leonarski_fandClaude Opus 5.5
63e0a85467
Copy number. The hard "Vm >= 4: MULTI_COPY, no decision" rule is gone. Copies are searched one after another up to the largest copy number with a Matthews probability of 1% (a Gumbel distribution with Kantardjieff & Rupp's 2003 mode and mean, no resolution dependence); COPIES_LIKELY reports the most probable. Sequential search. Copy n's translation function carries copies 1..n-1 as a known partial structure: the cross term 2 Re(conj(F_known) F(t)) goes on the same FFT grid (CPU FFTW and GPU cuFFT; KnownStructureFactors, AssemblyCorrelation). Its peaks, past those that clash, are ranked by the correlation of the whole assembly with E^2 (the TF itself, linear in |F|^2, rewards copying a placed copy onto an origin shift), the first that stands out (TF Z >= 8), packs and lowers R-free by 0.01 is kept; each copy is refined beside the others held fixed (RefineRigidBody's fixed copies), and the first copy again beside the second, the earlier ones once more at the end. Packing: ClashFraction counts C-alpha clashes with other copies and all their mates, binned (7mzt: 51 s of clash checks -> 1.9 s). Search quality: rotation-function peaks hill-climbed off the 6 deg sampling (6ze4: RF Z 10.4 -> 16.0, 3.3 deg off the deposited orientation -> 0.2); the first copy goes down the TF list until three placements that pack are refined, so a group is CLASH only where no offered orientation packs; groups are searched side by side, and every group the best one leads is searched again with the best one's copy orientations tried first, the better search kept. tNCS: the native Patterson of E^2 (5-10 A) off the lattice; placed copies' orientations join every further copy's search; and where the tNCS vector turns one group's screw axes into another's (TncsRelatesGroups), a group whose search stopped at fewer copies does not lose to the other - UNDECIDED. Measured on an in-house tNCS crystal (vector c/3 along the 3-fold): both hands fit with three copies to within 0.01 in R-free, and where one hand's search failed the other was taken as ENANTIOMORPH; now UNDECIDED. Null: the replicates are placed by the translation function in their own orientation, as the search placed the real one (a null at the real centroid reads high), and the gate is 4.51 = t(8) sqrt(1 + 1/9), 3 sd of a nine-draw null, the gate --model's MODEL_FIT is now read at. Speed: placements scored on the GPU structure-factor engines; further copies' trials score with the first copy's bulk solvent held, the assembly refitted at the end. Survey of 193 sets (jfjoch_mr_replay on stored merges, RTX 5080 shared with other jobs): MR median 1.15 s, max 24 s; demos 0.8-1.1 s. Report: COPIES and COPIES_LIKELY columns, MODEL_PRIOR_COPIES. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01EizBKhTqrAYago9KJG3dA3
40 lines
1.8 KiB
C++
40 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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// The molecular-replacement search on a GPU (CUDA builds only; the header itself needs no CUDA): the
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// rotation function and the translation function of MolecularReplacement.h, the same functions as the
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// CPU computes - the same trilinear interpolation of the same molecular transform, the same bins, the
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// same coefficients on the same grid - in float on the device, with cuFFT for FFTW. The two agree to
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// rounding, not bit for bit. Every reduction runs in a fixed order and nothing is summed with an
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// atomic, so the GPU is deterministic on its own.
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#include <memory>
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#include <vector>
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#include "MolecularReplacement.h"
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struct MolecularReplacementGPUState;
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struct MolecularReplacementGPUGroup;
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class MolecularReplacementGPU {
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public:
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// Uploads the molecular transform, on the calling thread's current device. Throws JFJochException on
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// a CUDA failure, as every call below does.
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explicit MolecularReplacementGPU(const MolecularTransform &ft);
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~MolecularReplacementGPU();
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std::vector<double> RotationFunction(const SearchReflections &refl, const gemmi::UnitCell &cell,
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const gemmi::SpaceGroup &sg, const std::vector<gemmi::Mat33> &rotations);
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// The translation function of one group at each of `rotations`; with `known`, beside a known partial
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// structure (KnownStructureFactors).
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std::vector<TranslationPeak> TranslationFunction(const TranslationSetup &setup,
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const std::vector<gemmi::Mat33> &rotations,
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const std::vector<std::complex<double>> *known = nullptr);
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private:
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std::unique_ptr<MolecularReplacementGPUState> state_;
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};
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