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

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Class water_changeable

ProtAssign.changeable --+
                        |
                       ProtAssign.water_changeable

Instance Methods

__init__(self, ct, iatom)

add_current_to_states(self, ct)

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

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

find_dihedrals(self, ct, atom1, atom2, atom3, acceptors, donors)

get_adjustable_atoms(self)

get_heavies(self)

get_penalty(self, istate)

get_state_sites(self, ct, istate)

get_view_atoms(self)

update_atom_indices(self, ct, new_indices)

Inherited from changeable: change_pka, get_atom_name, get_dihedral_atoms, get_new_index, get_residue_name, lock_protonation, pre_treat, pre_treat_1, pre_treat_2, swap_atoms

Class Variables

asl = '(water) AND (atom.ele O)'

redundancy_tolerance = 0.5

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__

add_current_to_states(self, ct)

Overrides: changeable.add_current_to_states

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

update_atom_indices(self, ct, new_indices)

Overrides: changeable.update_atom_indices