clogp

Daylight v4.9
Release Date: 1 February 2008

Name

clogp - calculate logp for molecules

Unix Synopsis

clogp [options] [infile.tdt [outfile.tdt]]
clogptalk

Description

clogp and clogptalk take TDTs (THOR Data Trees) as input, estimates logP(o/w) for the molecule, add a clogp datatype to the datatree, then write the TDT to its output.

clogp prints to standard output if second argument is missing, and reads from standard input if no arguments are given.

clogptalk is usually invoked as a program object (see dt_alloc_program(3)), and uses the "talk" protocol for input/output.

(Note: clogp(1) and clogptalk(1) are actually linked to the same executable file. The program looks at its own name to decide what to do. "Talk" behavior can be forced via "clogp -PIPETALK TRUE".)

The clogp datatype has 3 fields: CP<result;errlev;version>.

If a valid estimate of the logP(o/w) value can't be made (e.g. invalid input SMILES, or clogp can't make valid estimate), clogp copies the input TDT to its output unaltered.

Options

The clogptalk(1) program takes no command-line options. The following apply to clogp(1):

-HELP [TRUE|FALSE]

Displays command line summary and halts.

-PCMODELS_ERRORTEXT [TRUE|FALSE]

Displays English translations of all possible clogp errors as a TDT list of indirect-references. Format is: $I<-{errorlevel}P;{translation}>|

-PCMODELS_ERRORWORST [ERROR_VALUE]

For TDT output, suppresses any output above the given ERROR_LEVEL threshold. The default is '999', eg. all results are shown.

-PCMODELS_VERSION [TRUE|FALSE]

Displays the version number of the clogp program, the version number of the Biobyte algorithm, and the Biobyte database version number.

-PCMODELS_TABLEOUTPUT [TRUE|FALSE]

Produces verbose output as tables including fragment maps, values, and corrections used in the calculation.

-PCMODELS_DUMPFRAGDB [TRUE|FALSE]

Prints all data in current fragment database and exits. This option is not useful for the average user.

-PCMODELS_FRAGDB_BIN file
-PCMODELS_FRAGDB_NEW file
-PCMODELS_FRAGDB_DAT file
-PCMODELS_UPDATE_DEL file

Note: These options are only useful to advanced users who need maximum performance after changing the clogp algorithm. The normal way to add fragment data is to add lines to the delta file (doesn't require changing these options).
Normally, fragment database is built from binary data in the file defined by the option pcmodels_fragdb_bin and formatted data from that in pcmodels_update_del. If the binary file is unavailable, clogp will attempt to read formatted data from pcmodels_fragdb_dat, then read the delta file, then write the fragment database to pcmodels_fragdb_new as a binary file.

Return Value

Returns 0 to its environment if the program initializes correctly. Returns 1 if initialization fails, e.g. an invalid option or a file that can't be opened. Note that zero is returned even if no logP values are computed or errors are encountered during the computation for particular structures.

Files

$DY_ROOT/bin/clogp
$DY_ROOT/bin/clogptalk

Daylight License

programs: clogp

Bugs

None known.