dayprop

Daylight v4.9
Release Date: 1 February 2008

Name

dayprop - calculate physical properties for molecules

Unix Synopsis

dayprop [options] [infile.tdt [outfile.tdt]]
dayproptalk

Description

dayprop is a non-interactive program that takes Thor Data Tree (TDT) input containing SMILES and provides output in TDT format. If present, dayprop will read in the input from infile.tdt and write it's output to outfile.tdt. If filenames are not specified Dayprop will read from standard input and write to standard output.

dayproptalk is usually invoked as a program object (see dt_alloc_program(3)), and uses the "talk" protocol for input/output. See the Daylight Properties Package Manual for more information about the program object messages which dayproptalk uses.

If a valid estimate can't be made, dayprop copies the input TDT to its output unaltered.

The PPROP datatype has 4 fields: PPROP<property;result;method;comment>.

Options

The following apply to dayprop(1):

-HELP [TRUE]

Displays command line summary and halts.

-DUMP_INDIRECT

Displays English translations of all properties as a TDT list of indirect-references. Format is: $PI<Number;translation>|

-VERSION [TRUE]

Displays the version number of the toolkit program.

-SINGLE_PART [TRUE|FALSE]

When TRUE, treats the entire input SMILES as a single molecule and computes a single property value. When FALSE, computes a comma separated list of property values for the dot separated components within the input SMILES. The default is FALSE. SMILES as a single molecule. NOTE: -RXNDIFF TRUE can not be used with -SINGLE_PART FALSE option.

-RXNDIFF [TRUE|FALSE]

Calculates the difference between the property values of the product and reactant. The default for the RXNDIFF option is FALSE. NOTE: -RXNDIFF TRUE can not be used with -SINGLE_PART FALSE option.

-PROPERTY property_flag

Sets the property to be calculated. The following are valid property_flags:
NO_PROPERTY, AVERAGE_MOL_WT, MOL_FORM, ROTBOND_COUNT, HDONOR_COUNT, HACCEPTOR_COUNT, PARACHOR, ACCURATE_MASS, MOLAR_VOLUME, RING_COUNT, RIGIDITY, FRAGMENT_COUNT, FINGERPRINT, FLEXIBILITY, DEPICTION, STEREOCENTER_COUNT, PART_COUNT, POLAR_SURFACE_AREA, ATOM_COUNT, MATCH_COUNT, ALL

-SMARTS smarts_pattern

Defines the user pattern to be used with the MATCH_COUNT property.

-PROPID comment

Adds a comment to the comment field in PPROP.

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.

Files

$DY_ROOT/bin/dayprop
$DY_ROOT/bin/dayproptalk

Daylight License

programs: dayprop

Bugs

None known