polymer_crosslink_driver.py Command Help
Command: $SCHRODINGER/run polymer_crosslink_gui_dir/polymer_crosslink_driver.py
usage: $SCHRODINGER/run polymer_crosslink_gui_dir/polymer_crosslink_driver.py
[-h] [-icms ICMS] [-rm_md_dirs] [-mode {standard,fast,high_throughput}]
[-rxn [RXN ...]] [-cgrxn [CGRXN ...]] [-rate_type RATE_TYPE]
[-ab_smarts AB_SMARTS] [-cd_smarts CD_SMARTS] [-a_index SMARTS_INDEX]
[-b_index SMARTS_INDEX] [-c_index SMARTS_INDEX] [-d_index SMARTS_INDEX]
[-ab_bond INDEX1,INDEX2] [-cd_bond INDEX1,INDEX2]
[-threshold_bonds FORMING_BOND] [-ac_dist_thresh AC_DIST_THRESH]
[-ac_max_dist AC_MAX_DIST] [-ac_dist_step AC_DIST_STEP]
[-ac_delete_mol] [-ac_existing_bond] [-bd_dist_thresh BD_DIST_THRESH]
[-bd_max_dist BD_MAX_DIST] [-bd_dist_step BD_DIST_STEP]
[-bd_delete_mol] [-bd_existing_bond]
[-smarts_method {internal,canvas,rdkit}]
[-xlink_saturation XLINK_SATURATION] [-saturation_bond SMARTS]
[-saturation_type RXN,TYPE] [-max_xlink_iter MAX_XLINK_ITER]
[-xlinks_per_iter XLINKS_PER_ITER] [-intramonomer_xlinks]
[-max_bond_order MAX_BOND_ORDER] [-blocked_smarts [BLOCKED_SMARTS ...]]
[-sim_time SIM_TIME] [-sim_temp SIM_TEMP] [-seed SEED]
[-sim_timestep FEMTOSECONDS] [-sim_convergence SIM_CONVERGENCE]
[-max_sim_retries MAX_SIM_RETRIES] [-ensemble {NPT,NVT}]
[-pressure PRESSURE] [-ffld FFLD] [-cgffld FORCE_FIELD_NAME]
[-cgffld_loc_type FORCE_FIELD_LOCATION_TYPE] [-gpu] [-ramp RAMP_FILE]
[-extend_ramp] [-no_robust_eq] [-skip_analysis] [-skip_free_volume]
[-split_components] [-md_umbrella] [-use_zip_data PATH]
[-restart_proj PROJECT_NAME] [-restart_disp INCORPORATION]
[-restart_viewname VIEWNAME] [-restart_host HOSTNAME:PROCESSORS]
[-restart_jobname JOBNAME] [-HOST <hostname>] [-WAIT] [-LOCAL] [-D]
[-NOJOBID] [-VIEWNAME <viewname>] [-OPLSDIR OPLSDIR] [-JOBNAME JOBNAME]
options:
-h, -help Show this help message and exit.
-icms ICMS Disordered system containing monomers to crosslink.
(default: None)
-rm_md_dirs By default all job files for all equilibration steps
will be saved in sub-directories named according to
the xlinking/equilibration step. Use this option to
remove these sub-directories. Note that using this
option will prevent you from being able to view
trajectories in Maestro. (default: False)
-mode {standard,fast,high_throughput}
Specify the mode of crosslinking. {STANDARD_MODE} is
the default mode that performs crosslinking followed
by MD.{FAST_MODE} performs crosslinking followed by
local minimization and performs MD only when no
reactions are occurring. {HIGH_THROUGHPUT_MODE} is
same as {FAST_MODE} but has less rigorous structure
checks. (default: standard)
-smarts_method {internal,canvas,rdkit}
SMARTS matching method. (default: rdkit)
-skip_analysis Do not perform analysis calculations. (default: False)
-skip_free_volume Do not perform free volume calculations. (default:
False)
Reaction options:
-rxn [RXN ...] Use this flag to define all the breaking bond, forming
bond, and rate options for one atomistic crosslink
reaction. If only a single crosslink reaction is to be
specified, the specification can be done by either
this flag or the individual breaking bond and forming
bond flags, but -rxn and the individual flags may not
be mixed. If more than one reaction is to be
specified, then only multiple uses of this flag can be
used. In addition to the breaking and forming bond
options, the special -rxn option "rate" can be
supplied. "rate" can be used to control the relative
reactivity between reactions and can be either an
activation energy or Boltzmann factor (see the
-rate_type flag) and defaults to 1.0. When using -rxn,
follow it with the list of all breaking bond and
forming bond options WITHOUT the leading dashes, using
the "=" sign to join each option to its value, and
separate each option=value pair by a space. For
example: "-rxn ab_smarts=CCl cd_smarts=N[H]
ac_dist_thresh=3.0 ac_max_dist=8.0 bd_delete_mol=True"
or "-rxn ab_smarts=C=C cd_smarts=[R0,r5,r6]
ac_dist_thresh=4.0 bd_dist_thresh=3.0 bd_dist_step=1.0
-rxn ab_smarts=CCl cd_smarts=N[H] ac_dist_thresh=3.0
--". The first example shows single reaction where
bd_delete_mol results in deletion of HCl molecules
after every crosslinking step is performed. The second
example shows how two reactions would be defined and
also shows terminating the reaction specification
using the special flag "--". Since a -rxn group is
normally terminated by the next use of an option that
begins with "-", use "--" to terminate a -rxn group
when it is the last option that begins with "-" before
the end of the command line. Any option listed in the
Breaking bond or Forming bond option section may be
given following -rxn, but at least ab_smarts,
cd_smarts and one of ac_dist_thresh or bd_dist_thresh
are required for each -rxn group. The same defaults
and restrictions for each option apply whether they
are given as individual flags or part of a -rxn group.
(default: None)
-cgrxn [CGRXN ...] Use this flag to define all the forming bond, and rate
options for one coarse-grained crosslink reaction.
Unlike atomistic systems, coarse-grained reactions
must use this flag and may not use the flags in the
"Breaking bond options" or "Forming bond options"
sections. If more than one reaction is to be
specified, then multiple uses of this flag can be
used. The format of this flag is -cgrxn followed by a
series of space-separated option=value pairs which
define the reaction options. The following options are
supported: a_name, b_name, a_min_bonds, a_max_bonds,
b_min_bonds, b_max_bonds, dist_min, dist_max,
dist_step, angle, angle_pm, rate. "a_name" and
"b_name" give the names of the A and B particles
involved in the reaction. For each particle, the
"x_min_bonds" and "x_max_bonds" (x=a or b) options
give the minimum and maximum number of bonds allowed
for a particle of that type to be considered as a
crosslinking candidate. "dist_min" and "dist_max"
define the minimum and maximum distance between two
particles that are allowed to crosslink, and
"dist_step" is the amount to expand the allowed
distance each iteration as a search is performed from
dist_min to dist_max for eligible crosslinks.
"dist_min" and "dist_step" are ignored for when
multiple reactions are defined. "angle" and "angle_pm"
define the desired angle and +/- tolerance (in
degrees) for eligible crosslinks. If "angle" is not
given, no angle restriction will be enforced."rate"
can be used to control the relative reactivity between
reactions and can be either an activation energy or
Boltzmann factor (see the -rate_type flag) and
defaults to 1.0. "rate" is ignored when only a single
reaction is defined. For example: "-cgrxn a_name=phnh2
b_name=acetyl a_min_bonds=1 a_max_bonds=2
b_min_bonds=1 b_max_bonds=1 dist_min=5.0 dist_max=15.0
dist_step=1.0" or "-cgrxn a_name=phnh2 b_name=acetyl
a_min_bonds=1 a_max_bonds=1 b_min_bonds=1
b_max_bonds=1 dist_min=5.0 dist_max=15.0 dist_step=1.0
rate=3 -cgrxn a_name=phnh2 b_name=acetyl a_min_bonds=2
a_max_bonds=2 b_min_bonds=1 b_max_bonds=1 dist_min=5.0
dist_max=15.0 dist_step=1.0 rate=1 --". The second
example shows how two reactions would be defined (the
first reaction uses phnh2 particles that only have one
bond and the second uses phnh2 particles that only
have two bonds) and also shows terminating the
reaction specification using the special flag "--".
Since a -cgrxn group is normally terminated by the
next use of an option that begins with "-", use "--"
to terminate a -cgrxn group when it is the last option
that begins with "-" before the end of the command
line. (default: None)
-rate_type RATE_TYPE Define the type of rates provided with the -rxn or
-cgrxn flags. Choices are "energy" for activation
energies in kcal/mol or boltzmann for Boltzmann
factors. If the rates are activation energies,
Boltzmann factors will be computed from the energies
and temperature of the simulation. (default:
boltzmann)
Breaking bond options:
-ab_smarts AB_SMARTS SMARTS pattern to define the AB atom pair in the AB +
CD -> AC + BD crosslink reaction. (default: None)
-cd_smarts CD_SMARTS SMARTS pattern to define the CD atom pair in the AB +
CD -> AC + BD crosslink reaction. (default: None)
-a_index SMARTS_INDEX
The index of atom A in the AB SMARTS pattern (default:
1)
-b_index SMARTS_INDEX
The index of atom B in the AB SMARTS pattern (default:
2)
-c_index SMARTS_INDEX
The index of atom C in the CD SMARTS pattern (default:
1)
-d_index SMARTS_INDEX
The index of atom D in the CD SMARTS pattern (default:
2)
-ab_bond INDEX1,INDEX2
The index in the AB SMARTS pattern of the two atoms
whose bond should be broken. Values should be
index1,index2, such as 1,3. The default is to use the
A,B bond. (default: -1000.0)
-cd_bond INDEX1,INDEX2
The index in the CD SMARTS pattern of the two atoms
whose bond should be broken. Values should be
index1,index2, such as 1,3. The default is to use the
C,D bond. (default: -1000.0)
Forming bond options:
-threshold_bonds FORMING_BOND
Specify which forming bonds must be within a threshold
distance before the bond can be considered for
crosslinking. Choices are "AC", "BD" or "AC,BD" - the
latter specifies that both bonds must be within the
threshold distance (default: None)
-ac_dist_thresh AC_DIST_THRESH
Distance threshold in Angstroms for an A and C atom to
be considered as candidates for crosslinking. At least
1 of -ac_dist_thresh and -bd_dist_thresh must be
specified. Note that the -ac_max_dist and
-ac_dist_step flags are ignored if -ac_dist_thresh is
not given. (default: 3.0)
-ac_max_dist AC_MAX_DIST
Maximum distance (Angstroms) that should be used when
increasing step size to search for A and C atom
distances. Only used if -ac_dist_thresh is also
specified. (default: 7.0)
-ac_dist_step AC_DIST_STEP
Specify the step size (Angstroms) by which A and C
atom distance search should be incremented by. Only
usd if -ac_dist_thresh is also specified. (default:
0.5)
-ac_delete_mol Option to delete the crosslinked molecule containing A
and C bond. (default: False)
-ac_existing_bond Reaction will occur only if the AC bond already
exists. (default: False)
-bd_dist_thresh BD_DIST_THRESH
Distance threshold in Angstroms for a B and D atom to
be considered as candidates for crosslinking. At least
1 of -ac_dist_thresh and -bd_dist_thresh must be
specified. Note that the -bd_max_dist and
-bd_dist_step flags are ignored if -bd_dist_thresh is
not given. (default: None)
-bd_max_dist BD_MAX_DIST
Maximum distance (Angstroms) that should be used when
increasing step size to search for B and D atom
distances. Only used if -bd_dist_threshis also be
specified. (default: 7.0)
-bd_dist_step BD_DIST_STEP
Specify the step size (Angstroms) by which b and d
atom distance search should be incremented by. Only
used if -bd_dist_thresh is also specified. (default:
0.5)
-bd_delete_mol Option to delete the crosslinked molecule containing B
and D bond. (default: False)
-bd_existing_bond Reaction will occur only if the AC bond already
exists. (default: False)
Crosslinking options:
-xlink_saturation XLINK_SATURATION
Target crosslink saturation percent. (default: 75)
-saturation_bond SMARTS
The use of this argument is discouraged in favor of
-saturation_type, and this flag may not be used for
coarse-grained systems. SMARTS specifying which bond
the target crosslink saturation applies to. Must match
one of the SMARTS patterns given for breaking bonds.
(default: None)
-saturation_type RXN,TYPE
Particle which the target crosslink saturation applies
to. The format for the value of this flag is RXN,TYPE,
where RXN is the reaction containing the particle of
interest (1 for the first defined reaction, 2 for the
second, etc.) and TYPE is the participant type that is
the saturation target. For atomistic systems, TYPE
must be "AB" or "CD". For coarse-grained systems, TYPE
must be "A" or "B". If not provided, the type with the
fewest initial matches will be used (default: None)
-max_xlink_iter MAX_XLINK_ITER
Maximum number of successive unproductive crosslink +
equilibration iterations to attempt before exiting.
(default: 50)
-xlinks_per_iter XLINKS_PER_ITER
Limit the number of crosslinks formed per iteration to
a given value, allowed values are positive integers.
If -ramp is used, this flag must still be used to
indicate that the number of crosslinks should be
limited, but the value supplied with this flag is
ignored in favor of the values supplied with the ramp.
If -ramp is used and -xlinks_per_iter is not
specified, the number of crosslinks per iteration will
not be limited. (default: None)
-intramonomer_xlinks Allow crosslinks between atoms that start as part of
the same monomer. The default is to not allow
crosslinks between atoms that begin on the same
monomer. Atoms that begin on different monomers but
become part of the same molecule due to a crosslink
reaction are always allowed to crosslink regardless of
this flag. Use this flag, for instance, if the initial
structure is entirely or almost entirely a single
molecule. (default: False)
-max_bond_order MAX_BOND_ORDER
Maximum bond order allowed for the crosslinked bonds
formed in an atomistic reaction. Currently it does not
support coarse grained systems. (default: 3)
-blocked_smarts [BLOCKED_SMARTS ...]
List of SMART patterns to be blocked during
crosslinking. (default: None)
Simulation options:
-sim_time SIM_TIME Simulation time (ps) for the equilibration stage.
(default: 20)
-sim_temp SIM_TEMP Temperature (K) to run equilibration simulations at.
(default: 725)
-seed SEED Seed for random number generator used in MD
simulations. For multiple reaction jobs, also used to
seed the random number generator used to pick between
different crosslinking reactions. (default: 1234)
-sim_timestep FEMTOSECONDS
The timestep in femtoseconds to use for equilibration
simulations. The default is to use 2.0 fs. This flag
is ignored if -ramp is used. (default: 2.0)
-sim_convergence SIM_CONVERGENCE
Convergence criteria for equilibration simulations,
defined as percentage change in density of system
during equilibriatiation stage. (default: 5)
-max_sim_retries MAX_SIM_RETRIES
Maximum iterations to run equilibrium simulation to
achieve convergence. Setting this to 1 (default)
disables the convergence check during equilibration.
(default: 1)
-ensemble {NPT,NVT} Select between NPT or NVT ensemble to use during
simulationduring the equilibration stage. (default:
NPT)
-pressure PRESSURE Pressure (bar) to run NPT equilibration simulations
at. (default: 1.01325)
-ffld FFLD Force field to use during creation of Desmond system
prior to each equilibration step for atomistic
systems. Valid force fields are OPLS_2005, S-OPLS and
SPFF Default is OPLS_2005. (default: OPLS_2005)
-cgffld FORCE_FIELD_NAME
Name of coarse-grained force field to use during
creation of Desmond system prior to each equilibration
step. Required for coarse-grained systems. See related
location type flag -cgffld_loc_type. (default: None)
-cgffld_loc_type FORCE_FIELD_LOCATION_TYPE
Location type for the force field specified with
-cgffld. Option 'installed' means from a standard
location in the Schrodinger installation while option
'local' means either from /Users/bozhang/.schrodinger/
matsci_templates/coarse_grain_force_field_parameters
or the job launch directory, i.e. the CWD. (default:
local)
-gpu Run the Desmond jobs on GPUs. (default: False)
-ramp RAMP_FILE Use the temperature ramp supplied in the given file.
The format of this file is json file and is best
obtained by creating a ramp with the Crosslinking gui
and writing the job files. See also the
-xlinks_per_iter and -extend_ramp flags. (default:
None)
-extend_ramp Extend the final temperature ramp interval until the
target saturation is reached. Only useful if the
{ramp} flag is also used. The default is to end the
crosslinking workflow at the end of the final
temperature interval. (default: False)
-no_robust_eq If an equilibration stage fails with an error, do not
attempt to retry with different settings. The script
should exit instead. (default: False)
-split_components Split system in components when Desmond system is
built. This can speed up the the force field
assignment for systems that contain multiple identical
molecules. (default: False)
-md_umbrella Run desmond subjobs on the driver host. (default:
False)
Restart options:
-use_zip_data PATH Extract the archive before running. Any completed
files in the archive will be used instead of
submitting new jobs. (default: None)
-restart_proj PROJECT_NAME
Project name the restart job is associated with.
(default: None)
-restart_disp INCORPORATION
Incorporation state for the restart job. Should be one
of: append, ignore. (default: None)
-restart_viewname VIEWNAME
Viewname for the panel submitting the restart job.
Leave blank if running from the command line.
(default: None)
-restart_host HOSTNAME:PROCESSORS
Host for restart in the form of "hostname:cpus".
(default: None)
-restart_jobname JOBNAME
Jobname for restart. (default: None)
Job Control Options:
-HOST <hostname> Run job remotely on the indicated host entry.
(default: localhost)
-WAIT Do not return a prompt until the job completes.
(default: False)
-LOCAL Do not use a temporary directory for job files. Keep
files in the current directory. (default: False)
-D, -DEBUG Show details of Job Control operation. (default:
False)
-NOJOBID Run the job directly, without Job Control layer.
(default: False)
-VIEWNAME <viewname> Specifies viewname used in job filtering in maestro.
(default: False)
-OPLSDIR OPLSDIR Specifies directory for custom forcefield parameters.
(default: None)
-JOBNAME JOBNAME Provide an explicit name for the job. (default: None)