leonarski_f
dd0bffb283
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This is an UNSTABLE release. It includes many experimental features, as well as many AI generated fixes. We recommend using rc.152 for production use. * rugnux: Add `--model model.pdb` - score the merged data against an atomic model and compute initial maps. It reports R-work/R-free (scaling the model to the observed amplitudes with an overall scale, an anisotropic B and a flat bulk solvent - the standard few-parameter model, so a batch of maps stays directly comparable) and writes 2Fo-Fc / Fo-Fc electron-density maps (CCP4) plus a map-coefficient MTZ. The structure itself is not refined; the model is only re-fractionalised into the data cell. * rugnux: The merged reflection output now carries French-Wilson amplitudes (|F| and its sigma) next to the intensities - MTZ `F`/`SIGF`, mmCIF `_refln.F_meas_au`, and the text HKL - computed with the correct centric/acentric Wilson prior and epsilon multiplicity, so a downstream program (e.g. phenix.refine) can refine against amplitudes. The intensity columns are unchanged. * rugnux: R-free test-set flags are now assigned deterministically and consistently across symmetry - a Bijvoet pair I(+)/I(-) is never split between the work and free sets, and the assignment is a reproducible per-hkl hash that depends only on the reflection index, so every dataset of one crystal form gets the same ~5% free set (what a multi-dataset campaign such as PanDDA needs). On small data the fraction is floored so the test set stays large enough for a stable R-free (~500 reflections, capped at 10%); it stays flat at 5% on ordinary data. When a reference MTZ carries a `FreeR_flag` column its test set is imported instead, letting a whole campaign inherit one shared free set. * rugnux: A reference MTZ (`--reference-mtz`) can now fix the space group and cell for rotation data too (previously rejected), without being used to scale - the rotation merge stays self-consistent. When the crystal has an indexing (merohedral) ambiguity - a lattice symmetry higher than its Laue symmetry, e.g. P3/P4/P6/C2 - the reference also resolves it: each candidate reindexing (identity plus the twin-law cosets of the metric symmetry) is scored by its intensity correlation against the reference and the data are re-merged in the best-correlating one. This is a metric-preserving relabelling of hkl (the cell is unchanged) and a no-op for a holohedral crystal such as lysozyme. * rugnux: `--model` validation now aligns the data to the model before scoring - the observed reflections are reindexed into the model's enantiomorph when the two differ only by hand (indistinguishable from merged intensities). A merohedral indexing ambiguity is resolved against the reference MTZ when one is given (so a whole campaign shares one indexing convention); only with a model and no reference does validation fall back to fitting each candidate reindexing and keeping the lowest R-free. * rugnux: De-novo symmetry - recover a genuine high-symmetry group whose data are imperfectly scaled. Such a merge's within-orbit chi² lands just past the self-consistency bound (each real symmetry step adds a little systematic scatter), right where a merohedral twin also lands, so the chi² ratio alone cannot separate them. The candidate is now rescued when the extra intensity-proportional systematic error it invokes stays small relative to the confirmed subgroup - a genuine symmetry step gains multiplicity without inflating the merge error model's b, whereas a twin forces non-equivalent reflections together and b balloons. Fixes cubic insulin (I23 instead of I222) with no change to any other crystal in the test battery, including the twins that must stay in their lower symmetry. * Docs: Document the French-Wilson amplitude estimation, R-free flagging, reference-based space-group/ambiguity resolution, and model-based validation/maps in CPU_DATA_ANALYSIS.md. * Frontend: The status-bar pill now shows a progress bar during detector calibration (previously only during measurement), and the calibration state and its button are labelled "Calibration"/"CALIBRATE" (the internal `Pedestal` state name is unchanged for back-compatibility).Reviewed-on: #69 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
69 lines
2.2 KiB
C++
69 lines
2.2 KiB
C++
// Copyright Global Phasing Ltd.
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//
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// Functions for working with sequences (other than alignment).
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#ifndef GEMMI_SEQTOOLS_HPP_
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#define GEMMI_SEQTOOLS_HPP_
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#include "resinfo.hpp" // for find_tabulated_residue
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#include "metadata.hpp" // for Entity::first_mon, PolymerType
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namespace gemmi {
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constexpr double h2o_weight() { return 2 * 1.00794 + 15.9994; }
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inline double calculate_sequence_weight(const std::vector<std::string>& seq,
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double unknown=100.) {
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double weight = 0.;
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for (const std::string& item : seq) {
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size_t idx = find_tabulated_residue_idx(Entity::first_mon(item));
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if (idx == unknown_tabulated_residue_idx())
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weight += unknown;
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else
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weight += get_residue_info(idx).weight;
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//ResidueInfo res_info = find_tabulated_residue(Entity::first_mon(item));
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//weight += res_info.found() ? res_info.weight : unknown;
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}
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return weight - (seq.size() - 1) * h2o_weight();
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}
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inline std::string one_letter_code(const std::vector<std::string>& seq) {
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std::string r;
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for (const std::string& item : seq)
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r += find_tabulated_residue(Entity::first_mon(item)).fasta_code();
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return r;
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}
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/// Returns the format used in _entity_poly.pdbx_seq_one_letter_code,
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/// in which non-standard amino acids/nucleotides are represented by CCD codes
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/// in parenthesis, e.g. AA(MSE)H.
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inline std::string pdbx_one_letter_code(const std::vector<std::string>& seq,
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ResidueKind kind) {
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std::string r;
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for (const std::string& item : seq) {
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std::string code = Entity::first_mon(item);
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const ResidueInfo ri = find_tabulated_residue(code);
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if (ri.is_standard() && ri.kind == kind)
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r += ri.one_letter_code;
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else
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cat_to(r, '(', code, ')');
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}
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return r;
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}
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/// used with expand_one_letter_sequence()
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inline ResidueKind sequence_kind(PolymerType ptype) {
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if (is_polypeptide(ptype))
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return ResidueKind::AA;
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if (ptype == PolymerType::Dna)
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return ResidueKind::DNA;
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if (ptype == PolymerType::Rna || ptype == PolymerType::DnaRnaHybrid)
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return ResidueKind::RNA;
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if (ptype == PolymerType::Unknown)
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fail("sequence_kind(): unknown polymer type");
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return ResidueKind::AA;
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}
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} // namespace gemmi
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#endif
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