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
- 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
- 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
start_res (residue.Residue) – starting residue
end_res (residue.Residue) – ending residue
- 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(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)¶
Bases:
enum.Enum
- NoPropensity = 1¶
- Likely = 2¶
- Weak = 3¶
- Ambivalent = 4¶
- HelixBreaking = 5¶
- class schrodinger.protein.residue.BETA_STRAND_PROPENSITY(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)¶
Bases:
enum.Enum
- NoPropensity = 1¶
- StrandBreaking = 2¶
- Ambivalent = 3¶
- StrandForming = 4¶
- class schrodinger.protein.residue.TURN_PROPENSITY(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)¶
Bases:
enum.Enum
- NoPropensity = 1¶
- TurnForming = 2¶
- Ambivalent = 3¶
- TurnBreaking = 4¶
- class schrodinger.protein.residue.HELIX_TERMINATION_TENDENCY(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)¶
Bases:
enum.Enum
- NoTendency = 1¶
- HelixStarting = 2¶
- Ambivalent = 3¶
- HelixEnding = 4¶
- class schrodinger.protein.residue.SOLVENT_EXPOSURE_TENDENCY(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)¶
Bases:
enum.Enum
- NoTendency = 1¶
- Surface = 2¶
- Ambivalent = 3¶
- Buried = 4¶
- class schrodinger.protein.residue.STERIC_GROUP(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)¶
Bases:
enum.Enum
- NoSteric = 1¶
- Small = 2¶
- Ambivalent = 3¶
- Polar = 4¶
- Aromatic = 5¶
- class schrodinger.protein.residue.SIDE_CHAIN_CHEM(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)¶
Bases:
enum.Enum
- NoSideChainChem = 1¶
- AcidicHydrophilic = 2¶
- BasicHydrophilic = 3¶
- NeutralHydrophobicAliphatic = 4¶
- NeutralHydrophobicAromatic = 5¶
- NeutralHydrophilic = 6¶
- PrimaryThiol = 7¶
- IminoAcid = 8¶
- class schrodinger.protein.residue.RESIDUE_CHARGE(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)¶
Bases:
enum.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
- 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)¶
- 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)¶
- 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)¶
- 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)¶
- 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:
schrodinger.models.json.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:
schrodinger.protein.residue.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:
schrodinger.protein.residue.AbstractSequenceElement
An amino acid residue.
- is_gap = False¶
- pred_accessibility: schrodinger.protein.predictors.SolventAccessibility¶
- pred_disordered: schrodinger.protein.predictors.Disordered¶
- pred_domain_arr: schrodinger.protein.predictors.DomainArrangement¶
- kinase_features: schrodinger.protein.annotation.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
- property helix_propensity¶
- Returns
Helix propensity for the ResidueType of the residue
- Return type
- property beta_strand_propensity¶
- Returns
Beta-strand propensity for the ResidueType of the residue
- Return type
- property turn_propensity¶
- Returns
Turn propensity for the ResidueType of the residue
- Return type
- property helix_termination_tendency¶
- Returns
Helix termination tendency for the ResidueType of the residue
- Return type
- property exposure_tendency¶
- Returns
Solvent exposure tendency for the ResidueType of the residue
- Return type
- property steric_group¶
- Returns
Steric group for the ResidueType of the residue
- Return type
- property side_chain_chem¶
- Returns
Side chain chemistry for the ResidueType of the residue
- Return type
- 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
ref_res (
schrodinger.protein.residue.Residue
) – The reference residuesimilarity_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 residuesimilarity_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
- 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¶
- 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
res (AbstractSequenceElement) – The residue or gap to wrap
combined_chain_seq (sequence.CombinedChainProteinSequence) – The combined-chain sequence that the residue is part of.
- 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
- 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
- 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)¶
- 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:
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.
- 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:
schrodinger.protein.residue.Residue
- type¶
- seqres_only¶
- disulfide_bond¶
- pred_disulfide_bond¶
- b_factor¶
- molecule_number¶
- pfam¶
- pred_secondary_structure¶
- secondary_structure¶
- pred_accessibility: schrodinger.protein.predictors.SolventAccessibility¶
- pred_disordered: schrodinger.protein.predictors.Disordered¶
- pred_domain_arr: schrodinger.protein.predictors.DomainArrangement¶
- area¶
- composition¶
- domains¶
- kinase_features: schrodinger.protein.annotation.KinaseFeatureLabel¶
- gpcr_segment¶
- gpcr_generic_number¶
- t_cell_receptor¶
- custom_annotation¶