Daylight v4.9
Release Date: 1 February 2008

Name

convertStructure - converts structures and data between MDL and Daylight formats

Description

convertStructure parses input and interconverts data and structures between MDL chemical table-based file formats [molfile (MOL), SDfile (SDF), RGfile, RXNfile (RDF) and RDfile (RDF)] and Daylight SMILES-based formats [SMILES (SMI), isomeric SMILES (ISM), SMARTS (SMA), SMIRKS (SMRK), and Thor Data Tree (TDT) using a Java-based service with SOAP messaging.

As defined by the WSDL the input/output SOAP messages are as follows.

Note: If changes to the default ptable are to be used for conversions from MDL format to Daylight format, then the optionaal ptable information must be supplied.

Input: List of input strings, input format string, output format string, options as a list of name-value pairs, optional ptable changes as a list of [(atom number, atom symbol, atom mass, list of valence-charge pairs)], ERRORLEVEL

Output: List of objects with one object [(output string, error message)] per input SMILES

Valid input/output combinations include: 

    SMI --> SDF or RDF 
    TDT --> SDF or RDF
    SDF --> SMI, ISM, SMA, TDT or TDTSMA
    RDF --> SMI, ISM, SMA, SMRK, TDT, TDTSMA or TDTSMRK

Note: MOL is a valid input value that is interchangeable with SDF regardless of the actual input format. In addition, MOL is a valid output format value if the input value is SMI or TDT. However, the output will always be written n SDF format even if there is no associated data. In addition, either MOL or SDF is used with an RGfile input. Lastly, rxnfile format is not recognized as a separate format. RDF is used for both rxnfiles and RDfiles.

Options

ADD_2D [TRUE|FALSE]
Adds 2D coordinates to Daylight output. Default is TRUE.

ADD_3D [TRUE|FALSE]
Adds 3D coordinates to Daylight output. Default is TRUE.

CHI_EXPLICIT_H [TRUE|FALSE]
Determines whether chiral atoms must have explicit hydrogens. Default is FALSE.

DAYLIGHT_LIKE [TRUE|FALSE]
Sets all three DAYLIGHT options. Default is TRUE.

DAYLIGHT_HCOUNT [TRUE|FALSE]
Determines whether both the explicit H and H-count fields are used. Default is TRUE.

DAYLIGHT_STEREO [TRUE|FALSE]
Determines whether only specified stereochemistry is used. Default is TRUE.

DAYLIGHT_CHI_H [TRUE|FALSE]
Determines whether chiral atoms in the input file must have explicit hydrogens. Default is TRUE.

DB_EXPLICIT_H [TRUE|FALSE]
Determines whether double bonds in the input file must have explicit hydrogens. Default is FALSE.

DB_RING_CSITRANS [TRUE|FALSE]
Determines whether stereochemistry for ring double bonds is indicated. Default is FALSE.

FIX_RADICAL_RINGS [TRUE|FALSE]
Determines if radical rings are converted to aromatic. Default is TRUE.

ID_FIELD [NAME]
Specifies the data field identifier to be used as the unique ID. Default th first line of header block for molecules and $RIREG for reactions.

IMPLICIT_CHIRALITY [TRUE|FALSE]
Specifies how chirality is determined in order to detect implicit chiral centers. Default is FALSE.

M__ISO_ARE_DEFECTS [TRUE|FALSE]
Indicates whether values in the M ISO line are mass defects or or actual masses. Default is FALSE.

NAME_DATATAG [NAME]
Designates the data tag to be used as the unique ID. Default is LINE1, if available otherwise $NAM.

PREFIX [NAME]
Parses the designated prefix from data field identifiers. The default is to use the full $DTYPE name.

SMI_COMMENT [TRUE|FALSE]
Determines whether the SMILES is placed in the comment line of the connection table. Default is FALSE.

SMI_IS_ISM [TRUE|FALSE]
Replaces SMILES with isomeric SMILES in the output. Default is FALSE.

SMI_WITH_TUPLES [TRUE|FALSE]
Determines whether output tuple information is associated with SMILES or isomeric SMILES. Default is TRUE.

SPLIT_FIELDS [TRUE|FALSE]
Splits data that is spread across multiple lines in an input into separate entries. Default is FALSE.

USE_3D [TRUE|FALSE]
Designates whether 3D coordinates are included in the MDL output. Default is FALSE.

ERRORLEVEL [INTEGER]
Sets minimum level for errors to be reported along with more serious errors. Possible values are: 

     0  No messages
     1  Might be of interest but not an error
     2  Something abnormal; may require attention
     3  Requested operation cannot be carried out
     4  Serious error; program cannot continue

Return Value

convertStructure returns a blank string if it does not succeed. In addtion, it returns a set of error messages if the errorlevel is not set to 0.

Related Topics

mol2smi(1) smi2mol(1) rd2smi(1) smi2rd(1) sd2smarts(1) rd2smarts(1) rd2smirks(1) licensing(5)