2.3 Editing spacer libraries

Use the program nfe to add spacers to the spacer library, and to the group file. This program can be accessed through NEWLEAD_Vectors in InsightII, or by typing "nfe" at the UNIX prompt.

nfe consists of the three modules Main, Spacers, and Groups. In each module you find a menu with commands at the bottom of the screen (see figures 3, 4, and 5).

To execute a command

  • use the arrow keys (left, right, up, down) to highlight the command, and then press <CR> to activate it
            -- OR --
  • press the key corresponding to the first letter of the command name (e.g. "q" for Quit, "s" for Save, etc.). Use this second option carefully, because it can interfere with the input of data.

Fig. 3

The main menu of program nfe

Main module

The main module contains three commands

  • Spacers...
    to load the spacers module
  • Groups...
    to load the groups module
  • Quit
    to exit the program. Prompts to save to disk the spacer library and spacer groups currently in memory. Enter the filenames (<CR> = default names) for the spacer library file and the group file, or choose to discard the current work.
    The program can not be exited unless the files are written successfully (check for user's privileges!), or the user chooses to discard the session's changes.

Fig. 4

The Spacer menu of program nfe. Shown here is the result of the command "List".

Spacers module

This module deals with creating and modifying spacer libraries. The following commands are available

  • Find...
    to look up all occurrences of a spacer, enter its name at the prompt
  • Delete...
    to delete all occurrences of a spacer, enter its name at the prompt
  • Rename...
    to change name to a spacer in all its occurrences, enter the old and new names at the prompts
  • New Entry...
    to add one or more new entries. You are prompted to enter
    • geometrical data (in one line)
      • distance between heavy atoms
      • dihedral angle + 180
      • valence angle 1
      • valence angle 2
    • name of the spacer
    • atom numbers (in one line)
      • # H-atom 1
      • # heavy atom 1
      • # heavy atom 2
      • # H-atom 2
      • Atom types for heavy atoms 1 and 2
    • quit by entering <CR> at the "geometrical data" prompt
  • List...
    to display all entries in the library. Stop by entering "q"
  • Open...
    to load a library from a binary file. The memory is cleared before this operation. Enter the name of the file at the prompt. A <CR> implies the default spacer library, but the name of the fused-ring spacer library should be entered explicitly
  • Merge...
    to add the contents of an ASCII file -- typically created with the InsightII command NEWLEAD_Vectors -- to the current library in memory. Unlike the "Open..." command, "Merge..." does not clear the current library from memory. Enter the name of the ASCII file at the prompt
  • Save...
    to save permanently the current library in memory to disk. Enter the name of the target file at the prompt (<CR> = default spacer library -- take care to provide an explicit name if you have a special library, including the fused-ring library, currently in memory). This command has no effect if no library is currently in memory
  • Clear Memory
    to clear the spacer library in memory
  • Quit
    to return to the Main module.

Fig. 5

The Group menu of the program 'nfe'. Shown here is the result of the command "Find...", with argument "*" (Find All).

Groups module

Use this module to modify the spacer group file used by NEWLEAD to cluster the results of a run.

A group of spacers contains molecules whose heavy atoms can be nearly superimposed, irrespective of the atom type (e.g. benzene and pyridine, etc.) NEWLEAD uses the groups to cluster geometrically related results in families.

These are the commands of the Groups module

  • Find...
    to look up the contents of specific groups. The option are
    • look by spacer name: enter the full name of a spacer, or its partial name followed by the wild card "*" (e.g. "benzene", "benzene*"). The program displays all group containing the spacer(s)
    • retrieve a group by entering its number in the list
    • enter the wild card "*" to display all groups
  • Delete...
    to delete a spacer from all groups where it occurs. Enter the spacer name at the prompt
  • Rename...
    to rename a spacer in all groups where it occurs, enter the old and new names at the prompts
  • Add...
    to add a spacer to a group, enter the name of the spacer and the number of the target group at the prompts
  • New Group...
    to add a group at the bottom of the list. Enter a list of spacer names terminated by a <CR>
  • Open...
    to load a file from disk, after clearing the memory
  • Save...
    to save the spacer groups to disk. Enter a filename at the prompt (<CR> = default spacer group file)
  • Clear Group...
    to remove a group from memory. Enter the number of the group to be removed, or "*" to remove all groups
  • Quit
    to return to the Main module.