rxnchannel.py Command Help
Command: $SCHRODINGER/run rxnchannel.py
usage: $SCHRODINGER/run rxnchannel.py [-h] [-channels CHANNEL_FILE]
[-num_random_channels INT or 'all']
[-random_types RANDOM_TYPES [RANDOM_TYPES ...]]
[-seed SEED]
[-allow_adsorption_onto SMARTS or 'all' [SMARTS or 'all' ...]]
[-dissociation_bond_length DISSOCIATION_BOND_LENGTH]
[-no_minimization] [-isolate_products]
[-no_reactive_h] [-unique] [-verbose]
[-version]
input_file
Given reactant structures enumerate product structures that result from the
following types of reaction channels: (1) association, A + B --> A-B, (2)
dissociation, A-B --> A + B, (3) single-displacement, A + B-C --> A-B + C and
A-C + B, and (4) double-displacement, A-B + C-D --> A-C + B-D and A-D + B-C.
Copyright Schrodinger, LLC. All rights reserved.
positional arguments:
input_file Maestro input file containing a single reactant
structure.
options:
-h, -help Show this help message and exit.
-channels CHANNEL_FILE
Specify the name of the user supplied formatted input
text file that defines the reaction channels to
enumerate in this calculation. Each line should
contain a single reaction channel definition, which
amounts to two atom index sequences separated by a
semicolon. Unless the channel definition is for a
dissociation one of the sequences should contain atom
indicies from one of the reactant molecules and the
other sequence indicies from a different reactant
molecule. In the case of dissociation all atom
indicies should belong to the same reactant molecule.
All atom indicies must be unique and greater than
zero. These two sequences can each contain one or two
atom indicies separated by a whitespace, the former
specifies an atomic site that is available for single
bond formation while the latter specifies a single
bond to be broken. For a channel of type (1) or (2)
above add to the file the line '4; 8' to specify that
between atoms 4 and 8 a single bond should be formed
or broken, respectively. For a channel of type (3)
above add to the file the line '4; 8 9' to specify
that the single bond between atoms 8 and 9 should be
broken and that the resulting fragments should in turn
be bound to atom 4. For a channel of type (4) above
add to the file the line '2 4; 8 9' to specify that
the single bonds between atoms 2 and 4 and atoms 8 and
9 be broken and the resulting fragments in turn be
exchanged and bound. Note that reactive bonds can be
either single-order or zero-order bonds. (default:
None)
-num_random_channels INT or 'all'
Specify a number of random reaction channels to
generate or specify 'all' to calculate all possible
reaction channels for each type given by the argument
to -random_types. Unless 'all' is specified in order
to circumvent computational expense if the number of
reactant atoms becomes larger than 50 the protocol for
generating random channels will change from that of
taking a random sample of all possible reaction
channel definitions to that of generating the random
channel definitions on the fly without having
performed the expensive precomputation of all possible
reaction channel definitions. (default: 0)
-random_types RANDOM_TYPES [RANDOM_TYPES ...]
Specify the types of random reaction channels to
sample when generating random channels. The choices
are 'association', 'dissociation',
'single_displacement', 'double_displacement', and/or
'all'. Enter as many choices as desired. (default:
['double_displacement'])
-seed SEED, -random_seed SEED
Seed for random number generator. (default: 1234)
-allow_adsorption_onto SMARTS or 'all' [SMARTS or 'all' ...]
Specify a whitespace separated sequence of SMARTS
patterns onto which you wish to allow adsorption or
simply pass 'all' to allow all atoms to function as
adsorption sites. It is the first atom of the
specified SMARTS pattern that will serve as the
adsorption site. This option is useful for permitting
adsorption onto atoms that would ordinarly be skipped
due to the fact that the atomic valencies are already
complete, for example as in physisorption on graphene.
SMARTS patterns can automatically be determined in
Maestro by selecting the atoms of interest in the
workspace and doing Scripts > Workspace Tools > SMARTS
Index Identifier and clicking the 'Get from Selection'
button. The user should reorder the individual atomic
contributions to the obtained SMARTS pattern so that
the atomic adsorption site that they want comes first.
SMARTS patterns can be searched in Maestro by doing
Edit > Select Atoms > Select and then clicking the
'Substructure' tab and selecting the SMARTS option.
Here are a few arbitrary adsorption sites along with
descriptors (note you do not need to specify the
descriptor, only the SMARTS pattern): ['graphene: [c-
0X3][c-0X3]([c-0X3]([c-0X3]([c-0X3])[c-0X3])[c-
0X3]([c-0X3])[c-0X3])[c-0X3]']. (default: ['[c-0X3][c-
0X3]([c-0X3]([c-0X3]([c-0X3])[c-0X3])[c-0X3]([c-
0X3])[c-0X3])[c-0X3]'])
-dissociation_bond_length DISSOCIATION_BOND_LENGTH
Specify in Angstrom the bond length to use for
dissociation reaction channels. (default: 10.0)
-no_minimization Specify that the reactant and product geometries
should not be minimized. Note that by default and
regardless of this option that an attempt will be made
to eliminate any ring spears from any output
structures. If a minimization is being performed it
will be performed after the attempted ring spear
elimination. (default: False)
-isolate_products Use this option to return the isolated product
structures for each reaction channel. For example, for
a double displacement reaction, i.e. A-B + C-D --> A-C
+ B-D, rather than returning both A-C and B-D in a
given structure this option specifies to return two
structures, one with A-C and one with B-D. Note that
this option will not return atomic products. (default:
False)
-no_reactive_h Specify that R-H bonds be considered inert, i.e. those
bonds should not be allowed to dissociate or to
participate in a single displacement or double
displacement reaction. This option is particulary
useful for disabling the following, for example,
double displacement channels during an enumeration
run: R-H + R'-H' --> R-H' + R'-H or R-R' + H-H'.
(default: False)
-unique Specify this option to uniquify the final set of
returned structures. This option will firstly only
allow the calculation of unique single and/or double
displacement reaction channels, meaning that a SMILES
analysis is performed on fragments on either side of a
bond to recognize and skip channels for which the
products would be redundant with the given reactants.
If instead the two types of products are redundant
with each other then only a single type will be
computed. So these redundant channels will never be
calculated. This option will secondly apply a SMILES
filter to the final set of returned structures in
order to catch redundancies that have been calculated.
This filter will recognize conformational isomers and
will only return the first isomer. (default: False)
-verbose Turn on verbose printing. (default: False)
-version, -v Show the script's version number and exit.