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 schrodinger.protein.residue.BETA_STRAND_PROPENSITY¶

Bases: enum.Enum

An enumeration.

AMBIVALENT = 3¶

NO_PROPENSITY = 1¶

STRAND_BREAKING = 2¶

STRAND_FORMING = 4¶

class schrodinger.protein.residue.TURN_PROPENSITY¶

Bases: enum.Enum

An enumeration.

AMBIVALENT = 3¶

NO_PROPENSITY = 1¶

TURN_BREAKING = 4¶

TURN_FORMING = 2¶

class schrodinger.protein.residue.HELIX_TERMINATION_TENDENCY¶

Bases: enum.Enum

An enumeration.

AMBIVALENT = 3¶

HELIX_ENDING = 4¶

HELIX_STARTING = 2¶

NO_TENDENCY = 1¶

class schrodinger.protein.residue.SOLVENT_EXPOSURE_TENDENCY¶

Bases: enum.Enum

An enumeration.

AMBIVALENT = 3¶

BURIED = 4¶

NO_TENDENCY = 1¶

SURFACE = 2¶

class schrodinger.protein.residue.STERIC_GROUP¶

Bases: enum.Enum

An enumeration.

AMBIVALENT = 3¶

AROMATIC = 5¶

NO_STERIC = 1¶

POLAR = 4¶

SMALL = 2¶

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 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

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

__init__()¶: Initialize self. See help(type(self)) for accurate signature.

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 schrodinger.protein.residue.Gap¶

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

__init__()¶: Initialize self. See help(type(self)) for accurate signature.

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

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¶

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

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¶

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:	ref_res (`schrodinger.protein.residue.Residue`) – The reference residue similarity_matrix – The scoring matrix to use
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:	ref_res (`schrodinger.protein.residue.Residue`) – The reference residue similarity_matrix – The scoring matrix to use
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

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¶

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.seq_index 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:	res (AbstractSequenceElement) – The residue or gap to wrap combined_chain_seq (sequence.CombinedChainProteinSequence) – The combined-chain sequence that the residue is part of.

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

seq_index¶

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:	bond (DisulfideBond) – The split-chain disulfide bond. seq (sequence.CombinedChainProteinSequence) – The combined-chain sequence that this bond is in.

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)

res_pair¶

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

schrodinger.protein.residue.add_disulfide_bond(res1, res2)¶

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

schrodinger.protein.residue.remove_disulfide_bond(res1, res2)¶

Remove 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

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.

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:	ref_res (`schrodinger.protein.residue.Residue`) – The reference residue similarity_matrix – The scoring matrix to use
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:	ref_res (`schrodinger.protein.residue.Residue`) – The reference residue similarity_matrix – The scoring matrix to use
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_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¶

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`

schrodinger.protein.residue module¶

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