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IMP Reference Guide  develop.cd20b1e321,2019/12/14
The Integrative Modeling Platform
IMP.pmi.topology Namespace Reference

Set of Python classes to create a multi-state, multi-resolution IMP hierarchy. More...

Detailed Description

Set of Python classes to create a multi-state, multi-resolution IMP hierarchy.

Alternatively one can construct the entire topology and degrees of freedom via formatted text file with TopologyReader and IMP::pmi::macros::BuildSystem(). This is used in the PMI tutorial. Note that this only allows a limited set of the full options available to PMI users (rigid bodies only, fixed resolutions).

Classes

class  Molecule
 Stores a named protein chain. More...
 
class  PDBSequences
 Data_structure for reading and storing sequence data from pdb. More...
 
class  PMIMoleculeHierarchy
 Extends the functionality of IMP.atom.Molecule. More...
 
class  Sequences
 A dictionary-like wrapper for reading and storing sequence data. More...
 
class  State
 Stores a list of Molecules all with the same State index. More...
 
class  System
 This class initializes the root node of the global IMP.atom.Hierarchy. More...
 
class  TempResidue
 Temporarily stores residue information, even without structure available. More...
 
class  TopologyReader
 Automatically setup Sytem and Degrees of Freedom with a formatted text file. More...
 

Functions

def fasta_pdb_alignments
 This function computes and prints the alignment between the fasta file and the pdb sequence, computes the offsets for each contiguous fragment in the PDB. More...
 

Function Documentation

def IMP.pmi.topology.fasta_pdb_alignments (   fasta_sequences,
  pdb_sequences,
  show = False 
)

This function computes and prints the alignment between the fasta file and the pdb sequence, computes the offsets for each contiguous fragment in the PDB.

Parameters
fasta_sequencesIMP.pmi.topology.Sequences object
pdb_sequencesIMP.pmi.topology.PDBSequences object
showboolean default False, if True prints the alignments. The input objects should be generated using map_name dictionaries such that fasta_id and pdb_chain_id are mapping to the same protein name. It needs BioPython. Returns a dictionary of offsets, organized by peptide range (group): example: offsets={"ProtA":{(1,10):1,(20,30):10}}
Note
This function is only available in Python.

Definition at line 1001 of file pmi/topology/__init__.py.