IMP.pmi.topology.system_tools Namespace Reference

Tools to help build structures. More...

Detailed Description

Tools to help build structures.

Functions
def	build_along_backbone
	Group residues along the backbone, adding beads as needed. More...
def	build_bead
	Generates a single bead. More...
def	build_necklace
	Generates a string of beads with given length. More...
def	get_structure
	read a structure from a PDB file and return a list of residues More...
def	list_chunks_iterator
	Yield successive length-sized chunks from a list. More...

Function Documentation

def IMP.pmi.topology.system_tools.build_along_backbone	(		mdl,
			root,
			residues,
			rep_type,
			ca_centers = True
	)

Group residues along the backbone, adding beads as needed.

Currently this first groups into contiguous fragment regions ('folders') with identical sets of resolutions. However this behavior may change. The current resolutions used are 0 for atomic, and N for N residues per ball (see Resolution in PMI).

Parameters

mdl	the model
root	the hierarchy to which all the fragments and resolutions will be added
residues	list of PMI Residues, labeled with resolution
rep_type	Representation type (currently supports IMP.atom.BALLS)
ca_centers	If true, when making residue beads, will place the bead at the CA position

Note

This function is only available in Python.

Definition at line 107 of file system_tools.py.

def IMP.pmi.topology.system_tools.build_bead	(		model,
			residues,
			input_coord = None
	)

Generates a single bead.

Note

This function is only available in Python.

Definition at line 54 of file system_tools.py.

def IMP.pmi.topology.system_tools.build_necklace	(		model,
			residues,
			resolution,
			input_coord = None
	)

Generates a string of beads with given length.

Note

This function is only available in Python.

Definition at line 93 of file system_tools.py.

def IMP.pmi.topology.system_tools.get_structure	(		mdl,
			pdb_fn,
			chain_id,
			res_range = [],
			offset = 0,
			model_num = None,
			ca_only = False
	)

read a structure from a PDB file and return a list of residues

Parameters

mdl	The IMP model
pdb_fn	The file to read
chain_id	Chain ID to read
res_range	Add only a specific set of residues
offset	Apply an offset to the residue indexes of the PDB file
model_num	Read multi-model PDB and return that model
ca_only	Read only CA atoms (by default, all non-waters are read)

Note

This function is only available in Python.

Definition at line 23 of file system_tools.py.

def IMP.pmi.topology.system_tools.list_chunks_iterator	(		input_list,
			length
	)

Yield successive length-sized chunks from a list.

Note

This function is only available in Python.

Definition at line 11 of file system_tools.py.