A description of the Conversion Tools project and its initial release state is presented. The tools are scheduled to be included in Daylight Software v4.9.

Introduction

1. Languages
   • SMILES
   • SMARTS
   • SMIRKS
2. Formats
   • Chemical EXchange
   • Thor DataTree

• molfile
• RDfile
• RGfile
• rxnfile
• SDfile
• SData
• extended molfile
• extended rxnfile

• CTX
• TGF

• molfile and SDfile only
• estimated correct conversion rate of 99.9%
• incorrect conversion of 0.1% of a large database could be hundreds or thousands of structures.

• however they either fail to properly handle the language
• do not support other Daylight languages

• but neither do it according to our standards

Goals

• our customers needs
• our internal needs
• potential use by future customers

Objectives

• minimizing the number of supported file formats
• leaving the door open for extensibility
• focus on the CTfile formats and the ChemDraw sketcher

Methods

• The Toolkit approach maximizes robustness - it should never itself fail, only fail to convert malformed input.
• Users will not be required to know the input format, for example, where a structure ends and another begins within a SDfile.
• Direct I/O will be performed by applications, not the toolkit itself.
• The essence of the Conversion Toolkit will become part of DayCart.

Approach. The Conversion Toolkit interface will accept an object and input data, and outputs data in the correct format.

• The object will define the desired conversion, e.g., convert from a MDL SDfile to Daylight SMILES.
• Also, perception of input data will allow generic conversion of data.
• The interface will be extensible in order to easily support additional formats.

Issues. Dialects increase the complexity of converting a format. Do we take a hard or soft line on violations?

Technical Details

    dt_Handle <= dt_alloc_conversion(dt_Integer ifmt, dt_Integer ofmt)

• The parameters ifmt and ofmt will indicate the input and output formats, such as SDfile and SMILES.
• There will be integral definitions in the toolkit for format types.
  • DX_CONV_FMT_SMI
  • DX_CONV_FMT_SMA
  • DX_CONV_FMT_SMR
  • DX_CONV_FMT_MOL
  • DX_CONV_FMT_RDF
  • DX_CONV_FMT_RGF
  • DX_CONV_FMT_SDF
  • DX_CONV_FMT_SDT
  • DX_CONV_FMT_V30
  • DX_CONV_FMT_V3R
• For example, to indicate a SDfile to SMILES conversion, the input and output parameters will be DX_CONV_FMT_SDF and DX_CONV_FMT_SMI, respectively.

• The type DX_CONV_FMT_MDL will indicate any of the CTfile formats, and will not dictate which one or require that it be homogeneous. This is useful for converting an input stream of mixed types, such as a SDfile followed by a RDfile, or a RDfile containing molecules and reactions.
• The type DX_CONV_FMT_DAY will indicate any of the Daylight languages and will not dictate which one.
• In the case of generic types, the actual input type will be perceived and the actual output type will vary according to the input type.

The return value from the dt_alloc_conversion routine will be a conversion object that is passed with data into the second routine, which converts data from one format to another.

    dt_Handle <= dt_convert(dt_Handle conv, dt_Handle seq)

The list of supported formats will be as follows: MDL CTfile formats except XDfile (molfile, RGfile, rxnfile, SDfile, RDfile, extended molfile and extended rxnfile), SMILES, SMARTS, SMIRKS, Daylight Toolkit objects (molecule, reaction, pattern, and transform), and TDTs. Any CTfile format may be converted to the corresponding Daylight language or object, and vice versa.

Applications. Two powerful generic converters, mdl2daylight and daylight2mdl, will be provided for conversion to and from all of the supported MDL and Daylight formats. These converters perceive the input type and generate the most appropriate output type. The choice of which output type will be produced from an input type will be predetermined. For example, one input SMILES results in a molfile and multiple input SMILES result in a SDfile. The ability to recognize MDL input type will be limited. When the input or output type is known, the format may be specified.

All applications will be built on an internal conversion utility and support streaming of data, also known as \emph{feeder mode}. Conversion of data will be performed in parts and the size of the parts may be set by the user. Feeder mode will be necessary for processing large input files that would otherwise exceed hardware capabilities.

The main programming loop condition is:

    while (NULL_OB != (oseq = dt_convert(conv, iseq)))

Toolkit programmers wishing to convert to Daylight Toolkits objects (molecule, reaction, etc.), need to write their own programming loop to capture the objects as they are returned from \texttt{dt_convert}. For example, pseudo code for conversion of a SDfile to molecules is as follows:

#include "dt_smiles.h"  /* SMILES Toolkit */
#include "dt_conv.h"    /* Conversion Toolkit */

int main() {
    dt_Handle conv, iseq, oseq;

    /* create conversion object */
    conv = dt_alloc_conversion(DX_CONV_FMT_SDF, DX_CONV_FMT_OBJ);

    /* create input object */
    iseq = dt_alloc_seq();

    /* open and read part of an SDfile */
    ...

    /* convert data */
    while (NULL_OB != (oseq = dt_convert(conv, iseq))) {

        /* loop over molecules */
        while (NUL_OB != (obj = dt_next(oseq)))

            /* do something with the molecules */

        /* destroy output */
        dt_dealloc(oseq);

       /* read more from SDfile */
       ...
    }
    return 0;
}

Sample Conversions - MDl to Daylight

Atom List SMARTS: [#7,#6,#8]c1ccccc1

Any Atom SMARTS: [#0]c1ccccc1

Not Aliphatic SMARTS: [!#6]c1ccccc1

Wild Card Atom SMILES: *c1ccccc1

Lone Pair SMILES: c1ccncc1

R-groups SMARTS: [CO,N]c1cccc([CO,N])c1[C]

Isotope SMILES: [13CH3]c1ccccc1

Charge SMILES: [O-]c1ccccc1

Implicit Hydrogens SMARTS: [C&!h0&!h1&!h2&!h3]

Stereo Care (none) SMILES: C/C=C/C=C/C=C/C

Stereo Care (middle) SMILES: CC=C/C=C/C=CC

Stereo Care (ends) SMILES: C/C=C/C=C\C=C\C note: implied middle

Valence (connections) SMARTS: [C&X4]

Aromatic Bond SMARTS: [#6]:1:[#6]:[#6]:[#6]:[#6]:[#6]1

Single or Double Bond SMARTS: [#6]-,=1[#6]-,=[#6][#6]-,=[#6][#6]1

Double or Aromatic Bond SMARTS: [#6]=,:1-,:[#6]=,:[#6]-,:[#6]=,:[#6]-,:[#6]1

Wild Card Bond SMARTS: [#6]~1~[#6]~[#6]~[#6]~[#6]~[#6]1

Chirality SMILES: C[C@H](N)C(=O)O

Chirality (racemic) SMARTS: C[C&@,@@](N)C(=O)O

Stereo (racemic, care all) SMARTS: C/,\C=C/C

Stereo (racemic ends, care all) SMARTS: C/,\C=C/C=C/C=C/,\C

Stereo (racemic ends, care ends) SMARTS: C/,\C=C/C=C/,\C=C/C

Stereo (racemic middle, care all) SMARTS: C/C=C/C=C\C=C\C

Stereo (racemic middle, care middle and one end) SMARTS: CC=C/,\C=C/C=C/C

Stereo (racemic middle, care middle and both one end) warning: unsupported features SMARTS: CC=C/,\C=C(/C=C/C)/C=C/C warning: inconsistent bond directions SMARTS: CC=C/,\C=C(/C=C/C)\C=C/C warning: too much symmetry for directional bonds SMARTS: CC=C/,\C=C(/C)\C=C/C note: okay

Chain Bond SMARTS: CC-&!@O-&!@CC

Ring Bond SMARTS: CC-&@O-&@CC

Summary