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

Class rotatable_changeable

ProtAssign.changeable --+
                        |
                       ProtAssign.rotatable_changeable

Instance Methods

[hide private]

__init__(self, ct, iatom)

pre_treat_1(self, ct)

pre_treat_2(self, ct)

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

lock_protonation(self)

add_current_to_states(self, ct)

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

update_atom_indices(self, ct, new_indices)

get_heavies(self)

get_state_sites(self, ct, istate)

get_view_atoms(self)

get_penalty(self, istate)

get_adjustable_atoms(self)

change_pka(self, pka, propka_pH)

Inherited from changeable: get_atom_name, get_dihedral_atoms, get_new_index, get_residue_name, pre_treat, swap_atoms

Class Variables

[hide private]

asl = '((res.ptype "CYS ","CYT ") AND (atom.ptype " SG ") AND ...

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

Method Details

[hide private]

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

Overrides: changeable.enumerate_states

lock_protonation(self)

Overrides: changeable.lock_protonation

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

update_atom_indices(self, ct, new_indices)

Overrides: changeable.update_atom_indices

get_view_atoms(self)

Overrides: changeable.get_view_atoms

get_penalty(self, istate)

Overrides: changeable.get_penalty

get_adjustable_atoms(self)

Overrides: changeable.get_adjustable_atoms

change_pka(self, pka, propka_pH)

Overrides: changeable.change_pka

Class Variable Details

[hide private]

asl

Value:

'((res.ptype "CYS ","CYT ") AND (atom.ptype " SG ") AND (atom.formal -
1)) OR ((res.ptype "TYR ") AND (atom.ptype " OH ") AND (atom.formal -1
)) OR (( atom.ele H AND not /C0-H0/ AND not /N0-H0/ ) AND NOT (res.pty
pe "HOH","DOD","SPC","ASH","GLH","ASP","GLU" ))'

Class rotatable_changeable

__init__(self, ct, iatom) (Constructor)

pre_treat_1(self, ct)

pre_treat_2(self, ct)

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

lock_protonation(self)

add_current_to_states(self, ct)

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

update_atom_indices(self, ct, new_indices)

get_view_atoms(self)

get_penalty(self, istate)

get_adjustable_atoms(self)

change_pka(self, pka, propka_pH)

asl

init(self, ct, iatom)
(Constructor)