General Purpose Functions

ddpackage.ftestlicense - Test DayCart license validity.
ddpackage.fsetdebug - Get/set ession debug level; 0 = min, 9 = max.
ddpackage.fgeterrors - Return cartridge error queue; 0 = All messages, 1 = Notes, 2 = Warnings, 3 = Errors, 4 = Fatal.
ddpackage.fgetlog - Return cartridge log messages.
ddpackage.finfo - Get DayCart session-level option value.
ddpackage.fsetinfo - Set DayCart session-level option value.
ddpackage.fprogob - Access a program object through Daycart.

Molecule / Reaction Functions

ddpackage.fsmi2cansmi - Generate and return canonical SMILES; type is 0 = unique, 1 = isomeric.
ddpackage.fsmi2xsmi - Generate and return exchange SMILES; type of 0 = unique, 1 = isomeric; explicit of 0 = necessary hydrogens shown, 1 = all hydrogens shown specified.
ddpackage.fsmi2netch - Determine the net charge for a SMILES.
ddpackage.fsmi2hcount - Determine the total hydrogen count for a SMILES.
ddpackage.fsmi2mf - Calculate the molecular formula for a SMILES.
ddpackage.fsmi2amw - Calculate the average molecular weight for a SMILES.
ddpackage.fsmi2pmw - Calculate the high-precision molecular weight for a SMILES.
ddpackage.fmatchcover - Calculate the percentage atoms in the target SMILES matched by the given query SMARTS.
ddpackage.fsmi2graph - Generate a graph SMILES, with charges and bonding removed.

ddpackage.fvcs_desalt - Remove salt fragments from a structure based on the entries in the c$dcischem.salt table.
ddpackage.fvcs_normalize - Normalize structure based on SMIRKS rules in the c$dcischem.transform table.
ddpackage.fgen_molecules - Applies a transform SMIRKS to a set of input molecules (as SMILES) and generates the set of molecules resulting from the transform.
ddpackage.fgen_reactions - Applies a transform SMIRKS to a set of input molecules (as SMILES) and generates the set of reactions resulting from the transform.
ddpackage.fdayconvert - Converts the given chemical input representation into an alternate format.

ddpackage.fatomnorm - N-tuple atom reordering based on SMILES order.
ddpackage.fbondnorm - N-tuple bond reordering based on SMILES order.
ddpackage.fpartnorm - N-tuple component reordering based on SMILES order.
ddpackage.fsmi2scbits - Generate scaffold screening data.

Fingerprint Functions

ddpackage.fsmi2fp - Generate a fingerprint.
ddpackage.fsmi2xfp - Generate a difference fingerprint.
ddpackage.ffoldfp - Fold a fingerprint.
ddpackage.fbitcount - Determine the number of bits set in a fingerprint.
ddpackage.fnbits - Determine the total size of a fingerprint, in bits.
ddpackage.fisfp - Determine if a string is valid fingerprint.

Comparison Functions

Used with ddexact Indextype:

ddpackage.fexact - TRUE if input strings are identical.

Used with ddgraph Indextype:

ddpackage.fgraph - TRUE if input SMILES share the same canonical graph.
ddpackage.ftautomer - true if input SMILES are tautomeric (same graph, net charge and hydrogen count).
ddpackage.fusmiles - true if input SMILES share the same unique canonical SMILES.
ddpackage.fasmiles - true if input SMILES share the same absolute canonical SMILES.

Used with ddrole Indextype:

ddpackage.fcomponent - true if the second SMILES is a component of the first SMILES.
ddpackage.freactant - true if the second argument is a reactant of the reaction SMILES.
ddpackage.fagent - true if the second argument is an agent of the reaction SMILES.
ddpackage.fproduct - true if the second argument is a product of the reaction SMILES.

Used with ddblob Indextype:

ddpackage.fcontains - true if the second argument, a query SMILES, is a substructure of the first SMILES, assuming opened valences.
ddpackage.fisin - true if the first SMILES is a substructure of the second SMILES, assuming opened valences.
ddpackage.fmatches - true if the SMARTS query matches a given SMILES.
ddpackage.feuclid - calculate the euclidean distance between SMILES and/or fingerprints.
ddpackage.ftanimoto - calculate the tanimoto distance between SMILES and/or fingerprints.
ddpackage.ftversky - calculate the tversky distance between SMILES and/or fingerprints.
ddpackage.fsimilarity - calculate the similarity value between SMILES and/or fingerprints; uses the provided similarity measure.
ddpackage.ffingertest - true if all on bits in the second fingerprint or SMILES are also on in the first fingerprint or SMILES.

Session-Level Options

(Default in braces, if applicable).

Read-Only Options:

toolkit_version - Daylight Toolkit version used by Daycart.
daycart_version - Daycart shared library version.
extproc_pid - process ID for the extproc process attached to this DayCart session.
hostid - hardware hostid used for license key generation.
timeout_progress - applies to previous ddblob search. zero if the search completed or a positive integer if the search aborted due to timeout_abort.
count_value - number of hits expected (estimated or actual) for the previous ddblob query. Used with 'count_mode'.

Read/Write Options:

debug_level - Debug level set for log messages written either to /tmp/extproc.log or to the error queue (see fgeterrors()) {1}.
session_tag - Arbitrary tag written out with any log messages for the given session {none}.
exit_on_fault - TRUE or FALSE. When TRUE, each daycart process keeps track of severe errors and exits when fifty or more have occurred {FALSE}.
default_delimiter - Delimiter used to separate lines of multi-line output {newline on UNIX, CR/LF on Windows}.
force_delimiter - TRUE or FALSE. When TRUE, the default delimiter is always used for multi-line output. When FALSE, Daycart will attempt to detect the delimiter to use from input data {FALSE}.
vcs_table_cache - State of the VCS cache of salts and transforms. When off, each invocation of a vcs function causes the salt or transform table to be reread {on}.
default_fpsize - Default fingerprint size used for similarity comparisons and index creation when not otherwise inferred from input {512}.
timeout_interrupt - search interrupt time, in seconds {5}.
timeout_abort - search abort time, in seconds {3600}.
thread_count - number of worker threads used for contains(), isin() and matches() searches {0}.
count_mode - mode of query for ddblob searches. NONE - Normal behavior, returns hits to Oracle. ACTUAL - Runs full search, returns no hits. ESTIMATE - Runs partial search, projects hit count. Hit count can be retrieved with the 'count_value' option {NONE}.

Read/Write Conversion Options:

conv_smi_is_ism - When TRUE, conversions to tdt format include the isomeric SMILES in the root $SMI datatype {FALSE}.
conv_add_3d - When TRUE, conversion to tdt format includes 3D coordinates in the output file if present in the input {TRUE}.
conv_add_2d - When TRUE, conversion to tdt format includes 2D coordinates in the output file if present in the input {TRUE}.
conv_use_3d - When TRUE, conversion from tdt format uses 3D coordinates for the output if present in the input {FALSE}.
conv_split_fields - Controls handling of multi-line data from sdf and tdt files. TRUE causes these to be split into separate dataitems {FALSE}.
conv_id_field - Sets the id field to be used {for molecules, default ID is to the first line of each header block; for reactions, default is the value following $RIREG}.
conv_prefix - Sets the designated prefix to be parsed from the datatype names for conversion of rdf files {NONE}.
conv_implicit_chirality - Alters perception of chirality for implicit chiral centers. TRUE causes both ends of the chiral bonds to be used in the determination of chiral centers {TRUE}.
conv_ring_cistrans - When TRUE ignores cis/trans stereochemistry for all ring double bonds {FALSE}.
conv_db_explicit_h - When TRUE requires that double bonds have all hydrogens explicitly indicated for conversion from non-query MDL format to SMILES {FALSE}.
conv_chi_explicit_h - When TRUE chiral atoms have all hydrogens explicitly indicated for conversion from non-query MDL format to SMILES {FALSE}.
conv_fix_radical_rings - When TRUE, converts all-carbon, uncharged, radical rings to aromatic rings {TRUE}.
conv_nametag - Sets the tdt datatype tag used for the id {$NAM}.
conv_comment_smi - When TRUE output SMILES is written into the comment line of the header block in each connection table {FALSE}.
conv_smi_tuples - When FALSE the tuple information associated with the isomeric SMILES field in a tdt is printed in the output MDL file {TRUE}.
conv_day_hcount - When TRUE uses both explicit H and H-count fields for the conversion of query MDL files {TRUE}.
conv_day_stereo - When TRUE uses stereochemistry as specified for the conversion of query MDL files. When FALSE the program uses stereochemistry as specified and unspecified {TRUE}.
conv_day_chih - When TRUE chiral H are required to be explicit for the conversion of query MDL files. When FALSE implicit hydrogens used {TRUE}.