{ "_id": "6a207521cd65a98ecbd1300b", "Package": "crystract", "Type": "Package", "Title": "Crystallographic Information File (CIF) Data Processing Tools", "Version": "1.0.1", "Authors@R": "c(person(given = \"Don\", \nfamily = \"Ngo\",\nemail = \"dngo@carnegiescience.edu\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0009-0001-2779-2146\")),\nperson(given = \"Anirudh\",\nfamily = \"Prabhu\",\nemail = \"aprabhu@carnegiescience.edu\",\nrole = c(\"aut\"),\ncomment = c(ORCID = \"0000-0002-9921-6084\")),\nperson(given = \"Julia-Maria\",\nfamily = \"Hubner\",\nemail = \"julia-maria.huebner@tu-dresden.de\",\nrole = c(\"aut\"),\ncomment = c(ORCID = \"0000-0003-2048-6629\"))\n)", "Maintainer": "Don Ngo ", "Description": "Provides a suite of functions to parse Crystallographic\nInformation Files (.cif), extracting essential data such as\nchemical formulas, unit cell parameters, atomic coordinates,\nand symmetry operations. It also includes tools to calculate\ninteratomic distances, identify bonded pairs using various\nalgorithms (minimum_distance, brunner_nn_reciprocal, econ_nn,\ncrystal_nn), determine nearest neighbor counts, and calculate\nbond angles. The package is designed to facilitate the\npreparation of crystallographic data for further analysis,\nincluding machine learning applications in materials science.\nMethods are described in: Brunner (1977)\n; Hoppe (1979)\n; O'Keeffe (1979)\n; Shannon (1976)\n; Pan et al. (2021)\n; Pauling (1960,\nISBN:978-0801403330).", "License": "GPL (>= 3)", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "LazyData": "true", "URL": "https://prabhulab.github.io/ml-crystals/", "Config/pak/sysreqs": "libicu-dev", "Repository": "https://prabhulab.r-universe.dev", "Date/Publication": "2026-06-03 14:00:50 UTC", "RemoteUrl": "https://github.com/prabhulab/ml-crystals", "RemoteRef": "HEAD", "RemoteSha": "7d55348a44ed982de9a3db77a0b067e639e60b27", "RemoteSubdir": "packages/crystract", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-03 18:34:05 UTC", "User": "root" }, "Author": "Don Ngo [aut, cre] (ORCID: ),\nAnirudh Prabhu [aut] (ORCID: ),\nJulia-Maria Hubner [aut] (ORCID:\n)", "MD5sum": "98366331d77c33060119636915139f72", "_user": "prabhulab", "_type": "src", "_file": "crystract_1.0.1.tar.gz", "_fileid": "c21fab19f7c6fb4b4e177d49cd309be96627af8f475f592526951d66af7ea45e", "_filesize": 912825, "_sha256": "c21fab19f7c6fb4b4e177d49cd309be96627af8f475f592526951d66af7ea45e", "_created": "2026-06-03T18:34:05.000Z", "_published": "2026-06-03T18:40:33.759Z", "_distro": "noble", "_jobs": [ { "job": 79367852241, "time": 151, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7393532167" }, { "job": 79367852264, "time": 146, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7393530283" }, { "job": 79367852197, "time": 133, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7393603619" }, { "job": 79367852156, "time": 102, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7393592358" }, { "job": 79367111615, "time": 229, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7393477090" }, { "job": 79367852412, "time": 134, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7393525864" }, { "job": 79367852187, "time": 74, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7393504919" }, { "job": 79367852352, "time": 107, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7393515879" }, { "job": 79367852420, "time": 121, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7393522018" } ], "_buildurl": "https://github.com/r-universe/prabhulab/actions/runs/26904908673", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/prabhulab/ml-crystals", "_commit": { "id": "7d55348a44ed982de9a3db77a0b067e639e60b27", "author": "Don Ngo ", "committer": "Don Ngo ", "message": "Remove duplicate bibliography entries\n", "time": 1780495250 }, "_maintainer": { "name": "Don Ngo", "email": "dngo@carnegiescience.edu" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "data.table", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "future", "role": "Imports" }, { "package": "future.apply", "role": "Imports" }, { "package": "geometry", "role": "Imports" }, { "package": "DT", "role": "Suggests" }, { "package": "ggplot2", "role": "Suggests" }, { "package": "htmlwidgets", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "plotly", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "prabhulab", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-23", "n": 7 }, { "week": "2025-26", "n": 6 }, { "week": "2025-28", "n": 4 }, { "week": "2025-29", "n": 1 }, { "week": "2025-33", "n": 3 }, { "week": "2025-35", "n": 1 }, { "week": "2025-36", "n": 1 }, { "week": "2025-37", "n": 1 }, { "week": "2025-38", "n": 26 }, { "week": "2025-40", "n": 2 }, { "week": "2025-41", "n": 5 }, { "week": "2025-47", "n": 2 }, { "week": "2025-48", "n": 1 }, { "week": "2025-49", "n": 2 }, { "week": "2025-50", "n": 6 }, { "week": "2025-52", "n": 1 }, { "week": "2026-01", "n": 2 }, { "week": "2026-02", "n": 2 }, { "week": "2026-04", "n": 4 }, { "week": "2026-05", "n": 2 }, { "week": "2026-06", "n": 3 }, { "week": "2026-08", "n": 6 }, { "week": "2026-09", "n": 17 }, { "week": "2026-10", "n": 4 }, { "week": "2026-11", "n": 1 }, { "week": "2026-12", "n": 2 }, { "week": "2026-13", "n": 2 }, { "week": "2026-14", "n": 1 }, { "week": "2026-15", "n": 3 }, { "week": "2026-19", "n": 1 }, { "week": "2026-20", "n": 2 }, { "week": "2026-22", "n": 3 }, { "week": "2026-23", "n": 2 } ], "_tags": [ { "name": "v1.0.0", "date": "2025-09-16" }, { "name": "v1.0.1", "date": "2025-11-19" } ], "_stars": 3, "_contributors": [ { "user": "don-tat", "count": 179, "uuid": 105596803 } ], "_userbio": { "uuid": 175255884, "type": "organization", "name": "Prabhu Lab" }, "_downloads": { "count": 234, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/crystract" }, "_devurl": "https://github.com/prabhulab/ml-crystals", "_pkgdown": "https://prabhulab.github.io/ml-crystals/", "_searchresults": 12, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/crystract.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/prabhulab/ml-crystals", "_realowner": "prabhulab", "_cranurl": true, "_releases": [ { "version": "1.0.0", "date": "2026-03-20" }, { "version": "1.0.1", "date": "2026-05-28" } ], "_exports": [ "aggregate_batch_results", "analyze_cif_files", "analyze_single_cif", "apply_symmetry_operations", "brunner_nn_reciprocal", "calculate_angles", "calculate_distances", "calculate_expansion_factors", "calculate_neighbor_counts", "calculate_weighted_average_network_distance", "calculate_weighted_neighbor_counts", "covalent_radii", "crystal_nn", "econ_nn", "expand_transformed_coords", "export_analysis_to_csv", "extract_atomic_coordinates", "extract_chemical_formula", "extract_database_code", "extract_space_group_name", "extract_space_group_number", "extract_structure_type", "extract_symmetry_operations", "extract_unit_cell_metrics", "filter_atoms_by_symbol", "filter_by_elements", "filter_by_wyckoff_symbol", "filter_ghost_distances", "merge_sites_pbc", "minimum_distance", "propagate_angle_error", "propagate_distance_error", "read_cif_files", "set_radii_data", "voronoi_nn" ], "_datasets": [ { "name": "covalent_radii", "title": "Atomic Radii Data for Bond-Length Estimation", "object": "covalent_radii", "class": [ "data.table", "data.frame" ], "fields": [ "Symbol", "Radius", "Type" ], "rows": 74, "table": true, "tojson": true } ], "_help": [ { "page": "aggregate_batch_results", "title": "Aggregate Batched Analysis Results", "topics": [ "aggregate_batch_results" ] }, { "page": "analyze_cif_files", "title": "Analyze a Batch of CIF Files", "topics": [ "analyze_cif_files" ] }, { "page": "analyze_single_cif", "title": "Analyze the Content of a Single CIF File", "topics": [ "analyze_single_cif" ] }, { "page": "apply_symmetry_operations", "title": "Apply Symmetry Operations to Generate a Full Unit Cell", "concept": [ "coordinate processors" ], "topics": [ "apply_symmetry_operations" ] }, { "page": "brunner_nn_reciprocal", "title": "Identify Atomic Bonds using Brunner's Method (Reciprocal)", "concept": [ "bonding algorithms" ], "topics": [ "brunner_nn_reciprocal" ] }, { "page": "calculate_angles", "title": "Calculate Bond Angles", "concept": [ "property calculators" ], "topics": [ "calculate_angles" ] }, { "page": "calculate_distances", "title": "Calculate Interatomic Distances", "concept": [ "property calculators" ], "topics": [ "calculate_distances" ] }, { "page": "calculate_expansion_factors", "title": "Calculate Supercell Expansion Factors", "concept": [ "coordinate processors" ], "topics": [ "calculate_expansion_factors" ] }, { "page": "calculate_neighbor_counts", "title": "Calculate Coordination Numbers", "concept": [ "property calculators" ], "topics": [ "calculate_neighbor_counts" ] }, { "page": "calculate_weighted_average_network_distance", "title": "Calculate Weighted Average Network Bond Distance", "concept": [ "post-processing" ], "topics": [ "calculate_weighted_average_network_distance" ] }, { "page": "calculate_weighted_neighbor_counts", "title": "Calculate Weighted Coordination Numbers", "concept": [ "property calculators" ], "topics": [ "calculate_weighted_neighbor_counts" ] }, { "page": "covalent_radii", "title": "Atomic Radii Data for Bond-Length Estimation", "topics": [ "covalent_radii" ] }, { "page": "crystal_nn", "title": "Identify Atomic Bonds using CrystalNN", "concept": [ "bonding algorithms" ], "topics": [ "crystal_nn" ] }, { "page": "econ_nn", "title": "Identify Atomic Bonds using Hoppe's EconNN Method", "concept": [ "bonding algorithms" ], "topics": [ "econ_nn" ] }, { "page": "expand_transformed_coords", "title": "Expand Coordinates into a Supercell", "concept": [ "coordinate processors" ], "topics": [ "expand_transformed_coords" ] }, { "page": "export_analysis_to_csv", "title": "Export Analysis Results to a Directory of CSVs", "topics": [ "export_analysis_to_csv" ] }, { "page": "extract_atomic_coordinates", "title": "Extract Atomic Coordinates", "concept": [ "extractors" ], "topics": [ "extract_atomic_coordinates" ] }, { "page": "extract_chemical_formula", "title": "Extract Chemical Formula from CIF Content", "concept": [ "extractors" ], "topics": [ "extract_chemical_formula" ] }, { "page": "extract_database_code", "title": "Extract Database Code from CIF Content", "concept": [ "extractors" ], "topics": [ "extract_database_code" ] }, { "page": "extract_space_group_name", "title": "Extract Space Group Name from CIF Content", "concept": [ "extractors" ], "topics": [ "extract_space_group_name" ] }, { "page": "extract_space_group_number", "title": "Extract Space Group Number from CIF Content", "concept": [ "extractors" ], "topics": [ "extract_space_group_number" ] }, { "page": "extract_structure_type", "title": "Extract Structure Type from CIF Content", "concept": [ "extractors" ], "topics": [ "extract_structure_type" ] }, { "page": "extract_symmetry_operations", "title": "Extract Symmetry Operations", "concept": [ "extractors" ], "topics": [ "extract_symmetry_operations" ] }, { "page": "extract_unit_cell_metrics", "title": "Extract Unit Cell Metrics", "concept": [ "extractors" ], "topics": [ "extract_unit_cell_metrics" ] }, { "page": "filter_atoms_by_symbol", "title": "Filter Data by Atom Symbol Interactively", "concept": [ "property calculators" ], "topics": [ "filter_atoms_by_symbol" ] }, { "page": "filter_by_elements", "title": "Filter Distances by Element Symbols", "concept": [ "property calculators" ], "topics": [ "filter_by_elements" ] }, { "page": "filter_by_wyckoff_symbol", "title": "Filter Data by Wyckoff Symbol", "concept": [ "property calculators" ], "topics": [ "filter_by_wyckoff_symbol" ] }, { "page": "filter_ghost_distances", "title": "Filter Ghost Distances Using Atomic Radii", "concept": [ "post-processing" ], "topics": [ "filter_ghost_distances" ] }, { "page": "merge_sites_pbc", "title": "Merge Close Atoms (Pymatgen Style)", "topics": [ "merge_sites_pbc" ] }, { "page": "minimum_distance", "title": "Identify Atomic Bonds using the Minimum Distance Method", "concept": [ "bonding algorithms" ], "topics": [ "minimum_distance" ] }, { "page": "propagate_angle_error", "title": "Propagate Angle Error", "concept": [ "error propagators" ], "topics": [ "propagate_angle_error" ] }, { "page": "propagate_distance_error", "title": "Propagate Distance Error", "concept": [ "error propagators" ], "topics": [ "propagate_distance_error" ] }, { "page": "read_cif_files", "title": "Read CIF Files into Memory", "topics": [ "read_cif_files" ] }, { "page": "set_radii_data", "title": "Set or Reset a Custom Atomic Radii Table", "concept": [ "post-processing" ], "topics": [ "set_radii_data" ] }, { "page": "voronoi_nn", "title": "Identify Atomic Bonds using Voronoi Tessellation", "concept": [ "bonding algorithms" ], "topics": [ "voronoi_nn" ] } ], "_readme": "https://github.com/prabhulab/ml-crystals/raw/HEAD/packages/crystract/README.md", "_rundeps": [ "abind", "cli", "codetools", "data.table", "digest", "dplyr", "future", "future.apply", "generics", "geometry", "globals", "glue", "lifecycle", "linprog", "listenv", "lpSolve", "magic", "magrittr", "parallelly", "pillar", "pkgconfig", "R6", "Rcpp", "RcppProgress", "rlang", "stringi", "stringr", "tibble", "tidyselect", "utf8", "vctrs", "withr" ], "_vignettes": [ { "source": "crystract.Rmd", "filename": "crystract.html", "title": "Using the crystract Package for Crystallographic Analysis", "author": "Don Ngo, Julia Maria Hubner, Anirudh Prabhu", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Setup: Loading the Package", "1. The Core crystract Workflow", "1.1 The Full Pipeline for Batch Processing", "1.2 A Step-by-Step Walkthrough", "1.2.1 Loading CIF Data", "1.2.2 Extracting Metadata and Unit Cell Parameters", "1.2.3 Extracting Atomic and Symmetry Data", "1.2.4 Generating the Full Crystal Structure", "1.2.5 Calculating Interatomic Distances", "1.2.6 Identifying Bonds and Neighbors", "1.2.7 Calculating Bond Angles", "1.2.8 Error Propagation", "Uncertainty in Interatomic Distance ($\\sigma_d$)", "Uncertainty in Bond Angle ($\\sigma_\\theta$)", "2. Tools for Post-Processing and Analysis", "2.1 Filtering by Chemical Identity", "2.2 Filtering by Wyckoff Position", "2.3 Filtering Ghost Distances Using Atomic Radii", "2.4 Filtering by Element Exclusion", "2.5 Calculating Weighted Average Network Bond Distance", "Formula: Weighted Average Network Distance", "Best Practices for Accurate Calculation", "3. End-to-End Example: High-Throughput Batch Processing & CSV Extraction", "Conclusion" ], "created": "2025-08-12 13:47:23", "modified": "2026-05-28 17:41:08", "commits": 18 } ], "_score": 5.7737864449811935, "_indexed": true, "_nocasepkg": "crystract", "_universes": [ "prabhulab" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.0.1", "date": "2026-06-03T18:36:28.000Z", "distro": "noble", "commit": "7d55348a44ed982de9a3db77a0b067e639e60b27", "fileid": "17cd9291e488ee384a5c745ddcfc10c8eb23dbc6006d1a84ff449e691f0107fb", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/prabhulab/actions/runs/26904908673" }, { "r": "4.6.0", "os": "linux", "version": "1.0.1", "date": "2026-06-03T18:36:25.000Z", "distro": "noble", "commit": "7d55348a44ed982de9a3db77a0b067e639e60b27", "fileid": "d8d9b901631f79e9de47ed6173cbb9810ce7285ba975216e30edd9a3d9d57177", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/prabhulab/actions/runs/26904908673" }, { "r": "4.5.3", "os": "mac", "version": "1.0.1", "date": "2026-06-03T18:39:45.000Z", "commit": "7d55348a44ed982de9a3db77a0b067e639e60b27", "fileid": "81627e2839d82abd46f0746e4ad8c8fbefea233a8931a71c02e4b1b9c9fe5d64", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/prabhulab/actions/runs/26904908673" }, { "r": "4.6.0", "os": "mac", "version": "1.0.1", "date": "2026-06-03T18:39:15.000Z", "commit": "7d55348a44ed982de9a3db77a0b067e639e60b27", "fileid": "454b6ba975e4e2cc455436f06d5d4b3a0ea076a6f67db75cb68d2c9111130d9c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/prabhulab/actions/runs/26904908673" }, { "r": "4.6.0", "os": "wasm", "version": "1.0.1", "date": "2026-06-03T18:36:36.000Z", "commit": "7d55348a44ed982de9a3db77a0b067e639e60b27", "fileid": "7effc470a31f3f0808382de45d09cb7027a37a096995dc2c9cb09f1809a1d601", "status": "success", "buildurl": "https://github.com/r-universe/prabhulab/actions/runs/26904908673" }, { "r": "4.7.0", "os": "win", "version": "1.0.1", "date": "2026-06-03T18:35:18.000Z", "commit": "7d55348a44ed982de9a3db77a0b067e639e60b27", "fileid": "e5ccd55cee6f8794f5d6816c8feff5d52460ba0f3defc1b3f9944ae2ce51dcbc", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/prabhulab/actions/runs/26904908673" }, { "r": "4.5.3", "os": "win", "version": "1.0.1", "date": "2026-06-03T18:35:34.000Z", "commit": "7d55348a44ed982de9a3db77a0b067e639e60b27", "fileid": "68c297f416ab47258d3fd2a85aeb1cd9ce3d06b533fada953f67c58e1fd3b6a4", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/prabhulab/actions/runs/26904908673" }, { "r": "4.6.0", "os": "win", "version": "1.0.1", "date": "2026-06-03T18:35:53.000Z", "commit": "7d55348a44ed982de9a3db77a0b067e639e60b27", "fileid": "3cff7b871426505634dc991d2c4abce37a23445c5ec3243fc4061d4c25d3f4b7", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/prabhulab/actions/runs/26904908673" } ] }