SQQ

SQQ: Python Joint Toolkit for Water-Shell Topology Analysis.

Current release: 0.2.7

SQQ builds a water network, reports coordination diagnostics, and finds rings, standard half-cages, quasi-cages, closed cages, topology-wide hydrate clusters, per-frame phase domains and boundaries, cage guest occupancy, F3/F4/Q_l order parameters, MCG/DHOP hydrate-nucleation order parameters, and ice-like waters. Detailed algorithms are documented in docs/design.md; version notes are documented in docs/update.md.

Changed in 0.2.7

• Added one unified selector, --order-parameter NAME[,NAME...], for f3, f4, qN, mcg1, mcg3, dhop35, and dhop30; all and none are also supported.
• The new default is --order-parameter f3,f4. Q_l, MCG, and DHOP are now opt-in instead of default calculations.
• Root sqq / sqq -h output now places SQQ version: 0.2.7 Release date: Jul 15, 2026 immediately before usage:. sqq -v and sqq --version print only that version line; subcommand help keeps its existing layout.
• GRO and trajectory readers now reject non-finite coordinates; GRO accepts exactly one frame and rejects extra non-empty records after the box line.
• Water and guest selection groups contiguous residue blocks in source order, so wrapped or repeated five-digit GRO residue IDs do not merge distinct molecules.
• Configuration loading now parses textual on/off values explicitly and rejects invalid modes, non-finite cutoffs, nonpositive limits, and fractional integer settings before analysis.
• Selection is independent for F3 and F4, and the terminal, per-frame Markdown, per-water TSV, summary.xlsx, and run_config.yaml report only the selected parameters. With none, the workbook omits order_parameter.
• The old selectors --no-q, -q / --q-degree, --mcg3, and --dhop30 remain hidden compatibility options for 0.2.7 and emit a deprecation warning.
• Replaced the individual public --no-info, --no-*-gro, --no-xlsx, and --no-summary-detail switches with --no-output TYPE[,TYPE...]; its default is none, so existing default outputs remain enabled.
• Removed the redundant per-frame overview frame worksheet from summary.xlsx; dedicated analysis sheets retain the per-frame data.
• Fixed zero/partial-zero box handling, PBC-unwrapped guest centroids for occupancy/MCG, truncated GRO acceptance, and degenerate solid-angle triangles. Triclinic GRO/trajectory boxes now fail fast instead of being treated as orthorhombic.
• Non-strict serial read failures now become diagnostic rows; strict failures still write run_config.yaml. Failed inputs are recorded in run.failures, an optional failures workbook sheet, and summary_detail/failures.csv.
• Added configurable --xyz-scale / input.xyz_scale (default 0.1, angstrom to nm), removed repeated per-frame config normalization, skipped physical-core probing for one task, cached immutable ring topology properties, reused spatial Q_l cutoff pairs, and precomputed PBC-aware guest centers.
• XYZ now rejects negative/malformed declared counts, truncated records, extra non-empty records (multi-frame XYZ), and non-finite coordinates before analysis. One XYZ file represents one frame.
• Explicit --worker values are validated even for a single task or serial backend. Both process and compatibility-thread backends submit at most 3 * workers pending tasks, while preserving the configured active worker count.
• Trajectory readers reuse immutable MDAnalysis atom metadata across frames. The normal full orthorhombic minimum_image() path avoids temporary boolean-index arrays; MDAnalysis cutoff candidates accelerate large coordinate searches but every candidate is still rechecked with SQQ float64 PBC distances.
• Exact quasi-cage isomer counts remain sparse in memory and are written only to summary_detail/quasi_cage_isomer.csv; compact quasi composition counts remain in Markdown/XLSX. Detail-CSV replacement is transactional as a group, and workbook sheets are preflight-checked against Excel row/column limits.
• Summary output now records per-table dimensions and timing in run.summary_write, prints total summary-write seconds in the final terminal summary, writes XLSX/CSV/YAML through same-directory temporary files with atomic replacement, and uses lightweight Excel body formatting for sheets larger than 200,000 cells or 128 columns.
• Additional result-equivalent hot paths use a reusable guest-center spatial index plus batched occupancy solid angles, fixed 4/5/6 cage-grow count tuples and incidence pruning, batched DHOP plane-normal comparisons, and cached F4 local geometry vectors.
• Hydrate-cluster topology now always uses every detected cage in the search scope. --cage-size remains a reporting filter for cage tables/files and no longer changes cluster connectivity or phase classification.

Changed in 0.2.6

• Worker parsing is now form-based: -w 1 means one worker, while -w 1.0 or -w 100% means all detected physical cores before the reserve-one-core clamp.
• Runtime metadata is aligned with the summary.xlsx home sheet: terminal output now reports SQQ version, final effective Graph mode, worker policy, backend, and resolved workers using the same wording as the dashboard.
• Graph mode display now preserves both requested and effective modes: auto -> hbond, auto -> oo, or auto -> mixed (hbond, oo); explicit modes display as hbond, oo, or pairs.
• summary.xlsx keeps the quasi_cage sheet compact by aggregating quasi-cage isomers into composition-level columns; exact quasi-cage isomers are written to summary_detail/quasi_cage_isomer.csv.
• run_config.yaml keeps the raw configuration and adds a run block with resolved runtime metadata. Scientific analysis algorithms, coordinates, molecule membership, and topology counts are unchanged from 0.2.5.

Changed in 0.2.5

• Worker control: use --worker / -w with either a physical-core fraction (50%, 0.5, 1.0) or an explicit worker count (1, 4). SQQ reserves one physical core for the system and clamps by task count and platform limits.
• Summary dashboard clarity: the first workbook sheet reports SQQ version in Configuration and uses Analysis Results (min / mean / max) for per-frame result metrics. Frames total / ok / failed remains a run-level frame count.
• Single-file progress visibility: interactive serial runs now highlight the active stage with bold bright-blue text while keeping the compact three-row stage layout.

Install

Install the released package from PyPI:

pip install sqq

Upgrade an existing installation:

pip install -U sqq

For local development from a source checkout:

pip install -e .

Then use:

sqq -h
sqq --version
sqq init -o config.yaml
sqq analyze -i ./gro -c config.yaml -o ./result_sqq

Root help prints the SQQ version and release date immediately before the usage line. Use sqq -v or sqq --version for the version line alone.

During source-tree development without installation:

python -m sqq analyze -i ./gro -c config.yaml -o ./result_sqq

Quick Start

Single GRO file:

sqq analyze -i test1.gro -o ./result_sqq

Directory of GRO files:

sqq analyze -i ./gro --pattern "*.gro" -o ./result_sqq

Glob pattern:

sqq analyze -i "./gro/*.gro" -o ./result_sqq

XTC/TRR trajectory with a topology file:

sqq analyze -i traj.xtc --top topol.gro -c config.yaml -o ./result_sqq

Input Units and Boxes

GRO and MDAnalysis trajectory coordinates are interpreted in nm. GRO accepts exactly one frame per file and rejects truncated atom blocks, missing or malformed box lines, extra non-empty records, and non-finite coordinates. Trajectory frames also require finite coordinates. XYZ coordinates are multiplied by input.xyz_scale / --xyz-scale; the default 0.1 assumes angstrom input, while 1.0 keeps nm values. SQQ accepts exactly one declared XYZ frame per file and rejects truncated, extra, malformed, or non-finite atom records. XYZ has no periodic box unless converted through another format.

GRO atom counts and the mandatory box line are validated. A three-value positive box is orthorhombic; an all-zero box is treated as non-periodic. Nine-value GRO boxes with nonzero tilt terms and trajectory frames with non-90-degree angles are rejected because triclinic minimum-image calculations are not implemented. Molecules are formed from contiguous residue blocks in source order, preventing wrapped or repeated residue IDs from merging distinct molecules.

Analysis Modes

-m / --mode selects one of three base presets:

sqq analyze -i ./gro -m 00 -o ./result_rigorous
sqq analyze -i ./gro -m 50 -o ./result_standard
sqq analyze -i ./gro -m 99 -o ./result_performance

Modes do not change quasi_cage.max_layers or order.parameters; L1 and the f3,f4 order-parameter selection remain the defaults in every mode. Use --quasi-max-layer explicitly for L2/L3 and --order-parameter for another descriptor set. Automatic workers use the mode fraction of detected physical cores, reserve one physical core for the system, and are capped by the number of independent GRO/XYZ files or selected trajectory frames. Multiple standalone files use spawned processes by default; a single indexed XTC/TRR trajectory can also distribute frames across spawned workers. --worker N / -w N overrides the mode percentage; integer text such as 1 or 4 is a worker count, while decimal text such as 0.5 or 1.0 and percentages such as 50% or 100% are physical-core fractions. The old --workers spelling is retained as a compatibility alias.

Version 0.2.7 uses process-based parallelism for independent GRO/XYZ files and selected XTC/TRR frames, so CPU-bound ring, quasi-cage, and cage searches can run on multiple cores. The main process alone owns the terminal panel and final workbook; process workers report stage events through a process queue, analyze one file or a small trajectory-frame batch, write frame directories, and return summary rows. At most 3 * workers process or compatibility-thread tasks are kept in flight; this bounds Future and serialization overhead without reducing the worker count. parallel.math_threads: 1 prevents nested BLAS/OpenMP oversubscription.

The default chordless/bounded path preserves the established scientific definitions while accelerating neighbor generation, incremental chord pruning, L1 forward checking, cached layer growth, integer-mask subset ownership, and cage target/edge state pruning. Cage DFS also applies exact remaining-edge incidence and parity conditions before expansion. MDAnalysis supplies orthorhombic cutoff candidates when available, but SQQ still rechecks every distance and hydrogen-bond angle with its established float64 logic. F3 and graph-mode Q_l share one graph-vector cache; all Q_l degrees share candidate lists and spherical-angle work. Optional ring.definition: shortest_path applies the Franzblau shortest-path criterion and reuses bounded-BFS distance maps. Optional quasi_cage.search_policy: exact preserves distinct frontiers and enumerates connected L2/L3 subsets; these opt-in modes can change or add results. Candidate and state truncation is reported through frame warnings.

Optional scientific cage validation adds PBC-aware face planarity and edge-variation limits, manifold vertex-link checks, positive-volume validation, and volume-centroid cage centers. It remains disabled by default. SQQ uses an orthorhombic box representation and now rejects non-orthogonal/triclinic input explicitly.

The current release uses the same compact three-row stage model for serial and parallel progress: file preparation (reading, settings, selecting), core topology search (graph, ring, half/quasi, cage, and optional cluster), and post-processing (filtering, order, ice, output). In interactive single-file runs, the active stage is highlighted with bold bright-blue ANSI text. The cluster stage appears only when hydrate-cluster analysis is enabled. Parallel runs also show aggregate stage counts and up to six active files with per-stage and per-file timings.

Common Commands

Write a default configuration file:

sqq init -o config.yaml

Search 4/5/6 ring faces and report Type H cages:

sqq analyze -i md.gro -s 4,5,6 --cage-size H -o ./result_sqq_456

Explicitly report every detected cage composition in the selected search scope:

sqq analyze -i md.gro -s 4,5,6 --cage-size all -o ./result_sqq_all_cages

Analyze connected hydrate clusters from all detected cages:

sqq analyze -i md.gro -s 4,5,6 --hydrate-cluster on -o ./result_sqq_cluster

Enable bounded outer quasi-cage layers, or opt into exact connected-subset growth:

sqq analyze -i md.gro --quasi-max-layer 3 -o ./result_sqq_l3
sqq analyze -i md.gro --quasi-max-layer 3 --quasi-search-policy exact -o ./result_sqq_l3_exact

Opt into Franzblau shortest-path rings:

sqq analyze -i md.gro --ring-definition shortest_path -o ./result_sqq_sp_ring

Opt into stricter scientific cage validation:

sqq analyze -i md.gro --cage-scientific-validation on -o ./result_sqq_scientific

Select F3/F4 plus a LAMMPS-style Q_l degree list and neighbors:

sqq analyze -i md.gro --order-parameter f3,f4,q4,q6,q8,q10,q12 --q-neighbor-mode lammps --q-cutoff 0.35 --q-n-neighbor 12

Select all F3/F4 and hydrate-nucleation descriptors:

sqq analyze -i md.gro --order-parameter f3,f4,mcg1,mcg3,dhop35,dhop30 -o ./result_sqq_order

--order-parameter replaces the complete selection rather than adding to the default. Use all for f3,f4,q6,q12,mcg1,mcg3,dhop35,dhop30, or none to skip all order-parameter calculations.

Disable selected output categories with one option:

sqq analyze -i md.gro --no-output info,quasi-gro,cage-gro,xlsx -o ./result_sqq_report
sqq analyze -i md.gro --no-output all -o ./result_sqq_config_only

--no-output defaults to none. The mandatory run_config.yaml remains even with all.

Parallelize independent GRO/XYZ files with spawned processes (the default backend):

sqq analyze -i ./gro --pattern "*.gro" --parallel-backend process -w 4 -o ./result_sqq

The same process backend parallelizes selected frames of one indexed trajectory:

sqq analyze -i traj.xtc --top topol.gro -w 4 -o ./result_sqq

Use --parallel-backend serial for an exact one-process comparison. thread is retained as a compatibility backend, but CPU-bound Python topology search should normally use process.

Important Defaults

mode: "50"

input:
  pattern: "*.gro"
  xtc_stride: 1
  xyz_scale: 0.1

graph:
  bond_mode: auto
  oo_cutoff_nm: 0.35
  hbond_distance_nm: 0.35
  hbond_angle_deg: 30.0

ring:
  sizes: [5, 6]
  report_sizes: auto
  chordless: true
  definition: chordless

quasi_cage:
  enabled: true
  base_sizes: auto
  side_sizes: auto
  max_layers: 1
  search_policy: bounded

cage:
  enabled: true
  report_types: auto
  max_faces: 20
  search_mode: grow
  seed_mode: ring
  fast_closure: true
  fast_closure_max_states: 20000
  scientific_validation: false
  max_face_planarity_rms_nm: 0.06
  max_face_edge_cv: 0.35
  min_cage_volume_nm3: 1.0e-6
  occupancy_mode: polyhedron

hydrate_cluster:
  enabled: false
  min_cage: 2

hydrate_order:
  mcg_guest_resnames: [CH4, MET]
  mcg_guest_cutoff_nm: 0.90
  mcg_water_cutoff_nm: 0.60
  mcg_cone_half_angle_deg: 45.0
  mcg_min_waters: 5
  dhop_neighbor_cutoff_nm: 0.35
  dhop_planar_counts: [11, 12]
  dhop_min_qualified_neighbors: 3

order:
  parameters: [f3, f4]
  q_neighbor_mode: graph
  q_cutoff_nm: 0.35
  q_n_neighbor: null

output:
  disabled_outputs: []
  write_tsv: false
  write_order_tsv: false
  write_vmd: false
  summary_detail_dir: summary_detail
  cage_isomer_rows: nonzero
  write_empty_files: false
  structure_layout: grouped

parallel:
  backend: process
  workers: auto
  math_threads: 1

Configuration priority:

built-in defaults < mode preset < config.yaml < explicit command-line options

Parallel Execution

parallel.backend: process is the default for two or more independent GRO/XYZ inputs. SQQ uses the spawn start method on every supported platform. Each worker receives run configuration once, reads and writes its own frame, and sends only small stage events plus one summary row to the main process. This avoids the Python GIL limitation of the compatibility thread backend.

Automatic workers use the mode fraction of detected physical cores, then reserve one physical core for the operating system and cap the result by the number of files or selected trajectory frames. Physical-core detection prefers optional psutil, then platform probes such as Windows CIM, macOS sysctl, or Linux /proc/cpuinfo; if physical cores cannot be detected, SQQ falls back to the CPU count visible to the process. --worker / -w accepts either a fraction (50%, 0.5, or 1.0 for 100%) or an explicit positive integer worker count (1 means one worker). Windows ProcessPoolExecutor runs are capped at 61 workers; Linux workstations can use larger explicit values such as -w 100, subject to the reserve-one-core rule, task count, memory, and storage throughput.

One XTC/TRR file with --top is frame-parallel when the process backend resolves to more than one worker. Every worker opens a private MDAnalysis Universe once and seeks small contiguous batches of selected raw frame indexes; batch size is automatically bounded from 1 to 8, and complete coordinate arrays are not serialized between processes. Parent and worker trajectory readers are explicitly closed. Multiple trajectory files and the compatibility thread backend use the serial trajectory reader.

Process submission uses a bounded rolling queue of at most 3 * workers tasks. This is a queue-depth limit, not a CPU limit: with 100 effective workers SQQ may keep up to 300 tasks submitted while still running as many as 100 workers concurrently. Results are restored to original file/frame order before workbook writing.

The parent preserves input/frame order in summary.xlsx. Different standalone files must have unique case-insensitive stems because each stem is the output frame-directory name. Process runs set OMP_NUM_THREADS, OPENBLAS_NUM_THREADS, MKL_NUM_THREADS, VECLIB_MAXIMUM_THREADS, NUMEXPR_NUM_THREADS, and BLIS_NUM_THREADS to parallel.math_threads while workers are spawned, then restore the parent environment.

The scheduling and search-cache refinements themselves do not change existing scientific definitions or values. Before the new hydrate descriptors were enabled, they reduced the local 1200ns.gro serial run from about 26.6 s to 18.2 s. A 0.2.3 benchmark that also selected MCG-1 and DHOP35 completed in about 21.6 s on the same host; every overlapping pre-existing analysis column matched the earlier workbook. Performance depends on data, configuration, CPU, memory, and storage.

Search and Report Scope

-s / --size defines the ring-face sizes used during detection and, by default, reporting. With no dedicated report filter, SQQ reports all rings, quasi-cages, and cages found in that search scope. --ring-size and --cage-size can narrow the user-facing output afterward:

# Search 4/5/6, report only ring 5/6 and the Type H cage group
sqq analyze -i md.gro -s 4,5,6 --ring-size 5,6 --cage-size H

For example:

# Report every detected 4/5/6 ring, quasi-cage, and cage composition
sqq analyze -i md.gro -s 4,5,6

# Keep 4/5/6 rings and quasi-cages, but report only structure-I and structure-II cages
sqq analyze -i md.gro -s 4,5,6 --cage-size I,II

Cage report groups expand to scientific cage compositions:

I     -> 5¹², 5¹²6²
II    -> 5¹², 5¹²6⁴
H     -> 5¹², 5¹²6⁸, 4³5⁶6³
HS-I  -> 5¹², 5¹²6², 5¹²6³
TS-I  -> 5¹², 5¹²6², 5¹²6³
I2II  -> 5¹²6³

Repeated cage types contributed by multiple groups are reported once. All detected cages still participate in half-cage, quasi-cage, and free-ring filtering. An explicit --cage-size changes user-facing counts and files, not topology ownership. Cage detection supports 4/5/6 faces; ring and quasi-cage detection also support size 7.

--cage-size accepts the comma-separated groups I, II, H, HS-I, TS-I, and I2II. The default auto scope follows --size; all explicitly requests the same all-detected behavior. Use auto or all alone rather than combining either keyword with a group.

Cage Fast Closure and Scientific Validation

One frame-local ring topology index stores ring_by_id, ring centers, edge_to_ring_ids, ring adjacency, and the symmetric distance cache. Half/quasi and cage searches reuse this object instead of rebuilding the same incidence and geometry data.

cage.fast_closure: true is the default. Only when generic grow reaches a configured state limit, SQQ uses an indexed half-cage overlap graph to assemble connected combinations of two to four standard half-cage patches. Every candidate must still match one generated face composition and pass the ordinary closed-polyhedron test. Existing grow detections are retained first, so exhaustive grow output and object ids remain unchanged; fast closure only adds a cage when the bounded grow path missed it. --cage-fast-closure off disables this supplement for exact comparison.

cage.scientific_validation: false is the default. When enabled with --cage-scientific-validation on, every accepted cage must additionally satisfy the configured PBC-aware face-planarity RMS and edge-length coefficient-of-variation limits, an edge-connected face shell, a single cyclic face link around every vertex, and a positive minimum triangulated volume. Accepted cages then use the volume centroid instead of the mean cage-water position. Enabling it can therefore remove distorted cages and can change guest occupancy or geometry-resolved hydrate-cluster edges. Raw ring and half/quasi searches, order parameters, and ice classification are unchanged; ownership-filtered free-ring and free-patch outputs can increase when a rejected cage no longer consumes them.

Guest occupancy uses the configured center atom when available. Otherwise, guest atoms are PBC-unwrapped around one molecular anchor before calculating the centroid; the same helper is used by MCG. This correction can intentionally change occupancy counts relative to 0.2.6 or early 0.2.7 results for multi-atom guests crossing a periodic boundary.

Hydrate Cluster

--hydrate-cluster on analyzes every detected cage in the selected search scope. Cages become graph nodes and are connected through complete shared ring faces. When several detected cages reference the same face, ring-plane geometry keeps at most one cage on each physical side. --cage-size filters user-facing cage tables and files only; it does not remove cages from cluster connectivity or phase evidence.

The hierarchy follows the HTR+ idea of classifying hydrate type, domains, and boundaries on a cage-connection graph (DOI 10.1088/1361-648X/ad52df). SQQ implements this independently with labelled shared-face fingerprints, strict local seeds, mutually compatible expansion, and exclusive per-frame domains.

--cluster-min-cage N sets the minimum connected-component size; the default is 2. Smaller components are counted as isolated cages.

Within each cluster, SQQ builds labelled first-shell fingerprints from neighboring cage types and shared-face sizes. Strict local sI/sII/sH seeds initialize phase evidence. The sH templates cover 5^12, 4^3 5^6 6^3, and 5^12 6^8 cages; the earlier two-anchor sH composite is retained as supplemental high-confidence evidence. All three phases expand through mutually compatible face-labelled edges when a candidate has at least two accepted phase contacts. Cages claimed exclusively by one phase form deterministic per-frame domains. Remaining cages are reported as single-phase boundaries, interphase boundaries, ambiguous, or unclassified.

The analysis is off by default and does not alter ring, patch, cage, occupancy, order-parameter, or ice results. Classification is per-frame and independent of the cage reporting filter; temporal grain tracking and crystallographic orientation matching are not implemented.

--cluster-detail on adds optional one-row-per-cluster summary_detail/hydrate_cluster_detail.csv. The workbook keeps the per-frame hydrate_cluster sheet, while one-row-per-domain details move to summary_detail/hydrate_domain.csv; public motif output is not generated. Hydrate clusters do not produce separate GRO files.

Hydrate Nucleation Order Parameters

MCG-1 and DHOP35 were introduced as defaults in 0.2.5. Since 0.2.7, every MCG/DHOP variant is selected explicitly through --order-parameter; the package default is only f3,f4. These descriptors are independent of the optional cage-topology hydrate_cluster classifier: MCG works on selected methane-like guest centers and surrounding waters, while DHOP works on a dedicated O-O neighbor graph. They do not change graph, ring, patch, cage, occupancy, F3/F4/Q_l, hydrate-cluster, or ice results.

MCG follows the mutually coordinated guest definition. Guest pairs within 0.90 nm are connected when at least five waters lie within 0.60 nm of both guests and inside both 45-degree opposing cones. The threshold is at least five, not exactly five. MCG-1 keeps guest nodes with at least one qualifying MCG edge; optional MCG-3 applies a one-pass degree-at-least-three filter to the same qualifying graph. Connected components are measured only through qualifying MCG edges. The default guest residue names are CH4 and MET; change hydrate_order.mcg_guest_resnames for another methane naming convention. If no configured guest type is present, MCG is reported as N/A, not zero.

DHOP builds its own orthorhombic-PBC oxygen graph with hydrate_order.dhop_neighbor_cutoff_nm: 0.35. This 0.35 nm default follows the all-atom TIP4P/Ice implementation used by Li et al.; use 0.325 in YAML when reproducing the original mW-water definition. For each central O-O bond, SQQ counts neighboring plane-normal pairs within 35 degrees (or 30 degrees for DHOP30), selects waters with counts 11 or 12, requires at least three similarly qualified neighbors, includes their first oxygen shell, and reports the largest connected water cluster. DHOP35 and DHOP30 name the angular thresholds, not the O-O cutoff. No transition-state value such as DHOP35=57 is hard-coded; such values are system- and condition-dependent.

Select any combination with names such as --order-parameter mcg1,mcg3,dhop35,dhop30. Selection is separate from the numerical hydrate_order cutoff settings. All cutoff searches use deterministic cell lists and exact float64 minimum-image rechecks; there are no fixed neighbor-array limits.

References: Barnes et al., MCG (DOI 10.1063/1.4871898); Knott et al., MCG nucleation coordinate (DOI 10.1021/jp507959q); DeFever and Sarupria, DHOP (DOI 10.1063/1.4996132); Li et al., all-atom DHOP nucleation pathway (DOI 10.1073/pnas.2011755117).

Useful Options

Bond Mode

Use -b / --bond-mode to override the graph setting supplied by the selected mode or config.yaml:

sqq analyze -i md.gro -b auto
sqq analyze -i md.gro --bond-mode hbond
sqq analyze -i md.gro -b oo
sqq analyze -i md.gro -b pairs --pairs pairs.txt

Available values are auto, hbond, oo, and pairs. --pairs PAIRS.txt used alone remains shorthand for pairs mode. Combining --pairs with -b auto, -b hbond, or -b oo is rejected. Pairs mode requires either --pairs or graph.pair_file in config.yaml.

Output Selection

--no-output TYPE[,TYPE...] replaces the complete configured disabled-output list. The default is none, equivalent to output.disabled_outputs: [].

Default-on outputs are per-frame info Markdown, all five GRO categories, summary.xlsx, and summary_detail/*.csv. membership-tsv, order-tsv, and vmd are default-off positive outputs; --write-order-tsv enables the order TSV unless order-tsv is listed in --no-output. run_config.yaml is mandatory and is always rewritten.

gro disables all GRO categories. all disables every optional output and must be used alone; none disables nothing and must also be used alone. Accepted aliases are info-md, half-cage-gro, quasi-cage-gro, and detail-csv. Explicit CLI selection has precedence:

--no-output > output.disabled_outputs > default none

The old individual --no-info, --no-gro, --no-ring-gro, --no-half-cage-gro, --no-quasi-cage-gro, --no-cage-gro, --no-ice-gro, --no-xlsx, and --no-summary-detail spellings remain hidden compatibility options for 0.2.7. When no unified option is present they are translated into disabled_outputs; otherwise they are ignored with a warning.

When an existing output directory is reused, SQQ removes known stale files for disabled categories while preserving unrelated user files. If all per-frame outputs are disabled and no unrelated file remains, the empty frame directory is removed.

Output Structure

With the default --no-output none, SQQ writes one folder per frame, a global workbook, and CSV detail tables:

result_sqq/
  summary.xlsx
  summary_detail/
    failures.csv                       # only when frames fail
    cage_occupancy.csv
    cage_isomer.csv
    quasi_cage_isomer.csv
    hydrate_domain.csv
    hydrate_cluster_detail.csv        # only with --cluster-detail on
  run_config.yaml
  test1/
    test1_info.md
    ring/
      test1_ring_5.gro
      test1_ring_6.gro
    half_cage/
      hc_5r_5^5/
        test1_hc_5r_5^5.gro
    quasi_cage/
      qc_5r_5^3-6^2_55566/
        test1_qc_5r_5^3-6^2_55566.gro
    cage/
      5^12/
        test1_cage_5^12.gro
        test1_cage_5^12_empty.gro
        test1_cage_5^12_occupied.gro
    ice/
      test1_ice.gro
    test1_order_parameter.tsv   # only with --write-order-tsv

Items named by --no-output are omitted from this layout. --no-output all leaves only run_config.yaml and does not create empty per-frame directories.

Without --strict, standalone serial/process/thread read failures become failed summary rows and analysis continues where the reader remains usable. Failed inputs appear in summary.xlsx/failures and summary_detail/failures.csv when those outputs are enabled, and always in the mandatory run_config.yaml run.failures list. With --strict, SQQ re-raises the error after updating run_config.yaml to status: failed.

GRO structure folders, filenames, and title lines use portable ASCII structure labels since version 0.2.4, for example 5^126^2 and qc_5r_5^36^2_56566. Markdown/Excel scientific labels retain their readable superscript notation. This avoids Windows GBK/legacy-reader failures caused by Unicode superscript or subscript characters in generated GRO paths and titles.

Each per-frame *_info.md report is arranged for inspection. Frame Information begins with the SQQ version, report-generation date and local timezone, absolute source path, frame name, and trajectory time. The report shows requested/effective graph_mode, the effective bond_mode, only reported ring sizes, final free-ring counts, the active network degree distribution, groups half-cage and quasi-cage isomers below composition totals, and keeps cage composition totals plus cage isomers in one vertical Cage table. When enabled, the same report adds Hydrate Cluster, hierarchy, detail, domain, and boundary sections. Internal hc_ and qc_ prefixes are omitted from report labels.

When quasi-cage or cage isomers are present, the same report adds description tables:

• Quasi Cage Isomer Description explains each observed layered quasi-cage isomer by base ring and L1/L2/L3 ring sequence.
• Cage Isomer Description explains each observed closed-cage isomer by face composition and 6-ring face adjacency pattern.

Cage Occupancy remains a separate table because it describes guest assignment rather than cage topology. It expands exact guest compositions across dynamic columns in source guest order.

summary.xlsx remains plotting-oriented when xlsx is enabled. Its first sheet is a dashboard: Configuration includes SQQ version, requested/effective Graph mode such as auto -> hbond, normalized Order parameters, and normalized Disabled outputs; Analysis Results (min / mean / max) reports per-frame min/mean/max values while Frames total / ok / failed stays a run-level count. Failed inputs add a compact failures sheet without restoring the removed redundant frame sheet. The remaining analysis sheets keep one input file or trajectory frame per row, including connection diagnostics, ring, half_cage, compact composition-level quasi_cage, cage, optional per-frame hydrate_cluster, optional order_parameter, ice, detail_index, and config. Multi-row and isomer detail tables are written as UTF-8-SIG CSV files in summary_detail/ when summary-detail is enabled: optional failures.csv, cage_occupancy.csv, cage_isomer.csv, quasi_cage_isomer.csv, hydrate_domain.csv, and, with --cluster-detail on, hydrate_cluster_detail.csv. The quasi_cage workbook sheet aggregates exact quasi-cage isomers into composition-level columns such as 5r_5²6³, while quasi_cage_isomer.csv keeps nonzero exact isomer rows with quasi_cage_type, isomer, and count. cage_isomer.csv defaults to observed nonzero isomer rows plus per-frame totals; use --cage-isomer-rows all to restore the full zero-filled matrix. The order_parameter sheet contains only the selected F3, F4, Q_l, MCG, and DHOP columns; --order-parameter none omits the sheet. Focus mean/count columns are written only when order.focus_waters is non-empty. Per-frame reports follow the same selection, and --write-order-tsv writes only selected per-water F3/F4/Q_l values because MCG/DHOP are frame-level descriptors.

Summary construction records rows, columns, cells, bytes, CSV/XLSX write time, formatting time, and final-save time in run_config.yaml -> run.summary_write; the terminal prints its total seconds. XLSX, detail CSV, and run_config.yaml are written to same-directory temporary files and atomically replaced on success. Data sheets above 200,000 cells or 128 columns keep header styling, filter, freeze pane, and fixed column widths but skip costly body-cell formatting; scientific values and table schemas are unchanged.

Output ownership is:

cage > quasi_cage > half_cage > ring

Cage files include cage waters, CNT center atoms, and assigned guests. Exact guest-composition files are generated from the guest names present in the frame, such as CH4, CH4x2, or CH4+CO2.

See docs/design.md for algorithm details and docs/update.md for release changes.