corefinder Command Help
Command: $SCHRODINGER/utilities/corefinder
Usage: corefinder [OPTIONS] -o output_file input_file [input_file ...]
Extract cores and prepare them for use with ligand-based core hopping.
Input and output files can be sqlite or structure files (.mae,
.sdf, etc.). Input structure files are presumed to contain molecules
from which cores are to be extracted. Output files contain the
extracted cores. With the -w option, each new "core" consists of
a whole molecule from the input. This is for use if a user has
created cores by some other method.
The ligand-based core-hopping back-end program requires sqlite input.
If a structure file is given to the ligand-based driver, it will
first be converted to an sqlite file using "corefinder -w"
and this file will be used by the back-end program.
struct->sqlite is the normal work flow. It extracts cores from the
structures into an sqlite file used by core hopping.
The structure files (if there are several) will be processed in
separate subjobs and the resulting sqlite files will be combined at
the end. It usually suffices to issue the command as
$SCHRODINGER/utilities/corefinder -HOST <hostname> -o output.sqlite \
<list of input file names>
If there are too many input files to list on the command line, list them,
one per line, in a separate file and supply this file as the argument to
the "-a" option.
sqlite->sqlite combines multiple core-hopping sqlite files into a
single file in a single process.
sqlite->struct processes a single sqlite file into a file of cores.
This option is useful mainly for debugging purposes.
struct->struct extracts cores from a single input file into a
structure file containing cores, albeit without the extra information
that appears in the sqlite format. This option is useful mainly for
debugging purposes.
Options:
-v, -version Show the program's version and exit.
-h, -help Show this help message and exit.
Options controlling general program operation:
-first FIRST When reading input structure files, start with the
FIRST input structure, where the first in the file is
numbered 1. This is useful mainly for debugging. Not
passed to subjobs.
-last LAST When reading input structure files, end with the LAST
input structure, where the first in the file is
numbered 1. This is useful mainly for debugging. Not
passed to subjobs.
-o OUTFILE, -outfile OUTFILE
Combine and deduplicate cores into a file with the
specified name, which may have a .mae, .maegz or
.sqlite suffix.
-a ARGFILE, -argfile ARGFILE
Take program arguments from the named file. This
allows a long argument list, which could otherwise
exceed system limits on line length, to be specified.
If the same optional argument is specified in the
argument file and the command line, the command-line
value overrides the value in the argument file.
However, input-file names specified on the command
line are appended to those listed in the argument
file. An argument file may not containe a -a or
-argfile option. Finally, the arguments and options
must appear one string per line. For example '-o
outfile.mae' should appear as '-o' on one line and
'outfile.mae' on the next line, with no quotes.
Similarly, an input file whose path is 'dir with
spaces/in.mae' should appear on a single line, with no
quotes. Finally, comments, beginning with '#' and
ending with a newline, can be added anywhere.
-w, -whole_mol Do not extract cores from the input structures;
instead, treat each entire input structure as a core.
Supported for the mae->sqlite work flow.
-m, -do_skip_metal_only
Skip cores having the "b_epik_Metal_Only" property.
These are tautomers/ionomers appropriate only for use
in metal-containing receptors. Default is to skip them
unless -w is specified, in which case we keep them, on
the grounds that if the user is specifying his own
whole molecules to use as cores, he might possibly
know what the heck he is doing. :-).
-no_m, -dont_skip_metal_only
Do not skip cores having the "b_epik_Metal_Only"
property. See the description of "-m" for details.
-u, -do_skip_undesirable
Skip cores having undesirable chemistry, such as
Het-C(sp3)-Het. Default is to skip them unless -w is
specified, in which case we keep them. N.B. "-verbose"
lists the structures skipped.
-no_u, -dont_skip_undesirable
Skip cores having undesirable chemistry, such as
Het-C(sp3)-Het. See the description of "-u" for
details.
-j JOINING_RULES_FNAME, -joining_rules_fname JOINING_RULES_FNAME
File from which joining rules are to be read. If not
specified, installed version in
$SCHRODINGER/combiglide-v*/data/corefinder will be
used.
-r RING_MAX, -ring_max RING_MAX
Maximum ring size to allow in the library. This is the
maximum of the sizes of the 'smallest rings'
constituting a core ring system. For example,
naphthalene would be considered to have a maximum ring
size of 6, not 10. Default is 9.
-t TITLE_PROPERTY, -title_property TITLE_PROPERTY
Structure-level property of the parent structure to
use when composing the title of the core. If the
special string "PSMILES" is supplied, the SMILES of
the parent compound will be used. In the above cases,
the core title will be "Core <n> from parent
<property_value>". If the special string CSMILES is
specified, the core title will be set simply to the
SMILES of the core. Parent title, parent smiles and
core smiles will in any case appear in the core
structures as properties s_ch_parent_title,
s_ch_parent_smiles and s_ch_core_smiles, respectively.
The default is "s_m_title".
-WAIT When using Schrodinger job control (the default),
don't return from the command-line invocation until
the job is complete. Default is to return as soon as
the job has been launched by the job-control layer.
-NOJOBID Run immediately and locally, without Schrodinger job-
control. Cannot be called from the commandline with
-HOST, or used when there are subjobs.
-HOST HOST Host for execution of job or driver (if there are
subjobs). If not specified, then the local host is
used. If there are subjobs and no -SUBHOST option is
specified, then the subjobs, as well as the driver,
are executed on this host. This option must be
supplied on the command line, not in an argument file.
-SUBHOST SUBHOST Host for execution of subjobs. See also -HOST. This
option must be supplied on the command line, not in an
argument file.
Options controlling output verbosity:
-quiet Emit fatal error messages only
-normal_output Default verbosity specification. Writes error
messages, and brief information at the beginning and
end.
-verbose Prints default information plus a few lines per
structure read. Any input structures or cores skipped
because of undesirable features will be listed.
-DEBUG Emit verbose output at the job-control level
-DDEBUG Emit very verbose output at the job-control level
Options for private use, in some cases to assist with debugging:
-debug Prints -verbose output plus copious output useful for
debugging.
-debug_mae Prints -debug output and also write parents,
supercores, duplicates, etc. to the output structure
file. This output file cannot be used for core
hopping. Operates only when input and output files are
both structure files.
-e, -exceptional_mae_files
If specified, return Maestro files containing
structures that encountered exceptional conditions,
such as failure to match their own SMILES
-coverage When finished, report the list of rules that were not
matched. This option is ignored if -quiet is
specified.
-sqlite_chunksize SQLITE_CHUNKSIZE
Chunk size for performing certain SQL operations.
Default is 999 which is a compiled-in value for
certain operations. Setting this to a lower value
allows testing the chunking algorithm on small data
sets.
-verbosity VERBOSITY
The program specifies this option to a subjob based on
user specification of -verbose, -quiet or -debug.
-accept_bad_lewis Retain bad Lewis structures. Default discards them.
-jlaunched The program specifies this option to a job launched by
job control.