Incorporation of 2D Coordinates in Daylight Applications Michael A. Kappler Daylight CIS

The 2D datatype identifier has been incorporated into depiction of structures in THOR and Merlin applications. Daylight options allow the user to specify a preference for depictions with 2D data. SMILES can be depicted with 2D data, or inversely, 2D data with SMILES. Two new Daylight Depict Toolkit routines are provided to 1) associate SMILES and 2D data and 2) set depiction coordinates.

Background

Previously, the 2D datatype was incorporated into SMI2GIF and allows the user to depict structures in a familiar layout. The user can control whether the layout is determined by the Daylight depiction algorithm or 2D data (Figure 1).

Figure 1: Previosly, the 2D datatype was incorporated into the SMI2GIF and allows the user to depict structures in a familair layout. The user can control whether the layout is determined by the Daylight depiction algorithm (left) or 2D data (right).

Two Wrongs Make it Look Right! Use of 2D data (without bond type information) is dangerous! By reversing 2D coordinates of geminal substituients, the original depiction (left) will show an inverted stereocenter. Additionally, if the stereocenter is inverted in the SMILES string, the depiction will appear to be the original structure (right).

Figure 2: By reversing 2D coordinates of geminal substituients, the original depiction will show an inverted stereocenter. Additionally, if the stereocenter is inverted in the SMILES string (right), the depiction will appear to be the original structure.

Daylight Options

• THOR

  The '-TDT_GRAPHIC_PREFS' option, as described in the xvthor manual page, allows the user to specify a preference for depiction of SMILES with 2D data, and 2D data with its associated SMILES.

  Syntax: xvthor -TDT_GRAPHICS_PREFS D2D

  
  Figure 3: TDT Widget Properties allow the user to specify a preference for depiction of SMILES with 2D data and 2D data with its associated SMILES.

• Merlin

  The '-MERLIN_DEPICT_SMILES_2D' and '-MERLIN_DEPICT_2D_COORDS' options, as described in the xvmerlin manual page, allows the user to specify preference for depiction of a SMILES column with 2D data and a 2D column with its associated SMILES.

  Syntax: xvmerlin -MERLIN_DEPICT_2D_SMILES TRUE

Application Prgrammer Interface

• Association of SMILES and 2D Data

  #include "dy_xv_widget.h"
  dt_String dy_tdt_smi2d (dt_Handle datatree, dt_Integer slen, dt_String str, dt_Handle stype)

  • dual purpose
    • get SMILES for 2D data
    • get 2D data for a SMILES
  • datatree may contain subtrees
  • slen is length of variable str
  • str is a SMILES or 2D ntuple data
  • stype is datatype of str

• Applying 2D Data to a Depiction

  #include "dy_xv_widget.h"
  dt_String dy_dep_set2d (dt_Handle dep, dt_String str2d)

  • dep is a depiction object and is altered
  • str2d is 2D ntuple data

Sample Depictions

• THOR

  
  Figure 4: TDT Widget with default view (top) and with depiction of 2D data with its associated SMILES (bottom).

• Merlin

  Use of 2D data is particularly useful in Merlin when viewing a virtual combinatorial library, such as that produced by GADDwiCC.

  
  Figure 5: Merlin spreadsheet with default view (top) and with depiction of the SMILES column with 2D data (bottom). The 2D coordinates of all structures wer aligned to the first structure using T. J. O'Donnell's MOLALIGN program

Conclusions

• Incorporation of 2D data in depictions adds a dependency for correctly presenting stereochemistry.
• The 2D datatype identifier has been incorporated into THOR and Merlin aaplications.
• Daylight options allow the user to specify a preference for their depictions.
• Two new Daylight Depiction Toolkit routines have been introduced.

Future Direction

• Incorporation of 2D coordinates into all relevant Daylight tools.

Acknowlegdements

• Dave Weininger, Daylight
• Jeremy Yang, Daylight
• Jack Delany, Daylight
• T. J. O'Donnell, O'Donnell Associates