Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Example of parsing a CIF file #14

Merged
merged 2 commits into from
Dec 20, 2024
Merged

Example of parsing a CIF file #14

Show file tree
Hide file tree
Changes from 1 commit
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
f6af312
Example and doc
Kolaru Nov 27, 2024
1b4472f
Made example work from command line, expanded README.
Dec 18, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
285 changes: 285 additions & 0 deletions examples/parse_geometry/7706719.cif
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,285 @@
#------------------------------------------------------------------------------
#$Date: 2021-04-05 17:55:09 +0300 (Mon, 05 Apr 2021) $
#$Revision: 263781 $
#$URL: file:///home/coder/svn-repositories/cod/cif/7/70/67/7706719.cif $
#------------------------------------------------------------------------------
#
# This file is available in the Crystallography Open Database (COD),
# http://www.crystallography.net/
#
# All data on this site have been placed in the public domain by the
# contributors.
#
data_7706719
loop_
_publ_author_name
'Awwadi, Firas F.'
'Alwahsh, Manal I.'
'Turnbull, Mark M.'
'Landee, Christopher P.'
'Twamley, Brendan'
_publ_section_title
;
Two new canted antiferromagnetic systems: magnetic, theoretical, and
crystallographic studies on trans-bis(2-iodopyridine)dihalocopper(ii).
;
_journal_issue 12
_journal_name_full
'Dalton transactions (Cambridge, England : 2003)'
_journal_page_first 4167
_journal_page_last 4178
_journal_paper_doi 10.1039/d0dt04071a
_journal_volume 50
_journal_year 2021
_chemical_formula_sum 'C10 H8 Br2 Cu I2 N2'
_chemical_formula_weight 633.34
_space_group_IT_number 15
_space_group_name_Hall '-C 2yc'
_space_group_name_H-M_alt 'C 1 2/c 1'
_symmetry_cell_setting monoclinic
_symmetry_space_group_name_H-M 'C 1 2/c 1'
_atom_sites_solution_hydrogens geom
_atom_sites_solution_primary direct
_atom_sites_solution_secondary difmap
_audit_creation_method 'CrysAlisPro 1.171.38.46 (Rigaku OD, 2015)'
_audit_update_record
;
2020-10-10 deposited with the CCDC. 2021-03-01 downloaded from the CCDC.
;
_cell_angle_alpha 90.00
_cell_angle_beta 108.162(7)
_cell_angle_gamma 90.00
_cell_formula_units_Z 4
_cell_length_a 15.5605(10)
_cell_length_b 7.9626(4)
_cell_length_c 12.9489(7)
_cell_measurement_reflns_used 1246
_cell_measurement_temperature 293(2)
_cell_measurement_theta_max 29.0240
_cell_measurement_theta_min 3.6100
_cell_volume 1524.46(16)
_computing_cell_refinement 'CrysAlisPro 1.171.38.46 (Rigaku OD, 2015)'
_computing_data_collection 'CrysAlisPro 1.171.38.46 (Rigaku OD, 2015)'
_computing_data_reduction 'CrysAlisPro 1.171.38.46 (Rigaku OD, 2015)'
_computing_molecular_graphics 'shelxtl, Bruker,2002'
_computing_publication_material 'shelxtl, Bruker,2002'
_computing_structure_refinement 'shelxtl, Bruker,2002'
_computing_structure_solution 'shelxtl, Bruker,2002'
_diffrn_ambient_temperature 293(2)
_diffrn_detector_area_resol_mean 16.0534
_diffrn_measured_fraction_theta_full 0.998
_diffrn_measured_fraction_theta_max 0.998
_diffrn_measurement_device_type 'Xcalibur, Eos'
_diffrn_measurement_method '\w scans'
_diffrn_radiation_monochromator graphite
_diffrn_radiation_source 'fine-focus sealed tube'
_diffrn_radiation_type MoK\a
_diffrn_radiation_wavelength 0.71073
_diffrn_reflns_av_R_equivalents 0.0223
_diffrn_reflns_av_sigmaI/netI 0.0358
_diffrn_reflns_limit_h_max 18
_diffrn_reflns_limit_h_min -19
_diffrn_reflns_limit_k_max 9
_diffrn_reflns_limit_k_min -9
_diffrn_reflns_limit_l_max 10
_diffrn_reflns_limit_l_min -16
_diffrn_reflns_number 3023
_diffrn_reflns_theta_full 26.30
_diffrn_reflns_theta_max 26.30
_diffrn_reflns_theta_min 3.31
_exptl_absorpt_coefficient_mu 10.705
_exptl_absorpt_correction_T_max 1.00000
_exptl_absorpt_correction_T_min 0.47314
_exptl_absorpt_correction_type multi-scan
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.38.46 (Rigaku Oxford Diffraction, 2015)
Empirical absorption correction using spherical harmonics,
implemented in SCALE3 ABSPACK scaling algorithm.
;
_exptl_crystal_colour green
_exptl_crystal_density_diffrn 2.760
_exptl_crystal_density_method 'not measured'
_exptl_crystal_description parallelepiped
_exptl_crystal_F_000 1148
_exptl_crystal_preparation 'Magnetic properties'
_exptl_crystal_size_max 0.25
_exptl_crystal_size_mid 0.15
_exptl_crystal_size_min 0.10
_refine_diff_density_max 0.559
_refine_diff_density_min -0.944
_refine_diff_density_rms 0.186
_refine_ls_extinction_method none
_refine_ls_goodness_of_fit_ref 1.036
_refine_ls_hydrogen_treatment constra
_refine_ls_matrix_type full
_refine_ls_number_parameters 79
_refine_ls_number_reflns 1538
_refine_ls_number_restraints 0
_refine_ls_restrained_S_all 1.036
_refine_ls_R_factor_all 0.0396
_refine_ls_R_factor_gt 0.0320
_refine_ls_shift/su_max 0.000
_refine_ls_shift/su_mean 0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'calc w=1/[\s^2^(Fo^2^)+(0.0370P)^2^+0.0000P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme calc
_refine_ls_wR_factor_gt 0.0706
_refine_ls_wR_factor_ref 0.0745
_reflns_number_gt 1314
_reflns_number_total 1538
_reflns_threshold_expression >2sigma(I)
_cod_data_source_file d0dt04071a2.cif
_cod_data_source_block exp_2198
_cod_depositor_comments
'Adding full bibliography for 7706719--7706724.cif.'
_cod_original_cell_volume 1524.46(15)
_cod_database_code 7706719
loop_
_symmetry_equiv_pos_as_xyz
'x, y, z'
'-x, y, -z+1/2'
'x+1/2, y+1/2, z'
'-x+1/2, y+1/2, -z+1/2'
'-x, -y, -z'
'x, -y, z-1/2'
'-x+1/2, -y+1/2, -z'
'x+1/2, -y+1/2, z-1/2'
loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_U_iso_or_equiv
_atom_site_adp_type
_atom_site_occupancy
_atom_site_symmetry_multiplicity
_atom_site_calc_flag
_atom_site_refinement_flags
_atom_site_disorder_assembly
_atom_site_disorder_group
I1 I 0.14259(3) 0.80733(5) 0.69013(3) 0.04124(15) Uani 1 1 d . . .
Cu1 Cu 0.2500 0.7500 0.5000 0.0245(2) Uani 1 2 d S . .
Br1 Br 0.12243(3) 0.85448(7) 0.35677(4) 0.03650(17) Uani 1 1 d . . .
N1 N 0.1739(2) 0.5694(5) 0.5299(3) 0.0258(9) Uani 1 1 d . . .
C5 C 0.1653(3) 0.4250(7) 0.4732(4) 0.0348(12) Uani 1 1 d . . .
H5A H 0.1923 0.4176 0.4187 0.042 Uiso 1 1 calc R . .
C1 C 0.1332(3) 0.5791(6) 0.6066(4) 0.0285(11) Uani 1 1 d . . .
C3 C 0.0789(3) 0.2999(6) 0.5723(5) 0.0406(14) Uani 1 1 d . . .
H3A H 0.0480 0.2081 0.5878 0.049 Uiso 1 1 calc R . .
C4 C 0.1188(4) 0.2894(7) 0.4918(5) 0.0418(14) Uani 1 1 d . . .
H4A H 0.1143 0.1919 0.4509 0.050 Uiso 1 1 calc R . .
C2 C 0.0848(3) 0.4465(7) 0.6299(4) 0.0392(13) Uani 1 1 d . . .
H2A H 0.0568 0.4566 0.6834 0.047 Uiso 1 1 calc R . .
loop_
_atom_site_aniso_label
_atom_site_aniso_U_11
_atom_site_aniso_U_22
_atom_site_aniso_U_33
_atom_site_aniso_U_23
_atom_site_aniso_U_13
_atom_site_aniso_U_12
I1 0.0547(3) 0.0377(2) 0.0355(2) -0.00672(17) 0.02011(19) 0.00020(16)
Cu1 0.0290(4) 0.0223(4) 0.0244(4) -0.0004(4) 0.0114(3) -0.0059(3)
Br1 0.0352(3) 0.0372(3) 0.0336(3) 0.0069(2) 0.0056(2) -0.0030(2)
N1 0.028(2) 0.026(2) 0.024(2) 0.0038(18) 0.0090(17) -0.0047(17)
C5 0.041(3) 0.032(3) 0.035(3) -0.004(3) 0.017(2) -0.003(2)
C1 0.032(3) 0.028(3) 0.025(2) 0.001(2) 0.008(2) -0.002(2)
C3 0.034(3) 0.026(3) 0.060(4) 0.014(3) 0.012(3) -0.007(2)
C4 0.040(3) 0.027(3) 0.055(4) -0.007(3) 0.010(3) -0.008(2)
C2 0.039(3) 0.042(3) 0.042(3) 0.010(3) 0.020(2) -0.001(3)
loop_
_atom_type_symbol
_atom_type_description
_atom_type_scat_dispersion_real
_atom_type_scat_dispersion_imag
_atom_type_scat_source
C C 0.0033 0.0016 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
H H 0.0000 0.0000 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
N N 0.0061 0.0033 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
Cu Cu 0.3201 1.2651 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
Br Br -0.2901 2.4595 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
I I -0.4742 1.8119 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
loop_
_geom_angle_atom_site_label_1
_geom_angle_atom_site_label_2
_geom_angle_atom_site_label_3
_geom_angle
_geom_angle_site_symmetry_1
_geom_angle_site_symmetry_3
_geom_angle_publ_flag
N1 Cu1 N1 180.0 7_566 . ?
N1 Cu1 Br1 90.10(11) 7_566 7_566 ?
N1 Cu1 Br1 89.91(11) . 7_566 ?
N1 Cu1 Br1 89.90(11) 7_566 . ?
N1 Cu1 Br1 90.09(11) . . ?
Br1 Cu1 Br1 180.0 7_566 . ?
C1 N1 C5 117.7(4) . . ?
C1 N1 Cu1 123.7(3) . . ?
C5 N1 Cu1 118.5(3) . . ?
N1 C5 C4 123.2(5) . . ?
N1 C5 H5A 118.4 . . ?
C4 C5 H5A 118.4 . . ?
N1 C1 C2 122.3(5) . . ?
N1 C1 I1 117.4(3) . . ?
C2 C1 I1 120.2(4) . . ?
C2 C3 C4 119.6(5) . . ?
C2 C3 H3A 120.2 . . ?
C4 C3 H3A 120.2 . . ?
C5 C4 C3 118.5(5) . . ?
C5 C4 H4A 120.8 . . ?
C3 C4 H4A 120.8 . . ?
C3 C2 C1 118.6(5) . . ?
C3 C2 H2A 120.7 . . ?
C1 C2 H2A 120.7 . . ?
loop_
_geom_bond_atom_site_label_1
_geom_bond_atom_site_label_2
_geom_bond_distance
_geom_bond_site_symmetry_2
_geom_bond_publ_flag
I1 C1 2.097(5) . ?
Cu1 N1 1.976(4) 7_566 ?
Cu1 N1 1.976(4) . ?
Cu1 Br1 2.4036(5) 7_566 ?
Cu1 Br1 2.4036(5) . ?
N1 C1 1.336(5) . ?
N1 C5 1.349(6) . ?
C5 C4 1.361(7) . ?
C5 H5A 0.9300 . ?
C1 C2 1.384(7) . ?
C3 C2 1.373(8) . ?
C3 C4 1.374(7) . ?
C3 H3A 0.9300 . ?
C4 H4A 0.9300 . ?
C2 H2A 0.9300 . ?
loop_
_geom_torsion_atom_site_label_1
_geom_torsion_atom_site_label_2
_geom_torsion_atom_site_label_3
_geom_torsion_atom_site_label_4
_geom_torsion
_geom_torsion_site_symmetry_1
_geom_torsion_site_symmetry_2
_geom_torsion_site_symmetry_3
_geom_torsion_site_symmetry_4
_geom_torsion_publ_flag
N1 Cu1 N1 C1 -112(100) 7_566 . . . ?
Br1 Cu1 N1 C1 84.2(4) 7_566 . . . ?
Br1 Cu1 N1 C1 -95.8(4) . . . . ?
N1 Cu1 N1 C5 71(100) 7_566 . . . ?
Br1 Cu1 N1 C5 -92.9(3) 7_566 . . . ?
Br1 Cu1 N1 C5 87.1(3) . . . . ?
C1 N1 C5 C4 -1.2(7) . . . . ?
Cu1 N1 C5 C4 176.1(4) . . . . ?
C5 N1 C1 C2 1.0(7) . . . . ?
Cu1 N1 C1 C2 -176.1(4) . . . . ?
C5 N1 C1 I1 -177.6(3) . . . . ?
Cu1 N1 C1 I1 5.3(5) . . . . ?
N1 C5 C4 C3 -0.1(8) . . . . ?
C2 C3 C4 C5 1.5(8) . . . . ?
C4 C3 C2 C1 -1.7(8) . . . . ?
N1 C1 C2 C3 0.4(8) . . . . ?
I1 C1 C2 C3 179.0(4) . . . . ?
Loading
Loading