ffeatools.modules.FFEA_trajectory.FFEA_trajectory Class Reference

Public Member Functions
def	__init__ (self, fname="", surf=None, load_all=1, frame_rate=1, num_frames_to_read=1000000, start=0, onlyNodes=False)
def	load (self, fname, surf=None, load_all=1, frame_rate=1, num_frames_to_read=1000000, start=0, onlyNodes=False)
def	load_header (self, fname)
def	set_header (self, num_blobs, num_conformations, num_nodes)
def	load_frame (self, surf=None, onlyNodes=False)
def	rescale (self, factor, frame_index)
def	translate (self, trans)
def	skip_frame (self)
def	delete_frame (self, index=-1)
def	build_from_pdb (self, pdb, scale=1e-10)
def	set_single_frame (self, node, surf=None, step=0)
def	set_single_blob (self, bindex)
def	reset (self)
def	write_to_file (self, fname, frames=None, frame_rate=1)
def	write_header_to_file (self, fout)
def	write_frame_to_file (self, fout, index)
def	reset (self)

Data Fields
	valid
	empty
	traj
	num_blobs
	num_conformations
	blob
	num_frames

Static Public Attributes
	motion_state
	frame = None
	num_nodes
	success = frame.load_from_traj_onlynodes_faster(self.traj)
bool	eof = True
	fpos

Constructor & Destructor Documentation

__init__()

def ffeatools.modules.FFEA_trajectory.FFEA_trajectory.__init__	(		self,
			fname = "",
			surf = None,
			load_all = 1,
			frame_rate = 1,
			num_frames_to_read = 1000000,
			start = 0,
			onlyNodes = False
	)

Member Function Documentation

build_from_pdb()

def ffeatools.modules.FFEA_trajectory.FFEA_trajectory.build_from_pdb	(		self,
			pdb,
			scale = 1e-10
	)

delete_frame()

def ffeatools.modules.FFEA_trajectory.FFEA_trajectory.delete_frame	(		self,
			index = -1
	)

load()

def ffeatools.modules.FFEA_trajectory.FFEA_trajectory.load	(		self,
			fname,
			surf = None,
			load_all = 1,
			frame_rate = 1,
			num_frames_to_read = 1000000,
			start = 0,
			onlyNodes = False
	)

load_frame()

def ffeatools.modules.FFEA_trajectory.FFEA_trajectory.load_frame	(		self,
			surf = None,
			onlyNodes = False
	)

Referenced by ffeatools.modules.FFEA_trajectory.FFEA_trajectory.load().

load_header()

def ffeatools.modules.FFEA_trajectory.FFEA_trajectory.load_header	(		self,
			fname
	)

Referenced by ffeatools.modules.FFEA_trajectory.FFEA_trajectory.load().

rescale()

def ffeatools.modules.FFEA_trajectory.FFEA_trajectory.rescale	(		self,
			factor,
			frame_index
	)

reset() [1/2]

def ffeatools.modules.FFEA_trajectory.FFEA_trajectory.reset

(

self

)

Referenced by ffeatools.modules.FFEA_vdw.FFEA_vdw.__init__(), ffeatools.modules.FFEA_trajectory.FFEA_trajectory.__init__(), ffeatools.modules.FFEA_trajectory.FFEA_traj_blob.__init__(), ffeatools.modules.FFEA_trajectory.FFEA_trajectory.build_from_pdb(), ffeatools.modules.FFEA_trajectory.FFEA_trajectory.load(), ffeatools.modules.FFEA_trajectory.FFEA_trajectory.reset(), and ffeatools.modules.FFEA_trajectory.FFEA_trajectory.set_single_frame().

reset() [2/2]

def ffeatools.modules.FFEA_trajectory.FFEA_trajectory.reset

(

self

)

Referenced by ffeatools.modules.FFEA_vdw.FFEA_vdw.__init__(), and ffeatools.modules.FFEA_trajectory.FFEA_traj_blob.__init__().

set_header()

def ffeatools.modules.FFEA_trajectory.FFEA_trajectory.set_header	(		self,
			num_blobs,
			num_conformations,
			num_nodes
	)

Referenced by ffeatools.modules.FFEA_trajectory.FFEA_trajectory.build_from_pdb().

set_single_blob()

def ffeatools.modules.FFEA_trajectory.FFEA_trajectory.set_single_blob	(		self,
			bindex
	)

set_single_frame()

def ffeatools.modules.FFEA_trajectory.FFEA_trajectory.set_single_frame	(		self,
			node,
			surf = None,
			step = 0
	)

skip_frame()

def ffeatools.modules.FFEA_trajectory.FFEA_trajectory.skip_frame

(

self

)

Referenced by ffeatools.modules.FFEA_trajectory.FFEA_trajectory.load().

translate()

def ffeatools.modules.FFEA_trajectory.FFEA_trajectory.translate	(		self,
			trans
	)

write_frame_to_file()

def ffeatools.modules.FFEA_trajectory.FFEA_trajectory.write_frame_to_file	(		self,
			fout,
			index
	)

Referenced by ffeatools.modules.FFEA_trajectory.FFEA_trajectory.write_to_file().

write_header_to_file()

def ffeatools.modules.FFEA_trajectory.FFEA_trajectory.write_header_to_file	(		self,
			fout
	)

Referenced by ffeatools.modules.FFEA_trajectory.FFEA_trajectory.write_to_file().

write_to_file()

def ffeatools.modules.FFEA_trajectory.FFEA_trajectory.write_to_file	(		self,
			fname,
			frames = None,
			frame_rate = 1
	)

Field Documentation

blob

ffeatools.modules.FFEA_trajectory.FFEA_trajectory.blob

Referenced by ffeatools.modules.FFEA_trajectory.FFEA_trajectory.build_from_pdb(), ffeatools.modules.FFEA_trajectory.FFEA_trajectory.delete_frame(), ffeatools.modules.FFEA_trajectory.FFEA_trajectory.load_frame(), 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(), and ffeatools.modules.FFEA_trajectory.FFEA_trajectory.write_frame_to_file().

empty

ffeatools.modules.FFEA_trajectory.FFEA_trajectory.empty

Referenced by ffeatools.modules.FFEA_vdw.FFEA_vdw.reset(), and ffeatools.modules.FFEA_trajectory.FFEA_trajectory.reset().

eof

bool ffeatools.modules.FFEA_trajectory.FFEA_trajectory.eof = True

static

fpos

ffeatools.modules.FFEA_trajectory.FFEA_trajectory.fpos

static

Referenced by ffeatools.modules.FFEA_trajectory.FFEA_trajectory.load_frame().

frame

ffeatools.modules.FFEA_trajectory.FFEA_trajectory.frame = None

static

Referenced by ffeatools.modules.FFEA_trajectory.FFEA_traj_blob.calc_centroid_trajectory(), and ffeatools.modules.FFEA_trajectory.FFEA_traj_blob.set_frame().

motion_state

ffeatools.modules.FFEA_trajectory.FFEA_trajectory.motion_state

static

num_blobs

ffeatools.modules.FFEA_trajectory.FFEA_trajectory.num_blobs

Referenced by ffeatools.modules.FFEA_trajectory.FFEA_trajectory.delete_frame(), 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(), and ffeatools.modules.FFEA_trajectory.FFEA_trajectory.write_header_to_file().

num_conformations

ffeatools.modules.FFEA_trajectory.FFEA_trajectory.num_conformations

Referenced by ffeatools.modules.FFEA_trajectory.FFEA_trajectory.delete_frame(), 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(), and ffeatools.modules.FFEA_trajectory.FFEA_trajectory.write_header_to_file().

num_frames

ffeatools.modules.FFEA_trajectory.FFEA_trajectory.num_frames

Referenced by ffeatools.modules.FFEA_trajectory.FFEA_trajectory.delete_frame(), ffeatools.modules.FFEA_trajectory.FFEA_trajectory.load(), ffeatools.modules.FFEA_trajectory.FFEA_trajectory.load_frame(), ffeatools.modules.FFEA_trajectory.FFEA_trajectory.reset(), ffeatools.modules.FFEA_trajectory.FFEA_trajectory.set_single_frame(), ffeatools.modules.FFEA_trajectory.FFEA_trajectory.translate(), ffeatools.modules.FFEA_trajectory.FFEA_trajectory.write_frame_to_file(), and ffeatools.modules.FFEA_trajectory.FFEA_trajectory.write_to_file().

num_nodes

ffeatools.modules.FFEA_trajectory.FFEA_trajectory.num_nodes

static

Referenced by ffeatools.modules.FFEA_kinetic_rates.FFEA_kinetic_rates.add_node(), ffeatools.modules.FFEA_trajectory.FFEA_traj_blob.calc_centroid_trajectory(), 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_traj_blob.set_subblob(), and ffeatools.modules.FFEA_trajectory.FFEA_trajectory.write_header_to_file().

success

ffeatools.modules.FFEA_trajectory.FFEA_trajectory.success = frame.load_from_traj_onlynodes_faster(self.traj)

static

traj

ffeatools.modules.FFEA_trajectory.FFEA_trajectory.traj

Referenced by ffeatools.modules.FFEA_trajectory.FFEA_trajectory.load_frame(), ffeatools.modules.FFEA_trajectory.FFEA_trajectory.reset(), and ffeatools.modules.FFEA_trajectory.FFEA_trajectory.skip_frame().

valid

ffeatools.modules.FFEA_trajectory.FFEA_trajectory.valid

Referenced by ffeatools.modules.FFEA_trajectory.FFEA_trajectory.load(), ffeatools.modules.FFEA_vdw.FFEA_vdw.load(), ffeatools.modules.FFEA_vdw.FFEA_vdw.reset(), and ffeatools.modules.FFEA_trajectory.FFEA_trajectory.reset().

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

• FFEA_trajectory.py