2.1 Introduction

These pages shows how to build, enlarge, and modify a spacer library for NEWLEAD. The intended audience are advanced users who need customized libraries for their own use, or for the use of a group of researchers.

a few words about NEWLEAD's spacer libraries...

  • A spacer library for NEWLEAD consists of the following elements
    • key files for the spacers and the fused-ring spacers
    • a group file for the clustering of the results
    • data files for each spacer and fused-ring spacer
  • NEWLEAD loads a default spacer library during each run. This library is defined by the UNIX environment variable NEWLEAD_ROOT and by the following default file names
    • for the key files
        $NEWLEAD_ROOT/databases/ringbase.bnf (fused-rings)
    • for the group file
    • for the data files
      where <spacer> is the name of a spacer as it appears in a key file
  • The environment variable NEWLEAD_ROOT can be defined in various ways in order to access specific libraries
    • A system administrator can set NEWLEAD_ROOT to define the location of a default library for a group of users
    • Individual users can set different values for NEWLEAD_ROOT to define their customized libraries
    • If NEWLEAD_ROOT is set to null (use the unsetenv UNIX command), NEWLEAD looks for the directories "databases" and "bridges" inside the working directory. This feature allows to store special libraries in the directories dedicated to given projects, and to access these libraries automatically as needed
  • Optionally, the user can use one or more custom libraries to link specific pairs of fragments. The definition of spacers and the editing of a custom library is identical
  • "database.bnf" and "ringbase.bnf" are binary files which need the use of the special program nfe to be edited. "groups.prf" is an ASCII file which can also be edited with the program nfe. The data files "<spacer>.dat" can be either in the Columbia (MacroModel) or the MOL2 (Sybyl) format.