Protein class library in C++
weider at CUHHCA.HHMI.COLUMBIA.EDU
Tue Nov 16 11:03:04 EST 1993
>>|> Hello everybody!
>>|> We are developing methods and algorithms for doing calculations
>>|> on proteins. Now we change our programming language from
>>|> c to c++. Some months ago I found a C++-Class Library specially
>>|> created for proteins and I think also for handling Brookhaven files.
>>|> And of course now I cannot remember were this library was located.
>>|> Anybody who knows anything about it??? Anybody who can tell me????
>>|> Hannes Floeckner
>>|> Grazer-Bundesstr. 24
>>|> A-5020 SALZBURG
>> Are there any C libraries around for proteins? If you could let me know...
>>MRC Protein Function and Design,
>>"They can make me do it, but they can't make me do it with dignity."
Here is the announcement we made earlier this year.
PDBlib Version 1.0
What is PDBlib?
PDBlib is a class library written in C++ for modeling a
macromolecular structure at the level of detail (excluding symmetry
information) found in a Protein Data Back (PDB) file. A class is
supplied to read a PDB file into a PDBlib representation. This class
is independent of the actual representation and other forms of
input, for example from a relational database like SESAM, are
The library is made extensible by a close coupling between
intrinsic and external classes. By writing only to the external
classes you will remain compliant with future versions of the
What do I get?
bin: executable files.
include: PDBLib header files that should not be altered
by library users in general.
include_ext: user extensible header files.
lib: PDBLib library file.
examples: Example source and header files.
What don't I get?
You don't get source code. This is a temporary situation while we
attempt to centralize bug fixes and additions to the library. If you
find this situation unworkable source code is available by signing
a copyright agreement which is available with the distribution.
How do I use it?
Three examples are included for you to see how to use the library:
o example.C demonstrates the utilities of the class library;
o XDrawProtein.C is a simply drawing program that accesses a
PDB file through the class library and displays a static view
of the protein in a window;
o PDBview will render a PDB file using only X/Motif; no
special graphics hardware or software is needed.
How do I get it?
Via anonymous ftp from cuhhca.hhmi.columbia.edu (18.104.22.168) in the
On what platforms is it available?
PDBLib.1.0.SGI.tar.Z Compressed tar file of PDB object classes library
and header files for SGI. AT&T C++ release 2.1 & 3.0
PDBLib.1.0.Sun.tar.Z Compressed tar file of PDB object classes library
and header files for Sun Sparc station. AT&T C++
release 2.1 & 3.0 compatible.
PDBLib.1.0.Cvx.tar.Z Compressed tar file of PDB object classes library
and header files for Convex. AT&T C++ release 2.1
PDBLib.1.0.Alpha.tar.Z Compressed tar file of PDB object classes library
and header files for Dec 3000 (Alpha AXP) with OSF1.
Dec C++ (cxx) release 1.2 compatible.
What about future versions?
Version 2.0 (in 2-3 months) will contain support for crystallographic
symmetry and use of templates as found in C++ AT&T v3.0 and beyond.
Version 3.0 (in 1 year) will contain support for the macromolecular
Crystallographic Information File (CIF) format to be adopted by the PDB.
Who do I contact?
Address specific programming questions on PDBlib to Weider Chang, the
author of most of the code (weider at cuhhca.hhmi.columbia.edu).
Address questions concerning PDBview to Ilya Shindyalov
(shindyal at cuhhca.hhmi.columbia.edu)
Address general comments, criticisms, questions about future directions
etc. to Phil Bourne (system at cuhhca.hhmi.columbia.edu).
Phil Bourne June 7,1993
This work was supported by NSF grant IRI-9116798 with special thanks to
Drs Maria Zemankova and John Wooley.
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