stand-alone use You start the program through the command line:

newlead [-r or -R] [-v] [-d] [-h] [-t] \
[-i <file>] [-o <file>] \
[-l <file>] [-p <file>]

The options -r (-R), -v, -d, -h, and -t can also be typed together, e.g. "-rvh", "-hd", etc. A description of the available options follows.

  1. -i <nld.inp> input file (Columbia, MOL2, or CAR-archive format)
  2. -o <nld.out> output file
  3. -l <nld.log> log file
  4. -p <nld.prf> preference file
  5. -r (-R) ring option. -r fused-rings and linear spacers. -R only fused-ring spacers are connected in the first pass: each and every solution has one fused- ring. Default is no rings
  6. -d duplicates kept. Superimposable spacers such as benzene and pyridine are considered as duplicates. Default is only the first of a series is kept
  7. -h H-atoms kept. Default is H-atoms are removed from the results
  8. -v verbose log file. Default is short log file
  9. -t test run option. Information on the number and type of atoms for each fragment is given in the log file. No spacers are attached and no output file is produced. Default is no test run.

In 1-4), the default values for the files used by the program are given in <> brackets.

newlead -rhd -i ~/project2/complex.mmod \
-o 10.01.94.out

rings are fused; H-atoms and duplicates are kept; the input is the file "complex.mmod" in the directory "project2", the output is the file "10.01.94.out" in the working directory. Default names are assumed for the preference file and the log file.

Fig. 4

Accelrys interface After using the Fragments and the Preferences commands, activate the command NEWLEAD_Run (Custom menu) and click on the buttons displayed (Fig. 4). The buttons are,

  • "Fuse Rings", for fusing rings (-r option)
  • "Only Rings", for fusing only rings in the first pass (-R option). This button is available only if "Fuse Rings" is checked
  • "Delete H", for removing H-atoms from the output
  • "Delete Duplicates", to keep only the first in a series of results with superimposable spacers such as benzene and pyridine.

An editable field is given for the name of the output file (option -o).

Click the button "Execute" to run the program. The "Textport" window appears and a message is displayed when the run is completed.