# Example for: restraints.add(), restraints.unpick()

# This will enforce cis conformation for Pro-56.

# Make a model and stereochemical restraints:

from modeller import *
from modeller.scripts import complete_pdb, cispeptide

log.level(output=1, notes=1, warnings=1, errors=1, memory=0)
env = environ()
env.io.atom_files_directory = ['../atom_files']

env.libs.topology.read(file='$(LIB)/top_heav.lib')
env.libs.parameters.read(file='$(LIB)/par.lib')

code = '1fas'
mdl = complete_pdb(env, code)
rsr = mdl.restraints
atmsel = selection(mdl)
rsr.make(atmsel, restraint_type='stereo', spline_on_site=False)

# Change the Pro-56 restraint from trans to cis:
a = mdl.atoms
cispeptide(rsr, atom_ids1=(a['O:56'], a['C:56'], a['N:57'], a['CA:57']),
                atom_ids2=(a['CA:56'], a['C:56'], a['N:57'], a['CA:57']))

# Constrain the distance between alpha carbons in residues 5 and 15 to
# be less than 10 angstroms:
rsr.add(forms.upper_bound(group=physical.xy_distance,
                          feature=features.distance(a['CA:5'], a['CA:15']),
                          mean=10., stdev=0.1))

rsr.write(file='1fas.rsr')
atmsel.energy()

52c3baa159729e428d57dbce26320faf53d64056
<mask token>

<mask token>
log.level(output=1, notes=1, warnings=1, errors=1, memory=0)
<mask token>
env.libs.topology.read(file='$(LIB)/top_heav.lib')
env.libs.parameters.read(file='$(LIB)/par.lib')
<mask token>
rsr.make(atmsel, restraint_type='stereo', spline_on_site=False)
<mask token>
cispeptide(rsr, atom_ids1=(a['O:56'], a['C:56'], a['N:57'], a['CA:57']),
    atom_ids2=(a['CA:56'], a['C:56'], a['N:57'], a['CA:57']))
rsr.add(forms.upper_bound(group=physical.xy_distance, feature=features.
    distance(a['CA:5'], a['CA:15']), mean=10.0, stdev=0.1))
rsr.write(file='1fas.rsr')
atmsel.energy()

<mask token>
log.level(output=1, notes=1, warnings=1, errors=1, memory=0)
env = environ()
env.io.atom_files_directory = ['../atom_files']
env.libs.topology.read(file='$(LIB)/top_heav.lib')
env.libs.parameters.read(file='$(LIB)/par.lib')
code = '1fas'
mdl = complete_pdb(env, code)
rsr = mdl.restraints
atmsel = selection(mdl)
rsr.make(atmsel, restraint_type='stereo', spline_on_site=False)
a = mdl.atoms
cispeptide(rsr, atom_ids1=(a['O:56'], a['C:56'], a['N:57'], a['CA:57']),
    atom_ids2=(a['CA:56'], a['C:56'], a['N:57'], a['CA:57']))
rsr.add(forms.upper_bound(group=physical.xy_distance, feature=features.
    distance(a['CA:5'], a['CA:15']), mean=10.0, stdev=0.1))
rsr.write(file='1fas.rsr')
atmsel.energy()

from modeller import *
from modeller.scripts import complete_pdb, cispeptide
log.level(output=1, notes=1, warnings=1, errors=1, memory=0)
env = environ()
env.io.atom_files_directory = ['../atom_files']
env.libs.topology.read(file='$(LIB)/top_heav.lib')
env.libs.parameters.read(file='$(LIB)/par.lib')
code = '1fas'
mdl = complete_pdb(env, code)
rsr = mdl.restraints
atmsel = selection(mdl)
rsr.make(atmsel, restraint_type='stereo', spline_on_site=False)
a = mdl.atoms
cispeptide(rsr, atom_ids1=(a['O:56'], a['C:56'], a['N:57'], a['CA:57']),
    atom_ids2=(a['CA:56'], a['C:56'], a['N:57'], a['CA:57']))
rsr.add(forms.upper_bound(group=physical.xy_distance, feature=features.
    distance(a['CA:5'], a['CA:15']), mean=10.0, stdev=0.1))
rsr.write(file='1fas.rsr')
atmsel.energy()

# Example for: restraints.add(), restraints.unpick()

# This will enforce cis conformation for Pro-56.

# Make a model and stereochemical restraints:

from modeller import *
from modeller.scripts import complete_pdb, cispeptide

log.level(output=1, notes=1, warnings=1, errors=1, memory=0)
env = environ()
env.io.atom_files_directory = ['../atom_files']

env.libs.topology.read(file='$(LIB)/top_heav.lib')
env.libs.parameters.read(file='$(LIB)/par.lib')

code = '1fas'
mdl = complete_pdb(env, code)
rsr = mdl.restraints
atmsel = selection(mdl)
rsr.make(atmsel, restraint_type='stereo', spline_on_site=False)

# Change the Pro-56 restraint from trans to cis:
a = mdl.atoms
cispeptide(rsr, atom_ids1=(a['O:56'], a['C:56'], a['N:57'], a['CA:57']),
                atom_ids2=(a['CA:56'], a['C:56'], a['N:57'], a['CA:57']))

# Constrain the distance between alpha carbons in residues 5 and 15 to
# be less than 10 angstroms:
rsr.add(forms.upper_bound(group=physical.xy_distance,
                          feature=features.distance(a['CA:5'], a['CA:15']),
                          mean=10., stdev=0.1))

rsr.write(file='1fas.rsr')
atmsel.energy()
