Crystallographic Information Framework

CIFTEST2

based in part on the package trip by B. McMahon

Release 2.1

© Copyright 2005, 2006 by Georgi Todorov
Work supported in part by the U.S. National Science Foundation under grants DBI-0315281 and DBI-0610407, by the U.S. Department of Energy under grants ER63601-1021466-0009501 and ER64212-1027708-0011962 and by the International Union of Crystallography.

COPYING

This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License (GPL) as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.

Installing CIFTEST2

Download the tarball CIFTEST.tar.gz and unpack it to create the CIFTEST_2.1 directory in the current directory. See the following material to then use what you have unpacked.

File name File size (bytes)
CIFTEST_README.html 11000
COPYING 18009
README.txt File size (bytes)
[folder]  args 
   [folder]  cif2cbf 
      c2ctest0.cif.args 21
      c2ctest1.cif.args 23
      ciftest0.cif.args 8
      ciftest1.cif.args 8
      ciftest10.cif.args 8
      ciftest11.cif.args 7
      ciftest2.cif.args 8
      ciftest3.cif.args 8
      ciftest4.cif.args 8
      ciftest5.cif.args 8
      ciftest6.cif.args 8
      ciftest7.cif.args 8
      ciftest8.cif.args 8
      ciftest9.cif.args 8
   [folder]  ciffold 
      1ejg.cif.args 4
      longcomments.cif.args 4
      longtext.cif.args 4
   [folder]  vcif 
      ciftest0.args 27
      ciftest1.args 27
      ciftest10.args 27
      ciftest11.args 27
      ciftest2.args 27
      ciftest3.args 27
      ciftest4.args 27
      ciftest5.args 27
      ciftest6.args 27
      ciftest7.args 27
      ciftest8.args 27
      ciftest9.args 27
[folder]  descriptions 
   [folder]  cif2cbf 
      c2ctest0.cif.purpose 47
      c2ctest1.cif.purpose 44
      ciftest0.cif.purpose 21
      ciftest1.cif.purpose 53
      ciftest10.cif.purpose 35
      ciftest11.cif.purpose 41
      ciftest2.cif.purpose 51
      ciftest3.cif.purpose 38
      ciftest4.cif.purpose 54
      ciftest5.cif.purpose 69
      ciftest6.cif.purpose 71
      ciftest7.cif.purpose 71
      ciftest8.cif.purpose 68
      ciftest9.cif.purpose 35
   [folder]  vcif 
      ciftest0.purpose 21
      ciftest1.purpose 53
      ciftest10.purpose 35
      ciftest11.purpose 43
      ciftest2.purpose 51
      ciftest3.purpose 38
      ciftest4.purpose 54
      ciftest5.purpose 69
      ciftest6.purpose 71
      ciftest7.purpose 71
      ciftest8.purpose 68
      ciftest9.purpose 35
[folder]  origs 
   [folder]  cif2cbf 
      c2ctest0.cif 627
      c2ctest1.cif 739
      cif_cml.dic
      cif_core.dic
      cif_mm.dic
      ciftest0.cif 0
      ciftest1.cif 53
      ciftest10.cif 655
      ciftest11.cif 1308
      ciftest2.cif 67
      ciftest3.cif 68
      ciftest4.cif 300
      ciftest5.cif 2828
      ciftest6.cif 455
      ciftest7.cif 774
      ciftest8.cif 482
      ciftest9.cif 756
   [folder]  ciffold 
      1ejg.cif 147122
      1zrt.cif 1522666
      longcomments.cif 9157
      longtext.cif 27247
   [folder]  ciftbx 
      1ace.cif 403645
      1crn.cif 49695
      1cro.cif 51790
      1cwp.cif 375613
      1hyh.cif 898487
      1zrt.cif 1522666
      2ace.cif 448851
      4hir.cif 2130699
      4ins.cif 130342
      5hvp.cif 190663
      ADH041.cif 21959
      BDL001.cif 48510
      BDLB13.cif 49814
      c2ctest0.cif 627
      c2ctest1.cif 739
      cif_cml.dic
      cif_core.dic
      cif_mm.dic
      DDF040.cif 23420
      mtest.prt 81627
      qtest.cif 1100
      qtest.req 788
      STARDICT 30
      test.cif 3221
      test.prt 9861
      test.req 1799
      testrle.prt 0
      xtalt2.cif 7908
   [folder]  vcif 
      ciftest0 0
      ciftest1 53
      ciftest10 655
      ciftest11 1308
      ciftest2 67
      ciftest3 68
      ciftest4 300
      ciftest5 2828
      ciftest6 455
      ciftest7 774
      ciftest8 482
      ciftest9 756
[folder]  outs 
   [folder]  cif2cbf 
      c2ctest0.cif.result 891
      c2ctest1.cif.result 547
      ciftest0.cif.result 131
      ciftest1.cif.result 131
      ciftest10.cif.result 594
      ciftest11.cif.result 595
      ciftest2.cif.result 219
      ciftest3.cif.result 156
      ciftest4.cif.result 310
      ciftest5.cif.result 1403
      ciftest6.cif.result 552
      ciftest7.cif.result 1467
      ciftest8.cif.result 931
      ciftest9.cif.result 1486
   [folder]  ciffold 
      1ejg_out.cif 143162
      1ejg_out2.cif 143162
      1ejg_rebuilt.cif 143325
      1ejg_rebuilt2.cif 143325
      1zrt_out.cif 1491557
      1zrt_out2.cif 1491476
      1zrt_rebuilt.cif 1491813
      1zrt_rebuilt2.cif 1491813
      longcomments_out.cif 9517
      longcomments_out2.cif 9517
      longcomments_out2.cif~ 9528
      longtext_out.cif 27963
      longtext_out2.cif 27993
   [folder]  ciftbx 
      1ace.stwid 628455
      1ace.tpdb 394065
      1ace.twid 628509
      1crn.tpdb 51121
      1crn.twid 74191
      1cro.tpdb 53956
      1cro.twid 78576
      1cwp.tpdb 373393
      1cwp.twid 592373
      1hyh.tpdb 910097
      1hyh.twid 1428868
      1zrt.tpdb 1257321
      1zrt.twid 1999023
      2ace.tpdb 426220
      2ace.twid 673233
      4hir.tpdb 3716929
      4hir.twid 6312772
      4ins.out 202597
      4ins.out.x 109518
      4ins.prt 52650
      4ins.prt.x 39351
      4ins.tpdb 136676
      4ins.twid 207908
      4insuw.out 179943
      4insuw.prt 0
      4insw.out 179644
      4insw.prt 52650
      5hvp.tpdb 194658
      5hvp.twid 298750
      ADH041.tpdb 24512
      ADH041.twid 36305
      BDL001.tpdb 58530
      BDL001.twid 92034
      BDLB13.tpdb 59651
      BDLB13.twid 93434
      c2ctest0.out 682
      c2ctest1.out 794
      cyclops_test.prt 24665
      DDF040.tpdb 27784
      DDF040.twid 41555
      mtest.cyc 21144
      mtest.out 3513
      mtest.prt 81627
      mtest.xml 12273
      qtest.out 1994
      qtest.prt 360
      test.out 2223
      test.prt 9861
      testrle.prt 0
      xtalt2.out 9138
      xtalt2.out.x 12922
      xte29.out 9205
      xte29.out.x 12261
      xttne9.out 6561
      xttne9.out.x 8675
   [folder]  vcif 
      ciftest0.result 19
      ciftest1.result 19
      ciftest10.result 178
      ciftest11.result 0
      ciftest2.result 39
      ciftest3.result 0
      ciftest4.result 0
      ciftest5.result 0
      ciftest6.result 158
      ciftest7.result 1153
      ciftest8.result 188
      ciftest9.result 1036

What is CIFTEST2?

CIFTEST2 is a test kit for CIF software. The current version supports vcif, CIFFOLD, cif2cif, cif2xml, ciftbx, cif2pdb and cyclops. It is a shell script (sh) assuming the following directory tree structure:

|-- CIFTEST_2.1.tar.gz -> ../CIFTEST_2.1.tar.gz
|-- CIFTEST_README.html
|-- COPYING
|-- README.odt
|-- README.txt
|-- args
|   |-- cif2cbf
|   |   |-- c2ctest0.cif.args
|   |   |-- c2ctest1.cif.args
|   |   |-- ciftest0.cif.args
|   |   |-- ciftest1.cif.args
|   |   |-- ciftest10.cif.args
|   |   |-- ciftest11.cif.args
|   |   |-- ciftest2.cif.args
|   |   |-- ciftest3.cif.args
|   |   |-- ciftest4.cif.args
|   |   |-- ciftest5.cif.args
|   |   |-- ciftest6.cif.args
|   |   |-- ciftest7.cif.args
|   |   |-- ciftest8.cif.args
|   |   `-- ciftest9.cif.args
|   |-- ciffold
|   |   |-- 1ejg.cif.args
|   |   |-- longcomments.cif.args
|   |   `-- longtext.cif.args
|   |-- ciftbx
|   `-- vcif
|       |-- ciftest0.args
|       |-- ciftest1.args
|       |-- ciftest10.args
|       |-- ciftest11.args
|       |-- ciftest2.args
|       |-- ciftest3.args
|       |-- ciftest4.args
|       |-- ciftest5.args
|       |-- ciftest6.args
|       |-- ciftest7.args
|       |-- ciftest8.args
|       `-- ciftest9.args
|-- ciftest2
|-- descriptions
|   |-- cif2cbf
|   |   |-- c2ctest0.cif.purpose
|   |   |-- c2ctest1.cif.purpose
|   |   |-- ciftest0.cif.purpose
|   |   |-- ciftest1.cif.purpose
|   |   |-- ciftest10.cif.purpose
|   |   |-- ciftest11.cif.purpose
|   |   |-- ciftest2.cif.purpose
|   |   |-- ciftest3.cif.purpose
|   |   |-- ciftest4.cif.purpose
|   |   |-- ciftest5.cif.purpose
|   |   |-- ciftest6.cif.purpose
|   |   |-- ciftest7.cif.purpose
|   |   |-- ciftest8.cif.purpose
|   |   `-- ciftest9.cif.purpose
|   |-- ciffold
|   |-- ciftbx
|   `-- vcif
|       |-- ciftest0.purpose
|       |-- ciftest1.purpose
|       |-- ciftest10.purpose
|       |-- ciftest11.purpose
|       |-- ciftest2.purpose
|       |-- ciftest3.purpose
|       |-- ciftest4.purpose
|       |-- ciftest5.purpose
|       |-- ciftest6.purpose
|       |-- ciftest7.purpose
|       |-- ciftest8.purpose
|       `-- ciftest9.purpose
|-- dictionaries
|   |-- cif_cml.dic
|   |-- cif_core.dic
|   `-- cif_mm.dic
|-- errs
|   |-- cif2cbf
|   |-- ciffold
|   |-- ciftbx
|   `-- vcif
|-- gens
|   |-- cif2cbf
|   |-- ciffold
|   |-- ciftbx
|   `-- vcif
|-- origs
|   |-- cif2cbf
|   |   |-- c2ctest0.cif
|   |   |-- c2ctest1.cif
|   |   |-- cif_cml.dic -> ../../dictionaries/cif_cml.dic
|   |   |-- cif_core.dic -> ../../dictionaries/cif_core.dic
|   |   |-- cif_mm.dic -> ../../dictionaries/cif_mm.dic
|   |   |-- ciftest0.cif
|   |   |-- ciftest1.cif
|   |   |-- ciftest10.cif
|   |   |-- ciftest11.cif
|   |   |-- ciftest2.cif
|   |   |-- ciftest3.cif
|   |   |-- ciftest4.cif
|   |   |-- ciftest5.cif
|   |   |-- ciftest6.cif
|   |   |-- ciftest7.cif
|   |   |-- ciftest8.cif
|   |   `-- ciftest9.cif
|   |-- ciffold
|   |   |-- 1ejg.cif
|   |   |-- 1zrt.cif
|   |   |-- longcomments.cif
|   |   `-- longtext.cif
|   |-- ciftbx
|   |   |-- 1ace.cif
|   |   |-- 1crn.cif
|   |   |-- 1cro.cif
|   |   |-- 1cwp.cif
|   |   |-- 1hyh.cif
|   |   |-- 1zrt.cif
|   |   |-- 2ace.cif
|   |   |-- 4hir.cif
|   |   |-- 4ins.cif
|   |   |-- 5hvp.cif
|   |   |-- ADH041.cif
|   |   |-- BDL001.cif
|   |   |-- BDLB13.cif
|   |   |-- DDF040.cif
|   |   |-- STARDICT
|   |   |-- c2ctest0.cif
|   |   |-- c2ctest1.cif
|   |   |-- cif_cml.dic -> ../../dictionaries/cif_cml.dic
|   |   |-- cif_core.dic -> ../../dictionaries/cif_core.dic
|   |   |-- cif_mm.dic -> ../../dictionaries/cif_mm.dic
|   |   |-- mtest.prt
|   |   |-- qtest.cif
|   |   |-- qtest.req
|   |   |-- test.cif
|   |   |-- test.req
|   |   `-- xtalt2.cif
|   `-- vcif
|       |-- ciftest0
|       |-- ciftest1
|       |-- ciftest10
|       |-- ciftest11
|       |-- ciftest2
|       |-- ciftest3
|       |-- ciftest4
|       |-- ciftest5
|       |-- ciftest6
|       |-- ciftest7
|       |-- ciftest8
|       `-- ciftest9
`-- outs
    |-- cif2cbf
    |   |-- c2ctest0.cif.result
    |   |-- c2ctest1.cif.result
    |   |-- ciftest0.cif.result
    |   |-- ciftest1.cif.result
    |   |-- ciftest10.cif.result
    |   |-- ciftest11.cif.result
    |   |-- ciftest2.cif.result
    |   |-- ciftest3.cif.result
    |   |-- ciftest4.cif.result
    |   |-- ciftest5.cif.result
    |   |-- ciftest6.cif.result
    |   |-- ciftest7.cif.result
    |   |-- ciftest8.cif.result
    |   `-- ciftest9.cif.result
    |-- ciffold
    |   |-- 1ejg_out.cif
    |   |-- 1ejg_out2.cif
    |   |-- 1ejg_rebuilt.cif
    |   |-- 1ejg_rebuilt2.cif
    |   |-- 1zrt_out.cif
    |   |-- 1zrt_out2.cif
    |   |-- 1zrt_rebuilt.cif
    |   |-- 1zrt_rebuilt2.cif
    |   |-- longcomments_out.cif
    |   |-- longcomments_out2.cif
    |   |-- longcomments_out2.cif~
    |   |-- longtext_out.cif
    |   `-- longtext_out2.cif
    |-- ciftbx
    |   |-- 1ace.stwid
    |   |-- 1ace.tpdb
    |   |-- 1ace.twid
    |   |-- 1crn.tpdb
    |   |-- 1crn.twid
    |   |-- 1cro.tpdb
    |   |-- 1cro.twid
    |   |-- 1cwp.tpdb
    |   |-- 1cwp.twid
    |   |-- 1hyh.tpdb
    |   |-- 1hyh.twid
    |   |-- 1zrt.tpdb
    |   |-- 1zrt.twid
    |   |-- 2ace.tpdb
    |   |-- 2ace.twid
    |   |-- 4hir.tpdb
    |   |-- 4hir.twid
    |   |-- 4ins.out
    |   |-- 4ins.out.x
    |   |-- 4ins.prt
    |   |-- 4ins.prt.x
    |   |-- 4ins.tpdb
    |   |-- 4ins.twid
    |   |-- 4insuw.out
    |   |-- 4insuw.prt
    |   |-- 4insw.out
    |   |-- 4insw.prt
    |   |-- 5hvp.tpdb
    |   |-- 5hvp.twid
    |   |-- ADH041.tpdb
    |   |-- ADH041.twid
    |   |-- BDL001.tpdb
    |   |-- BDL001.twid
    |   |-- BDLB13.tpdb
    |   |-- BDLB13.twid
    |   |-- DDF040.tpdb
    |   |-- DDF040.twid
    |   |-- c2ctest0.out
    |   |-- c2ctest1.out
    |   |-- cyclops_test.prt
    |   |-- mtest.cyc
    |   |-- mtest.out
    |   |-- mtest.prt
    |   |-- mtest.xml
    |   |-- qtest.out
    |   |-- qtest.prt
    |   |-- test.out
    |   |-- test.prt
    |   |-- testrle.prt
    |   |-- xtalt2.out
    |   |-- xtalt2.out.x
    |   |-- xte29.out
    |   |-- xte29.out.x
    |   |-- xttne9.out
    |   `-- xttne9.out.x
    `-- vcif
        |-- ciftest0.result
        |-- ciftest1.result
        |-- ciftest10.result
        |-- ciftest11.result
        |-- ciftest2.result
        |-- ciftest3.result
        |-- ciftest4.result
        |-- ciftest5.result
        |-- ciftest6.result
        |-- ciftest7.result
        |-- ciftest8.result
        `-- ciftest9.result

BEFORE USING:

Before using CIFTEST v.2 please update the paths in the file "ciftest2". This can be done by setting the appropriate environment variables:

Variable Meaning
CIFTEST2DIR path to the CIFTEST2 directory
VCIF full path of vcif program
CIF2CIF full path of cif2cif program
CIF2CBF full path of cif2cbf program
CIF2PDB full path of cif2pdb program
CIF2XML full path to cif2xml program
CIFTBX_EX full path to CIFtbx tbx_ex program
CIFTBX_EXM full path to CIFtbx tbx_exm program
CIFTBX_TESTRLE full path to CIFtbx testrle program
PREFIX prefix for the bin directory containing programs to be tested
e.g. /usr/local
only used for programs not specified above

If you are using one of the sh-style shells, and you have put the programs to be tested into /usr/local/bin, and will execute ciftest2 from from the installation directory, you might do:

CIFTEST2DIR=.
PREFIX=/usr/local/bin
export CIFTEST2DIR
export PREFIX

or, if you use csh, you might do:

setenv CIFTEST2DIR .
setenv PREFIX /usr/local/bin

If you are trying out, some new version of, say, ciffold_0.5.4, and installed that binary as ~/bin/ciffold_0.5.4, you might override the use of PREFIX, above, for that particular program with:

CIFFOLD=~/bin/ciffold_0.5.4
EXPORT CIFFOLD

or

setenv CIFFOLD ~/bin/ciffold_0.5.4

USAGE:

ciftest2 vcif -> performs vcif tests
ciftest2 ciffold -> performs CIFFOLD tests
ciftest2 cif2cbf -> performs cif2cbf tests
ciftest2 cif2cif -> performs cif2cif tests
ciftest2 cif2pdb -> performs cif2pdb tests
ciftest2 cif2xml -> performs cif2xml tests
ciftest2 ciftbx -> performs ciftbx tests
ciftest2 cyclops -> performs cyclops tests
ciftest2 ciftbx3 -> performs all ciftbx3 tests
ciftest2 all -> perfoms all tests
ciftest2 clean -> removes all output and diff files
Version 1.9.96, G. Todorov, 27 Nov 05
Version 1.9.96, G. Todorov, 28 Nov 05
Version 1.9.97, G. Todorov, 30 Nov 05
Version 2.0, H. J. Bernstein, 30 Jan 06
Version 2.1, H. J. Bernstein, 3 Sep 06

International Tables for Crystallography

Volume G: Definition and exchange of crystallographic data

First online edition (2006)

Edited by S. R. Hall and B. McMahon

An essential guide and reference to CIF for programmers, data managers handling crystal-structure information and practising crystallographers.