IMP.pmi.topology.State Class Reference

Stores a list of Molecules all with the same State index. More...

Inherits _SystemBase.

Detailed Description

Stores a list of Molecules all with the same State index.

Also stores number of copies of each Molecule for easy selection.

Note

This class is only available in Python.

Definition at line 218 of file pmi/topology/__init__.py.

Public Member Functions
def	__init__
	Define a new state. More...
def	build
	Build all molecules (automatically makes clones) More...
def	create_molecule
	Create a new Molecule within this State. More...
def	get_hierarchy
	Get the IMP.atom.Hierarchy node for this state. More...
def	get_molecule
	Access a molecule by name and copy number. More...
def	get_molecules
	Return a dictionary where key is molecule name and value is a list of all copies of that molecule in setup order. More...
def	get_number_of_copies
	Get the number of copies of the given molecule (by name) More...

Constructor & Destructor Documentation

def IMP.pmi.topology.State.__init__	(		self,
			system,
			state_index
	)

Define a new state.

Parameters

system	the PMI System
state_index	the index of the new state

Note

It's expected that you will not use this constructor directly, but rather create it with System.create_state()

Definition at line 224 of file pmi/topology/__init__.py.

Member Function Documentation

def IMP.pmi.topology.State.build	(		self,
			kwargs
	)

Build all molecules (automatically makes clones)

Definition at line 314 of file pmi/topology/__init__.py.

def IMP.pmi.topology.State.create_molecule	(		self,
			name,
			sequence = '',
			chain_id = '',
			alphabet = IMP.pmi.alphabets.amino_acid,
			uniprot = None
	)

Create a new Molecule within this State.

Parameters

name	the name of the molecule (string); it must not be already used
sequence	sequence (string)
chain_id	Chain ID to assign to this molecule
alphabet	Mapping from FASTA codes to residue types
uniprot	UniProt accession, if available

Definition at line 269 of file pmi/topology/__init__.py.

def IMP.pmi.topology.State.get_hierarchy

(

self

)

Get the IMP.atom.Hierarchy node for this state.

Definition at line 299 of file pmi/topology/__init__.py.

def IMP.pmi.topology.State.get_molecule	(		self,
			name,
			copy_num = 0
	)

Access a molecule by name and copy number.

Parameters

name	The molecule name used during setup
copy_num	The copy number based on input order. Default: 0. Set to 'all' to get all copies

Definition at line 257 of file pmi/topology/__init__.py.

def IMP.pmi.topology.State.get_molecules

(

self

)

Return a dictionary where key is molecule name and value is a list of all copies of that molecule in setup order.

Definition at line 251 of file pmi/topology/__init__.py.

def IMP.pmi.topology.State.get_number_of_copies	(		self,
			molname
	)

Get the number of copies of the given molecule (by name)

Parameters

molname

The name of the molecule

Definition at line 304 of file pmi/topology/__init__.py.

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

• pmi/topology/__init__.py