IMP  2.3.0
The Integrative Modeling Platform
IMP.pmi.representation Namespace Reference

Representation of the system. More...

Detailed Description

Representation of the system.

This class creates the molecular hierarchies, representation, sequence connectivity for the various involved proteins and nucleic acid macromolecules:

Create a protein, DNA or RNA, represent it as a set of connected balls of appropriate radii and number of residues, pdb at given resolution(s), or ideal helices.

To initialize the class:

m the model upperharmonic Bool This flag uses either harmonic (False) or upperharmonic (True) in the intra-pair connectivity restraint. Default is True. disorderedlength Bool This flag uses either disordered length calculated for random coil peptides (True) or zero surface-to-surface distance between beads (False) as optimal distance for the sequence connectivity restraint. Default is False.

How to use the SimplifiedModel class (typical use):

see test/test_hierarchy_contruction.py

examples:

1) Create a chain of helices and flexible parts

c_1_119 =self.add_component_necklace("prot1",1,119,20) c_120_131 =self.add_component_ideal_helix("prot1",resolutions=[1,10],resrange=(120,131)) c_132_138 =self.add_component_beads("prot1",[(132,138)]) c_139_156 =self.add_component_ideal_helix("prot1",resolutions=[1,10],resrange=(139,156)) c_157_174 =self.add_component_beads("prot1",[(157,174)]) c_175_182 =self.add_component_ideal_helix("prot1",resolutions=[1,10],resrange=(175,182)) c_183_194 =self.add_component_beads("prot1",[(183,194)]) c_195_216 =self.add_component_ideal_helix("prot1",resolutions=[1,10],resrange=(195,216)) c_217_250 =self.add_component_beads("prot1",[(217,250)])

self.set_rigid_body_from_hierarchies(c_120_131) self.set_rigid_body_from_hierarchies(c_139_156) self.set_rigid_body_from_hierarchies(c_175_182) self.set_rigid_body_from_hierarchies(c_195_216)

clist=[c_1_119,c_120_131,c_132_138,c_139_156,c_157_174,c_175_182,c_183_194,c_195_216, c_217_250]

self.set_chain_of_super_rigid_bodies(clist,2,3)

self.set_super_rigid_bodies(["prot1"])

Note
This class is only available in Python.