schrodinger.protein.residue module

class schrodinger.protein.residue.ResidueChainKey

Bases: tuple

Key to partially identify a structured residue relative to its chain

resnum

Alias for field number 0

inscode

Alias for field number 1

__contains__

Return key in self.

__init__

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

__len__

Return len(self).

count(value) → integer -- return number of occurrences of value
index(value[, start[, stop]]) → integer -- return first index of value.

Raises ValueError if the value is not present.

class schrodinger.protein.residue.ResidueKey

Bases: tuple

Key to partially identify a structured residue.

Order and items based on MaestroStructureModel._getKey

entry_id

Alias for field number 0

chain

Alias for field number 1

resnum

Alias for field number 2

inscode

Alias for field number 3

chainKey()
__contains__

Return key in self.

__init__

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

__len__

Return len(self).

count(value) → integer -- return number of occurrences of value
index(value[, start[, stop]]) → integer -- return first index of value.

Raises ValueError if the value is not present.

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
schrodinger.protein.residue.get_structure_residue_chain_key(structure_residue)

Creates residue key relative to entry and chain for structure residue.

Returns:(resnum, inscode)
Return type:tuple(int, str)
schrodinger.protein.residue.get_residue_key(residue, entry_id, chain)

Creates residue key for residue.

Parameters:
  • residue (Residue) – Residue
  • entry_id (str or int) – Entry ID
  • chain (str) – Chain name
Returns:

The residue key containing entry_id, chain, resnum, and inscode

Return type:

ResidueKey

schrodinger.protein.residue.get_structure_residue_key(structure_residue, entry_id)

Creates residue key for structure residue.

Parameters:
Returns:

The residue key containing entry_id, chain, resnum, and inscode

Return type:

ResidueKey

class schrodinger.protein.residue.HELIX_PROPENSITY

Bases: enum.Enum

An enumeration.

Ambivalent = 4
HelixBreaking = 5
Likely = 2
NoPropensity = 1
Weak = 3
class schrodinger.protein.residue.BETA_STRAND_PROPENSITY

Bases: enum.Enum

An enumeration.

Ambivalent = 3
NoPropensity = 1
StrandBreaking = 2
StrandForming = 4
class schrodinger.protein.residue.TURN_PROPENSITY

Bases: enum.Enum

An enumeration.

Ambivalent = 3
NoPropensity = 1
TurnBreaking = 4
TurnForming = 2
class schrodinger.protein.residue.HELIX_TERMINATION_TENDENCY

Bases: enum.Enum

An enumeration.

Ambivalent = 3
HelixEnding = 4
HelixStarting = 2
NoTendency = 1
class schrodinger.protein.residue.SOLVENT_EXPOSURE_TENDENCY

Bases: enum.Enum

An enumeration.

Ambivalent = 3
Buried = 4
NoTendency = 1
Surface = 2
class schrodinger.protein.residue.STERIC_GROUP

Bases: enum.Enum

An enumeration.

Ambivalent = 3
Aromatic = 5
NoSteric = 1
Polar = 4
Small = 2
class schrodinger.protein.residue.SIDE_CHAIN_CHEM

Bases: enum.Enum

An enumeration.

AcidicHydrophilic = 2
BasicHydrophilic = 3
IminoAcid = 8
NeutralHydrophilic = 6
NeutralHydrophobicAliphatic = 4
NeutralHydrophobicAromatic = 5
NoSideChainChem = 1
PrimaryThiol = 7
class schrodinger.protein.residue.RESIDUE_CHARGE

Bases: enum.Enum

An enumeration.

Negative = 2
Neutral = 3
Positive = 1
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.

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.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.

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

__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.

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.DeoxyribonucleotideType(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.NucleotideType

__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.

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.RibonucleotideType(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.NucleotideType

__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.

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: schrodinger.models.json.JsonableClassMixin

is_res

Utility function to check whether a residue is not a gap

sequence

The sequence that this element is part of. Will be None if this residue is not part of a sequence. Stored as a weakref to avoid circular references. :rtype: sequence.AbstractSingleChainSequence

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

corresponding XYZ coordinates in Maestro. :rtype: bool

idx_in_seq
gapless_idx_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
__init__

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

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_dict)

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

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.

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
class schrodinger.protein.residue.Gap

Bases: schrodinger.protein.residue.AbstractSequenceElement

is_gap = True
__init__()

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

sequence

The sequence that this element is part of. Will be None if this residue is not part of a sequence. Stored as a weakref to avoid circular references. :rtype: sequence.AbstractSingleChainSequence

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

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

gapless_idx_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
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

idx_in_seq
is_res

Utility function to check whether a residue is not a gap

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.Residue(element_type, inscode=None, resnum=None, seqres_only=False)

Bases: schrodinger.protein.residue.AbstractSequenceElement

An amino acid residue.

is_gap = False
descriptors
__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.
type
seqres_only
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

getChainKey()
getKey()

Get a key that uniquely identifies the residue relative to structures.

Returns:Residue key as (entry_id, chain, inscode, resnum, molnum, pdbname), or None if residue is unparented or has no structure
Return type:ResidueKey or NoneType
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
chain

The name of the sequence chain that this residue belongs to. :rtype: str

structure_chain

The name of chain for the structure that this sequence is associated with. This is normally the same as chain, but it can be different if the user manually links this sequence to a structure with differing chain names.

Return type:str
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
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
getStructureResProperties()

Return all properties for the corresponding structure residue’s alpha carbon. Properties that apply to the whole residue are stored as atom properties on this atom. An empty dictionary will be returned if this residue doesn’t have a corresponding alpha carbon.

Returns:A dictionary-like object containing the properties.
Return type:structure._StructureAtomProperty or dict
updateDescriptors(descriptors)

Updates the descriptor dicts with new descriptor values

Parameters:descriptors (dict[str, float]) – A dict mapping descriptor names to their values
getDescriptorValue(descriptor_name)
getDescriptorKeys()
getProperty(seq_prop)

Get the residue’s value corresponding to the given SequenceProperty object

Parameters:seq_prop (schrodinger.protein.properties.SequenceProperty) – The object describing the residue property
Returns:The value of the sequence property
Return type:float or None
area
b_factor
composition
disulfide_bond
domains
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

gapless_idx_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
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

idx_in_seq
is_res

Utility function to check whether a residue is not a gap

molecule_number
pfam
pred_accessibility
pred_disordered
pred_disulfide_bond
pred_domain_arr
pred_secondary_structure
secondary_structure
sequence

The sequence that this element is part of. Will be None if this residue is not part of a sequence. Stored as a weakref to avoid circular references. :rtype: sequence.AbstractSingleChainSequence

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.CombinedChainResidueWrapper(res, combined_chain_seq)

Bases: object

A wrapper for a residue or gap so that res.sequence points to the combined-chain sequence and res.idx_in_seq gives the index within the combined-chain sequence.

Note that these wrappers are generated as needed and the combined-chain sequence does not store any reference to the generated instances. As such, these residues should not be stored using weakrefs and should not be compared using identity. Also note that these residues will not compare equal to the split-chain residues that they wrap.

__init__(res, combined_chain_seq)
Parameters:
sequence

The combined-chain sequence that the residue is part of, or None if the residue has been removed from the sequence.

Return type:sequence.CombinedChainProteinSequence or None
idx_in_seq

This residue’s index in the combined-chain sequence, or None if the residue has been removed from the sequence.

Return type:int or None
split_res

The split-chain residue or gap that this residue is wrapping.

Return type:AbstractSequenceElement
split_sequence

The split-chain sequence that this residue is part or, or None if the residue has been removed from the sequence.

Return type:sequence.ProteinSequence or None
disulfide_bond

The current disulfide bond, if any, that this residue is involved in. :rtype: CombinedChainDisulfideBond or None

class schrodinger.protein.residue.DisulfideBond(res1, res2)

Bases: object

Representation of a disulfide bond.

__init__(res1, res2)
Parameters:
  • res1 (Residue) – A residue in the bond
  • res2 (Residue) – The other residue in the bond
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)
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
class schrodinger.protein.residue.CombinedChainDisulfideBond(bond, seq)

Bases: schrodinger.protein.residue.DisulfideBond

A disulfide bond in a sequence.CombinedChainProteinSequence.

__init__(bond, seq)
Parameters:
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)
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
res_pair
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
schrodinger.protein.residue.add_disulfide_bond(res1, res2, known=True)

Add a disulfide bond between two residues.

Parameters:
  • res1 (residue.Residue) – A residue to link with a disulfide bond
  • res2 (residue.Residue) – Another residue to link with a disulfide bond
  • known (bool) – Whether the bond is a known bond or a predicted bond.
schrodinger.protein.residue.remove_disulfide_bond(bond)

Remove a disulfide bond between two residues.

Parameters:bond (residue.DisulfideBond) – The bond to disconnect
class schrodinger.protein.residue.Nucleotide(element_type, inscode=None, resnum=None, seqres_only=False)

Bases: schrodinger.protein.residue.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.
area
b_factor
beta_strand_propensity
Returns:Beta-strand propensity for the ResidueType of the residue
Return type:BETA_STRAND_PROPENSITY
chain

The name of the sequence chain that this residue belongs to. :rtype: str

charge
Returns:charge of the ResidueType of the residue
Return type:RESIDUE_CHARGE
composition
descriptors
disulfide_bond
domains
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_idx_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
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

getChainKey()
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
getDescriptorKeys()
getDescriptorValue(descriptor_name)
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
getKey()

Get a key that uniquely identifies the residue relative to structures.

Returns:Residue key as (entry_id, chain, inscode, resnum, molnum, pdbname), or None if residue is unparented or has no structure
Return type:ResidueKey or NoneType
getProperty(seq_prop)

Get the residue’s value corresponding to the given SequenceProperty object

Parameters:seq_prop (schrodinger.protein.properties.SequenceProperty) – The object describing the residue property
Returns:The value of the sequence property
Return type:float or None
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

getStructureResProperties()

Return all properties for the corresponding structure residue’s alpha carbon. Properties that apply to the whole residue are stored as atom properties on this atom. An empty dictionary will be returned if this residue doesn’t have a corresponding alpha carbon.

Returns:A dictionary-like object containing the properties.
Return type:structure._StructureAtomProperty or dict
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
idx_in_seq
inscode

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

is_gap = False
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
molecule_number
pfam
pred_accessibility
pred_disordered
pred_disulfide_bond
pred_domain_arr
pred_secondary_structure
rescode
resnum

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

secondary_structure
seqres_only
sequence

The sequence that this element is part of. Will be None if this residue is not part of a sequence. Stored as a weakref to avoid circular references. :rtype: sequence.AbstractSingleChainSequence

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
structure_chain

The name of chain for the structure that this sequence is associated with. This is normally the same as chain, but it can be different if the user manually links this sequence to a structure with differing chain names.

Return type:str
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
type
updateDescriptors(descriptors)

Updates the descriptor dicts with new descriptor values

Parameters:descriptors (dict[str, float]) – A dict mapping descriptor names to their values