placed,
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const UnitCell &cell,
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const gemmi::SpaceGroup &space_group,
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const std::string &output_prefix,
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Logger &logger);
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// The mmCIF text of `placed` exactly as WritePlacedModel writes it to <prefix>_model.cif, in memory.
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std::string PlacedModelMmcif(const gemmi::Structure &placed, const UnitCell &cell,
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const gemmi::SpaceGroup &space_group);
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