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.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.38.2.
.TH FMCS "1" "June 2012" "fmcs 1.0" "User Commands"
.SH NAME
fmcs \- fmcs
.SH DESCRIPTION
usage: fmcs [\-h] [\-\-maximize {atoms,bonds}] [\-\-min\-num\-atoms INT]
.IP
[\-\-compare {topology,elements,types}]
[\-\-atom\-compare {any,elements,isotopes}]
[\-\-bond\-compare {any,bondtypes}] [\-\-atom\-class\-tag TAG]
[\-\-ring\-matches\-ring\-only] [\-\-complete\-rings\-only]
[\-\-select SELECT] [\-\-timeout SECONDS] [\-\-output FILENAME]
[\-\-output\-format {smarts,fragment\-smiles,fragment\-sdf,complete\-sdf}]
[\-\-output\-all] [\-\-save\-atom\-class\-tag TAG] [\-\-save\-counts\-tag TAG]
[\-\-save\-atom\-indices\-tag TAG] [\-\-save\-smarts\-tag TAG]
[\-\-save\-smiles\-tag TAG] [\-\-times] [\-v] [\-\-version]
filename
.PP
Find the maximum common substructure of a set of structures
.SS "positional arguments:"
.TP
filename
SDF or SMILES file
.SS "optional arguments:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-\-maximize\fR {atoms,bonds}
Maximize the number of 'atoms' or 'bonds' in the MCS.
(Default: bonds)
.TP
\fB\-\-min\-num\-atoms\fR INT
Minimimum number of atoms in the MCS (Default: 2)
.TP
\fB\-\-compare\fR {topology,elements,types}
Use 'topology' as a shorthand for '\-\-atom\-compare any
\fB\-\-bond\-compare\fR any', 'elements' is '\-\-atom\-compare
elements \fB\-\-bond\-compare\fR any', and 'types' is '\-\-atomcompare elements \fB\-\-bond\-compare\fR bondtypes' (Default:
types)
.TP
\fB\-\-atom\-compare\fR {any,elements,isotopes}
Specify the atom comparison method. With 'any', every
atom matches every other atom. With 'elements', atoms
match only if they contain the same element. With
\&'isotopes', atoms match only if they have the same
isotope number; element information is ignored so [5C]
and [5P] are identical. This can be used to implement
user\-defined atom typing. (Default: elements)
.TP
\fB\-\-bond\-compare\fR {any,bondtypes}
Specify the bond comparison method. With 'any', every
bond matches every other bond. With 'bondtypes', bonds
are the same only if their bond types are the same.
(Default: bondtypes)
.TP
\fB\-\-atom\-class\-tag\fR TAG
Use atom class assignments from the field 'TAG'. The
tag data must contain a space separated list of
integers in the range 1\-10000, one for each atom.
Atoms are identical if and only if their corresponding
atom classes are the same. Note that '003' and '3' are
treated as identical values. (Not used by default)
.TP
\fB\-\-ring\-matches\-ring\-only\fR
Modify the bond comparison so that ring bonds only
match ring bonds and chain bonds only match chain
bonds. (Ring atoms can still match non\-ring atoms.)
.TP
\fB\-\-complete\-rings\-only\fR
If a bond is a ring bond in the input structures and a
bond is in the MCS then the bond must also be in a
ring in the MCS. Selecting this option also enables
\fB\-\-ring\-matches\-ring\-only\fR.
.TP
\fB\-\-select\fR SELECT
Select a subset of the input records to process.
Example: 1\-10,13,20,50\- (Default: '1\-', which selects
all structures)
.TP
\fB\-\-timeout\fR SECONDS
Report the best solution after running for at most
\&'timeout' seconds. Use 'none' for no timeout.
(Default: none)
.TP
\fB\-\-output\fR FILENAME, \fB\-o\fR FILENAME
Write the results to FILENAME (Default: use stdout)
.TP
\fB\-\-output\-format\fR {smarts,fragment\-smiles,fragment\-sdf,complete\-sdf}
\&'smarts' writes the SMARTS pattern including the atom
and bond criteria. 'fragment\-smiles' writes a matching
fragment as a SMILES string. 'fragment\-sdf' writes a
matching fragment as a SD file; see \fB\-\-save\-atom\-class\fR
for details on how atom class information is saved.
\&'complete\-sdf' writes the entire SD file with the
fragment information stored in the tag specified by
\fB\-\-save\-fragment\-indices\-tag\fR. (Default: smarts)
.TP
\fB\-\-output\-all\fR
By default the structure output formats only show an
MCS for the first input structure. If this option is
enabled then an MCS for all of the structures are
shown.
.TP
\fB\-\-save\-atom\-class\-tag\fR TAG
If atom classes are specified (via \fB\-\-class\-tag\fR) and
the output format is 'fragment\-sdf' then save the
substructure atom classes to the tag TAG, in fragment
atom order. By default this is the value of \fB\-\-atomclass\-tag\fR.
.TP
\fB\-\-save\-counts\-tag\fR TAG
Save the fragment count, atom count, and bond count to
the specified SD tag as space separated integers, like
\&'1 9 8'. (The fragment count will not be larger than 1
until fmcs supports disconnected MCSes.)
.TP
\fB\-\-save\-atom\-indices\-tag\fR TAG
If atom classes are specified and the output format is
\&'complete\-sdf' then save the MCS fragment atom indices
to the tag TAG, in MCS order. (Default: mcs\-atomindices)
.TP
\fB\-\-save\-smarts\-tag\fR TAG
Save the MCS SMARTS to the specified SD tag. Uses '\-'
if there is no MCS
.TP
\fB\-\-save\-smiles\-tag\fR TAG
Save the fragment SMILES to the specified SD tag. Uses
\&'\-' if there is no MCS
.TP
\fB\-\-times\fR
Print timing information to stderr
.TP
\fB\-v\fR, \fB\-\-verbose\fR
Print progress statistics to stderr. Use twice for
higher verbosity.
.HP
\fB\-\-version\fR
.PP
For more details on these options, see https://bitbucket.org/dalke/fmcs/
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