(IUCr) CIF: Accessing a CIF: the program QUASAR

Acta Cryst. (1991). A47, 655-685

Accessing a CIF: the program QUASAR

A data file conforming to the STAR File syntax is accessed by locating the appropriate data names. That is, search procedures rely on the grammatical rules of the STAR format to find the relevant data. This method of searching a file, referred to as parsing, is used by QUASAR (Hall & Sievers, 1990). It is described here as a suitable template for other CIF manipulation software.

QUASAR retrieves those data items contained in a request list of data names. As part of the access procedure it (a) outputs data items and data blocks in the order requested, (b) automatically checks the input file for logical integrity, (c) outputs the requested items in STAR File format (i.e. it spawns another CIF containing requested items), (d) permits multiple requests for a data item within the same data block, and (e) processes multiple data blocks in a single run.

An example of a QUASAR run is shown in Table 2. The first two lines of the request list in Table 2(a) specify the input and output STAR File names. These are input as extensions to the strings star_arc_ and star_out_, respectively. This example shows how specific data are extracted from the file toz.cif shown in Appendix II. The contents of the QUASAR output file, toz.out, are shown in Table 2(b). The contents of Tables 2(a) and (b) should be carefully compared with the data items in Appendix II.

Table 2. Accessing a CIF using QUASAR

(a) The QUASAR request file.

star_arc_toz.cif
star_out_toz.out

data_TOZ

_audit_creation_date

_chemical_name_systematic
_chemical_formula_sum

_cell_length_a
_cell_length_b
_cell_length_c
_cell_angle_alpha
_cell_angle_beta
_cell_angle_gamma

_reflns_scale_group_code
_reflns_scale_meas_F

_symmetry_equiv_pos_as_xyz

_atom_type_symbol
_atom_type_number_in_cell
_atom_type_scat_dispersion_real
_atom_type_scat_dispersion_imag


_atom_site_label
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_test_rubbish    #<<< ask for item not there
_atom_site_thermal_displace_type
_atom_site_U_iso_or_equiv

_refln_index_h
_refln_index_k
_refln_index_l
_refln_F_meas
_refln_F_sigma
_refln_observed_status
_refln_scale_group_code

(b) The QUASAR output file toz.out.

data_TOZ

_audit_creation_date                 91-03-20

_chemical_name_systematic
;trans-3-Benzoyl-2-(tert-butyl)-4-(iso-butyl)-1,3-oxazolidin-5-one
;
_chemical_formula_sum             'C18 H25 N O3'


_cell_length_a                       5.959(1)
_cell_length_b                       14.956(1)
_cell_length_c                       19.737(3)
_cell_angle_alpha                    90
_cell_angle_beta                     90
_cell_angle_gamma                    90

loop_
_reflns_scale_group_code
_reflns_scale_meas_F
             1 .960926

loop_
_symmetry_equiv_pos_as_xyz
        +x,+y,+z
  1/2-x,-y,1/2+z
  1/2+x,1/2-y,-z
  -x,1/2+y,1/2-z

loop_
_atom_type_symbol
_atom_type_number_in_cell
_atom_type_scat_dispersion_real
_atom_type_scat_dispersion_imag
  C  72 .017 .009
  H 100    0    0
  O  12 .047 .032
  N   4 .029 .018


loop_
_atom_site_label
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_test_rubbish     # requested item not present
_atom_site_thermal_displace_type
_atom_site_U_iso_or_equiv
  O1    .4154(4) .5699(1) .3026(1) ? Uani  .060(1)
  C2    .5630(5) .5087(2) .3246(1) ? Uani  .060(2)
  C3    .5350(5) .4920(2) .3997(1) ? Uani  .048(1)
  N4    .3570(3) .5558(1) .4167(1) ? Uani  .039(1)
  C5    .3000(5) .6122(2) .3581(1) ? Uani  .045(1)
  O21   .6958(5) .4738(2) .2874(1) ? Uani  .090(2)
  C31   .4869(6) .3929(2) .4143(2) ? Uani  .059(2)
  C32   .2552(7) .3558(2) .3953(2) ? Uani  .073(2)
  C321   .209(1) .3542(4) .3211(3) ? Uani  .111(4)
  C322   .230(1) .2626(3) .4264(3) ? Uani  .149(5)
  C41   .2034(4) .5476(2) .4682(1) ? Uani  .041(1)
  H321C   .04(1)  .318(3)  .320(2) ? Uiso  .14000
  H322A   .25(1)  .272(4)  .475(3) ? Uiso  .19000
  H322B   .34976   .22118   .40954 ? Uiso  .19000
  H322C   .08(1)  .234(4)  .397(3) ? Uiso  .19000
  H412  -.007(6)  .447(2)  .552(2) ? Uiso  .08000
  H513B  .115(7)  .757(3)  .426(2) ? Uiso  .09000
  H513C  .329(6)  .817(2)  .430(2) ? Uiso  .09000

loop_
_refln_index_h
_refln_index_k
_refln_index_l
_refln_F_meas
_refln_F_sigma
_refln_observed_status
_refln_scale_group_code
  ? ? ? ? ? ? ?


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