NAME¶
fmcs - fmcs
DESCRIPTION¶
usage: fmcs [-h] [--maximize {atoms,bonds}] [--min-num-atoms INT]
- [--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
Find the maximum common substructure of a set of structures
positional arguments:¶
- filename
- SDF or SMILES file
optional arguments:¶
- -h, --help
- show this help message and exit
- --maximize {atoms,bonds}
- Maximize the number of 'atoms' or 'bonds' in the MCS. (Default:
bonds)
- --min-num-atoms INT
- Minimimum number of atoms in the MCS (Default: 2)
- --compare {topology,elements,types}
- Use 'topology' as a shorthand for '--atom-compare any
--bond-compare any', 'elements' is '--atom-compare elements
--bond-compare any', and 'types' is '--atomcompare elements
--bond-compare bondtypes' (Default: types)
- --atom-compare {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)
- --bond-compare {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)
- --atom-class-tag 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)
- --ring-matches-ring-only
- 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.)
- --complete-rings-only
- 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 --ring-matches-ring-only.
- --select SELECT
- Select a subset of the input records to process. Example: 1-10,13,20,50-
(Default: '1-', which selects all structures)
- --timeout SECONDS
- Report the best solution after running for at most 'timeout' seconds. Use
'none' for no timeout. (Default: none)
- --output FILENAME, -o FILENAME
- Write the results to FILENAME (Default: use stdout)
- --output-format
{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
--save-atom-class 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
--save-fragment-indices-tag. (Default: smarts)
- --output-all
- 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.
- --save-atom-class-tag TAG
- If atom classes are specified (via --class-tag) 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
--atomclass-tag.
- --save-counts-tag 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.)
- --save-atom-indices-tag 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)
- --save-smarts-tag TAG
- Save the MCS SMARTS to the specified SD tag. Uses '-' if there is no
MCS
- --save-smiles-tag TAG
- Save the fragment SMILES to the specified SD tag. Uses '-' if there is no
MCS
- --times
- Print timing information to stderr
- -v, --verbose
- Print progress statistics to stderr. Use twice for higher verbosity.
--version
For more details on these options, see
https://bitbucket.org/dalke/fmcs/