schrodinger.protein.assignment module

Module for optimizing hydroxyl, thiol and water orientiations, Chi-flips of asparagine, glutamine and histidine, and protonation states of aspartic acid, glutamic acid, and histidine.

Usage: ProtAssign(st)

Copyright Schrodinger, LLC. All rights reserved.

exception schrodinger.protein.assignment.PropKaException(value)

Bases: Exception

__init__(value)

Initialize self. See help(type(self)) for accurate signature.

__cause__

exception cause

__class__

alias of builtins.type

__context__

exception context

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.protein.assignment', '__init__': <function PropKaException.__init__>, '__weakref__': <attribute '__weakref__' of 'PropKaException' objects>, '__doc__': None})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.protein.assignment'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__setstate__()
__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__suppress_context__
__traceback__
__weakref__

list of weak references to the object (if defined)

args
with_traceback()

Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

schrodinger.protein.assignment.report(message_level=1, message='')
schrodinger.protein.assignment.measure(ct, atom1=None, atom2=None, atom3=None, atom4=None, use_xtal=False, max_dist=10.0)
class schrodinger.protein.assignment.ProtAssign(ct, interactive=False, do_flips=True, asl='', noprot_asl='', atoms=[], use_xtal=False, torsion_penalty=False, sample_waters=True, sample_acids=True, freeze_existing=False, include_initial=False, max_comb=10000, logging_level=1, quiet_flag=False, debug_flag=False, add_labels=True, label_pkas=False, pH='neutral', use_propka=True, propka_pH=7.0, user_states=[], minimize=False)

Bases: object

clustering_distance = 4.0
class changeable(ct, iatom)

Bases: object

asl = 'none'
OH_length = 1.0
HOH_angle = 109.5
max_hbond_distance = 3.5
hbond_min_angle = 150.0
hbond_heavy_min_angle = 80.0
hbond_heavy_max_angle = 140.0
__init__(ct, iatom)

Initialize self. See help(type(self)) for accurate signature.

pre_treat_1(ct)
pre_treat_2(ct)
pre_treat(ct)
enumerate_states(ct, acceptors, donors, pH, do_flips=True, include_initial=False)
lock_protonation()
add_current_to_states(ct)
assign_state(ct, istate, add_labels=True, label_pkas=False)
update_atom_indices(ct, new_indices)
get_new_index(ct, atom_index, new_indices)
get_view_atoms()
get_residue_name(ct, iatom)
get_atom_name(ct, iatom)
swap_atoms(ct, atom1, atom2)
get_penalty(istate)
get_adjustable_atoms()
change_pka(pka, propka_pH)
get_dihedral_atoms(ct, h)
__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.protein.assignment', 'asl': 'none', 'OH_length': 1.0, 'HOH_angle': 109.5, 'max_hbond_distance': 3.5, 'hbond_min_angle': 150.0, 'hbond_heavy_min_angle': 80.0, 'hbond_heavy_max_angle': 140.0, '__init__': <function ProtAssign.changeable.__init__>, 'pre_treat_1': <function ProtAssign.changeable.pre_treat_1>, 'pre_treat_2': <function ProtAssign.changeable.pre_treat_2>, 'pre_treat': <function ProtAssign.changeable.pre_treat>, 'enumerate_states': <function ProtAssign.changeable.enumerate_states>, 'lock_protonation': <function ProtAssign.changeable.lock_protonation>, 'add_current_to_states': <function ProtAssign.changeable.add_current_to_states>, 'assign_state': <function ProtAssign.changeable.assign_state>, 'update_atom_indices': <function ProtAssign.changeable.update_atom_indices>, 'get_new_index': <function ProtAssign.changeable.get_new_index>, 'get_view_atoms': <function ProtAssign.changeable.get_view_atoms>, 'get_residue_name': <function ProtAssign.changeable.get_residue_name>, 'get_atom_name': <function ProtAssign.changeable.get_atom_name>, 'swap_atoms': <function ProtAssign.changeable.swap_atoms>, 'get_penalty': <function ProtAssign.changeable.get_penalty>, 'get_adjustable_atoms': <function ProtAssign.changeable.get_adjustable_atoms>, 'change_pka': <function ProtAssign.changeable.change_pka>, 'get_dihedral_atoms': <function ProtAssign.changeable.get_dihedral_atoms>, '__dict__': <attribute '__dict__' of 'changeable' objects>, '__weakref__': <attribute '__weakref__' of 'changeable' objects>, '__doc__': None})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.protein.assignment'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

class amide_changeable(ct, iatom)

Bases: schrodinger.protein.assignment.changeable

This is the primary amide -NH2 group of ASN and GLN residues.

asl = '((res.ptype "ASN " AND atom.ptype " CG ") OR (res.ptype "GLN " AND atom.ptype " CD "))'
__init__(ct, iatom)

Initialize self. See help(type(self)) for accurate signature.

pre_treat_1(ct)
pre_treat_2(ct)
enumerate_states(ct, acceptors, donors, pH, do_flips=True, include_initial=False)
assign_state(ct, istate, add_labels=True, label_pkas=False)
update_atom_indices(ct, new_indices)
get_heavies()
get_state_sites(ct, istate)
get_view_atoms()
get_penalty(istate)
get_adjustable_atoms()
HOH_angle = 109.5
OH_length = 1.0
__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.protein.assignment', '__doc__': '\n This is the primary amide -NH2 group of ASN and GLN residues.\n ', 'asl': '((res.ptype "ASN " AND atom.ptype " CG ") OR (res.ptype "GLN " AND atom.ptype " CD "))', '__init__': <function ProtAssign.amide_changeable.__init__>, 'pre_treat_1': <function ProtAssign.amide_changeable.pre_treat_1>, 'pre_treat_2': <function ProtAssign.amide_changeable.pre_treat_2>, 'enumerate_states': <function ProtAssign.amide_changeable.enumerate_states>, 'assign_state': <function ProtAssign.amide_changeable.assign_state>, 'update_atom_indices': <function ProtAssign.amide_changeable.update_atom_indices>, 'get_heavies': <function ProtAssign.amide_changeable.get_heavies>, 'get_state_sites': <function ProtAssign.amide_changeable.get_state_sites>, 'get_view_atoms': <function ProtAssign.amide_changeable.get_view_atoms>, 'get_penalty': <function ProtAssign.amide_changeable.get_penalty>, 'get_adjustable_atoms': <function ProtAssign.amide_changeable.get_adjustable_atoms>})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.protein.assignment'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

add_current_to_states(ct)
change_pka(pka, propka_pH)
get_atom_name(ct, iatom)
get_dihedral_atoms(ct, h)
get_new_index(ct, atom_index, new_indices)
get_residue_name(ct, iatom)
hbond_heavy_max_angle = 140.0
hbond_heavy_min_angle = 80.0
hbond_min_angle = 150.0
lock_protonation()
max_hbond_distance = 3.5
pre_treat(ct)
swap_atoms(ct, atom1, atom2)
class histidine_changeable(ct, iatom)

Bases: schrodinger.protein.assignment.changeable

Imidazole group of Histidine residues.

asl = '((res.ptype "HIS ","HID ","HIE ","HIP ")) AND ((atom.ptype " CG "))'
__init__(ct, iatom)

Initialize self. See help(type(self)) for accurate signature.

pre_treat_1(ct)
pre_treat_2(ct)
enumerate_states(ct, acceptors, donors, pH, do_flips=True, include_initial=False)
lock_protonation()
assign_state(ct, istate, add_labels=True, label_pkas=False)
update_atom_indices(ct, new_indices)
get_heavies()
get_state_sites(ct, istate)
get_view_atoms()
get_penalty(istate)
get_adjustable_atoms()
change_pka(pka, propka_pH)
HOH_angle = 109.5
OH_length = 1.0
__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.protein.assignment', '__doc__': '\n Imidazole group of Histidine residues.\n ', 'asl': '((res.ptype "HIS ","HID ","HIE ","HIP ")) AND ((atom.ptype " CG "))', '__init__': <function ProtAssign.histidine_changeable.__init__>, 'pre_treat_1': <function ProtAssign.histidine_changeable.pre_treat_1>, 'pre_treat_2': <function ProtAssign.histidine_changeable.pre_treat_2>, 'enumerate_states': <function ProtAssign.histidine_changeable.enumerate_states>, 'lock_protonation': <function ProtAssign.histidine_changeable.lock_protonation>, 'assign_state': <function ProtAssign.histidine_changeable.assign_state>, 'update_atom_indices': <function ProtAssign.histidine_changeable.update_atom_indices>, 'get_heavies': <function ProtAssign.histidine_changeable.get_heavies>, 'get_state_sites': <function ProtAssign.histidine_changeable.get_state_sites>, 'get_view_atoms': <function ProtAssign.histidine_changeable.get_view_atoms>, 'get_penalty': <function ProtAssign.histidine_changeable.get_penalty>, 'get_adjustable_atoms': <function ProtAssign.histidine_changeable.get_adjustable_atoms>, 'change_pka': <function ProtAssign.histidine_changeable.change_pka>})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.protein.assignment'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

add_current_to_states(ct)
get_atom_name(ct, iatom)
get_dihedral_atoms(ct, h)
get_new_index(ct, atom_index, new_indices)
get_residue_name(ct, iatom)
hbond_heavy_max_angle = 140.0
hbond_heavy_min_angle = 80.0
hbond_min_angle = 150.0
max_hbond_distance = 3.5
pre_treat(ct)
swap_atoms(ct, atom1, atom2)
class carboxyl_changeable(ct, iatom)

Bases: schrodinger.protein.assignment.changeable

asl = '(res.ptype "ASP ","ASH " AND atom.ptype " CG ") OR (res.ptype "GLU ","GLH " AND atom.ptype " CD ")'
__init__(ct, iatom)

Initialize self. See help(type(self)) for accurate signature.

pre_treat_1(ct)
pre_treat_2(ct)
enumerate_states(ct, acceptors, donors, pH, do_flips=True, include_initial=False)
lock_protonation()
assign_state(ct, istate, add_labels=True, label_pkas=False)
update_atom_indices(ct, new_indices)
get_heavies()
get_state_sites(ct, istate)
get_view_atoms()
get_penalty(istate)
get_adjustable_atoms()
change_pka(pka, propka_pH)
HOH_angle = 109.5
OH_length = 1.0
__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.protein.assignment', 'asl': '(res.ptype "ASP ","ASH " AND atom.ptype " CG ") OR (res.ptype "GLU ","GLH " AND atom.ptype " CD ")', '__init__': <function ProtAssign.carboxyl_changeable.__init__>, 'pre_treat_1': <function ProtAssign.carboxyl_changeable.pre_treat_1>, 'pre_treat_2': <function ProtAssign.carboxyl_changeable.pre_treat_2>, 'enumerate_states': <function ProtAssign.carboxyl_changeable.enumerate_states>, 'lock_protonation': <function ProtAssign.carboxyl_changeable.lock_protonation>, 'assign_state': <function ProtAssign.carboxyl_changeable.assign_state>, 'update_atom_indices': <function ProtAssign.carboxyl_changeable.update_atom_indices>, 'get_heavies': <function ProtAssign.carboxyl_changeable.get_heavies>, 'get_state_sites': <function ProtAssign.carboxyl_changeable.get_state_sites>, 'get_view_atoms': <function ProtAssign.carboxyl_changeable.get_view_atoms>, 'get_penalty': <function ProtAssign.carboxyl_changeable.get_penalty>, 'get_adjustable_atoms': <function ProtAssign.carboxyl_changeable.get_adjustable_atoms>, 'change_pka': <function ProtAssign.carboxyl_changeable.change_pka>, '__doc__': None})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.protein.assignment'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

add_current_to_states(ct)
get_atom_name(ct, iatom)
get_dihedral_atoms(ct, h)
get_new_index(ct, atom_index, new_indices)
get_residue_name(ct, iatom)
hbond_heavy_max_angle = 140.0
hbond_heavy_min_angle = 80.0
hbond_min_angle = 150.0
max_hbond_distance = 3.5
pre_treat(ct)
swap_atoms(ct, atom1, atom2)
class rotatable_changeable(ct, iatom)

Bases: schrodinger.protein.assignment.changeable

asl = '((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.ptype "HOH","DOD","SPC","ASH","GLH","ASP","GLU" ))'
__init__(ct, iatom)

Initialize self. See help(type(self)) for accurate signature.

pre_treat_1(ct)
pre_treat_2(ct)
enumerate_states(ct, acceptors, donors, pH, do_flips=True, include_initial=False)
lock_protonation()
add_current_to_states(ct)
assign_state(ct, istate, add_labels=True, label_pkas=False)
update_atom_indices(ct, new_indices)
get_heavies()
get_state_sites(ct, istate)
get_view_atoms()
get_penalty(istate)
get_adjustable_atoms()
change_pka(pka, propka_pH)
HOH_angle = 109.5
OH_length = 1.0
__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.protein.assignment', 'asl': '((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.ptype "HOH","DOD","SPC","ASH","GLH","ASP","GLU" ))', '__init__': <function ProtAssign.rotatable_changeable.__init__>, 'pre_treat_1': <function ProtAssign.rotatable_changeable.pre_treat_1>, 'pre_treat_2': <function ProtAssign.rotatable_changeable.pre_treat_2>, 'enumerate_states': <function ProtAssign.rotatable_changeable.enumerate_states>, 'lock_protonation': <function ProtAssign.rotatable_changeable.lock_protonation>, 'add_current_to_states': <function ProtAssign.rotatable_changeable.add_current_to_states>, 'assign_state': <function ProtAssign.rotatable_changeable.assign_state>, 'update_atom_indices': <function ProtAssign.rotatable_changeable.update_atom_indices>, 'get_heavies': <function ProtAssign.rotatable_changeable.get_heavies>, 'get_state_sites': <function ProtAssign.rotatable_changeable.get_state_sites>, 'get_view_atoms': <function ProtAssign.rotatable_changeable.get_view_atoms>, 'get_penalty': <function ProtAssign.rotatable_changeable.get_penalty>, 'get_adjustable_atoms': <function ProtAssign.rotatable_changeable.get_adjustable_atoms>, 'change_pka': <function ProtAssign.rotatable_changeable.change_pka>, '__doc__': None})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.protein.assignment'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

get_atom_name(ct, iatom)
get_dihedral_atoms(ct, h)
get_new_index(ct, atom_index, new_indices)
get_residue_name(ct, iatom)
hbond_heavy_max_angle = 140.0
hbond_heavy_min_angle = 80.0
hbond_min_angle = 150.0
max_hbond_distance = 3.5
pre_treat(ct)
swap_atoms(ct, atom1, atom2)
class amine_changeable(ct, iatom)

Bases: schrodinger.protein.assignment.changeable

asl = '((res.ptype "LYS ","LYN ") AND (atom.ptype " NZ "))'
__init__(ct, iatom)

Initialize self. See help(type(self)) for accurate signature.

pre_treat_1(ct)
pre_treat_2(ct)
enumerate_states(ct, acceptors, donors, pH, do_flips=True, include_initial=False)
lock_protonation()
assign_state(ct, istate, add_labels=True, label_pkas=False)
update_atom_indices(ct, new_indices)
get_heavies()
get_state_sites(ct, istate)
get_view_atoms()
get_penalty(istate)
change_pka(pka, propka_pH)
HOH_angle = 109.5
OH_length = 1.0
__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.protein.assignment', 'asl': '((res.ptype "LYS ","LYN ") AND (atom.ptype " NZ "))', '__init__': <function ProtAssign.amine_changeable.__init__>, 'pre_treat_1': <function ProtAssign.amine_changeable.pre_treat_1>, 'pre_treat_2': <function ProtAssign.amine_changeable.pre_treat_2>, 'enumerate_states': <function ProtAssign.amine_changeable.enumerate_states>, 'lock_protonation': <function ProtAssign.amine_changeable.lock_protonation>, 'assign_state': <function ProtAssign.amine_changeable.assign_state>, 'update_atom_indices': <function ProtAssign.amine_changeable.update_atom_indices>, 'get_heavies': <function ProtAssign.amine_changeable.get_heavies>, 'get_state_sites': <function ProtAssign.amine_changeable.get_state_sites>, 'get_view_atoms': <function ProtAssign.amine_changeable.get_view_atoms>, 'get_penalty': <function ProtAssign.amine_changeable.get_penalty>, 'change_pka': <function ProtAssign.amine_changeable.change_pka>, '__doc__': None})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.protein.assignment'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

add_current_to_states(ct)
get_adjustable_atoms()
get_atom_name(ct, iatom)
get_dihedral_atoms(ct, h)
get_new_index(ct, atom_index, new_indices)
get_residue_name(ct, iatom)
hbond_heavy_max_angle = 140.0
hbond_heavy_min_angle = 80.0
hbond_min_angle = 150.0
max_hbond_distance = 3.5
pre_treat(ct)
swap_atoms(ct, atom1, atom2)
class water_changeable(ct, iatom)

Bases: schrodinger.protein.assignment.changeable

asl = '(water) AND (atom.ele O)'
redundancy_tolerance = 0.5
__init__(ct, iatom)

Initialize self. See help(type(self)) for accurate signature.

find_dihedrals(ct, atom1, atom2, atom3, acceptors, donors)
enumerate_states(ct, acceptors, donors, pH, do_flips=True, include_initial=False)
add_current_to_states(ct)
assign_state(ct, istate, add_labels=True, label_pkas=False)
update_atom_indices(ct, new_indices)
get_heavies()
get_state_sites(ct, istate)
get_view_atoms()
get_penalty(istate)
get_adjustable_atoms()
HOH_angle = 109.5
OH_length = 1.0
__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.protein.assignment', 'asl': '(water) AND (atom.ele O)', 'redundancy_tolerance': 0.5, '__init__': <function ProtAssign.water_changeable.__init__>, 'find_dihedrals': <function ProtAssign.water_changeable.find_dihedrals>, 'enumerate_states': <function ProtAssign.water_changeable.enumerate_states>, 'add_current_to_states': <function ProtAssign.water_changeable.add_current_to_states>, 'assign_state': <function ProtAssign.water_changeable.assign_state>, 'update_atom_indices': <function ProtAssign.water_changeable.update_atom_indices>, 'get_heavies': <function ProtAssign.water_changeable.get_heavies>, 'get_state_sites': <function ProtAssign.water_changeable.get_state_sites>, 'get_view_atoms': <function ProtAssign.water_changeable.get_view_atoms>, 'get_penalty': <function ProtAssign.water_changeable.get_penalty>, 'get_adjustable_atoms': <function ProtAssign.water_changeable.get_adjustable_atoms>, '__doc__': None})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.protein.assignment'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

change_pka(pka, propka_pH)
get_atom_name(ct, iatom)
get_dihedral_atoms(ct, h)
get_new_index(ct, atom_index, new_indices)
get_residue_name(ct, iatom)
hbond_heavy_max_angle = 140.0
hbond_heavy_min_angle = 80.0
hbond_min_angle = 150.0
lock_protonation()
max_hbond_distance = 3.5
pre_treat(ct)
pre_treat_1(ct)
pre_treat_2(ct)
swap_atoms(ct, atom1, atom2)
class hbond_cluster

Bases: object

get_residue_name(ct, iatom)
get_atom_name(ct, iatom)
__init__()

Initialize self. See help(type(self)) for accurate signature.

setup_xtal(ct, interact, clustering_distance)
optimize(ct, interact, static_donors, static_acceptors, static_clashers, max_comb, use_propka, propka_pH=7.0, xtal_ct=None)
score_combination(ct, interact, states)
single_point(ct, interact, static_donors, static_acceptors, static_clashers, xtal_ct=None)
setup_local_static_alt(ct, static_acceptors, static_donors, static_clashers)
setup_local_static(ct, static_acceptors, static_donors, static_clashers)
initialize_score_storage()
pre_score_self(ct)
pre_score_pairs(ct, interact)
score_pair(ct, iacceptors, idonors, iclashers, icharge, jacceptors, jdonors, jclashers, jcharge, use_xtal=False)
score_donor_acceptor(ct, donor_heavy, donor_hydrogen, acceptor_heavy, use_xtal=False)
score_donor_donor(ct, donor1_heavy, donor1_hydrogen, donor2_heavy, donor2_hydrogen, use_xtal=False)
score_exhaustively(ct, interact, find_all_solutions=True, tolerate_clashes=False)
score_sequentially(ct, interact)

This routine uses an algorithm similar to Prime’s iteration to convergence. Starting from a random configuration, each species is optimized in turn, keeping the others fixed in their current state. This continues until the system reaches convergence (no more changes in the most optimal state for all residues).

expand_solutions(ct, interact)

This takes an existing set of good solutions and generates more by deconverging them and then iterating them back to convergence. Generates at least 10 new solutions.

recombine_solutions(ct, interact)

This is similar to score_sequentially, but begins with some pre-existing good solutions in self.combinations, and then creates hybrids to try to improve on them.

deconverge(ct, interact, comb, problem_cutoff=50.0)

This starts with what is assumed to be a good solution, and then randomizes the states, but not to anything that produces a problem.

iterate_to_convergence(ct, interact, comb, problem_cutoff=50.0)

This iterates the combination ‘comb’ to convergence. Maximum of 10 cycles.

create_hybrid(local_combinations, interact, random_scaffold=False)

This takes the lowest energy solution, and for each problematic region it searches other solutions (in random order) for any which may have had better luck for just that part of the overall cluster. It then splices those solutions into the lowest energy one. If random_scaffold, then it selects a random solution as the basis in stead of the lowest energy one.

trim_redundant_combinations()
assign_combination(ct, icombination, add_labels, label_pkas)
__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.protein.assignment', 'get_residue_name': <function ProtAssign.hbond_cluster.get_residue_name>, 'get_atom_name': <function ProtAssign.hbond_cluster.get_atom_name>, '__init__': <function ProtAssign.hbond_cluster.__init__>, 'setup_xtal': <function ProtAssign.hbond_cluster.setup_xtal>, 'optimize': <function ProtAssign.hbond_cluster.optimize>, 'score_combination': <function ProtAssign.hbond_cluster.score_combination>, 'single_point': <function ProtAssign.hbond_cluster.single_point>, 'setup_local_static_alt': <function ProtAssign.hbond_cluster.setup_local_static_alt>, 'setup_local_static': <function ProtAssign.hbond_cluster.setup_local_static>, 'initialize_score_storage': <function ProtAssign.hbond_cluster.initialize_score_storage>, 'pre_score_self': <function ProtAssign.hbond_cluster.pre_score_self>, 'pre_score_pairs': <function ProtAssign.hbond_cluster.pre_score_pairs>, 'score_pair': <function ProtAssign.hbond_cluster.score_pair>, 'score_donor_acceptor': <function ProtAssign.hbond_cluster.score_donor_acceptor>, 'score_donor_donor': <function ProtAssign.hbond_cluster.score_donor_donor>, 'score_exhaustively': <function ProtAssign.hbond_cluster.score_exhaustively>, 'score_sequentially': <function ProtAssign.hbond_cluster.score_sequentially>, 'expand_solutions': <function ProtAssign.hbond_cluster.expand_solutions>, 'recombine_solutions': <function ProtAssign.hbond_cluster.recombine_solutions>, 'deconverge': <function ProtAssign.hbond_cluster.deconverge>, 'iterate_to_convergence': <function ProtAssign.hbond_cluster.iterate_to_convergence>, 'create_hybrid': <function ProtAssign.hbond_cluster.create_hybrid>, 'trim_redundant_combinations': <function ProtAssign.hbond_cluster.trim_redundant_combinations>, 'assign_combination': <function ProtAssign.hbond_cluster.assign_combination>, '__dict__': <attribute '__dict__' of 'hbond_cluster' objects>, '__weakref__': <attribute '__weakref__' of 'hbond_cluster' objects>, '__doc__': None})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.protein.assignment'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

__init__(ct, interactive=False, do_flips=True, asl='', noprot_asl='', atoms=[], use_xtal=False, torsion_penalty=False, sample_waters=True, sample_acids=True, freeze_existing=False, include_initial=False, max_comb=10000, logging_level=1, quiet_flag=False, debug_flag=False, add_labels=True, label_pkas=False, pH='neutral', use_propka=True, propka_pH=7.0, user_states=[], minimize=False)

Initialize self. See help(type(self)) for accurate signature.

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.protein.assignment', 'clustering_distance': 4.0, 'changeable': <class 'schrodinger.protein.assignment.ProtAssign.changeable'>, 'amide_changeable': <class 'schrodinger.protein.assignment.ProtAssign.amide_changeable'>, 'histidine_changeable': <class 'schrodinger.protein.assignment.ProtAssign.histidine_changeable'>, 'carboxyl_changeable': <class 'schrodinger.protein.assignment.ProtAssign.carboxyl_changeable'>, 'rotatable_changeable': <class 'schrodinger.protein.assignment.ProtAssign.rotatable_changeable'>, 'amine_changeable': <class 'schrodinger.protein.assignment.ProtAssign.amine_changeable'>, 'water_changeable': <class 'schrodinger.protein.assignment.ProtAssign.water_changeable'>, 'hbond_cluster': <class 'schrodinger.protein.assignment.ProtAssign.hbond_cluster'>, '__init__': <function ProtAssign.__init__>, 'fix_elements': <function ProtAssign.fix_elements>, 'freeze_existing_hydrogens': <function ProtAssign.freeze_existing_hydrogens>, 'setup': <function ProtAssign.setup>, 'remove_zero_order_bonds': <function ProtAssign.remove_zero_order_bonds>, 'extend_targeted_to_hyds': <function ProtAssign.extend_targeted_to_hyds>, 'delete_atoms': <function ProtAssign.delete_atoms>, 'run_propka': <function ProtAssign.run_propka>, 'generate_mates': <function ProtAssign.generate_mates>, 'apply_pkas': <function ProtAssign.apply_pkas>, 'find_protonation_state_changes': <function ProtAssign.find_protonation_state_changes>, 'identify_species': <function ProtAssign.identify_species>, 'identify_all_hbonders': <function ProtAssign.identify_all_hbonders>, 'enumerate_changeable_states': <function ProtAssign.enumerate_changeable_states>, 'lock_protonation_states': <function ProtAssign.lock_protonation_states>, 'remove_changeables_from_hbonders': <function ProtAssign.remove_changeables_from_hbonders>, 'cluster': <function ProtAssign.cluster>, 'set_user_states': <function ProtAssign.set_user_states>, 'assign_state_of_changeable': <function ProtAssign.assign_state_of_changeable>, 'increment_state_of_changeable': <function ProtAssign.increment_state_of_changeable>, 'decrement_state_of_changeable': <function ProtAssign.decrement_state_of_changeable>, 'record_current_indices': <function ProtAssign.record_current_indices>, 'assign_best_combinations': <function ProtAssign.assign_best_combinations>, 'assign_cluster_combination': <function ProtAssign.assign_cluster_combination>, 'single_point_cluster': <function ProtAssign.single_point_cluster>, 'optimize_cluster': <function ProtAssign.optimize_cluster>, 'optimize': <function ProtAssign.optimize>, 'minimize_hydrogens': <function ProtAssign.minimize_hydrogens>, 'restore_zobs': <function ProtAssign.restore_zobs>, 'cleanup': <function ProtAssign.cleanup>, 'summarize_pkas': <function ProtAssign.summarize_pkas>, '__dict__': <attribute '__dict__' of 'ProtAssign' objects>, '__weakref__': <attribute '__weakref__' of 'ProtAssign' objects>, '__doc__': None})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.protein.assignment'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

fix_elements(ct)
freeze_existing_hydrogens(ct)
setup(ct)
remove_zero_order_bonds(ct)
extend_targeted_to_hyds(ct)
delete_atoms(ct, atoms)
run_propka(changeables, ct, use_xtal=False)
generate_mates(ct)
apply_pkas(changeables, changes, propka_pH)
find_protonation_state_changes(ct, clusters='all')
identify_species(ct)
identify_all_hbonders(ct)
enumerate_changeable_states(ct)
lock_protonation_states(ct)
remove_changeables_from_hbonders()
cluster(ct)
set_user_states(ct)
assign_state_of_changeable(ct, ichangeable, istate)
increment_state_of_changeable(ct, ichangeable)
decrement_state_of_changeable(ct, ichangeable)
record_current_indices(ct)
assign_best_combinations(ct)
assign_cluster_combination(ct, icluster, icombination)
single_point_cluster(ct, icluster)
optimize_cluster(ct, icluster, assign=True)
optimize(ct)
minimize_hydrogens(ct)
restore_zobs(ct)
cleanup(ct)
summarize_pkas()