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)