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PDBML2CIF
Installation Notes: V2-0-07

                    Installation, Building and Usage Notes
                        for the Pdbml2Cif Application


Note: Prior to utilizing Pdbml2Cif application, it is necessary to install
      Xerces-C XML parser on the target system. Pdbml2Cif uses this parser
      for XML parsing. Xerces-C XML parser can be downloaded from:

      http://xml.apache.org/xerces-c/


1.  Application Installation

a.  Uncompress and unbundle the distribution using the following command:

        zcat pdbml2cif-vX.XXX-prod-src.tar.gz | tar -xf -

    The result of this command is a subdirectory pdbml2cif-vX.XXX-prod-src in
    the current directory. It contains the subdirectories of various source
    modules and helper directories:

        bin - subdirectory in which the application executable
          will be placed after the build process.
        pdbml-parser-vX.X - subdirectory of the main application module,
          that contains a test example in its "test" subdirectory.

b.  Set up the environment variables.

    - Add Xerces-C library directory to LD_LIBRARY_PATH. For example,
      if Xerces-C library directory is "/opt/xerces-c-src_2_5_0/lib":

        For C shell users:
          setenv LD_LIBRARY_PATH "/opt/xerces-c-src_2_5_0/lib:"$LD_LIBRARY_PATH

        For Bourne shell users:
          LD_LIBRARY_PATH="/opt/xerces-c-src_2_5_0/lib:"$LD_LIBRARY_PATH;
          export LD_LIBRARY_PATH


2.  Application Building

    Position in the pdbml2cif-vX.XXX-prod-src directory and run "make" command:

        cd pdbml2cif-vX.XXX-prod-src
        make

    The application executable will be placed in the "bin" subdirectory.


    NOTE: The users who are working on Sun platform are strongly advised to
    check the compiler flags in etc/make.platform.sunos5 file. Depending on
    the compiler version, users may be required to make modifications to those
    compiler flags.


3.  Demonstration

a.  To do the demonstration of this application, position in the
    pdbml2cif-vX.XXX-prod-src directory and run "make test" command:

        cd pdbml2cif-vX.XXX-prod-src
        make test

    This command invokes a testing script, "test.sh", which invokes
    pdbml2cif application that converts a PDBML test file to MMCIF file.

b.  The tool command line options can be displayed by typing the name of the
    executable without arguments:

        cd pdbml2cif-vX.XXX-prod-src/bin
        pdbml2cif

 

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