canvasMCS Command Help
Command: $SCHRODINGER/utilities/canvasMCS
canvasMCS - Finds maximum common substructure(s) among a given set of molecules.
Usage: canvasMCS [<job control options>] <program options>
Job Control Options: [-JOB <jobName> [-HOST <host>]
[-LOCAL]
[-TMPDIR <dir>]
[-WAIT]
[-INTERVAL <n>]
[-NICE]]
-JOB <jobName> - Job name. If omitted, no other job control options are
permitted.
-HOST <host> - Run job on <host>. Only single-CPU jobs are supported.
-LOCAL - Store temporary job files in current directory.
-TMPDIR <dir> - Store temporary job files in <dir>.
-WAIT - Do not return prompt until job completes.
-INTERVAL <n> - Update log file every <n> seconds.
-NICE - Run job at reduced priority.
Program Options: -ismi <smiFile>
|-isd <sdFile> [-fieldAsName <field>]
|-imae <maeFile> [-fieldAsName <field>]
|-iproj <projFile>
|-icsv <csvFile> [-noHeader]
[-d <delimiter>]
[-smi <SMILESCol>]
[-name <nameCol>]
-ocsv <csvOutput>
|-opw <pwOutput>
|-osd <sdOutput> [-nodetail]
|-omae <maeOutput> [-nodetail]
[-min <minMatch>]
[-max <maxMatch>]
[-stop <size>]
[-n <structRange> [-file]]
[-rs [<numMols>]]
[-limit <numMols>]
[-showall [<int>] | -exclusive]
[-nodetail]
[-sortname]
[-addring]
[-v3]
[-ordinal]
[-atomtype <type>]
[-timeout] <seconds>
[-nobreakring] | [-nobreakaring]
[-allH]
[-disconnect]
[-prochiral]
-ismi <smiFile> - Input SMILES file, with one SMILES string per line.
An optional structure name may follow the SMILES,
with a space or tab separator.
-isd <sdFile> - Input SD file, standard or compressed.
-imae <maeFile> - Input Maestro file, standard or compressed.
-iproj <projFile> - Canvas project file, including absolute path.
-icsv <csvFile> - Input CSV file. By default, the file is expected to
contain a column header line and SMILES in the first
column.
-noHeader - Input CSV file has no header line.
-d <delimiter> - Input CSV file delimiter. The default is ','. Use
-d ' ' for space and -d ' ' for tab. Consecutive
space delimiters are treated as one.
-smi <SMILESCol> - Input CSV SMILES column, either by name or by index,
starting at 1. By default, SMILES is the first column.
-name <nameCol> - Input CSV molecule name column, either by name or by
index. By default, it is the second column.
-min <minMatch> - Minimum number of molecules that must match the MCS.
The default is all. If <minMatch> exceeds the number
of inputs, it is perceived as requiring all to match.
Note that the largest substructure common to at least
<minMatch> molecules may actually match additional
molecules, so the number of matches reported may be
larger than <minMatch>.
-max <maxMatch> - Target upper bound on the minimum number of molecules
that must match the MCS. The default is all. When
<maxMatch> is larger than <minMatch>, a series of
solutions is produced, where the first solution matches
at least <minMatch> molecules, and subsequent solutions
match larger numbers of molecules. Ideally, there will
be a unique MCS for each match count between <minMatch>
and <maxMatch>, but this rarely happens in practice.
Furthermore, the last reported solution may match more
than <maxMatch> molecules, for the reasons given above.
-stop <size> - Stop processing when MCS Atom + Bond Count falls below
this threshold.
-ocsv <csvOutput> - Output CSV file for MCS results.
-opw <pwOutput> - Output MCS for all pairs in columnar format.
-omae <fileName> - Output Maestro file for MCS results.
-osd <fileName> - Output SD file for MCS results.
-nodetail - Omit MCS atom and bond lists in output file. These are
never reported in CSV output.
-n <structRange> - The set of input structures to process:
1,4 - structures 1 and 4
1:10,14 - structures 1 through 10 and 14
2: - structures 2 through the end of file
:5,13:18 - structures 1 through 5 and 13 through 18
All structures are processed by default.
-file - If specified, <structRange> in the above is taken as
a filename, which contains range selection. If used
together with -iproj option, this file must be the
binary set file written from Canvas GUI. For other
input formats, this file should contain a valid
structure range string as specified above in each line.
-rs [<numMols>] - Process only a random subset of the input molecules.
If <numMols> is omitted, it will be set to sqrt(total).
-limit <numMols> - Maximum number of molecules to process (default=2000).
Processing more than 2000 may exceed available memory.
-showall [<int>] - Output all equivalents for each MCS. 2 by default.
Not compatible with -exclusive and -opw. 0 is 'off',
1 reports all patterns, 2 (default) reports only unique
patterns, and 3 reports these same unique patterns on
a single line.
-exclusive - If an input molecule matches more than one MCS, report
only the match to the largest MCS. Not compatible with
-showall.
-sortname - Sort output on molecule name. By default, input order
is preserved.
-addring - In output MCS SMARTS patterns, mark each atom as cyclic
(R) or acyclic (R0). Off by default.
-addh - In output MCS SMARTS patterns, include hydrogen counts for
each atom. Off by default.
-nox - In output MCS SMARTS patterns, suppress addition of a
connectivity qualification [nX3] for pyrrolic nitrogens.
Default is on.
-v3 - Output MDL version 3 SD Format.
-ordinal - Use the ordinal position of each structure in the source
file as its identifier (e.g. '1' for first, '2' for second)
-atomtype <type> - Atom typing scheme. Must be an integer value between
1 and 13 or C (details below). The default is 11.
-timeout <seconds>- Abort further calculations when cpu time exceeds this
integer.
-nobreakring - Do not consider partial rings as part of MCS.
-nobreakaring - Do not consider partial aromatic rings as part of MCS.
-allH - Consider hydrogens as explicit atoms. Implies -addh.
-disconnect - Allow the MCS to have one or more disconnections.
-u - Use unique SMILES for all SMILES output."
-prochiral - Use 3D geometry to distinguish prochirality. Requires.
3D all-atom inputs to work properly.
Atom Typing Schemes
-------------------
1 - All atoms equivalent; all bonds equivalent.
2 - Atoms distinguished by HB acceptor/donor; all bonds equivalent.
3 - Atoms distinguished by hybridization state; all bonds equivalent.
4 - Atoms distinguished by functional type: {H}, {C}, {F,Cl}, {Br,I}, {N,0},
{S}, {other}; bonds by hybridization.
5 - Mol2 atom types; all bonds equivalent.
6 - Atoms distinguished by whether terminal, halogen, HB acceptor/donor;
bonds distinguished by bond order.
7 - Atomic number and bond order.
8 - Atoms distinguished by ring size, aromaticity, HB acceptor/donor,
ionization potential, whether terminal, whether halogen; bonds
distinguished by bond order.
9 - Carhart atom types (atom-pairs approach); all bonds equivalent.
10 - Daylight invariant atom types; bonds distinguished by bond order.
11 - Same as 7, but distinguishing aromatic from non-aromatic.
12 - Same as 11, but distinguishing aliphatic atoms by ring/acyclic.
13 - Same as 12, but distinguishing rings by size.
C - Custom. Must be followed by location of a type definitions file.