Package: cry 0.5.1.9000

cry: Statistics for Structural Crystallography

Reading and writing of files in the most commonly used formats of structural crystallography. It includes functions to work with a variety of statistics used in this field and functions to perform basic crystallographic computing. References: D. G. Waterman, J. Foadi, G. Evans (2011) <doi:10.1107/S0108767311084303>.

Authors:James Foadi [cre, aut], David Waterman [aut], Rita Giordano [aut], Kutumbarao Nidamarthi [aut]

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cry/json (API)

# Install 'cry' in R:
install.packages('cry', repos = c('https://jfoadi.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/jfoadi/cry/issues

On CRAN:

5.03 score 1 packages 12 scripts 253 downloads 56 exports 29 dependencies

Last updated 2 years agofrom:ed4947d49e. Checks:OK: 3 NOTE: 4. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 10 2024
R-4.5-winNOTENov 10 2024
R-4.5-linuxNOTENov 10 2024
R-4.4-winNOTENov 10 2024
R-4.4-macNOTENov 10 2024
R-4.3-winOKNov 10 2024
R-4.3-macOKNov 10 2024

Exports:angleavei_vs_resbravaiscalculate_cell_volumechange_COLSRCcheck_angle_validitycheck_bravais_validitycheck_cryst_symm_validitycheck_merged_reflections_validitycheck_rec_unit_cell_validitycheck_unit_cell_validitycheck_validitycreate_merged_reflectionscreate_rec_unit_cellcreate_unit_cellcryst_symmcrystal_familycrystal_systemdeplete_systematic_absencesextract_symmetry_infofind_symm_settingfindHMfrac_to_orthfull_symm_stringsgenerate_millerhkl_to_resolattice_stufflowest_uc_compatible_SGmerged_reflectionsnum_symm_settingsop_xyz_list_to_matrix_listop_xyz_to_matrixorth_to_fracplot_SHELXread_SHELX_logreadCIFreadmm_CIFreadMTZreadMTZHeaderreadpd_rtvreadSF_CIFreadsm_REFLreadXDS_ASCIIreadXDS_ASCIIHeaderrec_unit_cellsyminfo_to_matrix_listsyminfo_to_op_xyz_listsymm_to_cell_constsysabstheme_crytranslate_SGunit_cellwriteMTZwriteXDS_ASCIIxtal_mat01xtal_mat02

Dependencies:clicolorspacefansifarverggplot2gluegtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigR6RColorBrewerrlangscalestibbleutf8vctrsviridisLitewithrzoo

Read and analyse an MTZ file

Rendered fromMTZ.Rmdusingknitr::rmarkdownon Nov 10 2024.

Last update: 2022-06-14
Started: 2021-04-02

Read and analyse an XDS file

Rendered fromXDS.Rmdusingknitr::rmarkdownon Nov 10 2024.

Last update: 2021-04-29
Started: 2021-04-15

Read SHELXC/D/E log file

Rendered fromSHELX.Rmdusingknitr::rmarkdownon Nov 10 2024.

Last update: 2022-06-14
Started: 2021-04-18

Readme and manuals

Help Manual

Help pageTopics
Constructor for an S3 object of class "angle"angle
Mean and standard deviation in resolution shells.avei_vs_res
Constructor for an S3 object of class "bravais"bravais
S3 generic to compute cell volumecalculate_cell_volume
Volume of a reciprocal unit cell (in angstroms^(-3))calculate_cell_volume.rec_unit_cell
Volume of a unit cell (in angstroms^3)calculate_cell_volume.unit_cell
Change COLSRC date and time stampchange_COLSRC
Validity and compatibility of a cry object of class 'angle'check_angle_validity
Validity and compatibility of a cry object of class 'bravais'check_bravais_validity
Validity and compatibility of a cry object of class 'cryst_symm'check_cryst_symm_validity
Validity and compatibility of a cry object of class 'merged_reflections'check_merged_reflections_validity
Validity and compatibility of a cry object of class 'rec_unit_cell'check_rec_unit_cell_validity
Validity and compatibility of a cry object of class 'unit_cell'check_unit_cell_validity
Validity and compatibility of cry objectscheck_validity
S3 generic to create merged_reflections objectscreate_merged_reflections
Default method for generic "create_merged_reflections"create_merged_reflections.default
S3 generic to create rec_unit_cell objectscreate_rec_unit_cell
Reciprocal unit cell starting from a Bravais symbolcreate_rec_unit_cell.bravais
Reciprocal unit cell from a 'cryst_symm' objectcreate_rec_unit_cell.cryst_symm
Default method for generic "create_rec_unit_cell"create_rec_unit_cell.default
Reciprocal unit cell starting from a unit cellcreate_rec_unit_cell.unit_cell
S3 generic to create unit_cell objectscreate_unit_cell
Unit cell starting from a Bravais symbolcreate_unit_cell.bravais
Unit cell from a 'cryst_symm' objectcreate_unit_cell.cryst_symm
Default method for generic "create_unit_cell"create_unit_cell.default
Unit cell starting from a reciprocal unit cellcreate_unit_cell.rec_unit_cell
Constructor for an S3 object of class "cryst_symm".cryst_symm
Crystal family corresponding to given space group.crystal_family
Crystal system corresponding to given space group.crystal_system
Deplete systematic absencesdeplete_systematic_absences
Information on a specific space groupextract_symmetry_info
Find specific space group settingfind_symm_setting
Correct spelling for Herman-Mauguin space groups symbolsfindHM
From fractional to orthogonal coordinatesfrac_to_orth
Symmetry operations in human readable formfull_symm_strings
Generate Miller indicesgenerate_miller
Calculates resolution, given the Miller indiceshkl_to_reso
Calculation of useful lattice parameterslattice_stuff
Space group compatible with given celllowest_uc_compatible_SG
Constructor for an S3 object of class "merged_reflections".merged_reflections
Number of space group settingsnum_symm_settings
List of matrices and vectors of a specific space groupop_xyz_list_to_matrix_list
Human-readable symmetry operator into matrix and vectorop_xyz_to_matrix
From orthogonal to fractional coordinatesorth_to_frac
Plot SHELXC log filesplot_SHELX
Print method for an object of class "angle".print.angle
Print method for an object of class "bravais".print.bravais
Print method for an object of class "cryst_symm".print.cryst_symm
Print method for an object of class "rec_unit_cell".print.rec_unit_cell
Print method for an object of class "unit_cell".print.merged_reflections print.unit_cell
Reads and SHELXD log filesread_SHELX_log
Reads and output a CIF filereadCIF
Reads and output an mmCIF filereadmm_CIF
Load an MTZ filereadMTZ
Reads and output an MTZ headerreadMTZHeader
Reads and output a CIF file for powder diffractionreadpd_rtv
Reads and output an CIF filereadSF_CIF
Reads and output an CIF filereadsm_REFL
Load an XDS_ASCII file.readXDS_ASCII
Load an XDS_ASCII file's header.readXDS_ASCIIHeader
Constructor for an S3 object of class "rec_unit_cell.rec_unit_cell
Operators of a specific space group in matrix formsyminfo_to_matrix_list
Operators of a specific space groupsyminfo_to_op_xyz_list
Cell parameter constrains from symmetrysymm_to_cell_const
Locate systematic absencessysabs
cry theme for ggplot2theme_cry
Translation of space group symbols, numbers, etc.translate_SG
Constructor for an S3 object of class "unit_cell.unit_cell
Write data to an MTZ filewriteMTZ
Write data to an XDS_ASCII file.writeXDS_ASCII
Matrix for cell orthogonalisation (first choice)xtal_mat01
Matrix for cell orthogonalisation (second choice)xtal_mat02