testlicense - Test DayCart license validity.
geterrors - Return cartridge error queue; 0 = All messages, 1 =
Notes, 2 = Warnings, 3 = Errors, 4 = Fatal.
getlog - Return cartridge log messages.
getinfo - Get DayCart session-level option value.
setinfo - Set DayCart session-level option value.
smi2cansmi - Generate and return canonical SMILES; type is
0 = unique, 1 = isomeric.
smi2xsmi - Generate and return exchange SMILES;
type of 0 = unique, 1 = isomeric; explicit of 0 = necessary
hydrogens shown, 1 = all hydrogens shown specified.
smi2netch - Determine the net charge for a SMILES.
smi2hcount - Determine the total hydrogen count for a SMILES.
smi2mf - Calculate the molecular formula for a SMILES.
smi2amw - Calculate the average molecular weight for a SMILES.
smi2pmw - Calculate the high-precision molecular weight for a
SMILES.
matchcover - Calculate the percentage atoms in the target SMILES
matched by the given query SMARTS.
smi2graph - Generate a graph SMILES, with charges and bonding
removed.
gen_molecules - Applies a transform SMIRKS to a set of input
molecules (as SMILES) and generates the set of molecules resulting from the
transform.
gen_reactions - Applies a transform SMIRKS to a set of input
molecules (as SMILES) and generates the set of reactions resulting from the
transform.
dayconvert - Converts the given chemical input representation
into an alternate format.
atomnorm - N-tuple atom reordering based on SMILES order.
bondnorm - N-tuple bond reordering based on SMILES order.
partnorm - N-tuple component reordering based on SMILES order.
smi2fp - Generate a fingerprint.
smi2xfp - Generate a difference fingerprint.
smi2screen - Generate screening data for search performance.
foldfp - Fold a fingerprint.
bitcount - Determine the number of bits set in a fingerprint.
nbits - Determine the total size of a fingerprint, in bits.
isfp - Determine if a string is valid fingerprint.
graph - TRUE if input SMILES share the same canonical graph.
tautomer - true if input SMILES are tautomeric (same graph, net
charge and hydrogen count).
usmiles - true if input SMILES share the same unique canonical
SMILES.
asmiles - true if input SMILES share the same absolute canonical
SMILES.
component - true if the second SMILES is a component of the
first SMILES.
reactant - true if the second argument is a reactant of the
reaction SMILES.
agent - true if the second argument is an agent of the
reaction SMILES.
product - true if the second argument is a product of the
reaction SMILES.
contains - true if the second argument, a query SMILES, is a
substructure of the first SMILES, assuming opened valences.
isin - true if the first SMILES is a substructure of the
second SMILES, assuming opened valences.
matches - true if the SMARTS query matches a given SMILES.
euclid - calculate the euclidean distance between SMILES
and/or fingerprints.
tanimoto - calculate the tanimoto distance between SMILES
and/or fingerprints.
tversky - calculate the tversky distance between SMILES and/or
fingerprints.
similarity - calculate the similarity value between SMILES and/or
fingerprints; uses the provided similarity measure.
fingertest - true if all on bits in the second fingerprint or
SMILES are also on in the first fingerprint or SMILES.
(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.
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}.
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}.
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}.
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