ffeatools.modules.FFEA_beads.FFEA_beads Class Reference

Public Member Functions
def	__init__ (self, fname="", motion_state="STATIC", scale=1.0, topology=None, node=None, assignBeads=True)
def	load (self, fname, motion_state, topology, node, assignBeads)
def	get_beads_preassignment (self, text)
def	assign_beads (self, topology, node)
def	rescale (self, factor)
def	reset (self)

Data Fields
	scale
	valid
	pdb
	empty
	b_elems

Constructor & Destructor Documentation

__init__()

def ffeatools.modules.FFEA_beads.FFEA_beads.__init__	(		self,
			fname = "",
			motion_state = "STATIC",
			scale = 1.0,
			topology = None,
			node = None,
			assignBeads = True
	)

Member Function Documentation

assign_beads()

def ffeatools.modules.FFEA_beads.FFEA_beads.assign_beads	(		self,
			topology,
			node
	)

get_beads_preassignment()

def ffeatools.modules.FFEA_beads.FFEA_beads.get_beads_preassignment	(		self,
			text
	)

Referenced by ffeatools.modules.FFEA_beads.FFEA_beads.assign_beads().

load()

def ffeatools.modules.FFEA_beads.FFEA_beads.load	(		self,
			fname,
			motion_state,
			topology,
			node,
			assignBeads
	)

Referenced by ffeatools.modules.FFEA_binding_sites.FFEA_binding_sites.__init__(), ffeatools.modules.FFEA_springs.FFEA_springs.__init__(), ffeatools.modules.FFEA_kinetic_states.FFEA_kinetic_states.__init__(), and ffeatools.modules.FFEA_kinetic_rates.FFEA_kinetic_rates.__init__().

rescale()

def ffeatools.modules.FFEA_beads.FFEA_beads.rescale	(		self,
			factor
	)

reset()

def ffeatools.modules.FFEA_beads.FFEA_beads.reset

(

self

)

Referenced by ffeatools.modules.FFEA_binding_sites.FFEA_binding_sites.__init__(), ffeatools.modules.FFEA_skeleton.FFEA_skeleton.__init__(), ffeatools.modules.FFEA_lj.FFEA_lj.__init__(), ffeatools.modules.FFEA_kinetic_map.FFEA_kinetic_map.__init__(), ffeatools.modules.FFEA_kinetic_rates.FFEA_kinetic_rates.__init__(), ffeatools.modules.FFEA_springs.FFEA_springs.__init__(), ffeatools.modules.FFEA_kinetic_states.FFEA_kinetic_states.__init__(), ffeatools.modules.FFEA_pdb_OLD.FFEA_pdb.__init__(), ffeatools.modules.FFEA_vdw.FFEA_vdw.__init__(), ffeatools.modules.FFEA_ctforces.FFEA_ctforce_linear.__init__(), ffeatools.modules.FFEA_stokes.FFEA_stokes.__init__(), ffeatools.modules.FFEA_node.FFEA_node.__init__(), ffeatools.modules.FFEA_trajectory.FFEA_trajectory.__init__(), ffeatools.modules.FFEA_pin.FFEA_pin.__init__(), ffeatools.modules.FFEA_material.FFEA_material.__init__(), ffeatools.modules.FFEA_beads.FFEA_beads.__init__(), ffeatools.modules.FFEA_topology.FFEA_topology.__init__(), ffeatools.modules.FFEA_pdb.FFEA_pdb.__init__(), ffeatools.modules.FFEA_measurement.FFEA_measurement.__init__(), ffeatools.modules.FFEA_script.FFEA_script.__init__(), ffeatools.modules.FFEA_surface.FFEA_surface.__init__(), ffeatools.modules.FFEA_ctforces.FFEA_ctforce_rotational.__init__(), ffeatools.modules.FFEA_ctforces.FFEA_ctforce_linear_surface.__init__(), ffeatools.modules.FFEA_ctforces.FFEA_ctforces.__init__(), ffeatools.modules.FFEA_kinetic_states.FFEA_kinetic_state.__init__(), ffeatools.modules.FFEA_springs.FFEA_spring.__init__(), ffeatools.modules.FFEA_lj.FFEA_lj_pair.__init__(), ffeatools.modules.FFEA_pdb_OLD.FFEA_pdb_blob.__init__(), ffeatools.modules.FFEA_trajectory.FFEA_traj_blob.__init__(), ffeatools.modules.FFEA_pdb_OLD.FFEA_pdb_frame.__init__(), ffeatools.modules.FFEA_pdb.FFEA_pdb_atom.__init__(), ffeatools.modules.FFEA_surface.FFEA_face.__init__(), ffeatools.modules.FFEA_topology.FFEA_element.__init__(), ffeatools.modules.FFEA_material.FFEA_material.build(), ffeatools.modules.FFEA_trajectory.FFEA_trajectory.build_from_pdb(), ffeatools.modules.FFEA_pdb.FFEA_pdb.build_from_rod(), ffeatools.modules.FFEA_pdb_OLD.FFEA_pdb.build_from_traj(), ffeatools.modules.FFEA_pdb.FFEA_pdb.build_from_traj(), ffeatools.modules.FFEA_trajectory.FFEA_trajectory.load(), ffeatools.modules.FFEA_binding_sites.FFEA_binding_sites.load_bsites(), ffeatools.modules.FFEA_measurement.FFEA_measurement.load_detailed(), ffeatools.modules.FFEA_surface.FFEA_surface.load_face(), ffeatools.modules.FFEA_measurement.FFEA_measurement.load_global(), ffeatools.modules.FFEA_kinetic_rates.FFEA_kinetic_rates.load_rates(), ffeatools.modules.FFEA_kinetic_states.FFEA_kinetic_states.load_states(), ffeatools.modules.FFEA_node.FFEA_node.load_vol(), ffeatools.modules.FFEA_surface.FFEA_surface.load_vol(), and ffeatools.modules.FFEA_pin.FFEA_pin.pin_radially().

Field Documentation

b_elems

ffeatools.modules.FFEA_beads.FFEA_beads.b_elems

Referenced by ffeatools.modules.FFEA_beads.FFEA_beads.assign_beads().

empty

ffeatools.modules.FFEA_beads.FFEA_beads.empty

Referenced by ffeatools.modules.FFEA_pdb.FFEA_pdb.build_from_rod(), ffeatools.modules.FFEA_pdb.FFEA_pdb.build_from_traj(), ffeatools.modules.FFEA_skeleton.FFEA_skeleton.reset(), ffeatools.modules.FFEA_lj.FFEA_lj.reset(), ffeatools.modules.FFEA_beads.FFEA_beads.reset(), ffeatools.modules.FFEA_vdw.FFEA_vdw.reset(), ffeatools.modules.FFEA_stokes.FFEA_stokes.reset(), ffeatools.modules.FFEA_trajectory.FFEA_trajectory.reset(), ffeatools.modules.FFEA_ctforces.FFEA_ctforces.reset(), ffeatools.modules.FFEA_measurement.FFEA_measurement.reset(), ffeatools.modules.FFEA_pdb.FFEA_pdb.reset(), ffeatools.modules.FFEA_script.FFEA_script.reset(), and ffeatools.modules.FFEA_node.FFEA_node.reset().

pdb

ffeatools.modules.FFEA_beads.FFEA_beads.pdb

Referenced by ffeatools.modules.FFEA_beads.FFEA_beads.assign_beads(), ffeatools.modules.FFEA_beads.FFEA_beads.rescale(), and ffeatools.modules.FFEA_beads.FFEA_beads.reset().

scale

ffeatools.modules.FFEA_beads.FFEA_beads.scale

Referenced by ffeatools.modules.FFEA_script.FFEA_script_blob.default(), ffeatools.modules.FFEA_node.FFEA_node.load_FFEA_node(), and ffeatools.modules.FFEA_script.FFEA_script_blob.write_to_file().

valid

ffeatools.modules.FFEA_beads.FFEA_beads.valid

Referenced by ffeatools.modules.FFEA_pdb.FFEA_pdb.build_from_rod(), ffeatools.modules.FFEA_pdb.FFEA_pdb.build_from_traj(), ffeatools.modules.FFEA_trajectory.FFEA_trajectory.load(), ffeatools.modules.FFEA_skeleton.FFEA_skeleton.load(), ffeatools.modules.FFEA_lj.FFEA_lj.load(), ffeatools.modules.FFEA_vdw.FFEA_vdw.load(), ffeatools.modules.FFEA_stokes.FFEA_stokes.load(), ffeatools.modules.FFEA_topology.FFEA_topology.load(), ffeatools.modules.FFEA_pdb.FFEA_pdb.load(), ffeatools.modules.FFEA_pin.FFEA_pin.load(), ffeatools.modules.FFEA_node.FFEA_node.load(), ffeatools.modules.FFEA_material.FFEA_material.load(), ffeatools.modules.FFEA_surface.FFEA_surface.load(), ffeatools.modules.FFEA_ctforces.FFEA_ctforces.load(), ffeatools.modules.FFEA_skeleton.FFEA_skeleton.reset(), ffeatools.modules.FFEA_lj.FFEA_lj.reset(), ffeatools.modules.FFEA_beads.FFEA_beads.reset(), ffeatools.modules.FFEA_vdw.FFEA_vdw.reset(), ffeatools.modules.FFEA_stokes.FFEA_stokes.reset(), ffeatools.modules.FFEA_trajectory.FFEA_trajectory.reset(), ffeatools.modules.FFEA_ctforces.FFEA_ctforces.reset(), ffeatools.modules.FFEA_measurement.FFEA_measurement.reset(), ffeatools.modules.FFEA_pdb.FFEA_pdb.reset(), ffeatools.modules.FFEA_script.FFEA_script.reset(), and ffeatools.modules.FFEA_node.FFEA_node.reset().

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

• FFEA_beads.py