Package schrodinger :: Package protein :: Module assignment :: Class ProtAssign :: Class amide_changeable

[frames] | no frames]

Class amide_changeable

ProtAssign.changeable --+
                        |
                       ProtAssign.amide_changeable

Instance Methods

__init__(self, ct, iatom)

assign_state(self, ct, istate, add_labels=True, label_pkas=False)

enumerate_states(self, ct, acceptors, donors, pH, do_flips=True, include_initial=False)

get_adjustable_atoms(self)

get_heavies(self)

get_penalty(self, istate)

get_state_sites(self, ct, istate)

get_view_atoms(self)

pre_treat_1(self, ct)

pre_treat_2(self, ct)

update_atom_indices(self, ct, new_indices)

Inherited from changeable: add_current_to_states, change_pka, get_atom_name, get_dihedral_atoms, get_new_index, get_residue_name, lock_protonation, pre_treat, swap_atoms

Class Variables

asl = '((res.ptype "ASN " AND atom.ptype " CG ") OR (res.ptype...

Inherited from changeable: HOH_angle, OH_length, hbond_heavy_max_angle, hbond_heavy_min_angle, hbond_min_angle, max_hbond_distance

Method Details

init(self, ct, iatom)
(Constructor)

Overrides: changeable.__init__

assign_state(self, ct, istate, add_labels=True, label_pkas=False)

Overrides: changeable.assign_state

enumerate_states(self, ct, acceptors, donors, pH, do_flips=True, include_initial=False)

Overrides: changeable.enumerate_states

get_adjustable_atoms(self)

Overrides: changeable.get_adjustable_atoms

get_penalty(self, istate)

Overrides: changeable.get_penalty

get_view_atoms(self)

Overrides: changeable.get_view_atoms

pre_treat_1(self, ct)

Overrides: changeable.pre_treat_1

pre_treat_2(self, ct)

Overrides: changeable.pre_treat_2

update_atom_indices(self, ct, new_indices)

Overrides: changeable.update_atom_indices

Class Variable Details

asl

Value:

'((res.ptype "ASN " AND atom.ptype " CG ") OR (res.ptype "GLN " AND at
om.ptype " CD "))'