convert

Daylight v4.9
Release Date: 1 February 2008

Name

convert - set of programs for the interconversion of MDL connection table-based
files and Daylight SMILES based-files.

Unix Synopsis

program_name [options] [infile [outfile]] - where program_name is mol2smi,
smi2mol, etc.

Description

convert(1) is a set of programs that transform structure information and data from an MDL chemical table file (molfile, SDfile, RDfile, RGfile, query SDfile, or query RDfile) into a Daylight SMILES (SMI), isomeric SMILES (ISM), SMARTS (SMA), SMIRKS (SMRK), Thor Data Tree (TDT), or SQL loader (SQLLDR) file. In addition, SMI, ISM, and TDT formatted files can be converted into MDL formats.

Sometimes it is convenient to take data directly from another source or to keep large files compressed. In these cases, input from stdin may be used. Note: If an output file is specified as part of the command, the input file must be designated as '-' (dash).

$ cat infile | program_name [options]  > outfile                       
$ gzip -cd infile.gz | program_name [options] - outfile

Default output is to stdout.

Users should be aware that the MDL representation is predicated on accurate knowledge of the bond orders in a particular valence bond representation. Implicit H atoms are added to make up a valid valence value. These data are stored in their proprietary P-table. Daylight relies on having accurate H-counts and makes up the valence by suitable bond order values against a Daylight default version of a P-table. On very rare occasions it is possible for the structure to be corrupted during conversion. Users are encouraged to compare molecular formulae generated from MDL formatted files against those generated from the SMILES where large critical conversions are carried out.

In addition, it should be noted that many of the program options allow the user to customize the resulting conversion in such a way as to follow particular business rules. For example, a user-defined P-table can be substituted for the default table or one can require that the input file have explicit hydrogen atoms on stereocenters. Note: The default value for any option can be changed by modifying $DY_ROOT/etc/unix/dy_covert.dat.

Below is a brief summary of each convert program. Each program has a separate manual page. Please see these pages for details.

mol2smi -  converts molfile/SDfile into a SMILES file 
smi2mol - converts a SMILES file into a molfile/SDfile
rd2smi - converts an RDfile into a SMILES file
smi2rd - converts a SMILES file into an RDfile
sd2smarts - converts a query SDfile or RGfile into a SMARTS file 
rd2smarts - converts a query RDfile into a SMARTS file
rd2smirks - converts a RDfile with a transform into a SMIRKS file

Options

The following options are common to all convert programs.

-VERSION [TRUE|FALSE]

Prints the program version. Default is FALSE. Setting -VERSION to TRUE prints the program version to stout.

-HELP [TRUE|FALSE]

Prints the help message. Default is FALSE. Setting -HELP to TRUE or using -h prints the help message to stout.

-SKIP_RECORDS <num>

Gives the number of records to skipped. Default is 0. Providing a value allows this number of records in the input file to be skipped during conversion.

-DO_RECORDS <num>

Gives the number of records to processed. Default is 10M. Providing a value allows this number of records in the input file to be processed during conversion.

-SHOW_ERRORLEVEL [ALL|NOTE|WARNING|ERROR|FATAL]

Sets minimum level for errors to be reported along with more serious errors. Possible values are:

     NOTE|ALL  Might be of interest but not an error
     WARNING   Something abnormal; may require attention
     ERROR     Requested operation cannot be carried out
     FATAL     Serious error; program cannot continue

Default is ERROR which shows this level and above.

-ERROR_LOG <file>

Sets file for error information. Default is stderr. Providing a filename for -ERROR_LOG redirects the error information to this file.

-REJECT_LOG <file>

Sets file for rejected input. Default is stderr. Providing a filename for -REJECT redirects the rejected records to this file.

Return Value

All convert programs return 0 to the environment if they succeed without errors or a non-zero value if there are errors.

Files

$DY_ROOT/bin/program_name

Daylight License

programs: convert