rxnpath_backend.py Command Help
Command: $SCHRODINGER/run rxnpath_backend.py
usage: $SCHRODINGER/run rxnpath_backend.py [-h] [-job_name JOB_NAME]
[-reorder] [-norxncomplex]
[-vdwscale VDWSCALE]
[-reverse_interpolation]
[-sample list of floats [list of floats ...]]
[-presumed_ts {reactant_like,midway,product_like}]
[-densearound]
[-interpolation {internal,distance,cartesian}]
[-bondweight BONDWEIGHT]
[-angleweight ANGLEWEIGHT]
[-dihedralweight DIHEDRALWEIGHT]
[-cartesianweight CARTESIANWEIGHT]
[-penaltyweight PENALTYWEIGHT]
[-mixprevious MIXPREVIOUS]
[-guess {beforesuperposition,aftersuperposition}]
[-connectivity {reactant,ts,product}]
[-verbose] [-version]
[-DRIVERHOST DRIVERHOST]
[-HOST HOST] [-SAVE]
[-TMPDIR TMPDIR] [-LOCAL] [-WAIT]
[-DEBUG]
input_files [input_files ...]
Given reactant and product structures interpolate the coordinates of
intermediate structures along the reaction path. Copyright Schrodinger, LLC.
All rights reserved.
positional arguments:
input_files White space delimited list of input Maestro files
where each file may contain multiple reactant/product
pairs of structures ordered like (1) reactants for
reaction 1, (2) products for reaction 1, (3) reactants
for reaction 2, (4) products for reaction 2, etc.
options:
-h, -help Show this help message and exit.
-job_name JOB_NAME Specify the job name of this calculation. (default:
rxnpath)
-reorder Attempts to automatically determine the appropriate
mapping of reactant atoms to product atoms. (default:
False)
-norxncomplex Disable the preprocessing of reactants and products
into reaction complexes for certain bimolecular
reactions. (default: False)
-vdwscale VDWSCALE Scales the inter-molecular VDW distance used to
separate reactants or products when forming reaction
complexes. This option will not used if the user
chooses the option '-norxncomplex'. (default: 1.0)
-reverse_interpolation
Specify that the reaction path should be interpolated
in reverse, i.e. the reactant and product definitions
do not change however the interpolation is done from
products to reactants rather than from reactants to
products. (default: False)
-sample list of floats [list of floats ...]
Specify the type of sampling used in generating the
reaction path. For uniform sampling between the
reactant and product pass N >= 1, where N is the
number of points to sample. For non-uniform sampling
pass a whitespace delimited list of numbers N, where
0.0 (reactant) < N < 1.0 (product), for example 0.5
might resemble the transition state. (default: [10.0])
-presumed_ts {reactant_like,midway,product_like}
Location of presumed transition state along the
reaction path. Choices are reactant_like (0.25),
midway (0.50), and product_like (0.75). Used only in
the '-densearound' and '-connectivity' options.
(default: midway)
-densearound Increase the density of sampling points in the
presumed transition state region by adding 10 sampling
points, with a step size of 0.02, centered on the
transition state location. These points will override
any pre-existing sampling points in these regions, for
example those obtained from the '-sample' option.
(default: False)
-interpolation {internal,distance,cartesian}
Specify the coordinate system in which to interpolate
reaction path points. Options include cartesian,
distance, and internal. Option cartesian is the
fastest and works for certain reactions, usually
simple reactions involving a small number of reactive
atoms. Option distance is more computationally
demanding but may have some advanages over cartesian,
for example it will not over-estimate bond lengths.
Option internal is also computationally demanding but
works for the greatest number of reactions, for
example it can be used to avoid certain types of
atomic collisions along the reaction path. (default:
cartesian)
-bondweight BONDWEIGHT
Specify the weight, w >= 0, of the bond terms used in
fitting the reaction path. Increase this value to
increase the rigidity of interpolated bonds or
decrease it if one experiences difficulty with
convergence. Typically this value will not need to be
decreased. (default: 1000.0)
-angleweight ANGLEWEIGHT
Specify the weight, w >= 0, of the angle terms used in
fitting the reaction path. Increase this value to
increase the rigidity of interpolated angles or
decrease it if one experiences difficulty with
convergence. Typically this value will not need to be
decreased. (default: 1000.0)
-dihedralweight DIHEDRALWEIGHT
Specify the weight, w >= 0, of the dihedral terms used
in fitting the reaction path. Increase this value to
increase the rigidity of interpolated dihedrals or
decrease it if one experiences difficulty with
convergence. Typically this value will not need to be
decreased. (default: 1000.0)
-cartesianweight CARTESIANWEIGHT
Specify the weight, w >= 0, of the Cartesian terms
used in fitting the reaction path. Increase this value
if one is confident that the interpolated Cartesian
coordinates well approximate the desired coordinates
of the reaction path point. Note that in such a
situation the user might prefer to use the option
-interpolation cartesian. Decrease this value if the
interpolated Cartesian coordinates are a poor guess or
if one experiences difficulty with convergence.
Increasing or decreasing this value can typically
remedy troublesome reaction paths more effectively
than by changing the other weighting terms. (default:
1000.0)
-penaltyweight PENALTYWEIGHT
Specify the weight, w >= 0, of the bond penalty terms
used in fitting the reaction path. Such weights
prevent bond lengths from becoming too small. Increase
this value if the reaction path features atom-atom
collisions or decrease it if the user wants
unconstrained bond lengths. Typically this value will
not need to be decreased. (default: 1.0)
-mixprevious MIXPREVIOUS
Specify the extent to which the optimized Cartesian
coordinates from the previous reaction path point are
mixed with the interpolated Cartesian coordinates for
the current reaction path point. Typically, the
interpolated Cartesian coordinates are used as a guess
solution to the optimizer. Mixing can help convergence
for certain types of reactions where these guesses can
involve overlapping atoms. Mixing additionally helps
to create continuous reaction paths. Accepted values
are in [0.0, 1.0]. (default: 0.5)
-guess {beforesuperposition,aftersuperposition}
Specify the type of guess solution to use from the
optimized Cartesian coordinates of the previous
reaction path point. Note that if the '-mixprevious'
option is zero then the '-guess' option is irrelevant.
Accepted values are beforesuperposition and
aftersuperposition. Option beforesuperposition uses
the optimized coordinates returned from the optimizer
while option aftersuperposition will first superpose
the optimized structure on to the reactant. (default:
beforesuperposition)
-connectivity {reactant,ts,product}
Specify the type of connectivity, i.e. bond
assignment, protocol to use in defining the structures
along the reaction path. Options include reactant, ts,
or product. Options reactant and product will use
those bonds defined in the reactant or product as the
bonds in the structures along the reaction path.
Option ts specifies that the bonding of the structures
along the reaction path will change from that of
reactants, to something resembling both reactants and
products in the specified transition state region, and
then finally to products. (default: ts)
-verbose Turn on verbose printing. (default: False)
-version, -v Show the script's version number and exit.
-DRIVERHOST DRIVERHOST
Job Control option - if used with -HOST specifies the
host on which to run the script itself. (default:
localhost)
-HOST HOST Job Control option - specifies the host on which to
run the script or if used with -DRIVERHOST specifies
the host to use for any subjobs. (default: localhost)
-SAVE Job Control option - copy the archived contents of the
job directory back to the submission directory after
the job finishes. (default: False)
-TMPDIR TMPDIR Job Control option - specify the scratch directory for
the job. (default: /scr)
-LOCAL Job Control option - write temporary files in the
submission directory instead of the scratch directory.
(default: False)
-WAIT Job Control option - wait for the job to finish before
executing another command. (default: False)
-DEBUG Job Control option - show the details of operation of
the top-level script. (default: False)