MUG'03 25th-28th February 2003, Santa Fe, NM.

Daylight Property Package

John Bradshaw
Daylight CIS Inc., Sheraton House, Castle Park, Cambridge, CB3 0AX, UK
Margaret Rittner
Daylight CIS Inc., 441, Greg Avenue, Santa Fe, NM 87501, USA


The calculation of molecular properties from structure has always been closely associated with the Daylight and its progenitors. For many, the calculation of CLOGP was their first introduction to our software. With the advent of virtual screening there has been a resurgence in the requirements for rapid estimation of appropriate properties directly from structure. To that end, Daylight is introducing a Property Package which will provide values for most of the commonly used properties. The architecture of the package allows for additional properties to be added should they be required. Use of the program object technology ensures that the same code ( and hence the same answers ) are accessible from many programs including DayCart™

Program Objects

Program objects are used to provide two-way communication with an external process, e.g., the clogptalk program for computing hydrophobicity for a structure represented in SMILES. Using program objects, a calling program can start an external program, send it input, receive its output, and perform other tasks while the external program remains running and ready for more input. This is particularly important for many property programs which spend significant amounts of time initializing themselves.

A number of programs supporting program objects are supplied with the release of Daylight Software. Most of these are supplied as contributed code, in the directory: $DY_ROOT/contrib/src/c/progob/. The commercial programs clogptalk and cmrtalk operate as program objects (in $DY_ROOT/bin). The propertytalk program will operate in the same way, using the PIPETALK protocol.

Using program objects with Daycart™

The PIPETALK protocol provides an ideal way for the Daylight Oracle cartridge to communicate with external function for instance to populate a table column with clogp values say with a sql line like

UPDATE my_table SET clogP = clogp(smiles);

The propertytalk program

One of the advantages of talk programs is that you only need to have one copy of the code and a whole variety of programs can access the same algorithm/code. This means, for physical property calculations for instance, for a given structure you always get the same answer, irrespective of the calling program. To this end we have produced a talk program which will calculate a variety of physical properties commonly used in molecular selection and design directly from the structures. These values can then be stored along with the structure from which they were derived. These functions are available via a program_object interface which allows them to be called from within DayCart™. described above. Many of these are included in the VCS building routines, calculated from the parent or version smiles, as appropriate. All values are returned as part_tuples except for PART_COUNT which is an integer, this ensures that data for mixtures and salts are handled correctly.

Note that the property values come in various types:-
  1. Counting the number of matches of a pattern of atoms and bonds, usually expressed as SMARTS.
  2. Additive constitutive properties where the patterns are counted and multiplied by a weighting factor e.g. molecular weight
  3. Daylight object properties such as atom, cycle or part counts
  4. Results of a Daylight algorithm such as fingerprint, depiction, conformation etc

In the future we will allow users to alter the paterns which are matched and the weights which are applied to the individual counts.

These programs can be accessed in the a demo form with the caveat that as it is running in a stateless world the program object is not persistent.

Plans and Futures

This package will be made available with a selection of some or all of the above properties in a 4.8 release. The appropriate SQL extensions are also available for use in conjunction with Daycart™. These may be accessed either in a parallel fashion or in a single user mode, depending on system resources.

In a later version there will be the equivalent of the algorithm manager in CLOGP and users will be allowed to edit the patterns which are mapped for the properties. This may be either via the talk protocol or an external file.

Daylight Chemical Information Systems, Inc.