Restraints.reindex() — renumber model restraints using another model

reindex(mdl)

Requirements:

restraints

This command renumbers atom indices in all restraints in memory. It is expected that the input restraints refer to atoms in the passed model mdl; the re-indexed restraints will correspond to the current model. Only those restraints that have all atoms in the current model will be selected. You can remove the others by Restraints.condense(). This command is useful when the old restraints have to be used while changing from one topology model to another.

Example: examples/commands/reindex_restraints.py

# Example for: restraints.reindex()

# This will reindex restraints obtained previously for a simpler topology so
# that they will now apply to a more complicated topology.

from modeller import *
from modeller.scripts import complete_pdb

env = environ()
env.io.atom_files_directory = ['../atom_files']
tpl = env.libs.topology
par = env.libs.parameters

# Generate the model for the simpler topology (CA only in this case):
tpl.read(file='$(LIB)/top_ca.lib')
par.read(file='$(LIB)/par_ca.lib')

code = '1fas'
mdl = complete_pdb(env, code)
mdl.write(file=code+'.ca')

# Generate the restraints for the simpler topology:
sel = selection(mdl)
mdl.restraints.make(sel, restraint_type='stereo', spline_on_site=False)
mdl.restraints.write(file='1fas-ca.rsr')
sel.energy()

# Generate the model for the more complicated topology:
tpl.read(file='$(LIB)/top_heav.lib')
par.read(file='$(LIB)/par.lib')

mdl.read(file=code)
aln = alignment(env)
aln.append_model(mdl, atom_files=code, align_codes=code)
aln.append_model(mdl, atom_files=code+'.ini', align_codes=code+'-ini')
mdl.clear_topology()
mdl.generate_topology(aln[code+'-ini'])
mdl.transfer_xyz(aln)
mdl.write(file='1fas.ini')

mdl2 = model(env, file='1fas.ca')
mdl.restraints.reindex(mdl2)
mdl.restraints.write(file='1fas.rsr')
sel = selection(mdl)
sel.energy()