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README
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[1][IUCr Home Page] [2][CIF Home Page] [3][ciftbx.src] [4][cyclops.src]
[5][cif2cif.src] [6][cif2xml.src] [7][cif2pdb.src]
__________________________________________________________________
CIFtbx, Cyclops, cif2cif, cif2xml, cif2pdb README FIRST Information
CIFtbx Version 4.1.1 Release, March 2024
Copyright © 2024 Sydney R. Hall and Herbert J. Bernstein
Cyclops Version 2.1.5, November 2009
Copyright © 2009 Sydney R. Hall and Herbert J. Bernstein
cif2cif Version 2.0.1, January 2024
Copyright © 1997, 1998, 2000, 2005, 2009, 2024 Herbert J. Bernstein
cif2xml Version 0.1.1 beta, November 2009
Copyright © 2000, 2009 Herbert J. Bernstein
cif2pdb Version 2.0.3, November 2009
Copyright © 2000, 2005, 2009 Herbert J. Bernstein and Frances C.
Bernstein
Sydney R. Hall
Crystallography Centre, University of Western Australia, Nedlands 6009,
Australia
Phone: +61 9 380 2725, e-mail: syd@crystal.uwa.edu.au
Herbert J. Bernstein
Bernstein+Sons, 11 Riverside Drive, Apt 5UE, NY 10023-1317, USA
Phone: 1-212-877-1686, e-mail: yayahjb@gmail.com.com
Frances C. Bernstein
Bernstein+Sons, 11 Riverside Drive, Apt 5UE, NY 10023-1317, USA
Phone: 1-212-877-1686, e-mail: fcb@bernstein-plus-sons.com
__________________________________________________________________
YOU MAY REDISTRIBUTE THE CBFLIB PACKAGE UNDER THE TERMS OF THE [8]GPL.
ALTERNATIVELY YOU MAY REDISTRIBUTE THE CBFLIB API UNDER THE TERMS OF
THE [9]LGPL.
__________________________________________________________________
Work on these programs has been supported by grants from various
government agencies and the IUCr. See the documentation of the
individual programs for further information.
CIFtbx4, Cyclops, cif2cif, cif2xml and cif2pdb are free software; you
can redistribute this software and/or modify this software under the
terms of the GNU General Public License as published by the Free
Software Foundation; either version 2 of the License, or (at your
option) any later version.
Alternatively you may reditribute and/or modify the CIFtbx API (but not
the programs) under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1 of the
License, or (at your option) any later version.
This software 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 software; if not, write to the Free Software Foundation,
Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
You should have received a copy of the GNU Lesser General Public
License along with this software; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
Before using this software, please read the
[10]NOTICE
and please read the IUCr
[11]Policy
on the Use of the Crystallographic Information File (CIF)
__________________________________________________________________
CIFtbx is a tool box of Fortran routines for manipulating CIF data.
CYCLOPS2, cif2cif, cif2xml and cif2pdb are open source Fortran programs
based on CIFtbx. CYCLOPS2 checks STAR data names against data name
dictionaries. cif2cif copies a CIF to a CIF while checking data names
against dictionaries and reformating numbers with esd's to conform to
the rule of 19. A request list may be specified. cif2xml is a variant
of cif2cif which produces XML output. cif2pdb converts mmCIF files to a
PDB or WPDB format.
In order to ensure continuing availability of source code and
documentation most programs and documents on this site are subject to
copyright. This does not prevent you from using the programs, from
making copies and changes, but prevents the creation of "closed source"
versions out of the open source versions. See [12]NOTICE.
Science is best served when the tools we use are fully understood by
those who wield those tools and by those who make used of results
obtained with those tools. When a scientific tool exists as software,
access to source code is an important element in achieving full
understanding of that tool. As our field evolves and new versions of
software are required, access to source allows us to adapt our tools
quickly and effectively.
In the early days of software development, most scientific software
source code was freely and openly shared with a minimum of formalities.
These days, it appears that carefully drawn legal documents are
necessary to protect free access to the source code of scientific
software. We are all deeply indebted to [13]Richard Stallman for
showing us how a creative combination of copyrights and seemingly
restrictive licenses could give us truly unfettered freedom to use
programs, to read their source code and to develop new versions. The
[14]GNU project, and the [15]Linux project have shown that an open
source approach works. We use the GNU General Public License (the
[16]"GPL") for our programs starting with the release of CIFtbx3. Older
versions use the license from [17]OpenRasmol. The OpenRasMol conditions
for use have correctly been called "GPL-like".
If you are a user of these programs, you will find that the copyrights
and notices ask little more of you than that you avoid mistakes by
others by keeping the notices with copies, display scientific integrity
by citing your sources properly and treating this like other shared
scientific developments by not inferring a warranty. If you are a
software developer and wish to incorporate what you find here into new
code, or to pick up bits and pieces and use them in another context,
the situation becomes more complex. Read the notices carefully. You
will find that they are "infectious". Whatever you make from our Open
Source code must itself be offered as Open Source code. In addition, in
order to allow users to understand what has changed and to ensure
orderly development you have to describe your changes.
__________________________________________________________________
[18]CIFtbx Primer Plus (320K in PDF format) provides documentation on
CIFtbx.
__________________________________________________________________
In order to get a complete release of CIFtbx4, CYCLOPS2, cif2cif,
cif2xml you will need either a C-shell archive or a shell archive of
each package. That is, you need either
[19]ciftbx.cshar.Z, [20]cyclops.cshar.Z, [21]cif2cif.cshar.Z,
[22]cif2xml.cshar.Z and [23]cif2pdb.cshar.Z or
[24]ciftbx.shar.Z, [25]cyclops.shar.Z, [26]cif2cif.shar.Z,
[27]cif2xml.shar.Z and [28]cif2pdb.shar.Z
You do not need both sets. If you cannot decompress files at your end,
then you may wish to have [29]ciftbx.cshar, [30]cyclops.cshar,
[31]cif2cif.cshar, [32]cif2xml.cshar and [33]cif2pdb.cshar
In order to test the programs, you will need at least the following CIF
dictionaries: [34]cif_core.dic.Z [35]cif_mm.dic.Z and
[36]cif_mm_pdbx.dic.Z Check the IUCr web page at
[37]http://www.iucr.org for latest versions.
The directory structure within which you will work is
top level directory
-------------------
|
|
--------------------------------------------------------------------------
| | | | | |
[38]dictionaries [39]ciftbx.src [40]cyclops.src [41]cif2cif.src [42]ci
f2xml.src [43]cif2pdb.src
------------ ---------- ----------- ----------- ----------- --------
---
In order to save space and transmission time, it is possible that each
archive will be compressed before you pick it up. Place the archives in
the top level directory and the dictionaries into the 'dictionaries'
directory. Be sure to uncompress the archives before trying to unpack
them. If you are on a UNIX system, leave the dictionaries compressed.
Each archive contains a detailed README file for the package involved.
Please do read the README. The general approach is:
1. unpack the archive
2. make all
3. make tests
Since all this code depends on CIFtbx, you must install CIFtbx before
installing CYCLOPS2, cif2cif, cif2xml or cif2pdb. If you don't need
CYCLOPS2 or cif2cif or cif2xml or cif2pdb, you may leave them out, but
they are good examples of working CIFtbx applications, so we suggest
taking a look at them if you are new to CIFtbx.
__________________________________________________________________
For further information contact Syd Hall ( syd@crystal.uwa.edu.au )
or Herbert Bernstein ( yayahjb@gmail.com )
__________________________________________________________________
The CIFtbx site is provided courtesy of [44]Bernstein + Sons,
Information Systems Consultants.
Portions © Copyright Herbert J. Bernstein 2000, 2005, 2009, 2024. All
Rights Reserved. Other copyrights apply. License to copy most pages on
this site will be granted if certain open source and other conditions
are adhered to. See
[45]http://www.bernstein-plus-sons.com/software/ciftbx_4.1.0/NOTICE.htm
l. To request permission to copy any elements from our pages, or to
send comments about our pages, please write to
[46]webmaster@bernstein-plus-sons.co m. If you establish a link to one
of our pages, please let us know! Updated 14 August 2024
References
1. http://www.iucr.org/iucr-top/welcome.html
2. http://www.iucr.org/iucr-top/cif/home.html
3. file:///home/yaya/cbf_imgcif_dictionary/ciftbx/ciftbx.src/README.ciftbx.html
4. file:///home/yaya/cbf_imgcif_dictionary/ciftbx/cyclops.src/README.cyclops.html
5. file:///home/yaya/cbf_imgcif_dictionary/ciftbx/cif2cif.src/README.cif2cif.html
6. file:///home/yaya/cbf_imgcif_dictionary/ciftbx/cif2xml.src/README.cif2xml.html
7. file:///home/yaya/cbf_imgcif_dictionary/ciftbx/cif2pdb.src/README.cif2pdb.html
8. file:///home/yaya/cbf_imgcif_dictionary/ciftbx/gpl.txt
9. file:///home/yaya/cbf_imgcif_dictionary/ciftbx/lgpl.txt
10. file:///home/yaya/cbf_imgcif_dictionary/ciftbx/NOTICE.html
11. file:///home/yaya/cbf_imgcif_dictionary/ciftbx/IUCR_POLICY.html
12. file:///home/yaya/cbf_imgcif_dictionary/ciftbx/NOTICE.html
13. http://www.stallman.org/
14. http://www.gnu.org/
15. http://www.linux.org/
16. http://www.gnu.org/copyleft/gpl.html
17. http://www.openrasmol.org/
18. file:///home/yaya/cbf_imgcif_dictionary/ciftbx/CIFtbx_Primer.pdf
19. file:///home/yaya/cbf_imgcif_dictionary/ciftbx/ciftbx.cshar.Z
20. file:///home/yaya/cbf_imgcif_dictionary/ciftbx/cyclops.cshar.Z
21. file:///home/yaya/cbf_imgcif_dictionary/ciftbx/cif2cif.cshar.Z
22. file:///home/yaya/cbf_imgcif_dictionary/ciftbx/cif2xml.cshar.Z
23. file:///home/yaya/cbf_imgcif_dictionary/ciftbx/cif2pdb.cshar.Z
24. file:///home/yaya/cbf_imgcif_dictionary/ciftbx/ciftbx.shar.Z
25. file:///home/yaya/cbf_imgcif_dictionary/ciftbx/cyclops.shar.Z
26. file:///home/yaya/cbf_imgcif_dictionary/ciftbx/cif2cif.shar.Z
27. file:///home/yaya/cbf_imgcif_dictionary/ciftbx/cif2xml.shar.Z
28. file:///home/yaya/cbf_imgcif_dictionary/ciftbx/cif2pdb.shar.Z
29. file:///cgi-bin/yaya/decomp.cgi/NDB/mmcif/software/ciftbx_4.1.0/ciftbx.cshar
30. file:///cgi-bin/yaya/decomp.cgi/NDB/mmcif/software/ciftbx_4.1.0/cyclops.cshar
31. file:///cgi-bin/yaya/decomp.cgi/NDB/mmcif/software/ciftbx_4.1.0/cif2cif.cshar
32. file:///cgi-bin/yaya/decomp.cgi/NDB/mmcif/software/ciftbx_4.1.0/cif2xml.cshar
33. file:///cgi-bin/yaya/decomp.cgi/NDB/mmcif/software/ciftbx_4.1.0/cif2pdb.cshar
34. file:///home/yaya/cbf_imgcif_dictionary/ciftbx/dictionaries/cif_core.dic.Z
35. file:///home/yaya/cbf_imgcif_dictionary/ciftbx/dictionaries/cif_mm.dic.Z
36. file:///home/yaya/cbf_imgcif_dictionary/ciftbx/dictionaries/cif_mm_pdbx.dic.Z
37. http://www.iucr.org/
38. file:///home/yaya/cbf_imgcif_dictionary/ciftbx/dictionaries
39. file:///home/yaya/cbf_imgcif_dictionary/ciftbx/ciftbx.src
40. file:///home/yaya/cbf_imgcif_dictionary/ciftbx/cyclops.src
41. file:///home/yaya/cbf_imgcif_dictionary/ciftbx/cif2cif.src
42. file:///home/yaya/cbf_imgcif_dictionary/ciftbx/cif2xml.src
43. file:///home/yaya/cbf_imgcif_dictionary/ciftbx/cif2pdb.src
44. http://www.bernstein-plus-sons.com/
45. http://www.bernstein-plus-sons.com/software/ciftbx_4.1.0/NOTICE.html
46. mailto:webmaster@bernstein-plus-sons.com