schrodinger.protein.residue module

schrodinger.protein.residue.check_if_comparable(default_return=0)

Decorator to return early from residue comparison methods.

Returns default_return if: - the other residue is a gap - the residues are different types (e.g. protein/DNA or DNA/RNA) - either residue is an unknown residue

class schrodinger.protein.residue.ResidueChainKey(resnum: int, inscode: str)

Bases: NamedTuple

Key to partially identify a structured residue relative to its chain

resnum: int

Alias for field number 0

inscode: str

Alias for field number 1

class schrodinger.protein.residue.ResidueKey(entry_id: int, chain: str, resnum: int, inscode: str)

Bases: NamedTuple

Key to partially identify a structured residue.

Order and items based on MaestroStructureModel._getKey

entry_id: int

Alias for field number 0

chain: str

Alias for field number 1

resnum: int

Alias for field number 2

inscode: str

Alias for field number 3

chainKey()
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:

  • structure_residue (schrodinger.structure._Residue) – Structure residue

  • entry_id (str or int) – Entry ID

Returns:

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

Return type:

ResidueKey

schrodinger.protein.residue.get_formatted_residue(res) → str

Create the formatted residue string.

Parameters:

res (residue.Residue) – residue

Returns:

formatted string

schrodinger.protein.residue.get_formatted_residue_range(start_res, end_res) → str

Create the residue range tooltip.

Parameters:
Returns:

a formatted string to be used

schrodinger.protein.residue.order_contiguous(residues)

Check if a list of residues is contiguous, and put them in contiguous order if they are not.

Parameters:

residues (list) – List of schrodinger.structure._Residue objects

Return type:

list

Returns:

List of schrodinger.structure._Residue objects in contiguous order, or None if the residues were not contiguous.

class schrodinger.protein.residue.HELIX_PROPENSITY

Bases: Enum

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

Bases: Enum

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

Bases: Enum

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

Bases: Enum

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

Bases: Enum

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

Bases: Enum

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

Bases: Enum

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

Bases: Enum

Positive = 1
Negative = 2
Neutral = 3
class schrodinger.protein.residue.ElementType(short_code, long_code, name)

Bases: object

__init__(short_code, long_code, name)
makeVariant(long_code, short_code=None, *, nonstandard=True)

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

  • nonstandard (bool) – Whether the variant should be considered nonstandard. If False, the residue will be generally treated identically to its standard (e.g. HIE/HIS)

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: 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)
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: ResidueType

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: NucleotideType

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: NucleotideType

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.get_protein_alphabet()

Return a cached map of amino acid element types.

Includes definitions from the nonstandard residues database.

Return type:

types.MappingProxyType

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: JsonableClassMixin

property is_res

Utility function to check whether a residue is not a gap

property 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.

Return type:

bool

property idx_in_seq
property 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

class schrodinger.protein.residue.Gap

Bases: AbstractSequenceElement

is_gap = True
__init__()
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.

Return type:

cls

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

Bases: AbstractSequenceElement

An amino acid residue.

is_gap = False
pred_accessibility: SolventAccessibility
pred_disordered: Disordered
pred_domain_arr: DomainArrangement
kinase_features: KinaseFeatureLabel
SLOT_BLOCKLIST = {'disulfide_bond', 'pred_disulfide_bond', 'sequence', 'type'}
property descriptors
property kinase_conservation
__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.

Return type:

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

property resnum

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

property inscode

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

property rescode
property short_code
property long_code
property chain

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

property 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

property hydrophobicity
Returns:

Hydrophobicity for the ResidueType on the Kyte-Doolittle scale, if available; otherwise None.

Return type:

float

property hydrophilicity
Returns:

Hydrophilicity for the ResidueType on the Hopp-Woods scale, if available; otherwise None

Return type:

float

property charge
Returns:

charge of the ResidueType of the residue

Return type:

RESIDUE_CHARGE

property helix_propensity
Returns:

Helix propensity for the ResidueType of the residue

Return type:

HELIX_PROPENSITY

property beta_strand_propensity
Returns:

Beta-strand propensity for the ResidueType of the residue

Return type:

BETA_STRAND_PROPENSITY

property turn_propensity
Returns:

Turn propensity for the ResidueType of the residue

Return type:

TURN_PROPENSITY

property helix_termination_tendency
Returns:

Helix termination tendency for the ResidueType of the residue

Return type:

HELIX_TERMINATION_TENDENCY

property exposure_tendency
Returns:

Solvent exposure tendency for the ResidueType of the residue

Return type:

SOLVENT_EXPOSURE_TENDENCY

property steric_group
Returns:

Steric group for the ResidueType of the residue

Return type:

STERIC_GROUP

property side_chain_chem
Returns:

Side chain chemistry for the ResidueType of the residue

Return type:

SIDE_CHAIN_CHEM

property ss_prediction_psipred

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

property ss_prediction_sspro

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

property 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

getIdentityStrict(ref_res)

Return the identity between the residue and a reference residue without considering nonstandard amino acids identical to their related standard amino acid.

See getIdentity for additional documentation.

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:

str, int, float or None

disulfide_bond
pred_disulfide_bond
b_factor
molecule_number
pfam
pred_secondary_structure
secondary_structure
area
composition
domains
gpcr_segment
gpcr_generic_number
t_cell_receptor
antibody_region
custom_annotation
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:
property 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

property 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

property split_res

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

Return type:

AbstractSequenceElement

property 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

property 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

property 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)

property 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

property 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: DisulfideBond

A disulfide bond in a sequence.CombinedChainProteinSequence.

__init__(bond, seq)
Parameters:
property 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

property 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: Residue

type
seqres_only
disulfide_bond
pred_disulfide_bond
b_factor
molecule_number
pfam
pred_secondary_structure
secondary_structure
pred_accessibility: SolventAccessibility
pred_disordered: Disordered
pred_domain_arr: DomainArrangement
area
composition
domains
kinase_features: KinaseFeatureLabel
gpcr_segment
gpcr_generic_number
t_cell_receptor
antibody_region
custom_annotation