ffeatools.modules.FFEA_script.FFEA_script_params Class Reference

Public Member Functions
def	__init__ (self)
def	assign_param (self, lvalue, rvalue, scriptdir=".")
def	check_params (self)
def	fix_params (self)
def	completed (self)
def	test_traj (self)
def	write_to_file (self, fout, fname, verbose=False)

Data Fields
	restart
	dt
	kT
	rng_seed
	kt
	check
	num_steps
	trajectory_out_fname
	measurement_out_fname
	vdw_forcefield_params
	kinetics_out_fname
	binding_site_params
	beads_out_fname
	checkpoint_in
	checkpoint_out
	epsilon
	max_iterations_cg
	kappa
	epsilon_0
	dielec_ext
	calc_stokes
	stokes_visc
	calc_ssint
	calc_noise
	calc_springs
	calc_ctforces
	inc_self_vdw
	vdw_cutoff
	calc_preComp
	calc_es
	calc_kinetics
	kinetics_update
	es_update
	es_N
	ssint_type
	steric_factor
	move_into_box
	sticky_wall_xz
	wall_x_1
	wall_x_2
	wall_y_1
	wall_y_2
	wall_z_1
	wall_z_2
	es_h
	num_blobs
	num_conformations
	num_states
	num_rods

Constructor & Destructor Documentation

__init__()

def ffeatools.modules.FFEA_script.FFEA_script_params.__init__

(

self

)

Member Function Documentation

assign_param()

def ffeatools.modules.FFEA_script.FFEA_script_params.assign_param	(		self,
			lvalue,
			rvalue,
			scriptdir = "."
	)

check_params()

def ffeatools.modules.FFEA_script.FFEA_script_params.check_params

(

self

)

completed()

def ffeatools.modules.FFEA_script.FFEA_script_params.completed

(

self

)

fix_params()

def ffeatools.modules.FFEA_script.FFEA_script_params.fix_params

(

self

)

test_traj()

def ffeatools.modules.FFEA_script.FFEA_script_params.test_traj

(

self

)

write_to_file()

def ffeatools.modules.FFEA_script.FFEA_script_params.write_to_file	(		self,
			fout,
			fname,
			verbose = False
	)

Field Documentation

beads_out_fname

ffeatools.modules.FFEA_script.FFEA_script_params.beads_out_fname

Referenced by ffeatools.modules.FFEA_script.FFEA_script_params.assign_param(), and ffeatools.modules.FFEA_script.FFEA_script_params.write_to_file().

binding_site_params

ffeatools.modules.FFEA_script.FFEA_script_params.binding_site_params

Referenced by ffeatools.modules.FFEA_script.FFEA_script_params.assign_param(), and ffeatools.modules.FFEA_script.FFEA_script_params.write_to_file().

calc_ctforces

ffeatools.modules.FFEA_script.FFEA_script_params.calc_ctforces

Referenced by ffeatools.modules.FFEA_script.FFEA_script_params.assign_param().

calc_es

ffeatools.modules.FFEA_script.FFEA_script_params.calc_es

Referenced by ffeatools.modules.FFEA_script.FFEA_script_params.assign_param(), and ffeatools.modules.FFEA_script.FFEA_script_params.write_to_file().

calc_kinetics

ffeatools.modules.FFEA_script.FFEA_script_params.calc_kinetics

Referenced by ffeatools.modules.FFEA_script.FFEA_script_params.assign_param().

calc_noise

ffeatools.modules.FFEA_script.FFEA_script_params.calc_noise

Referenced by ffeatools.modules.FFEA_script.FFEA_script_params.assign_param(), and ffeatools.modules.FFEA_script.FFEA_script_params.write_to_file().

calc_preComp

ffeatools.modules.FFEA_script.FFEA_script_params.calc_preComp

Referenced by ffeatools.modules.FFEA_script.FFEA_script_params.assign_param(), and ffeatools.modules.FFEA_script.FFEA_script_params.write_to_file().

calc_springs

ffeatools.modules.FFEA_script.FFEA_script_params.calc_springs

Referenced by ffeatools.modules.FFEA_script.FFEA_script_params.assign_param(), and ffeatools.modules.FFEA_script.FFEA_script_params.write_to_file().

calc_ssint

ffeatools.modules.FFEA_script.FFEA_script_params.calc_ssint

Referenced by ffeatools.modules.FFEA_script.FFEA_script_params.assign_param(), and ffeatools.modules.FFEA_script.FFEA_script_params.write_to_file().

calc_stokes

ffeatools.modules.FFEA_script.FFEA_script_params.calc_stokes

Referenced by ffeatools.modules.FFEA_script.FFEA_script_params.assign_param(), and ffeatools.modules.FFEA_script.FFEA_script_params.write_to_file().

check

ffeatools.modules.FFEA_script.FFEA_script_params.check

Referenced by ffeatools.modules.FFEA_script.FFEA_script_params.assign_param(), and ffeatools.modules.FFEA_script.FFEA_script_params.write_to_file().

checkpoint_in

ffeatools.modules.FFEA_script.FFEA_script_params.checkpoint_in

Referenced by ffeatools.modules.FFEA_script.FFEA_script_params.assign_param(), and ffeatools.modules.FFEA_script.FFEA_script_params.write_to_file().

checkpoint_out

ffeatools.modules.FFEA_script.FFEA_script_params.checkpoint_out

Referenced by ffeatools.modules.FFEA_script.FFEA_script_params.assign_param(), and ffeatools.modules.FFEA_script.FFEA_script_params.write_to_file().

dielec_ext

ffeatools.modules.FFEA_script.FFEA_script_params.dielec_ext

Referenced by ffeatools.modules.FFEA_script.FFEA_script_params.assign_param(), and ffeatools.modules.FFEA_script.FFEA_script_params.write_to_file().

dt

ffeatools.modules.FFEA_script.FFEA_script_params.dt

Referenced by ffeatools.modules.FFEA_script.FFEA_script_params.assign_param(), and ffeatools.modules.FFEA_script.FFEA_script_params.write_to_file().

epsilon

ffeatools.modules.FFEA_script.FFEA_script_params.epsilon

Referenced by ffeatools.modules.FFEA_script.FFEA_script_params.assign_param(), and ffeatools.modules.FFEA_script.FFEA_script_params.write_to_file().

epsilon_0

ffeatools.modules.FFEA_script.FFEA_script_params.epsilon_0

Referenced by ffeatools.modules.FFEA_script.FFEA_script_params.assign_param(), and ffeatools.modules.FFEA_script.FFEA_script_params.write_to_file().

es_h

ffeatools.modules.FFEA_script.FFEA_script_params.es_h

Referenced by ffeatools.modules.FFEA_script.FFEA_script_params.assign_param(), and ffeatools.modules.FFEA_script.FFEA_script_params.write_to_file().

es_N

ffeatools.modules.FFEA_script.FFEA_script_params.es_N

Referenced by ffeatools.modules.FFEA_script.FFEA_script_params.assign_param(), and ffeatools.modules.FFEA_script.FFEA_script_params.write_to_file().

es_update

ffeatools.modules.FFEA_script.FFEA_script_params.es_update

Referenced by ffeatools.modules.FFEA_script.FFEA_script_params.assign_param(), and ffeatools.modules.FFEA_script.FFEA_script_params.write_to_file().

inc_self_vdw

ffeatools.modules.FFEA_script.FFEA_script_params.inc_self_vdw

Referenced by ffeatools.modules.FFEA_script.FFEA_script_params.assign_param(), and ffeatools.modules.FFEA_script.FFEA_script_params.write_to_file().

kappa

ffeatools.modules.FFEA_script.FFEA_script_params.kappa

Referenced by ffeatools.modules.FFEA_script.FFEA_script_params.assign_param(), and ffeatools.modules.FFEA_script.FFEA_script_params.write_to_file().

kinetics_out_fname

ffeatools.modules.FFEA_script.FFEA_script_params.kinetics_out_fname

Referenced by ffeatools.modules.FFEA_script.FFEA_script_params.assign_param(), and ffeatools.modules.FFEA_script.FFEA_script_params.write_to_file().

kinetics_update

ffeatools.modules.FFEA_script.FFEA_script_params.kinetics_update

Referenced by ffeatools.modules.FFEA_script.FFEA_script_params.assign_param().

kT

ffeatools.modules.FFEA_script.FFEA_script_params.kT

Referenced by ffeatools.modules.FFEA_script.FFEA_script_params.assign_param(), and ffeatools.modules.FFEA_script.FFEA_script_params.write_to_file().

kt

ffeatools.modules.FFEA_script.FFEA_script_params.kt

max_iterations_cg

ffeatools.modules.FFEA_script.FFEA_script_params.max_iterations_cg

Referenced by ffeatools.modules.FFEA_script.FFEA_script_params.assign_param(), and ffeatools.modules.FFEA_script.FFEA_script_params.write_to_file().

measurement_out_fname

ffeatools.modules.FFEA_script.FFEA_script_params.measurement_out_fname

Referenced by ffeatools.modules.FFEA_script.FFEA_script_params.assign_param(), and ffeatools.modules.FFEA_script.FFEA_script_params.write_to_file().

move_into_box

ffeatools.modules.FFEA_script.FFEA_script_params.move_into_box

Referenced by ffeatools.modules.FFEA_script.FFEA_script_params.assign_param().

num_blobs

ffeatools.modules.FFEA_script.FFEA_script_params.num_blobs

Referenced by ffeatools.modules.FFEA_script.FFEA_script_params.assign_param(), ffeatools.modules.FFEA_trajectory.FFEA_trajectory.delete_frame(), ffeatools.modules.FFEA_script.FFEA_script_params.fix_params(), ffeatools.modules.FFEA_trajectory.FFEA_trajectory.rescale(), ffeatools.modules.FFEA_trajectory.FFEA_trajectory.reset(), ffeatools.modules.FFEA_trajectory.FFEA_trajectory.set_header(), ffeatools.modules.FFEA_trajectory.FFEA_trajectory.set_single_blob(), ffeatools.modules.FFEA_trajectory.FFEA_trajectory.set_single_frame(), ffeatools.modules.FFEA_trajectory.FFEA_trajectory.translate(), ffeatools.modules.FFEA_trajectory.FFEA_trajectory.write_header_to_file(), and ffeatools.modules.FFEA_script.FFEA_script_params.write_to_file().

num_conformations

ffeatools.modules.FFEA_script.FFEA_script_params.num_conformations

Referenced by ffeatools.modules.FFEA_script.FFEA_script_blob.add_empty_conformation(), ffeatools.modules.FFEA_trajectory.FFEA_trajectory.delete_frame(), ffeatools.modules.FFEA_script.FFEA_script_params.fix_params(), ffeatools.modules.FFEA_trajectory.FFEA_trajectory.rescale(), ffeatools.modules.FFEA_trajectory.FFEA_trajectory.reset(), ffeatools.modules.FFEA_trajectory.FFEA_trajectory.set_header(), ffeatools.modules.FFEA_trajectory.FFEA_trajectory.set_single_blob(), ffeatools.modules.FFEA_trajectory.FFEA_trajectory.set_single_frame(), ffeatools.modules.FFEA_trajectory.FFEA_trajectory.translate(), ffeatools.modules.FFEA_trajectory.FFEA_trajectory.write_header_to_file(), ffeatools.modules.FFEA_script.FFEA_script_params.write_to_file(), and ffeatools.modules.FFEA_script.FFEA_script_blob.write_to_file().

num_rods

ffeatools.modules.FFEA_script.FFEA_script_params.num_rods

Referenced by ffeatools.modules.FFEA_script.FFEA_script_params.fix_params().

num_states

ffeatools.modules.FFEA_script.FFEA_script_params.num_states

num_steps

ffeatools.modules.FFEA_script.FFEA_script_params.num_steps

Referenced by ffeatools.modules.FFEA_script.FFEA_script_params.assign_param(), and ffeatools.modules.FFEA_script.FFEA_script_params.write_to_file().

restart

ffeatools.modules.FFEA_script.FFEA_script_params.restart

Referenced by ffeatools.modules.FFEA_script.FFEA_script_params.assign_param(), and ffeatools.modules.FFEA_script.FFEA_script_params.write_to_file().

rng_seed

ffeatools.modules.FFEA_script.FFEA_script_params.rng_seed

Referenced by ffeatools.modules.FFEA_script.FFEA_script_params.assign_param(), and ffeatools.modules.FFEA_script.FFEA_script_params.write_to_file().

ssint_type

ffeatools.modules.FFEA_script.FFEA_script_params.ssint_type

Referenced by ffeatools.modules.FFEA_script.FFEA_script_params.assign_param(), and ffeatools.modules.FFEA_script.FFEA_script_params.write_to_file().

steric_factor

ffeatools.modules.FFEA_script.FFEA_script_params.steric_factor

Referenced by ffeatools.modules.FFEA_script.FFEA_script_params.assign_param(), and ffeatools.modules.FFEA_script.FFEA_script_params.write_to_file().

sticky_wall_xz

ffeatools.modules.FFEA_script.FFEA_script_params.sticky_wall_xz

Referenced by ffeatools.modules.FFEA_script.FFEA_script_params.assign_param().

stokes_visc

ffeatools.modules.FFEA_script.FFEA_script_params.stokes_visc

Referenced by ffeatools.modules.FFEA_script.FFEA_script_params.assign_param(), and ffeatools.modules.FFEA_script.FFEA_script_params.write_to_file().

trajectory_out_fname

ffeatools.modules.FFEA_script.FFEA_script_params.trajectory_out_fname

Referenced by ffeatools.modules.FFEA_script.FFEA_script_params.assign_param(), ffeatools.modules.FFEA_script.FFEA_script_params.test_traj(), and ffeatools.modules.FFEA_script.FFEA_script_params.write_to_file().

vdw_cutoff

ffeatools.modules.FFEA_script.FFEA_script_params.vdw_cutoff

Referenced by ffeatools.modules.FFEA_script.FFEA_script_params.assign_param(), and ffeatools.modules.FFEA_script.FFEA_script_params.write_to_file().

vdw_forcefield_params

ffeatools.modules.FFEA_script.FFEA_script_params.vdw_forcefield_params

Referenced by ffeatools.modules.FFEA_script.FFEA_script_params.assign_param(), and ffeatools.modules.FFEA_script.FFEA_script_params.write_to_file().

wall_x_1

ffeatools.modules.FFEA_script.FFEA_script_params.wall_x_1

Referenced by ffeatools.modules.FFEA_script.FFEA_script_params.assign_param().

wall_x_2

ffeatools.modules.FFEA_script.FFEA_script_params.wall_x_2

Referenced by ffeatools.modules.FFEA_script.FFEA_script_params.assign_param().

wall_y_1

ffeatools.modules.FFEA_script.FFEA_script_params.wall_y_1

Referenced by ffeatools.modules.FFEA_script.FFEA_script_params.assign_param().

wall_y_2

ffeatools.modules.FFEA_script.FFEA_script_params.wall_y_2

Referenced by ffeatools.modules.FFEA_script.FFEA_script_params.assign_param().

wall_z_1

ffeatools.modules.FFEA_script.FFEA_script_params.wall_z_1

Referenced by ffeatools.modules.FFEA_script.FFEA_script_params.assign_param().

wall_z_2

ffeatools.modules.FFEA_script.FFEA_script_params.wall_z_2

Referenced by ffeatools.modules.FFEA_script.FFEA_script_params.assign_param().

---

The documentation for this class was generated from the following file:

• FFEA_script.py