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IMP Reference Guide  develop.cc86c9801d,2022/11/22
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 205 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
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 System.create_state()

Definition at line 211 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 299 of file pmi/topology/__init__.py.

def IMP.pmi.topology.State.create_molecule (   self,
  name,
  sequence = '',
  chain_id = '',
  alphabet = IMP.pmi.alphabets.amino_acid 
)

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 256 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 284 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 244 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 238 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
molnameThe name of the molecule

Definition at line 289 of file pmi/topology/__init__.py.


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