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='')¶
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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¶
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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})¶
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__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 "))'¶
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__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)¶
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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
()¶
-