def cispeptide(rsr, atom_ids1, atom_ids2):
"""To create cis-peptide bond stereochemical restraints.
Note: you must have done the STEREOCHEMICAL restraints already.
Example (cis-peptide between residues 4 and 5):
>>> a = mdl.atoms
>>> cispeptide(mdl.rsr,
... atom_ids1=(a['O:4'], a['C:4'], a['N:5'], a['CA:5']),
... atom_ids2=(a['CA:4'], a['C:4'], a['N:5'], a['CA:5']))
"""
rsr.unpick(atom_ids1)
rsr.add(
forms.gaussian(group=physical.dihedral,
feature=features.dihedral(atom_ids1),
mean=3.141593,
stdev=0.087))
rsr.unpick(atom_ids2)
rsr.add(
forms.gaussian(group=physical.dihedral,
feature=features.dihedral(atom_ids2),
mean=0.0,
stdev=0.087))
def make_restraints(atmsel, restraints, num_selected):
from modeller import forms, physical, features
for (res, weights, means, stdevs) in omega:
for a in atmsel.find_atoms(res, ("CA", "C", "+N", "+CA"), num_selected):
r = forms.multi_gaussian(physical.omega_dihedral, features.dihedral(*a), weights, means, stdevs)
restraints.add(r)
def make_restraints(atmsel, restraints, num_selected):
from modeller import forms, physical, features
for (res, atoms, mean, stdev) in impropers:
for a in atmsel.find_atoms(res, atoms, num_selected):
r = forms.gaussian(physical.improper, features.dihedral(*a), mean, stdev)
restraints.add(r)
def make_restraints(atmsel, restraints, num_selected):
from modeller import forms, physical, features
for (res, weights, means, stdevs) in omega:
for a in atmsel.find_atoms(res, ('CA', 'C', '+N', '+CA'), num_selected):
r = forms.multi_gaussian(physical.omega_dihedral,
features.dihedral(*a), weights, means,
stdevs)
restraints.add(r)
def make_restraints(atmsel, restraints, num_selected):
from modeller import forms, physical, features
for (res, weights, means, stdevs) in chi1:
for a in atmsel.find_chi1_dihedrals(res, num_selected):
r = forms.multi_gaussian(physical.chi1_dihedral,
features.dihedral(*a), weights, means,
stdevs)
restraints.add(r)
def make_restraints(atmsel, restraints, num_selected):
from modeller import forms, physical, features
for (res, values) in chi2:
arr = True
for a in atmsel.find_chi2_dihedrals(res, num_selected):
r = forms.spline(physical.chi2_dihedral,
features.dihedral(*a), open=False, low=-3.11978,
high=3.16341, delta=0.04363, lowderiv=0,
highderiv=0, values=values, use_array=arr)
arr = restraints.add(r)
