schrodinger.protein.residue module

schrodinger.protein.residue.get_matrix_value(matrix, first, second)

Return a similarity matrix value for a specified pair of residues.

schrodinger.protein.residue.box_letter(letter)

Map an ASCII letter to the circled Unicode variant

Parameters:letter (str) – ASCII letter to map
Raises:ValueError – if the input is not an ASCII letter
class schrodinger.protein.residue.HELIX_PROPENSITY

Bases: enum.Enum

An enumeration.

AMBIVALENT = 4
HELIX_BREAKING = 5
LIKELY = 2
NO_PROPENSITY = 1
WEAK = 3
__class__

alias of enum.EnumMeta

__members__ = mappingproxy(OrderedDict([('NO_PROPENSITY', <HELIX_PROPENSITY.NO_PROPENSITY: 1>), ('LIKELY', <HELIX_PROPENSITY.LIKELY: 2>), ('WEAK', <HELIX_PROPENSITY.WEAK: 3>), ('AMBIVALENT', <HELIX_PROPENSITY.AMBIVALENT: 4>), ('HELIX_BREAKING', <HELIX_PROPENSITY.HELIX_BREAKING: 5>)]))
__module__ = 'schrodinger.protein.residue'
class schrodinger.protein.residue.BETA_STRAND_PROPENSITY

Bases: enum.Enum

An enumeration.

AMBIVALENT = 3
NO_PROPENSITY = 1
STRAND_BREAKING = 2
STRAND_FORMING = 4
__class__

alias of enum.EnumMeta

__members__ = mappingproxy(OrderedDict([('NO_PROPENSITY', <BETA_STRAND_PROPENSITY.NO_PROPENSITY: 1>), ('STRAND_BREAKING', <BETA_STRAND_PROPENSITY.STRAND_BREAKING: 2>), ('AMBIVALENT', <BETA_STRAND_PROPENSITY.AMBIVALENT: 3>), ('STRAND_FORMING', <BETA_STRAND_PROPENSITY.STRAND_FORMING: 4>)]))
__module__ = 'schrodinger.protein.residue'
class schrodinger.protein.residue.TURN_PROPENSITY

Bases: enum.Enum

An enumeration.

AMBIVALENT = 3
NO_PROPENSITY = 1
TURN_BREAKING = 4
TURN_FORMING = 2
__class__

alias of enum.EnumMeta

__members__ = mappingproxy(OrderedDict([('NO_PROPENSITY', <TURN_PROPENSITY.NO_PROPENSITY: 1>), ('TURN_FORMING', <TURN_PROPENSITY.TURN_FORMING: 2>), ('AMBIVALENT', <TURN_PROPENSITY.AMBIVALENT: 3>), ('TURN_BREAKING', <TURN_PROPENSITY.TURN_BREAKING: 4>)]))
__module__ = 'schrodinger.protein.residue'
class schrodinger.protein.residue.HELIX_TERMINATION_TENDENCY

Bases: enum.Enum

An enumeration.

AMBIVALENT = 3
HELIX_ENDING = 4
HELIX_STARTING = 2
NO_TENDENCY = 1
__class__

alias of enum.EnumMeta

__members__ = mappingproxy(OrderedDict([('NO_TENDENCY', <HELIX_TERMINATION_TENDENCY.NO_TENDENCY: 1>), ('HELIX_STARTING', <HELIX_TERMINATION_TENDENCY.HELIX_STARTING: 2>), ('AMBIVALENT', <HELIX_TERMINATION_TENDENCY.AMBIVALENT: 3>), ('HELIX_ENDING', <HELIX_TERMINATION_TENDENCY.HELIX_ENDING: 4>)]))
__module__ = 'schrodinger.protein.residue'
class schrodinger.protein.residue.SOLVENT_EXPOSURE_TENDENCY

Bases: enum.Enum

An enumeration.

AMBIVALENT = 3
BURIED = 4
NO_TENDENCY = 1
SURFACE = 2
__class__

alias of enum.EnumMeta

__members__ = mappingproxy(OrderedDict([('NO_TENDENCY', <SOLVENT_EXPOSURE_TENDENCY.NO_TENDENCY: 1>), ('SURFACE', <SOLVENT_EXPOSURE_TENDENCY.SURFACE: 2>), ('AMBIVALENT', <SOLVENT_EXPOSURE_TENDENCY.AMBIVALENT: 3>), ('BURIED', <SOLVENT_EXPOSURE_TENDENCY.BURIED: 4>)]))
__module__ = 'schrodinger.protein.residue'
class schrodinger.protein.residue.STERIC_GROUP

Bases: enum.Enum

An enumeration.

AMBIVALENT = 3
AROMATIC = 5
NO_STERIC = 1
POLAR = 4
SMALL = 2
__class__

alias of enum.EnumMeta

__members__ = mappingproxy(OrderedDict([('NO_STERIC', <STERIC_GROUP.NO_STERIC: 1>), ('SMALL', <STERIC_GROUP.SMALL: 2>), ('AMBIVALENT', <STERIC_GROUP.AMBIVALENT: 3>), ('POLAR', <STERIC_GROUP.POLAR: 4>), ('AROMATIC', <STERIC_GROUP.AROMATIC: 5>)]))
__module__ = 'schrodinger.protein.residue'
class schrodinger.protein.residue.SIDE_CHAIN_CHEM

Bases: enum.Enum

An enumeration.

ACIDIC_HYDROPHILIC = 2
BASIC_HYDROPHILIC = 3
IMINO_ACID = 8
NEUTRAL_HYDROPHILIC = 6
NEUTRAL_HYDROPHOBIC_ALIPHATIC = 4
NEUTRAL_HYDROPHOBIC_AROMATIC = 5
NO_SIDE_CHAIN_CHEM = 1
PRIMARY_THIOL = 7
__class__

alias of enum.EnumMeta

__members__ = mappingproxy(OrderedDict([('NO_SIDE_CHAIN_CHEM', <SIDE_CHAIN_CHEM.NO_SIDE_CHAIN_CHEM: 1>), ('ACIDIC_HYDROPHILIC', <SIDE_CHAIN_CHEM.ACIDIC_HYDROPHILIC: 2>), ('BASIC_HYDROPHILIC', <SIDE_CHAIN_CHEM.BASIC_HYDROPHILIC: 3>), ('NEUTRAL_HYDROPHOBIC_ALIPHATIC', <SIDE_CHAIN_CHEM.NEUTRAL_HYDROPHOBIC_ALIPHATIC: 4>), ('NEUTRAL_HYDROPHOBIC_AROMATIC', <SIDE_CHAIN_CHEM.NEUTRAL_HYDROPHOBIC_AROMATIC: 5>), ('NEUTRAL_HYDROPHILIC', <SIDE_CHAIN_CHEM.NEUTRAL_HYDROPHILIC: 6>), ('PRIMARY_THIOL', <SIDE_CHAIN_CHEM.PRIMARY_THIOL: 7>), ('IMINO_ACID', <SIDE_CHAIN_CHEM.IMINO_ACID: 8>)]))
__module__ = 'schrodinger.protein.residue'
class schrodinger.protein.residue.RESIDUE_CHARGE

Bases: enum.Enum

An enumeration.

NEGATIVE = 2
NEUTRAL = 3
POSITIVE = 1
__class__

alias of enum.EnumMeta

__members__ = mappingproxy(OrderedDict([('POSITIVE', <RESIDUE_CHARGE.POSITIVE: 1>), ('NEGATIVE', <RESIDUE_CHARGE.NEGATIVE: 2>), ('NEUTRAL', <RESIDUE_CHARGE.NEUTRAL: 3>)]))
__module__ = 'schrodinger.protein.residue'
class schrodinger.protein.residue.ElementType(short_code, long_code, name)

Bases: object

__init__(short_code, long_code, name)

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

__str__()

Return str(self).

__repr__()

Return repr(self).

makeVariant(long_code, short_code)

Create a variant of an element type with a new long and short code.

Parameters:
  • long_code (str) – A 2+ character string representing the element type
  • short_code (str) – A 1 character string representing the element type
Returns:

The variant element type
Return type:

ElementType
__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.protein.residue', '__init__': <function ElementType.__init__>, '__str__': <function ElementType.__str__>, '__repr__': <function ElementType.__repr__>, 'makeVariant': <function ElementType.makeVariant>, '__dict__': <attribute '__dict__' of 'ElementType' objects>, '__weakref__': <attribute '__weakref__' of 'ElementType' 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.residue'
__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

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__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 schrodinger.protein.residue.ResidueType(short_code, long_code, name, charge=None, hydrophobicity=None, hydrophilicity=None, helix_propensity=None, beta_strand_propensity=None, turn_propensity=None, helix_termination_tendency=None, exposure_tendency=None, steric_group=None, side_chain_chem=None, isoelectric_point=None)

Bases: schrodinger.protein.residue.ElementType

__init__(short_code, long_code, name, charge=None, hydrophobicity=None, hydrophilicity=None, helix_propensity=None, beta_strand_propensity=None, turn_propensity=None, helix_termination_tendency=None, exposure_tendency=None, steric_group=None, side_chain_chem=None, isoelectric_point=None)

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

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.protein.residue', '__init__': <function ResidueType.__init__>, '__doc__': None, '__slotnames__': []})
__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.residue'
__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

__slotnames__ = []
__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)

makeVariant(long_code, short_code)

Create a variant of an element type with a new long and short code.

Parameters:
  • long_code (str) – A 2+ character string representing the element type
  • short_code (str) – A 1 character string representing the element type
Returns:

The variant element type
Return type:

ElementType
class schrodinger.protein.residue.NucleotideType(short_code, long_code, name, charge=None, hydrophobicity=None, hydrophilicity=None, helix_propensity=None, beta_strand_propensity=None, turn_propensity=None, helix_termination_tendency=None, exposure_tendency=None, steric_group=None, side_chain_chem=None, isoelectric_point=None)

Bases: schrodinger.protein.residue.ResidueType

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.protein.residue', '__doc__': None, '__slotnames__': []})
__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__(short_code, long_code, name, charge=None, hydrophobicity=None, hydrophilicity=None, helix_propensity=None, beta_strand_propensity=None, turn_propensity=None, helix_termination_tendency=None, exposure_tendency=None, steric_group=None, side_chain_chem=None, isoelectric_point=None)

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

__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.residue'
__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

__slotnames__ = []
__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)

makeVariant(long_code, short_code)

Create a variant of an element type with a new long and short code.

Parameters:
  • long_code (str) – A 2+ character string representing the element type
  • short_code (str) – A 1 character string representing the element type
Returns:

The variant element type
Return type:

ElementType
schrodinger.protein.residue.make_variants(variants)

Helper function to create modified amino acids and modified nucleotides

Parameters:
  • variants – A list of modified residues. The modified residue will have all the same properties as the standard one (hydophobicity, charge, etc.) but its long code (ie, its PDB residue name) will differ, and if a tuple of (string, string) is provided, both its long code and short code will differ.
  • variants – list of (ResidueType, list of string or (string,string))
Returns:

a list of residue variants
Return type:

list of ResidueType
schrodinger.protein.residue.merge_dicts(*dict_args)

Merge any number of dictionaries into a single dictionary.

Note that repeated keys will be silently overwritten with the last value.

schrodinger.protein.residue.make_one_letter_map(res_list)
schrodinger.protein.residue.make_three_letter_map(res_list)
schrodinger.protein.residue.any_structured_residues(residues)

Returns whether any of the given residues are structured.

Parameters:residues (iterable(residue.Residue)) – The iterable of residues to check
Returns:True if the given residues contain one that is structured.
Return type:bool
class schrodinger.protein.residue.AbstractSequenceElement

Bases: object

__slots__ = ['is_gap', 'sequence']
__init__()

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

is_gap
sequence
__copy__()
__deepcopy__(memo)
is_res

Utility function to check whether a residue is not a gap

hasStructure()
Returns:Whether this element has a structure i.e. whether it has

corresponding XYZ coordinates in Maestro. :rtype: bool

seq_index
__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__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.residue'
__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).

class schrodinger.protein.residue.Gap

Bases: schrodinger.models.json.JsonableClassMixin, schrodinger.protein.residue.AbstractSequenceElement

__slots__ = ['is_gap', 'sequence', '__weakref__']
__init__()

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

is_gap
__str__()

Return str(self).

toJsonImplementation()

Abstract method that must be defined by all derived classes. Converts an instance of the derived class into a jsonifiable object.

Returns:A dict made up of JSON native datatypes or Jsonable objects. See the link below for a table of such types. https://docs.python.org/2/library/json.html#encoders-and-decoders
classmethod fromJsonImplementation(json_obj)

Abstract method that must be defined by all derived classes. Takes in a dictionary and constructs an instance of the derived class.

Parameters:json_dict (dict) – A dictionary loaded from a JSON string or file.
Returns:An instance of the derived class.

:rtype : cls

__class__

alias of builtins.type

__copy__()
__deepcopy__(memo)
__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.protein.residue', '__slots__': ['is_gap', 'sequence', '__weakref__'], '__init__': <function Gap.__init__>, '__str__': <function Gap.__str__>, 'toJsonImplementation': <function Gap.toJsonImplementation>, 'fromJsonImplementation': <classmethod object>, 'is_gap': <member 'is_gap' of 'Gap' objects>, 'sequence': <member 'sequence' of 'Gap' objects>, '__dict__': <attribute '__dict__' of 'Gap' objects>, '__weakref__': <attribute '__weakref__' of 'Gap' objects>, '__doc__': None, '_Gap_jsonAdapters': []})
__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).

classmethod __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.residue'
__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

__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)

classmethod fromJson(json_obj)

A factory method which constructs a new object from a given dict loaded from a json string or file.

Parameters:json_obj (dict) – A json-loaded dictionary to create an object from.
Returns:An instance of this class.

:rtype : cls

get_version()

Method to get the version of a particular object. Defaults to the current version of mmshare. This class can be overridden for custom versioning behavior.

hasStructure()
Returns:Whether this element has a structure i.e. whether it has

corresponding XYZ coordinates in Maestro. :rtype: bool

is_res

Utility function to check whether a residue is not a gap

seq_index
sequence
toJson(_mark_version=True)

Create and returns a data structure made up of jsonable items.

Return type:An instance of one the classes from NATIVE_JSON_DATATYPES
class schrodinger.protein.residue.SequenceElement(element_type)

Bases: schrodinger.protein.residue.AbstractSequenceElement

__init__(element_type)
Parameters:element_type (ElementType) – The kind of the residue
__str__()

Returns the short code for the residue

__repr__()

Return repr(self).

__copy__()
__deepcopy__(memo)
__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.protein.residue', '__init__': <function SequenceElement.__init__>, '__str__': <function SequenceElement.__str__>, '__repr__': <function SequenceElement.__repr__>, '_getNewInstance': <function SequenceElement._getNewInstance>, '__copy__': <function SequenceElement.__copy__>, '__deepcopy__': <function SequenceElement.__deepcopy__>, '_getCopyBlackList': <function SequenceElement._getCopyBlackList>, '_getReprKwargList': <function SequenceElement._getReprKwargList>, '__dict__': <attribute '__dict__' of 'SequenceElement' objects>, '__weakref__': <attribute '__weakref__' of 'SequenceElement' 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.residue'
__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

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__slots__ = ['is_gap', 'sequence']
__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)

hasStructure()
Returns:Whether this element has a structure i.e. whether it has

corresponding XYZ coordinates in Maestro. :rtype: bool

is_gap
is_res

Utility function to check whether a residue is not a gap

seq_index
sequence
class schrodinger.protein.residue.Residue(element_type, inscode=None, resnum=None, seqres_only=False)

Bases: schrodinger.models.json.JsonableClassMixin, schrodinger.protein.residue.SequenceElement

An amino acid residue.

__init__(element_type, inscode=None, resnum=None, seqres_only=False)
Parameters:
  • element_type (ResidueType) – The kind of the residue
  • inscode (str) – The insertion code
  • resnum (int) – PDB residue number
  • seqres_only (bool) – Whether this residue only appears in the SEQRES record of a structure. Only applies to sequences associated with a structure.
toJsonImplementation()

Abstract method that must be defined by all derived classes. Converts an instance of the derived class into a jsonifiable object.

Returns:A dict made up of JSON native datatypes or Jsonable objects. See the link below for a table of such types. https://docs.python.org/2/library/json.html#encoders-and-decoders
classmethod fromJsonImplementation(json_obj)

Abstract method that must be defined by all derived classes. Takes in a dictionary and constructs an instance of the derived class.

Parameters:json_dict (dict) – A dictionary loaded from a JSON string or file.
Returns:An instance of the derived class.

:rtype : cls

hasSetResNum() → bool
Returns:Whether a specific resnum has been set
resnum

If resnum is set to None, resnum will be auto-generated from column number.

inscode

If inscode and rescode are both set to None, the inscode will be ‘+’.

rescode
short_code
long_code
hydrophobicity
Returns:Hydrophobicity for the ResidueType on the Kyte-Doolittle scale, if available; otherwise None.
Return type:float
hydrophilicity
Returns:Hydrophilicity for the ResidueType on the Hopp-Woods scale, if available; otherwise None
Return type:float
charge
Returns:charge of the ResidueType of the residue
Return type:RESIDUE_CHARGE
helix_propensity
Returns:Helix propensity for the ResidueType of the residue
Return type:HELIX_PROPENSITY
beta_strand_propensity
Returns:Beta-strand propensity for the ResidueType of the residue
Return type:BETA_STRAND_PROPENSITY
turn_propensity
Returns:Turn propensity for the ResidueType of the residue
Return type:TURN_PROPENSITY
helix_termination_tendency
Returns:Helix termination tendency for the ResidueType of the residue
Return type:HELIX_TERMINATION_TENDENCY
exposure_tendency
Returns:Solvent exposure tendency for the ResidueType of the residue
Return type:SOLVENT_EXPOSURE_TENDENCY
steric_group
Returns:Steric group for the ResidueType of the residue
Return type:STERIC_GROUP
side_chain_chem
Returns:Side chain chemistry for the ResidueType of the residue
Return type:SIDE_CHAIN_CHEM
gapped_index_in_seq

Return the index of this residue within its sequence counting gaps

Returns:Index of this residue in its sequence or None if it is not part of a sequence.
Return type:int or None
gapless_index_in_seq

Return the index of this residue within its sequence ignoring gaps

Returns:Index of this residue in its sequence or None if it is not part of a sequence.
Return type:int or None
ss_prediction_psipred

Returns a DSSP code matching the secondary structure prediction for the residue or None. Value is calculated from thePsiPred backend.

ss_prediction_sspro

Returns a DSSP code matching the secondary structure prediction for the residue or None. Value is calculated from the SSpro backend.

isoelectric_point
Returns:A float representing the isoelectric point value for the ResidueType of the residue
getSimilarity(ref_res, similarity_matrix={('A', 'A'): 4, ('A', 'B'): -2, ('A', 'C'): 0, ('A', 'D'): -2, ('A', 'E'): -1, ('A', 'F'): -2, ('A', 'G'): 0, ('A', 'H'): -2, ('A', 'I'): -1, ('A', 'K'): -1, ('A', 'L'): -1, ('A', 'M'): -1, ('A', 'N'): -2, ('A', 'P'): -1, ('A', 'Q'): -1, ('A', 'R'): -1, ('A', 'S'): 1, ('A', 'T'): 0, ('A', 'V'): 0, ('A', 'W'): -3, ('A', 'X'): 0, ('A', 'Y'): -2, ('A', 'Z'): -1, ('B', 'A'): -2, ('B', 'B'): 4, ('B', 'C'): -3, ('B', 'D'): 4, ('B', 'E'): 1, ('B', 'F'): -3, ('B', 'G'): -1, ('B', 'H'): 0, ('B', 'I'): -3, ('B', 'K'): 0, ('B', 'L'): -4, ('B', 'M'): -3, ('B', 'N'): 3, ('B', 'P'): -2, ('B', 'Q'): 0, ('B', 'R'): -1, ('B', 'S'): 0, ('B', 'T'): -1, ('B', 'V'): -3, ('B', 'W'): -4, ('B', 'X'): -1, ('B', 'Y'): -3, ('B', 'Z'): 1, ('C', 'A'): 0, ('C', 'B'): -3, ('C', 'C'): 9, ('C', 'D'): -3, ('C', 'E'): -4, ('C', 'F'): -2, ('C', 'G'): -3, ('C', 'H'): -3, ('C', 'I'): -1, ('C', 'K'): -3, ('C', 'L'): -1, ('C', 'M'): -1, ('C', 'N'): -3, ('C', 'P'): -3, ('C', 'Q'): -3, ('C', 'R'): -3, ('C', 'S'): -1, ('C', 'T'): -1, ('C', 'V'): -1, ('C', 'W'): -2, ('C', 'X'): -2, ('C', 'Y'): -2, ('C', 'Z'): -3, ('D', 'A'): -2, ('D', 'B'): 4, ('D', 'C'): -3, ('D', 'D'): 6, ('D', 'E'): 2, ('D', 'F'): -3, ('D', 'G'): -1, ('D', 'H'): -1, ('D', 'I'): -3, ('D', 'K'): -1, ('D', 'L'): -4, ('D', 'M'): -3, ('D', 'N'): 1, ('D', 'P'): -1, ('D', 'Q'): 0, ('D', 'R'): -2, ('D', 'S'): 0, ('D', 'T'): -1, ('D', 'V'): -3, ('D', 'W'): -4, ('D', 'X'): -1, ('D', 'Y'): -3, ('D', 'Z'): 1, ('E', 'A'): -1, ('E', 'B'): 1, ('E', 'C'): -4, ('E', 'D'): 2, ('E', 'E'): 5, ('E', 'F'): -3, ('E', 'G'): -2, ('E', 'H'): 0, ('E', 'I'): -3, ('E', 'K'): 1, ('E', 'L'): -3, ('E', 'M'): -2, ('E', 'N'): 0, ('E', 'P'): -1, ('E', 'Q'): 2, ('E', 'R'): 0, ('E', 'S'): 0, ('E', 'T'): -1, ('E', 'V'): -2, ('E', 'W'): -3, ('E', 'X'): -1, ('E', 'Y'): -2, ('E', 'Z'): 4, ('F', 'A'): -2, ('F', 'B'): -3, ('F', 'C'): -2, ('F', 'D'): -3, ('F', 'E'): -3, ('F', 'F'): 6, ('F', 'G'): -3, ('F', 'H'): -1, ('F', 'I'): 0, ('F', 'K'): -3, ('F', 'L'): 0, ('F', 'M'): 0, ('F', 'N'): -3, ('F', 'P'): -4, ('F', 'Q'): -3, ('F', 'R'): -3, ('F', 'S'): -2, ('F', 'T'): -2, ('F', 'V'): -1, ('F', 'W'): 1, ('F', 'X'): -1, ('F', 'Y'): 3, ('F', 'Z'): -3, ('G', 'A'): 0, ('G', 'B'): -1, ('G', 'C'): -3, ('G', 'D'): -1, ('G', 'E'): -2, ('G', 'F'): -3, ('G', 'G'): 6, ('G', 'H'): -2, ('G', 'I'): -4, ('G', 'K'): -2, ('G', 'L'): -4, ('G', 'M'): -3, ('G', 'N'): 0, ('G', 'P'): -2, ('G', 'Q'): -2, ('G', 'R'): -2, ('G', 'S'): 0, ('G', 'T'): -2, ('G', 'V'): -3, ('G', 'W'): -2, ('G', 'X'): -1, ('G', 'Y'): -3, ('G', 'Z'): -2, ('H', 'A'): -2, ('H', 'B'): 0, ('H', 'C'): -3, ('H', 'D'): -1, ('H', 'E'): 0, ('H', 'F'): -1, ('H', 'G'): -2, ('H', 'H'): 8, ('H', 'I'): -3, ('H', 'K'): -1, ('H', 'L'): -3, ('H', 'M'): -2, ('H', 'N'): 1, ('H', 'P'): -2, ('H', 'Q'): 0, ('H', 'R'): 0, ('H', 'S'): -1, ('H', 'T'): -2, ('H', 'V'): -3, ('H', 'W'): -2, ('H', 'X'): -1, ('H', 'Y'): 2, ('H', 'Z'): 0, ('I', 'A'): -1, ('I', 'B'): -3, ('I', 'C'): -1, ('I', 'D'): -3, ('I', 'E'): -3, ('I', 'F'): 0, ('I', 'G'): -4, ('I', 'H'): -3, ('I', 'I'): 4, ('I', 'K'): -3, ('I', 'L'): 2, ('I', 'M'): 1, ('I', 'N'): -3, ('I', 'P'): -3, ('I', 'Q'): -3, ('I', 'R'): -3, ('I', 'S'): -2, ('I', 'T'): -1, ('I', 'V'): 3, ('I', 'W'): -3, ('I', 'X'): -1, ('I', 'Y'): -1, ('I', 'Z'): -3, ('K', 'A'): -1, ('K', 'B'): 0, ('K', 'C'): -3, ('K', 'D'): -1, ('K', 'E'): 1, ('K', 'F'): -3, ('K', 'G'): -2, ('K', 'H'): -1, ('K', 'I'): -3, ('K', 'K'): 5, ('K', 'L'): -2, ('K', 'M'): -1, ('K', 'N'): 0, ('K', 'P'): -1, ('K', 'Q'): 1, ('K', 'R'): 2, ('K', 'S'): 0, ('K', 'T'): -1, ('K', 'V'): -2, ('K', 'W'): -3, ('K', 'X'): -1, ('K', 'Y'): -2, ('K', 'Z'): 1, ('L', 'A'): -1, ('L', 'B'): -4, ('L', 'C'): -1, ('L', 'D'): -4, ('L', 'E'): -3, ('L', 'F'): 0, ('L', 'G'): -4, ('L', 'H'): -3, ('L', 'I'): 2, ('L', 'K'): -2, ('L', 'L'): 4, ('L', 'M'): 2, ('L', 'N'): -3, ('L', 'P'): -3, ('L', 'Q'): -2, ('L', 'R'): -2, ('L', 'S'): -2, ('L', 'T'): -1, ('L', 'V'): 1, ('L', 'W'): -2, ('L', 'X'): -1, ('L', 'Y'): -1, ('L', 'Z'): -3, ('M', 'A'): -1, ('M', 'B'): -3, ('M', 'C'): -1, ('M', 'D'): -3, ('M', 'E'): -2, ('M', 'F'): 0, ('M', 'G'): -3, ('M', 'H'): -2, ('M', 'I'): 1, ('M', 'K'): -1, ('M', 'L'): 2, ('M', 'M'): 5, ('M', 'N'): -2, ('M', 'P'): -2, ('M', 'Q'): 0, ('M', 'R'): -1, ('M', 'S'): -1, ('M', 'T'): -1, ('M', 'V'): 1, ('M', 'W'): -1, ('M', 'X'): -1, ('M', 'Y'): -1, ('M', 'Z'): -1, ('N', 'A'): -2, ('N', 'B'): 3, ('N', 'C'): -3, ('N', 'D'): 1, ('N', 'E'): 0, ('N', 'F'): -3, ('N', 'G'): 0, ('N', 'H'): 1, ('N', 'I'): -3, ('N', 'K'): 0, ('N', 'L'): -3, ('N', 'M'): -2, ('N', 'N'): 6, ('N', 'P'): -2, ('N', 'Q'): 0, ('N', 'R'): 0, ('N', 'S'): 1, ('N', 'T'): 0, ('N', 'V'): -3, ('N', 'W'): -4, ('N', 'X'): -1, ('N', 'Y'): -2, ('N', 'Z'): 0, ('P', 'A'): -1, ('P', 'B'): -2, ('P', 'C'): -3, ('P', 'D'): -1, ('P', 'E'): -1, ('P', 'F'): -4, ('P', 'G'): -2, ('P', 'H'): -2, ('P', 'I'): -3, ('P', 'K'): -1, ('P', 'L'): -3, ('P', 'M'): -2, ('P', 'N'): -2, ('P', 'P'): 7, ('P', 'Q'): -1, ('P', 'R'): -2, ('P', 'S'): -1, ('P', 'T'): -1, ('P', 'V'): -2, ('P', 'W'): -4, ('P', 'X'): -2, ('P', 'Y'): -3, ('P', 'Z'): -1, ('Q', 'A'): -1, ('Q', 'B'): 0, ('Q', 'C'): -3, ('Q', 'D'): 0, ('Q', 'E'): 2, ('Q', 'F'): -3, ('Q', 'G'): -2, ('Q', 'H'): 0, ('Q', 'I'): -3, ('Q', 'K'): 1, ('Q', 'L'): -2, ('Q', 'M'): 0, ('Q', 'N'): 0, ('Q', 'P'): -1, ('Q', 'Q'): 5, ('Q', 'R'): 1, ('Q', 'S'): 0, ('Q', 'T'): -1, ('Q', 'V'): -2, ('Q', 'W'): -2, ('Q', 'X'): -1, ('Q', 'Y'): -1, ('Q', 'Z'): 3, ('R', 'A'): -1, ('R', 'B'): -1, ('R', 'C'): -3, ('R', 'D'): -2, ('R', 'E'): 0, ('R', 'F'): -3, ('R', 'G'): -2, ('R', 'H'): 0, ('R', 'I'): -3, ('R', 'K'): 2, ('R', 'L'): -2, ('R', 'M'): -1, ('R', 'N'): 0, ('R', 'P'): -2, ('R', 'Q'): 1, ('R', 'R'): 5, ('R', 'S'): -1, ('R', 'T'): -1, ('R', 'V'): -3, ('R', 'W'): -3, ('R', 'X'): -1, ('R', 'Y'): -2, ('R', 'Z'): 0, ('S', 'A'): 1, ('S', 'B'): 0, ('S', 'C'): -1, ('S', 'D'): 0, ('S', 'E'): 0, ('S', 'F'): -2, ('S', 'G'): 0, ('S', 'H'): -1, ('S', 'I'): -2, ('S', 'K'): 0, ('S', 'L'): -2, ('S', 'M'): -1, ('S', 'N'): 1, ('S', 'P'): -1, ('S', 'Q'): 0, ('S', 'R'): -1, ('S', 'S'): 4, ('S', 'T'): 1, ('S', 'V'): -2, ('S', 'W'): -3, ('S', 'X'): 0, ('S', 'Y'): -2, ('S', 'Z'): 0, ('T', 'A'): 0, ('T', 'B'): -1, ('T', 'C'): -1, ('T', 'D'): -1, ('T', 'E'): -1, ('T', 'F'): -2, ('T', 'G'): -2, ('T', 'H'): -2, ('T', 'I'): -1, ('T', 'K'): -1, ('T', 'L'): -1, ('T', 'M'): -1, ('T', 'N'): 0, ('T', 'P'): -1, ('T', 'Q'): -1, ('T', 'R'): -1, ('T', 'S'): 1, ('T', 'T'): 5, ('T', 'V'): 0, ('T', 'W'): -2, ('T', 'X'): 0, ('T', 'Y'): -2, ('T', 'Z'): -1, ('V', 'A'): 0, ('V', 'B'): -3, ('V', 'C'): -1, ('V', 'D'): -3, ('V', 'E'): -2, ('V', 'F'): -1, ('V', 'G'): -3, ('V', 'H'): -3, ('V', 'I'): 3, ('V', 'K'): -2, ('V', 'L'): 1, ('V', 'M'): 1, ('V', 'N'): -3, ('V', 'P'): -2, ('V', 'Q'): -2, ('V', 'R'): -3, ('V', 'S'): -2, ('V', 'T'): 0, ('V', 'V'): 4, ('V', 'W'): -3, ('V', 'X'): -1, ('V', 'Y'): -1, ('V', 'Z'): -2, ('W', 'A'): -3, ('W', 'B'): -4, ('W', 'C'): -2, ('W', 'D'): -4, ('W', 'E'): -3, ('W', 'F'): 1, ('W', 'G'): -2, ('W', 'H'): -2, ('W', 'I'): -3, ('W', 'K'): -3, ('W', 'L'): -2, ('W', 'M'): -1, ('W', 'N'): -4, ('W', 'P'): -4, ('W', 'Q'): -2, ('W', 'R'): -3, ('W', 'S'): -3, ('W', 'T'): -2, ('W', 'V'): -3, ('W', 'W'): 11, ('W', 'X'): -2, ('W', 'Y'): 2, ('W', 'Z'): -3, ('X', 'A'): 0, ('X', 'B'): -1, ('X', 'C'): -2, ('X', 'D'): -1, ('X', 'E'): -1, ('X', 'F'): -1, ('X', 'G'): -1, ('X', 'H'): -1, ('X', 'I'): -1, ('X', 'K'): -1, ('X', 'L'): -1, ('X', 'M'): -1, ('X', 'N'): -1, ('X', 'P'): -2, ('X', 'Q'): -1, ('X', 'R'): -1, ('X', 'S'): 0, ('X', 'T'): 0, ('X', 'V'): -1, ('X', 'W'): -2, ('X', 'X'): -1, ('X', 'Y'): -1, ('X', 'Z'): -1, ('Y', 'A'): -2, ('Y', 'B'): -3, ('Y', 'C'): -2, ('Y', 'D'): -3, ('Y', 'E'): -2, ('Y', 'F'): 3, ('Y', 'G'): -3, ('Y', 'H'): 2, ('Y', 'I'): -1, ('Y', 'K'): -2, ('Y', 'L'): -1, ('Y', 'M'): -1, ('Y', 'N'): -2, ('Y', 'P'): -3, ('Y', 'Q'): -1, ('Y', 'R'): -2, ('Y', 'S'): -2, ('Y', 'T'): -2, ('Y', 'V'): -1, ('Y', 'W'): 2, ('Y', 'X'): -1, ('Y', 'Y'): 7, ('Y', 'Z'): -2, ('Z', 'A'): -1, ('Z', 'B'): 1, ('Z', 'C'): -3, ('Z', 'D'): 1, ('Z', 'E'): 4, ('Z', 'F'): -3, ('Z', 'G'): -2, ('Z', 'H'): 0, ('Z', 'I'): -3, ('Z', 'K'): 1, ('Z', 'L'): -3, ('Z', 'M'): -1, ('Z', 'N'): 0, ('Z', 'P'): -1, ('Z', 'Q'): 3, ('Z', 'R'): 0, ('Z', 'S'): 0, ('Z', 'T'): -1, ('Z', 'V'): -2, ('Z', 'W'): -3, ('Z', 'X'): -1, ('Z', 'Y'): -2, ('Z', 'Z'): 4})

Returns the similarity between the residue and a reference residue

Parameters:
Returns:

similarity score based on the similarity matrix
Return type:

float
getBinarySimilarity(ref_res, similarity_matrix={('A', 'A'): 4, ('A', 'B'): -2, ('A', 'C'): 0, ('A', 'D'): -2, ('A', 'E'): -1, ('A', 'F'): -2, ('A', 'G'): 0, ('A', 'H'): -2, ('A', 'I'): -1, ('A', 'K'): -1, ('A', 'L'): -1, ('A', 'M'): -1, ('A', 'N'): -2, ('A', 'P'): -1, ('A', 'Q'): -1, ('A', 'R'): -1, ('A', 'S'): 1, ('A', 'T'): 0, ('A', 'V'): 0, ('A', 'W'): -3, ('A', 'X'): 0, ('A', 'Y'): -2, ('A', 'Z'): -1, ('B', 'A'): -2, ('B', 'B'): 4, ('B', 'C'): -3, ('B', 'D'): 4, ('B', 'E'): 1, ('B', 'F'): -3, ('B', 'G'): -1, ('B', 'H'): 0, ('B', 'I'): -3, ('B', 'K'): 0, ('B', 'L'): -4, ('B', 'M'): -3, ('B', 'N'): 3, ('B', 'P'): -2, ('B', 'Q'): 0, ('B', 'R'): -1, ('B', 'S'): 0, ('B', 'T'): -1, ('B', 'V'): -3, ('B', 'W'): -4, ('B', 'X'): -1, ('B', 'Y'): -3, ('B', 'Z'): 1, ('C', 'A'): 0, ('C', 'B'): -3, ('C', 'C'): 9, ('C', 'D'): -3, ('C', 'E'): -4, ('C', 'F'): -2, ('C', 'G'): -3, ('C', 'H'): -3, ('C', 'I'): -1, ('C', 'K'): -3, ('C', 'L'): -1, ('C', 'M'): -1, ('C', 'N'): -3, ('C', 'P'): -3, ('C', 'Q'): -3, ('C', 'R'): -3, ('C', 'S'): -1, ('C', 'T'): -1, ('C', 'V'): -1, ('C', 'W'): -2, ('C', 'X'): -2, ('C', 'Y'): -2, ('C', 'Z'): -3, ('D', 'A'): -2, ('D', 'B'): 4, ('D', 'C'): -3, ('D', 'D'): 6, ('D', 'E'): 2, ('D', 'F'): -3, ('D', 'G'): -1, ('D', 'H'): -1, ('D', 'I'): -3, ('D', 'K'): -1, ('D', 'L'): -4, ('D', 'M'): -3, ('D', 'N'): 1, ('D', 'P'): -1, ('D', 'Q'): 0, ('D', 'R'): -2, ('D', 'S'): 0, ('D', 'T'): -1, ('D', 'V'): -3, ('D', 'W'): -4, ('D', 'X'): -1, ('D', 'Y'): -3, ('D', 'Z'): 1, ('E', 'A'): -1, ('E', 'B'): 1, ('E', 'C'): -4, ('E', 'D'): 2, ('E', 'E'): 5, ('E', 'F'): -3, ('E', 'G'): -2, ('E', 'H'): 0, ('E', 'I'): -3, ('E', 'K'): 1, ('E', 'L'): -3, ('E', 'M'): -2, ('E', 'N'): 0, ('E', 'P'): -1, ('E', 'Q'): 2, ('E', 'R'): 0, ('E', 'S'): 0, ('E', 'T'): -1, ('E', 'V'): -2, ('E', 'W'): -3, ('E', 'X'): -1, ('E', 'Y'): -2, ('E', 'Z'): 4, ('F', 'A'): -2, ('F', 'B'): -3, ('F', 'C'): -2, ('F', 'D'): -3, ('F', 'E'): -3, ('F', 'F'): 6, ('F', 'G'): -3, ('F', 'H'): -1, ('F', 'I'): 0, ('F', 'K'): -3, ('F', 'L'): 0, ('F', 'M'): 0, ('F', 'N'): -3, ('F', 'P'): -4, ('F', 'Q'): -3, ('F', 'R'): -3, ('F', 'S'): -2, ('F', 'T'): -2, ('F', 'V'): -1, ('F', 'W'): 1, ('F', 'X'): -1, ('F', 'Y'): 3, ('F', 'Z'): -3, ('G', 'A'): 0, ('G', 'B'): -1, ('G', 'C'): -3, ('G', 'D'): -1, ('G', 'E'): -2, ('G', 'F'): -3, ('G', 'G'): 6, ('G', 'H'): -2, ('G', 'I'): -4, ('G', 'K'): -2, ('G', 'L'): -4, ('G', 'M'): -3, ('G', 'N'): 0, ('G', 'P'): -2, ('G', 'Q'): -2, ('G', 'R'): -2, ('G', 'S'): 0, ('G', 'T'): -2, ('G', 'V'): -3, ('G', 'W'): -2, ('G', 'X'): -1, ('G', 'Y'): -3, ('G', 'Z'): -2, ('H', 'A'): -2, ('H', 'B'): 0, ('H', 'C'): -3, ('H', 'D'): -1, ('H', 'E'): 0, ('H', 'F'): -1, ('H', 'G'): -2, ('H', 'H'): 8, ('H', 'I'): -3, ('H', 'K'): -1, ('H', 'L'): -3, ('H', 'M'): -2, ('H', 'N'): 1, ('H', 'P'): -2, ('H', 'Q'): 0, ('H', 'R'): 0, ('H', 'S'): -1, ('H', 'T'): -2, ('H', 'V'): -3, ('H', 'W'): -2, ('H', 'X'): -1, ('H', 'Y'): 2, ('H', 'Z'): 0, ('I', 'A'): -1, ('I', 'B'): -3, ('I', 'C'): -1, ('I', 'D'): -3, ('I', 'E'): -3, ('I', 'F'): 0, ('I', 'G'): -4, ('I', 'H'): -3, ('I', 'I'): 4, ('I', 'K'): -3, ('I', 'L'): 2, ('I', 'M'): 1, ('I', 'N'): -3, ('I', 'P'): -3, ('I', 'Q'): -3, ('I', 'R'): -3, ('I', 'S'): -2, ('I', 'T'): -1, ('I', 'V'): 3, ('I', 'W'): -3, ('I', 'X'): -1, ('I', 'Y'): -1, ('I', 'Z'): -3, ('K', 'A'): -1, ('K', 'B'): 0, ('K', 'C'): -3, ('K', 'D'): -1, ('K', 'E'): 1, ('K', 'F'): -3, ('K', 'G'): -2, ('K', 'H'): -1, ('K', 'I'): -3, ('K', 'K'): 5, ('K', 'L'): -2, ('K', 'M'): -1, ('K', 'N'): 0, ('K', 'P'): -1, ('K', 'Q'): 1, ('K', 'R'): 2, ('K', 'S'): 0, ('K', 'T'): -1, ('K', 'V'): -2, ('K', 'W'): -3, ('K', 'X'): -1, ('K', 'Y'): -2, ('K', 'Z'): 1, ('L', 'A'): -1, ('L', 'B'): -4, ('L', 'C'): -1, ('L', 'D'): -4, ('L', 'E'): -3, ('L', 'F'): 0, ('L', 'G'): -4, ('L', 'H'): -3, ('L', 'I'): 2, ('L', 'K'): -2, ('L', 'L'): 4, ('L', 'M'): 2, ('L', 'N'): -3, ('L', 'P'): -3, ('L', 'Q'): -2, ('L', 'R'): -2, ('L', 'S'): -2, ('L', 'T'): -1, ('L', 'V'): 1, ('L', 'W'): -2, ('L', 'X'): -1, ('L', 'Y'): -1, ('L', 'Z'): -3, ('M', 'A'): -1, ('M', 'B'): -3, ('M', 'C'): -1, ('M', 'D'): -3, ('M', 'E'): -2, ('M', 'F'): 0, ('M', 'G'): -3, ('M', 'H'): -2, ('M', 'I'): 1, ('M', 'K'): -1, ('M', 'L'): 2, ('M', 'M'): 5, ('M', 'N'): -2, ('M', 'P'): -2, ('M', 'Q'): 0, ('M', 'R'): -1, ('M', 'S'): -1, ('M', 'T'): -1, ('M', 'V'): 1, ('M', 'W'): -1, ('M', 'X'): -1, ('M', 'Y'): -1, ('M', 'Z'): -1, ('N', 'A'): -2, ('N', 'B'): 3, ('N', 'C'): -3, ('N', 'D'): 1, ('N', 'E'): 0, ('N', 'F'): -3, ('N', 'G'): 0, ('N', 'H'): 1, ('N', 'I'): -3, ('N', 'K'): 0, ('N', 'L'): -3, ('N', 'M'): -2, ('N', 'N'): 6, ('N', 'P'): -2, ('N', 'Q'): 0, ('N', 'R'): 0, ('N', 'S'): 1, ('N', 'T'): 0, ('N', 'V'): -3, ('N', 'W'): -4, ('N', 'X'): -1, ('N', 'Y'): -2, ('N', 'Z'): 0, ('P', 'A'): -1, ('P', 'B'): -2, ('P', 'C'): -3, ('P', 'D'): -1, ('P', 'E'): -1, ('P', 'F'): -4, ('P', 'G'): -2, ('P', 'H'): -2, ('P', 'I'): -3, ('P', 'K'): -1, ('P', 'L'): -3, ('P', 'M'): -2, ('P', 'N'): -2, ('P', 'P'): 7, ('P', 'Q'): -1, ('P', 'R'): -2, ('P', 'S'): -1, ('P', 'T'): -1, ('P', 'V'): -2, ('P', 'W'): -4, ('P', 'X'): -2, ('P', 'Y'): -3, ('P', 'Z'): -1, ('Q', 'A'): -1, ('Q', 'B'): 0, ('Q', 'C'): -3, ('Q', 'D'): 0, ('Q', 'E'): 2, ('Q', 'F'): -3, ('Q', 'G'): -2, ('Q', 'H'): 0, ('Q', 'I'): -3, ('Q', 'K'): 1, ('Q', 'L'): -2, ('Q', 'M'): 0, ('Q', 'N'): 0, ('Q', 'P'): -1, ('Q', 'Q'): 5, ('Q', 'R'): 1, ('Q', 'S'): 0, ('Q', 'T'): -1, ('Q', 'V'): -2, ('Q', 'W'): -2, ('Q', 'X'): -1, ('Q', 'Y'): -1, ('Q', 'Z'): 3, ('R', 'A'): -1, ('R', 'B'): -1, ('R', 'C'): -3, ('R', 'D'): -2, ('R', 'E'): 0, ('R', 'F'): -3, ('R', 'G'): -2, ('R', 'H'): 0, ('R', 'I'): -3, ('R', 'K'): 2, ('R', 'L'): -2, ('R', 'M'): -1, ('R', 'N'): 0, ('R', 'P'): -2, ('R', 'Q'): 1, ('R', 'R'): 5, ('R', 'S'): -1, ('R', 'T'): -1, ('R', 'V'): -3, ('R', 'W'): -3, ('R', 'X'): -1, ('R', 'Y'): -2, ('R', 'Z'): 0, ('S', 'A'): 1, ('S', 'B'): 0, ('S', 'C'): -1, ('S', 'D'): 0, ('S', 'E'): 0, ('S', 'F'): -2, ('S', 'G'): 0, ('S', 'H'): -1, ('S', 'I'): -2, ('S', 'K'): 0, ('S', 'L'): -2, ('S', 'M'): -1, ('S', 'N'): 1, ('S', 'P'): -1, ('S', 'Q'): 0, ('S', 'R'): -1, ('S', 'S'): 4, ('S', 'T'): 1, ('S', 'V'): -2, ('S', 'W'): -3, ('S', 'X'): 0, ('S', 'Y'): -2, ('S', 'Z'): 0, ('T', 'A'): 0, ('T', 'B'): -1, ('T', 'C'): -1, ('T', 'D'): -1, ('T', 'E'): -1, ('T', 'F'): -2, ('T', 'G'): -2, ('T', 'H'): -2, ('T', 'I'): -1, ('T', 'K'): -1, ('T', 'L'): -1, ('T', 'M'): -1, ('T', 'N'): 0, ('T', 'P'): -1, ('T', 'Q'): -1, ('T', 'R'): -1, ('T', 'S'): 1, ('T', 'T'): 5, ('T', 'V'): 0, ('T', 'W'): -2, ('T', 'X'): 0, ('T', 'Y'): -2, ('T', 'Z'): -1, ('V', 'A'): 0, ('V', 'B'): -3, ('V', 'C'): -1, ('V', 'D'): -3, ('V', 'E'): -2, ('V', 'F'): -1, ('V', 'G'): -3, ('V', 'H'): -3, ('V', 'I'): 3, ('V', 'K'): -2, ('V', 'L'): 1, ('V', 'M'): 1, ('V', 'N'): -3, ('V', 'P'): -2, ('V', 'Q'): -2, ('V', 'R'): -3, ('V', 'S'): -2, ('V', 'T'): 0, ('V', 'V'): 4, ('V', 'W'): -3, ('V', 'X'): -1, ('V', 'Y'): -1, ('V', 'Z'): -2, ('W', 'A'): -3, ('W', 'B'): -4, ('W', 'C'): -2, ('W', 'D'): -4, ('W', 'E'): -3, ('W', 'F'): 1, ('W', 'G'): -2, ('W', 'H'): -2, ('W', 'I'): -3, ('W', 'K'): -3, ('W', 'L'): -2, ('W', 'M'): -1, ('W', 'N'): -4, ('W', 'P'): -4, ('W', 'Q'): -2, ('W', 'R'): -3, ('W', 'S'): -3, ('W', 'T'): -2, ('W', 'V'): -3, ('W', 'W'): 11, ('W', 'X'): -2, ('W', 'Y'): 2, ('W', 'Z'): -3, ('X', 'A'): 0, ('X', 'B'): -1, ('X', 'C'): -2, ('X', 'D'): -1, ('X', 'E'): -1, ('X', 'F'): -1, ('X', 'G'): -1, ('X', 'H'): -1, ('X', 'I'): -1, ('X', 'K'): -1, ('X', 'L'): -1, ('X', 'M'): -1, ('X', 'N'): -1, ('X', 'P'): -2, ('X', 'Q'): -1, ('X', 'R'): -1, ('X', 'S'): 0, ('X', 'T'): 0, ('X', 'V'): -1, ('X', 'W'): -2, ('X', 'X'): -1, ('X', 'Y'): -1, ('X', 'Z'): -1, ('Y', 'A'): -2, ('Y', 'B'): -3, ('Y', 'C'): -2, ('Y', 'D'): -3, ('Y', 'E'): -2, ('Y', 'F'): 3, ('Y', 'G'): -3, ('Y', 'H'): 2, ('Y', 'I'): -1, ('Y', 'K'): -2, ('Y', 'L'): -1, ('Y', 'M'): -1, ('Y', 'N'): -2, ('Y', 'P'): -3, ('Y', 'Q'): -1, ('Y', 'R'): -2, ('Y', 'S'): -2, ('Y', 'T'): -2, ('Y', 'V'): -1, ('Y', 'W'): 2, ('Y', 'X'): -1, ('Y', 'Y'): 7, ('Y', 'Z'): -2, ('Z', 'A'): -1, ('Z', 'B'): 1, ('Z', 'C'): -3, ('Z', 'D'): 1, ('Z', 'E'): 4, ('Z', 'F'): -3, ('Z', 'G'): -2, ('Z', 'H'): 0, ('Z', 'I'): -3, ('Z', 'K'): 1, ('Z', 'L'): -3, ('Z', 'M'): -1, ('Z', 'N'): 0, ('Z', 'P'): -1, ('Z', 'Q'): 3, ('Z', 'R'): 0, ('Z', 'S'): 0, ('Z', 'T'): -1, ('Z', 'V'): -2, ('Z', 'W'): -3, ('Z', 'X'): -1, ('Z', 'Y'): -2, ('Z', 'Z'): 4})

Returns if the residue and a reference residue are similar

Parameters:
Returns:

1 if the similarity score is positive, otherwise 0.
Return type:

int
getIdentity(ref_res)

Return the identity between the residue and a reference residue

Parameters:ref_res (schrodinger.protein.residue.Residue) – The reference residue
Returns:1 if same as the reference residue, 0 otherwise.
Return type:int
getConservation(ref_res)

Return whether the residue and a reference residue have similar side-chain chemistry.

The similarity criterion is based on “side chain chemistry” descriptor matching.

Parameters:ref_res (schrodinger.protein.residue.Residue) – The reference residue
Returns:1 if the residue and reference residue are have similar side chain chemistry, 0 otherwise.
Return type:int
__class__

alias of builtins.type

__copy__()
__deepcopy__(memo)
__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.protein.residue', '__doc__': '\n An amino acid residue.\n ', '__init__': <function Residue.__init__>, 'toJsonImplementation': <function Residue.toJsonImplementation>, 'fromJsonImplementation': <classmethod object>, '_getCopyBlackList': <function Residue._getCopyBlackList>, '_getReprKwargList': <function Residue._getReprKwargList>, 'hasSetResNum': <function Residue.hasSetResNum>, 'resnum': <property object>, 'inscode': <property object>, 'rescode': <property object>, 'short_code': <property object>, 'long_code': <property object>, 'hydrophobicity': <property object>, 'hydrophilicity': <property object>, 'charge': <property object>, 'helix_propensity': <property object>, 'beta_strand_propensity': <property object>, 'turn_propensity': <property object>, 'helix_termination_tendency': <property object>, 'exposure_tendency': <property object>, 'steric_group': <property object>, 'side_chain_chem': <property object>, 'ss_prediction_sspro': <property object>, 'ss_prediction_psipred': <property object>, 'gapped_index_in_seq': <property object>, 'gapless_index_in_seq': <property object>, '_indexInSeq': <function Residue._indexInSeq>, 'isoelectric_point': <property object>, 'getSimilarity': <function Residue.getSimilarity>, 'getBinarySimilarity': <function Residue.getBinarySimilarity>, 'getIdentity': <function Residue.getIdentity>, 'getConservation': <function Residue.getConservation>, '_Residue_jsonAdapters': []})
__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).

classmethod __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.residue'
__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

__slots__ = ['is_gap', 'sequence']
__str__()

Returns the short code for the residue

__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)

classmethod fromJson(json_obj)

A factory method which constructs a new object from a given dict loaded from a json string or file.

Parameters:json_obj (dict) – A json-loaded dictionary to create an object from.
Returns:An instance of this class.

:rtype : cls

get_version()

Method to get the version of a particular object. Defaults to the current version of mmshare. This class can be overridden for custom versioning behavior.

hasStructure()
Returns:Whether this element has a structure i.e. whether it has

corresponding XYZ coordinates in Maestro. :rtype: bool

is_gap
is_res

Utility function to check whether a residue is not a gap

seq_index
sequence
toJson(_mark_version=True)

Create and returns a data structure made up of jsonable items.

Return type:An instance of one the classes from NATIVE_JSON_DATATYPES
class schrodinger.protein.residue.DisulfideBond(res1, res2)

Bases: object

Representation of a disulfide bond.

__init__(res1, res2)
Parameters:res_pair (iterable(residue.Residue, residue.Residue)) – Pair of residues to link with a disulfide bond
__eq__(other)

Return self==value.

__ne__(other)

Return self!=value.

__hash__()

Return hash(self).

res_pair
isValid()

Check whether the disulfide bond is valid and if so, return its seqs.

Returns:False if the disulfide bond is invalid, the seqs otherwise.
Return type:bool or list(sequence.ProteinSequence, sequence.ProteinSequence)
__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.protein.residue', '__doc__': '\n Representation of a disulfide bond.\n ', '__init__': <function DisulfideBond.__init__>, '__eq__': <function DisulfideBond.__eq__>, '__ne__': <function DisulfideBond.__ne__>, '__hash__': <function DisulfideBond.__hash__>, 'res_pair': <property object>, 'isValid': <function DisulfideBond.isValid>, 'is_intra_sequence': <property object>, 'is_inter_sequence': <property object>, '__iter__': <function DisulfideBond.__iter__>, '__dict__': <attribute '__dict__' of 'DisulfideBond' objects>, '__weakref__': <attribute '__weakref__' of 'DisulfideBond' objects>})
__dir__() → list

default dir() implementation

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__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.residue'
__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)

is_intra_sequence

Check whether the bond is valid and intra-sequence.

Returns:Whether the bond is a valid, intra-sequence bond.
Return type:bool
Raises:ValueError – If the bond is not valid
is_inter_sequence

Check whether the bond is valid and inter-sequence.

Returns:Whether the bond is a valid, inter-sequence bond.
Return type:bool
Raises:ValueError – If the bond is not valid
__iter__()
schrodinger.protein.residue.add_disulfide_bond(res1, res2)

Add a disulfide bond between two residues.

Parameters:
schrodinger.protein.residue.remove_disulfide_bond(res1, res2)

Remove a disulfide bond between two residues.

Parameters:
class schrodinger.protein.residue.Nucleotide(element_type, inscode=None, resnum=None, seqres_only=False)

Bases: schrodinger.protein.residue.Residue

__class__

alias of builtins.type

__copy__()
__deepcopy__(memo)
__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.protein.residue', '__doc__': None, '_Nucleotide_jsonAdapters': []})
__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__(element_type, inscode=None, resnum=None, seqres_only=False)
Parameters:
  • element_type (ResidueType) – The kind of the residue
  • inscode (str) – The insertion code
  • resnum (int) – PDB residue number
  • seqres_only (bool) – Whether this residue only appears in the SEQRES record of a structure. Only applies to sequences associated with a structure.
classmethod __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.residue'
__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

__slots__ = ['is_gap', 'sequence']
__str__()

Returns the short code for the residue

__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)

beta_strand_propensity
Returns:Beta-strand propensity for the ResidueType of the residue
Return type:BETA_STRAND_PROPENSITY
charge
Returns:charge of the ResidueType of the residue
Return type:RESIDUE_CHARGE
exposure_tendency
Returns:Solvent exposure tendency for the ResidueType of the residue
Return type:SOLVENT_EXPOSURE_TENDENCY
classmethod fromJson(json_obj)

A factory method which constructs a new object from a given dict loaded from a json string or file.

Parameters:json_obj (dict) – A json-loaded dictionary to create an object from.
Returns:An instance of this class.

:rtype : cls

classmethod fromJsonImplementation(json_obj)

Abstract method that must be defined by all derived classes. Takes in a dictionary and constructs an instance of the derived class.

Parameters:json_dict (dict) – A dictionary loaded from a JSON string or file.
Returns:An instance of the derived class.

:rtype : cls

gapless_index_in_seq

Return the index of this residue within its sequence ignoring gaps

Returns:Index of this residue in its sequence or None if it is not part of a sequence.
Return type:int or None
gapped_index_in_seq

Return the index of this residue within its sequence counting gaps

Returns:Index of this residue in its sequence or None if it is not part of a sequence.
Return type:int or None
getBinarySimilarity(ref_res, similarity_matrix={('A', 'A'): 4, ('A', 'B'): -2, ('A', 'C'): 0, ('A', 'D'): -2, ('A', 'E'): -1, ('A', 'F'): -2, ('A', 'G'): 0, ('A', 'H'): -2, ('A', 'I'): -1, ('A', 'K'): -1, ('A', 'L'): -1, ('A', 'M'): -1, ('A', 'N'): -2, ('A', 'P'): -1, ('A', 'Q'): -1, ('A', 'R'): -1, ('A', 'S'): 1, ('A', 'T'): 0, ('A', 'V'): 0, ('A', 'W'): -3, ('A', 'X'): 0, ('A', 'Y'): -2, ('A', 'Z'): -1, ('B', 'A'): -2, ('B', 'B'): 4, ('B', 'C'): -3, ('B', 'D'): 4, ('B', 'E'): 1, ('B', 'F'): -3, ('B', 'G'): -1, ('B', 'H'): 0, ('B', 'I'): -3, ('B', 'K'): 0, ('B', 'L'): -4, ('B', 'M'): -3, ('B', 'N'): 3, ('B', 'P'): -2, ('B', 'Q'): 0, ('B', 'R'): -1, ('B', 'S'): 0, ('B', 'T'): -1, ('B', 'V'): -3, ('B', 'W'): -4, ('B', 'X'): -1, ('B', 'Y'): -3, ('B', 'Z'): 1, ('C', 'A'): 0, ('C', 'B'): -3, ('C', 'C'): 9, ('C', 'D'): -3, ('C', 'E'): -4, ('C', 'F'): -2, ('C', 'G'): -3, ('C', 'H'): -3, ('C', 'I'): -1, ('C', 'K'): -3, ('C', 'L'): -1, ('C', 'M'): -1, ('C', 'N'): -3, ('C', 'P'): -3, ('C', 'Q'): -3, ('C', 'R'): -3, ('C', 'S'): -1, ('C', 'T'): -1, ('C', 'V'): -1, ('C', 'W'): -2, ('C', 'X'): -2, ('C', 'Y'): -2, ('C', 'Z'): -3, ('D', 'A'): -2, ('D', 'B'): 4, ('D', 'C'): -3, ('D', 'D'): 6, ('D', 'E'): 2, ('D', 'F'): -3, ('D', 'G'): -1, ('D', 'H'): -1, ('D', 'I'): -3, ('D', 'K'): -1, ('D', 'L'): -4, ('D', 'M'): -3, ('D', 'N'): 1, ('D', 'P'): -1, ('D', 'Q'): 0, ('D', 'R'): -2, ('D', 'S'): 0, ('D', 'T'): -1, ('D', 'V'): -3, ('D', 'W'): -4, ('D', 'X'): -1, ('D', 'Y'): -3, ('D', 'Z'): 1, ('E', 'A'): -1, ('E', 'B'): 1, ('E', 'C'): -4, ('E', 'D'): 2, ('E', 'E'): 5, ('E', 'F'): -3, ('E', 'G'): -2, ('E', 'H'): 0, ('E', 'I'): -3, ('E', 'K'): 1, ('E', 'L'): -3, ('E', 'M'): -2, ('E', 'N'): 0, ('E', 'P'): -1, ('E', 'Q'): 2, ('E', 'R'): 0, ('E', 'S'): 0, ('E', 'T'): -1, ('E', 'V'): -2, ('E', 'W'): -3, ('E', 'X'): -1, ('E', 'Y'): -2, ('E', 'Z'): 4, ('F', 'A'): -2, ('F', 'B'): -3, ('F', 'C'): -2, ('F', 'D'): -3, ('F', 'E'): -3, ('F', 'F'): 6, ('F', 'G'): -3, ('F', 'H'): -1, ('F', 'I'): 0, ('F', 'K'): -3, ('F', 'L'): 0, ('F', 'M'): 0, ('F', 'N'): -3, ('F', 'P'): -4, ('F', 'Q'): -3, ('F', 'R'): -3, ('F', 'S'): -2, ('F', 'T'): -2, ('F', 'V'): -1, ('F', 'W'): 1, ('F', 'X'): -1, ('F', 'Y'): 3, ('F', 'Z'): -3, ('G', 'A'): 0, ('G', 'B'): -1, ('G', 'C'): -3, ('G', 'D'): -1, ('G', 'E'): -2, ('G', 'F'): -3, ('G', 'G'): 6, ('G', 'H'): -2, ('G', 'I'): -4, ('G', 'K'): -2, ('G', 'L'): -4, ('G', 'M'): -3, ('G', 'N'): 0, ('G', 'P'): -2, ('G', 'Q'): -2, ('G', 'R'): -2, ('G', 'S'): 0, ('G', 'T'): -2, ('G', 'V'): -3, ('G', 'W'): -2, ('G', 'X'): -1, ('G', 'Y'): -3, ('G', 'Z'): -2, ('H', 'A'): -2, ('H', 'B'): 0, ('H', 'C'): -3, ('H', 'D'): -1, ('H', 'E'): 0, ('H', 'F'): -1, ('H', 'G'): -2, ('H', 'H'): 8, ('H', 'I'): -3, ('H', 'K'): -1, ('H', 'L'): -3, ('H', 'M'): -2, ('H', 'N'): 1, ('H', 'P'): -2, ('H', 'Q'): 0, ('H', 'R'): 0, ('H', 'S'): -1, ('H', 'T'): -2, ('H', 'V'): -3, ('H', 'W'): -2, ('H', 'X'): -1, ('H', 'Y'): 2, ('H', 'Z'): 0, ('I', 'A'): -1, ('I', 'B'): -3, ('I', 'C'): -1, ('I', 'D'): -3, ('I', 'E'): -3, ('I', 'F'): 0, ('I', 'G'): -4, ('I', 'H'): -3, ('I', 'I'): 4, ('I', 'K'): -3, ('I', 'L'): 2, ('I', 'M'): 1, ('I', 'N'): -3, ('I', 'P'): -3, ('I', 'Q'): -3, ('I', 'R'): -3, ('I', 'S'): -2, ('I', 'T'): -1, ('I', 'V'): 3, ('I', 'W'): -3, ('I', 'X'): -1, ('I', 'Y'): -1, ('I', 'Z'): -3, ('K', 'A'): -1, ('K', 'B'): 0, ('K', 'C'): -3, ('K', 'D'): -1, ('K', 'E'): 1, ('K', 'F'): -3, ('K', 'G'): -2, ('K', 'H'): -1, ('K', 'I'): -3, ('K', 'K'): 5, ('K', 'L'): -2, ('K', 'M'): -1, ('K', 'N'): 0, ('K', 'P'): -1, ('K', 'Q'): 1, ('K', 'R'): 2, ('K', 'S'): 0, ('K', 'T'): -1, ('K', 'V'): -2, ('K', 'W'): -3, ('K', 'X'): -1, ('K', 'Y'): -2, ('K', 'Z'): 1, ('L', 'A'): -1, ('L', 'B'): -4, ('L', 'C'): -1, ('L', 'D'): -4, ('L', 'E'): -3, ('L', 'F'): 0, ('L', 'G'): -4, ('L', 'H'): -3, ('L', 'I'): 2, ('L', 'K'): -2, ('L', 'L'): 4, ('L', 'M'): 2, ('L', 'N'): -3, ('L', 'P'): -3, ('L', 'Q'): -2, ('L', 'R'): -2, ('L', 'S'): -2, ('L', 'T'): -1, ('L', 'V'): 1, ('L', 'W'): -2, ('L', 'X'): -1, ('L', 'Y'): -1, ('L', 'Z'): -3, ('M', 'A'): -1, ('M', 'B'): -3, ('M', 'C'): -1, ('M', 'D'): -3, ('M', 'E'): -2, ('M', 'F'): 0, ('M', 'G'): -3, ('M', 'H'): -2, ('M', 'I'): 1, ('M', 'K'): -1, ('M', 'L'): 2, ('M', 'M'): 5, ('M', 'N'): -2, ('M', 'P'): -2, ('M', 'Q'): 0, ('M', 'R'): -1, ('M', 'S'): -1, ('M', 'T'): -1, ('M', 'V'): 1, ('M', 'W'): -1, ('M', 'X'): -1, ('M', 'Y'): -1, ('M', 'Z'): -1, ('N', 'A'): -2, ('N', 'B'): 3, ('N', 'C'): -3, ('N', 'D'): 1, ('N', 'E'): 0, ('N', 'F'): -3, ('N', 'G'): 0, ('N', 'H'): 1, ('N', 'I'): -3, ('N', 'K'): 0, ('N', 'L'): -3, ('N', 'M'): -2, ('N', 'N'): 6, ('N', 'P'): -2, ('N', 'Q'): 0, ('N', 'R'): 0, ('N', 'S'): 1, ('N', 'T'): 0, ('N', 'V'): -3, ('N', 'W'): -4, ('N', 'X'): -1, ('N', 'Y'): -2, ('N', 'Z'): 0, ('P', 'A'): -1, ('P', 'B'): -2, ('P', 'C'): -3, ('P', 'D'): -1, ('P', 'E'): -1, ('P', 'F'): -4, ('P', 'G'): -2, ('P', 'H'): -2, ('P', 'I'): -3, ('P', 'K'): -1, ('P', 'L'): -3, ('P', 'M'): -2, ('P', 'N'): -2, ('P', 'P'): 7, ('P', 'Q'): -1, ('P', 'R'): -2, ('P', 'S'): -1, ('P', 'T'): -1, ('P', 'V'): -2, ('P', 'W'): -4, ('P', 'X'): -2, ('P', 'Y'): -3, ('P', 'Z'): -1, ('Q', 'A'): -1, ('Q', 'B'): 0, ('Q', 'C'): -3, ('Q', 'D'): 0, ('Q', 'E'): 2, ('Q', 'F'): -3, ('Q', 'G'): -2, ('Q', 'H'): 0, ('Q', 'I'): -3, ('Q', 'K'): 1, ('Q', 'L'): -2, ('Q', 'M'): 0, ('Q', 'N'): 0, ('Q', 'P'): -1, ('Q', 'Q'): 5, ('Q', 'R'): 1, ('Q', 'S'): 0, ('Q', 'T'): -1, ('Q', 'V'): -2, ('Q', 'W'): -2, ('Q', 'X'): -1, ('Q', 'Y'): -1, ('Q', 'Z'): 3, ('R', 'A'): -1, ('R', 'B'): -1, ('R', 'C'): -3, ('R', 'D'): -2, ('R', 'E'): 0, ('R', 'F'): -3, ('R', 'G'): -2, ('R', 'H'): 0, ('R', 'I'): -3, ('R', 'K'): 2, ('R', 'L'): -2, ('R', 'M'): -1, ('R', 'N'): 0, ('R', 'P'): -2, ('R', 'Q'): 1, ('R', 'R'): 5, ('R', 'S'): -1, ('R', 'T'): -1, ('R', 'V'): -3, ('R', 'W'): -3, ('R', 'X'): -1, ('R', 'Y'): -2, ('R', 'Z'): 0, ('S', 'A'): 1, ('S', 'B'): 0, ('S', 'C'): -1, ('S', 'D'): 0, ('S', 'E'): 0, ('S', 'F'): -2, ('S', 'G'): 0, ('S', 'H'): -1, ('S', 'I'): -2, ('S', 'K'): 0, ('S', 'L'): -2, ('S', 'M'): -1, ('S', 'N'): 1, ('S', 'P'): -1, ('S', 'Q'): 0, ('S', 'R'): -1, ('S', 'S'): 4, ('S', 'T'): 1, ('S', 'V'): -2, ('S', 'W'): -3, ('S', 'X'): 0, ('S', 'Y'): -2, ('S', 'Z'): 0, ('T', 'A'): 0, ('T', 'B'): -1, ('T', 'C'): -1, ('T', 'D'): -1, ('T', 'E'): -1, ('T', 'F'): -2, ('T', 'G'): -2, ('T', 'H'): -2, ('T', 'I'): -1, ('T', 'K'): -1, ('T', 'L'): -1, ('T', 'M'): -1, ('T', 'N'): 0, ('T', 'P'): -1, ('T', 'Q'): -1, ('T', 'R'): -1, ('T', 'S'): 1, ('T', 'T'): 5, ('T', 'V'): 0, ('T', 'W'): -2, ('T', 'X'): 0, ('T', 'Y'): -2, ('T', 'Z'): -1, ('V', 'A'): 0, ('V', 'B'): -3, ('V', 'C'): -1, ('V', 'D'): -3, ('V', 'E'): -2, ('V', 'F'): -1, ('V', 'G'): -3, ('V', 'H'): -3, ('V', 'I'): 3, ('V', 'K'): -2, ('V', 'L'): 1, ('V', 'M'): 1, ('V', 'N'): -3, ('V', 'P'): -2, ('V', 'Q'): -2, ('V', 'R'): -3, ('V', 'S'): -2, ('V', 'T'): 0, ('V', 'V'): 4, ('V', 'W'): -3, ('V', 'X'): -1, ('V', 'Y'): -1, ('V', 'Z'): -2, ('W', 'A'): -3, ('W', 'B'): -4, ('W', 'C'): -2, ('W', 'D'): -4, ('W', 'E'): -3, ('W', 'F'): 1, ('W', 'G'): -2, ('W', 'H'): -2, ('W', 'I'): -3, ('W', 'K'): -3, ('W', 'L'): -2, ('W', 'M'): -1, ('W', 'N'): -4, ('W', 'P'): -4, ('W', 'Q'): -2, ('W', 'R'): -3, ('W', 'S'): -3, ('W', 'T'): -2, ('W', 'V'): -3, ('W', 'W'): 11, ('W', 'X'): -2, ('W', 'Y'): 2, ('W', 'Z'): -3, ('X', 'A'): 0, ('X', 'B'): -1, ('X', 'C'): -2, ('X', 'D'): -1, ('X', 'E'): -1, ('X', 'F'): -1, ('X', 'G'): -1, ('X', 'H'): -1, ('X', 'I'): -1, ('X', 'K'): -1, ('X', 'L'): -1, ('X', 'M'): -1, ('X', 'N'): -1, ('X', 'P'): -2, ('X', 'Q'): -1, ('X', 'R'): -1, ('X', 'S'): 0, ('X', 'T'): 0, ('X', 'V'): -1, ('X', 'W'): -2, ('X', 'X'): -1, ('X', 'Y'): -1, ('X', 'Z'): -1, ('Y', 'A'): -2, ('Y', 'B'): -3, ('Y', 'C'): -2, ('Y', 'D'): -3, ('Y', 'E'): -2, ('Y', 'F'): 3, ('Y', 'G'): -3, ('Y', 'H'): 2, ('Y', 'I'): -1, ('Y', 'K'): -2, ('Y', 'L'): -1, ('Y', 'M'): -1, ('Y', 'N'): -2, ('Y', 'P'): -3, ('Y', 'Q'): -1, ('Y', 'R'): -2, ('Y', 'S'): -2, ('Y', 'T'): -2, ('Y', 'V'): -1, ('Y', 'W'): 2, ('Y', 'X'): -1, ('Y', 'Y'): 7, ('Y', 'Z'): -2, ('Z', 'A'): -1, ('Z', 'B'): 1, ('Z', 'C'): -3, ('Z', 'D'): 1, ('Z', 'E'): 4, ('Z', 'F'): -3, ('Z', 'G'): -2, ('Z', 'H'): 0, ('Z', 'I'): -3, ('Z', 'K'): 1, ('Z', 'L'): -3, ('Z', 'M'): -1, ('Z', 'N'): 0, ('Z', 'P'): -1, ('Z', 'Q'): 3, ('Z', 'R'): 0, ('Z', 'S'): 0, ('Z', 'T'): -1, ('Z', 'V'): -2, ('Z', 'W'): -3, ('Z', 'X'): -1, ('Z', 'Y'): -2, ('Z', 'Z'): 4})

Returns if the residue and a reference residue are similar

Parameters:
Returns:

1 if the similarity score is positive, otherwise 0.
Return type:

int
getConservation(ref_res)

Return whether the residue and a reference residue have similar side-chain chemistry.

The similarity criterion is based on “side chain chemistry” descriptor matching.

Parameters:ref_res (schrodinger.protein.residue.Residue) – The reference residue
Returns:1 if the residue and reference residue are have similar side chain chemistry, 0 otherwise.
Return type:int
getIdentity(ref_res)

Return the identity between the residue and a reference residue

Parameters:ref_res (schrodinger.protein.residue.Residue) – The reference residue
Returns:1 if same as the reference residue, 0 otherwise.
Return type:int
getSimilarity(ref_res, similarity_matrix={('A', 'A'): 4, ('A', 'B'): -2, ('A', 'C'): 0, ('A', 'D'): -2, ('A', 'E'): -1, ('A', 'F'): -2, ('A', 'G'): 0, ('A', 'H'): -2, ('A', 'I'): -1, ('A', 'K'): -1, ('A', 'L'): -1, ('A', 'M'): -1, ('A', 'N'): -2, ('A', 'P'): -1, ('A', 'Q'): -1, ('A', 'R'): -1, ('A', 'S'): 1, ('A', 'T'): 0, ('A', 'V'): 0, ('A', 'W'): -3, ('A', 'X'): 0, ('A', 'Y'): -2, ('A', 'Z'): -1, ('B', 'A'): -2, ('B', 'B'): 4, ('B', 'C'): -3, ('B', 'D'): 4, ('B', 'E'): 1, ('B', 'F'): -3, ('B', 'G'): -1, ('B', 'H'): 0, ('B', 'I'): -3, ('B', 'K'): 0, ('B', 'L'): -4, ('B', 'M'): -3, ('B', 'N'): 3, ('B', 'P'): -2, ('B', 'Q'): 0, ('B', 'R'): -1, ('B', 'S'): 0, ('B', 'T'): -1, ('B', 'V'): -3, ('B', 'W'): -4, ('B', 'X'): -1, ('B', 'Y'): -3, ('B', 'Z'): 1, ('C', 'A'): 0, ('C', 'B'): -3, ('C', 'C'): 9, ('C', 'D'): -3, ('C', 'E'): -4, ('C', 'F'): -2, ('C', 'G'): -3, ('C', 'H'): -3, ('C', 'I'): -1, ('C', 'K'): -3, ('C', 'L'): -1, ('C', 'M'): -1, ('C', 'N'): -3, ('C', 'P'): -3, ('C', 'Q'): -3, ('C', 'R'): -3, ('C', 'S'): -1, ('C', 'T'): -1, ('C', 'V'): -1, ('C', 'W'): -2, ('C', 'X'): -2, ('C', 'Y'): -2, ('C', 'Z'): -3, ('D', 'A'): -2, ('D', 'B'): 4, ('D', 'C'): -3, ('D', 'D'): 6, ('D', 'E'): 2, ('D', 'F'): -3, ('D', 'G'): -1, ('D', 'H'): -1, ('D', 'I'): -3, ('D', 'K'): -1, ('D', 'L'): -4, ('D', 'M'): -3, ('D', 'N'): 1, ('D', 'P'): -1, ('D', 'Q'): 0, ('D', 'R'): -2, ('D', 'S'): 0, ('D', 'T'): -1, ('D', 'V'): -3, ('D', 'W'): -4, ('D', 'X'): -1, ('D', 'Y'): -3, ('D', 'Z'): 1, ('E', 'A'): -1, ('E', 'B'): 1, ('E', 'C'): -4, ('E', 'D'): 2, ('E', 'E'): 5, ('E', 'F'): -3, ('E', 'G'): -2, ('E', 'H'): 0, ('E', 'I'): -3, ('E', 'K'): 1, ('E', 'L'): -3, ('E', 'M'): -2, ('E', 'N'): 0, ('E', 'P'): -1, ('E', 'Q'): 2, ('E', 'R'): 0, ('E', 'S'): 0, ('E', 'T'): -1, ('E', 'V'): -2, ('E', 'W'): -3, ('E', 'X'): -1, ('E', 'Y'): -2, ('E', 'Z'): 4, ('F', 'A'): -2, ('F', 'B'): -3, ('F', 'C'): -2, ('F', 'D'): -3, ('F', 'E'): -3, ('F', 'F'): 6, ('F', 'G'): -3, ('F', 'H'): -1, ('F', 'I'): 0, ('F', 'K'): -3, ('F', 'L'): 0, ('F', 'M'): 0, ('F', 'N'): -3, ('F', 'P'): -4, ('F', 'Q'): -3, ('F', 'R'): -3, ('F', 'S'): -2, ('F', 'T'): -2, ('F', 'V'): -1, ('F', 'W'): 1, ('F', 'X'): -1, ('F', 'Y'): 3, ('F', 'Z'): -3, ('G', 'A'): 0, ('G', 'B'): -1, ('G', 'C'): -3, ('G', 'D'): -1, ('G', 'E'): -2, ('G', 'F'): -3, ('G', 'G'): 6, ('G', 'H'): -2, ('G', 'I'): -4, ('G', 'K'): -2, ('G', 'L'): -4, ('G', 'M'): -3, ('G', 'N'): 0, ('G', 'P'): -2, ('G', 'Q'): -2, ('G', 'R'): -2, ('G', 'S'): 0, ('G', 'T'): -2, ('G', 'V'): -3, ('G', 'W'): -2, ('G', 'X'): -1, ('G', 'Y'): -3, ('G', 'Z'): -2, ('H', 'A'): -2, ('H', 'B'): 0, ('H', 'C'): -3, ('H', 'D'): -1, ('H', 'E'): 0, ('H', 'F'): -1, ('H', 'G'): -2, ('H', 'H'): 8, ('H', 'I'): -3, ('H', 'K'): -1, ('H', 'L'): -3, ('H', 'M'): -2, ('H', 'N'): 1, ('H', 'P'): -2, ('H', 'Q'): 0, ('H', 'R'): 0, ('H', 'S'): -1, ('H', 'T'): -2, ('H', 'V'): -3, ('H', 'W'): -2, ('H', 'X'): -1, ('H', 'Y'): 2, ('H', 'Z'): 0, ('I', 'A'): -1, ('I', 'B'): -3, ('I', 'C'): -1, ('I', 'D'): -3, ('I', 'E'): -3, ('I', 'F'): 0, ('I', 'G'): -4, ('I', 'H'): -3, ('I', 'I'): 4, ('I', 'K'): -3, ('I', 'L'): 2, ('I', 'M'): 1, ('I', 'N'): -3, ('I', 'P'): -3, ('I', 'Q'): -3, ('I', 'R'): -3, ('I', 'S'): -2, ('I', 'T'): -1, ('I', 'V'): 3, ('I', 'W'): -3, ('I', 'X'): -1, ('I', 'Y'): -1, ('I', 'Z'): -3, ('K', 'A'): -1, ('K', 'B'): 0, ('K', 'C'): -3, ('K', 'D'): -1, ('K', 'E'): 1, ('K', 'F'): -3, ('K', 'G'): -2, ('K', 'H'): -1, ('K', 'I'): -3, ('K', 'K'): 5, ('K', 'L'): -2, ('K', 'M'): -1, ('K', 'N'): 0, ('K', 'P'): -1, ('K', 'Q'): 1, ('K', 'R'): 2, ('K', 'S'): 0, ('K', 'T'): -1, ('K', 'V'): -2, ('K', 'W'): -3, ('K', 'X'): -1, ('K', 'Y'): -2, ('K', 'Z'): 1, ('L', 'A'): -1, ('L', 'B'): -4, ('L', 'C'): -1, ('L', 'D'): -4, ('L', 'E'): -3, ('L', 'F'): 0, ('L', 'G'): -4, ('L', 'H'): -3, ('L', 'I'): 2, ('L', 'K'): -2, ('L', 'L'): 4, ('L', 'M'): 2, ('L', 'N'): -3, ('L', 'P'): -3, ('L', 'Q'): -2, ('L', 'R'): -2, ('L', 'S'): -2, ('L', 'T'): -1, ('L', 'V'): 1, ('L', 'W'): -2, ('L', 'X'): -1, ('L', 'Y'): -1, ('L', 'Z'): -3, ('M', 'A'): -1, ('M', 'B'): -3, ('M', 'C'): -1, ('M', 'D'): -3, ('M', 'E'): -2, ('M', 'F'): 0, ('M', 'G'): -3, ('M', 'H'): -2, ('M', 'I'): 1, ('M', 'K'): -1, ('M', 'L'): 2, ('M', 'M'): 5, ('M', 'N'): -2, ('M', 'P'): -2, ('M', 'Q'): 0, ('M', 'R'): -1, ('M', 'S'): -1, ('M', 'T'): -1, ('M', 'V'): 1, ('M', 'W'): -1, ('M', 'X'): -1, ('M', 'Y'): -1, ('M', 'Z'): -1, ('N', 'A'): -2, ('N', 'B'): 3, ('N', 'C'): -3, ('N', 'D'): 1, ('N', 'E'): 0, ('N', 'F'): -3, ('N', 'G'): 0, ('N', 'H'): 1, ('N', 'I'): -3, ('N', 'K'): 0, ('N', 'L'): -3, ('N', 'M'): -2, ('N', 'N'): 6, ('N', 'P'): -2, ('N', 'Q'): 0, ('N', 'R'): 0, ('N', 'S'): 1, ('N', 'T'): 0, ('N', 'V'): -3, ('N', 'W'): -4, ('N', 'X'): -1, ('N', 'Y'): -2, ('N', 'Z'): 0, ('P', 'A'): -1, ('P', 'B'): -2, ('P', 'C'): -3, ('P', 'D'): -1, ('P', 'E'): -1, ('P', 'F'): -4, ('P', 'G'): -2, ('P', 'H'): -2, ('P', 'I'): -3, ('P', 'K'): -1, ('P', 'L'): -3, ('P', 'M'): -2, ('P', 'N'): -2, ('P', 'P'): 7, ('P', 'Q'): -1, ('P', 'R'): -2, ('P', 'S'): -1, ('P', 'T'): -1, ('P', 'V'): -2, ('P', 'W'): -4, ('P', 'X'): -2, ('P', 'Y'): -3, ('P', 'Z'): -1, ('Q', 'A'): -1, ('Q', 'B'): 0, ('Q', 'C'): -3, ('Q', 'D'): 0, ('Q', 'E'): 2, ('Q', 'F'): -3, ('Q', 'G'): -2, ('Q', 'H'): 0, ('Q', 'I'): -3, ('Q', 'K'): 1, ('Q', 'L'): -2, ('Q', 'M'): 0, ('Q', 'N'): 0, ('Q', 'P'): -1, ('Q', 'Q'): 5, ('Q', 'R'): 1, ('Q', 'S'): 0, ('Q', 'T'): -1, ('Q', 'V'): -2, ('Q', 'W'): -2, ('Q', 'X'): -1, ('Q', 'Y'): -1, ('Q', 'Z'): 3, ('R', 'A'): -1, ('R', 'B'): -1, ('R', 'C'): -3, ('R', 'D'): -2, ('R', 'E'): 0, ('R', 'F'): -3, ('R', 'G'): -2, ('R', 'H'): 0, ('R', 'I'): -3, ('R', 'K'): 2, ('R', 'L'): -2, ('R', 'M'): -1, ('R', 'N'): 0, ('R', 'P'): -2, ('R', 'Q'): 1, ('R', 'R'): 5, ('R', 'S'): -1, ('R', 'T'): -1, ('R', 'V'): -3, ('R', 'W'): -3, ('R', 'X'): -1, ('R', 'Y'): -2, ('R', 'Z'): 0, ('S', 'A'): 1, ('S', 'B'): 0, ('S', 'C'): -1, ('S', 'D'): 0, ('S', 'E'): 0, ('S', 'F'): -2, ('S', 'G'): 0, ('S', 'H'): -1, ('S', 'I'): -2, ('S', 'K'): 0, ('S', 'L'): -2, ('S', 'M'): -1, ('S', 'N'): 1, ('S', 'P'): -1, ('S', 'Q'): 0, ('S', 'R'): -1, ('S', 'S'): 4, ('S', 'T'): 1, ('S', 'V'): -2, ('S', 'W'): -3, ('S', 'X'): 0, ('S', 'Y'): -2, ('S', 'Z'): 0, ('T', 'A'): 0, ('T', 'B'): -1, ('T', 'C'): -1, ('T', 'D'): -1, ('T', 'E'): -1, ('T', 'F'): -2, ('T', 'G'): -2, ('T', 'H'): -2, ('T', 'I'): -1, ('T', 'K'): -1, ('T', 'L'): -1, ('T', 'M'): -1, ('T', 'N'): 0, ('T', 'P'): -1, ('T', 'Q'): -1, ('T', 'R'): -1, ('T', 'S'): 1, ('T', 'T'): 5, ('T', 'V'): 0, ('T', 'W'): -2, ('T', 'X'): 0, ('T', 'Y'): -2, ('T', 'Z'): -1, ('V', 'A'): 0, ('V', 'B'): -3, ('V', 'C'): -1, ('V', 'D'): -3, ('V', 'E'): -2, ('V', 'F'): -1, ('V', 'G'): -3, ('V', 'H'): -3, ('V', 'I'): 3, ('V', 'K'): -2, ('V', 'L'): 1, ('V', 'M'): 1, ('V', 'N'): -3, ('V', 'P'): -2, ('V', 'Q'): -2, ('V', 'R'): -3, ('V', 'S'): -2, ('V', 'T'): 0, ('V', 'V'): 4, ('V', 'W'): -3, ('V', 'X'): -1, ('V', 'Y'): -1, ('V', 'Z'): -2, ('W', 'A'): -3, ('W', 'B'): -4, ('W', 'C'): -2, ('W', 'D'): -4, ('W', 'E'): -3, ('W', 'F'): 1, ('W', 'G'): -2, ('W', 'H'): -2, ('W', 'I'): -3, ('W', 'K'): -3, ('W', 'L'): -2, ('W', 'M'): -1, ('W', 'N'): -4, ('W', 'P'): -4, ('W', 'Q'): -2, ('W', 'R'): -3, ('W', 'S'): -3, ('W', 'T'): -2, ('W', 'V'): -3, ('W', 'W'): 11, ('W', 'X'): -2, ('W', 'Y'): 2, ('W', 'Z'): -3, ('X', 'A'): 0, ('X', 'B'): -1, ('X', 'C'): -2, ('X', 'D'): -1, ('X', 'E'): -1, ('X', 'F'): -1, ('X', 'G'): -1, ('X', 'H'): -1, ('X', 'I'): -1, ('X', 'K'): -1, ('X', 'L'): -1, ('X', 'M'): -1, ('X', 'N'): -1, ('X', 'P'): -2, ('X', 'Q'): -1, ('X', 'R'): -1, ('X', 'S'): 0, ('X', 'T'): 0, ('X', 'V'): -1, ('X', 'W'): -2, ('X', 'X'): -1, ('X', 'Y'): -1, ('X', 'Z'): -1, ('Y', 'A'): -2, ('Y', 'B'): -3, ('Y', 'C'): -2, ('Y', 'D'): -3, ('Y', 'E'): -2, ('Y', 'F'): 3, ('Y', 'G'): -3, ('Y', 'H'): 2, ('Y', 'I'): -1, ('Y', 'K'): -2, ('Y', 'L'): -1, ('Y', 'M'): -1, ('Y', 'N'): -2, ('Y', 'P'): -3, ('Y', 'Q'): -1, ('Y', 'R'): -2, ('Y', 'S'): -2, ('Y', 'T'): -2, ('Y', 'V'): -1, ('Y', 'W'): 2, ('Y', 'X'): -1, ('Y', 'Y'): 7, ('Y', 'Z'): -2, ('Z', 'A'): -1, ('Z', 'B'): 1, ('Z', 'C'): -3, ('Z', 'D'): 1, ('Z', 'E'): 4, ('Z', 'F'): -3, ('Z', 'G'): -2, ('Z', 'H'): 0, ('Z', 'I'): -3, ('Z', 'K'): 1, ('Z', 'L'): -3, ('Z', 'M'): -1, ('Z', 'N'): 0, ('Z', 'P'): -1, ('Z', 'Q'): 3, ('Z', 'R'): 0, ('Z', 'S'): 0, ('Z', 'T'): -1, ('Z', 'V'): -2, ('Z', 'W'): -3, ('Z', 'X'): -1, ('Z', 'Y'): -2, ('Z', 'Z'): 4})

Returns the similarity between the residue and a reference residue

Parameters:
Returns:

similarity score based on the similarity matrix
Return type:

float
get_version()

Method to get the version of a particular object. Defaults to the current version of mmshare. This class can be overridden for custom versioning behavior.

hasSetResNum() → bool
Returns:Whether a specific resnum has been set
hasStructure()
Returns:Whether this element has a structure i.e. whether it has

corresponding XYZ coordinates in Maestro. :rtype: bool

helix_propensity
Returns:Helix propensity for the ResidueType of the residue
Return type:HELIX_PROPENSITY
helix_termination_tendency
Returns:Helix termination tendency for the ResidueType of the residue
Return type:HELIX_TERMINATION_TENDENCY
hydrophilicity
Returns:Hydrophilicity for the ResidueType on the Hopp-Woods scale, if available; otherwise None
Return type:float
hydrophobicity
Returns:Hydrophobicity for the ResidueType on the Kyte-Doolittle scale, if available; otherwise None.
Return type:float
inscode

If inscode and rescode are both set to None, the inscode will be ‘+’.

is_gap
is_res

Utility function to check whether a residue is not a gap

isoelectric_point
Returns:A float representing the isoelectric point value for the ResidueType of the residue
long_code
rescode
resnum

If resnum is set to None, resnum will be auto-generated from column number.

seq_index
sequence
short_code
side_chain_chem
Returns:Side chain chemistry for the ResidueType of the residue
Return type:SIDE_CHAIN_CHEM
ss_prediction_psipred

Returns a DSSP code matching the secondary structure prediction for the residue or None. Value is calculated from thePsiPred backend.

ss_prediction_sspro

Returns a DSSP code matching the secondary structure prediction for the residue or None. Value is calculated from the SSpro backend.

steric_group
Returns:Steric group for the ResidueType of the residue
Return type:STERIC_GROUP
toJson(_mark_version=True)

Create and returns a data structure made up of jsonable items.

Return type:An instance of one the classes from NATIVE_JSON_DATATYPES
toJsonImplementation()

Abstract method that must be defined by all derived classes. Converts an instance of the derived class into a jsonifiable object.

Returns:A dict made up of JSON native datatypes or Jsonable objects. See the link below for a table of such types. https://docs.python.org/2/library/json.html#encoders-and-decoders
turn_propensity
Returns:Turn propensity for the ResidueType of the residue
Return type:TURN_PROPENSITY