Release Date: 1 February 2008
Namerd2smirks - converts a query connection table-based reaction file into a
Unix Synopsisrd2smirks [options] [infile [outfile]]
Descriptionrd2smirks(1) converts an MDL RDfile containing a transform into a Daylight SMIRKS (SMRK) or Thor Data Tree (TDT) file. Alternatively, the output can be directed to two SQL loader (SQLLDR) files.
The input file must be an rxnfile or RDfile containing a reaction (no agent) in v2000 format. R-group and S-group features are not recognized. The input file can contain any query atom feature that can be represented in both MDL CTfile format and Daylight SMARTS. Query bond features are not permitted. In addition, if the input file contains query atoms, then the transform atoms must be mapped.
Default output is to stdout. In the case of SQLLDR output, the user must specify the rootname for the two output files.
Double bond stereochemistry and tetrahedral chirality are inferred from the atom coordinates and bond style information in the connection table and encoded as SMIRKS. SMIRKS and associated structural information including 2D or 3D-coordinates are automatically stored in the TDT and SQLLDR outputs.
Data in RDfiles are converted for TDT and SQLLDR outputs. The SQLLDR format stores data in one file (.dat) and structural information in another (.str). Legal characters for data tags are limited to: $, _, /, A-Z, a-z, and 0-9.
Unless otherwise specified using the ID_FIELD option, the value for $RIREG is used as the default ID. In the SMRK output, this ID follows the space-delimited SMIRKS. The ID is stored in the $NAM field for the TDT format and as the first line of the SQLLDR files. If there is no default ID available, the SMIRKS will be used as the ID for TDT and SQLLDR output.
The manual page for "convert" describes features common to this and the other "convert" programs. Please refer to it for more information on general usage and options such as -HELP, -VERSION, -SKIP_RECORDS, -DO_RECORDS, -ERROR_LEVEL, -ERROR_LOG, and -REJECT_LOG.
Controls whether the output is in SMIRKS, TDT, or SQLLDR format. The default is SMRK. For the TDT and SQLLDR formats, information for any non-standard atom labels in the input file are stored as as an atom-tuple in the ASYM datatype. The original atom is designated by '*' in the SMARTS. For TDT output, a special $SMIG datatype is written containing data about the conversion program name and version.
Adds 2D and/or 3D coordinates to the TDT or SQLLDR output. These data are taken from the actual coordinates in the input atom block and stored as a comma-separated list of values in unique SMILES order. Default is TRUE for both -ADD_2D and -ADD_3D. If non-zero coordinates are found in the atom block, then either 2D or 3D coordinates are written to the output file depending on which are available. Setting one of these values to FALSE eliminates the entry for that set of coordinates.-ID_FIELD <name>
Sets the data field identifier to be used as unique ID. The value for $RIREG or this value followed by '_' (underscore) and the RXN:VARIATION number if this is specified as the -PREFIX value is used as the default. Designating all or part of a datatype including REREG as the ID_FIELD causes the data in that field to be recognized as the ID. Note one may need to place the data field identifier in quotes and use `\\` before '$'. Input records not containing information in the designated field are rejected.-PREFIX <name>
Parses the designated prefix from data field identifiers. The default is to use the full $DTYPE name. Specifying a prefix removes the defined string from the output $DTYPE name and stores the prefix in the TDT/SQLLDR output files. For reactions, the string must cover from the beginning of the name to the first '('. For example RXN:VARIATION can be stripped from the following $DTYPE names: RXN:VARIATION(1) and RXN:VARIATION(2). Also note that in this case, the reaction is split on RXN:VARIATION number with the ID identified by the $RIREG value followed by '_' and the RXN:VARIATION number.-IMPLICIT_CHIRALITY [TRUE|FALSE]
Alters the way in which chirality is determined in order to detect implicit chiral centers. This is useful for some natural products. For a bond A-hash-B, the interpretation is that B is below A from the perspective of A and A is above B from the perspective of B. The default is FALSE. Setting -IMPLICIT_CHIRALITY to TRUE allows both ends of chiral bonds to be used in the determination of chiral centers.-DB_RINGS_CISTRANS [TRUE|FALSE]
Toggles whether stereochemistry for ring double bonds is indicated. Default is FALSE. Setting this option as TRUE, marks the cis/trans stereochemistry for all ring double bonds.-M__ISO_ARE_DEFECTS [TRUE|FALSE]
Indicates whether the values in the M ISO line of the property block are mass defects or actual masses for the isotopes listed. Default is FALSE. When -M__ISO_ARE_DEFECTS is set as TRUE, values in the line are treated as mass defects.-FIX_RADICAL_RINGS [TRUE|FALSE] Converts radical rings to aromatic. The default is TRUE which allows for the certain types of five, six, and seven-membered radical rings to be converted to aromatic. Changing this option to FALSE, keeps the rings as specified in the input file. In order for a ring to be converted, all atoms in the ring must be order for a ring to be converted, all atoms in the ring must be carbon and designated as doublet radicals. In addition, no atom in the ring may have a charge. -DAYLIGHT_CHI_H [TRUE|FALSE]
Determines whether chiral atoms in the input file must have explicit hydrogens. The default is TRUE. Setting this option to FALSE removes the requirement that chiral atoms have all hydrogens explicitly indicated.
Return Valuerd2smirks returns 0 to the environment if it succeeds without errors or a non-zero value if there are errors.
Related Topicsconvert(1) mol2smi(1) smi2mol(1) rd2smi(1) smi2rd(1) sd2smarts(1) rd2smarts(1) licensing(5) options(5)