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IMP Reference Guide  2.14.0
The Integrative Modeling Platform
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 172 of file pmi/topology/__init__.py.

Public Member Functions

def __init__
 Define a new state. More...
 
def build
 call build on all molecules (automatically makes clones) More...
 
def create_molecule
 Create a new Molecule within 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 are the list of all copies of that molecule in setup order. More...
 

Constructor & Destructor Documentation

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

Define a new state.

Parameters
systemthe PMI System
state_indexthe index of the new state
Note
It's expected that you will not use this constructor directly, but rather create it with pmi::System::create_state()

Definition at line 178 of file pmi/topology/__init__.py.

Member Function Documentation

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

call build on all molecules (automatically makes clones)

Definition at line 255 of file pmi/topology/__init__.py.

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

Create a new Molecule within this State.

Parameters
namethe name of the molecule (string); it must not be already used
sequencesequence (string)
chain_idChain ID to assign to this molecule
alphabetMapping from FASTA codes to residue types

Definition at line 222 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
nameThe molecule name used during setup
copy_numThe copy number based on input order. Default: 0. Set to 'all' to get all copies

Definition at line 210 of file pmi/topology/__init__.py.

def IMP.pmi.topology.State.get_molecules (   self)

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

Definition at line 204 of file pmi/topology/__init__.py.


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