schrodinger.protein.residue module¶
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class
schrodinger.protein.residue.
ResidueChainKey
¶ Bases:
tuple
Key to partially identify a structured residue relative to its chain
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resnum
¶ Alias for field number 0
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inscode
¶ Alias for field number 1
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__contains__
¶ Return key in self.
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__init__
¶ Initialize self. See help(type(self)) for accurate signature.
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__len__
¶ Return len(self).
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count
(value) → integer -- return number of occurrences of value¶
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index
(value[, start[, stop]]) → integer -- return first index of value.¶ Raises ValueError if the value is not present.
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class
schrodinger.protein.residue.
ResidueKey
¶ Bases:
tuple
Key to partially identify a structured residue.
Order and items based on
MaestroStructureModel._getKey
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entry_id
¶ Alias for field number 0
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chain
¶ Alias for field number 1
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resnum
¶ Alias for field number 2
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inscode
¶ Alias for field number 3
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chainKey
()¶
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__contains__
¶ Return key in self.
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__init__
¶ Initialize self. See help(type(self)) for accurate signature.
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__len__
¶ Return len(self).
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count
(value) → integer -- return number of occurrences of value¶
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index
(value[, start[, stop]]) → integer -- return first index of value.¶ Raises ValueError if the value is not present.
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schrodinger.protein.residue.
get_matrix_value
(matrix, first, second)¶ Return a similarity matrix value for a specified pair of residues.
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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
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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)
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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:
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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:
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class
schrodinger.protein.residue.
HELIX_PROPENSITY
¶ Bases:
enum.Enum
An enumeration.
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Ambivalent
= 4¶
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HelixBreaking
= 5¶
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Likely
= 2¶
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NoPropensity
= 1¶
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Weak
= 3¶
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class
schrodinger.protein.residue.
BETA_STRAND_PROPENSITY
¶ Bases:
enum.Enum
An enumeration.
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Ambivalent
= 3¶
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NoPropensity
= 1¶
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StrandBreaking
= 2¶
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StrandForming
= 4¶
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class
schrodinger.protein.residue.
TURN_PROPENSITY
¶ Bases:
enum.Enum
An enumeration.
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Ambivalent
= 3¶
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NoPropensity
= 1¶
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TurnBreaking
= 4¶
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TurnForming
= 2¶
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class
schrodinger.protein.residue.
HELIX_TERMINATION_TENDENCY
¶ Bases:
enum.Enum
An enumeration.
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Ambivalent
= 3¶
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HelixEnding
= 4¶
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HelixStarting
= 2¶
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NoTendency
= 1¶
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class
schrodinger.protein.residue.
SOLVENT_EXPOSURE_TENDENCY
¶ Bases:
enum.Enum
An enumeration.
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Ambivalent
= 3¶
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Buried
= 4¶
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NoTendency
= 1¶
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Surface
= 2¶
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class
schrodinger.protein.residue.
STERIC_GROUP
¶ Bases:
enum.Enum
An enumeration.
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Ambivalent
= 3¶
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Aromatic
= 5¶
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NoSteric
= 1¶
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Polar
= 4¶
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Small
= 2¶
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class
schrodinger.protein.residue.
SIDE_CHAIN_CHEM
¶ Bases:
enum.Enum
An enumeration.
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AcidicHydrophilic
= 2¶
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BasicHydrophilic
= 3¶
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IminoAcid
= 8¶
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NeutralHydrophilic
= 6¶
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NeutralHydrophobicAliphatic
= 4¶
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NeutralHydrophobicAromatic
= 5¶
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NoSideChainChem
= 1¶
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PrimaryThiol
= 7¶
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class
schrodinger.protein.residue.
RESIDUE_CHARGE
¶ Bases:
enum.Enum
An enumeration.
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Negative
= 2¶
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Neutral
= 3¶
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Positive
= 1¶
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class
schrodinger.protein.residue.
ElementType
(short_code, long_code, name)¶ Bases:
object
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__init__
(short_code, long_code, name)¶ Initialize self. See help(type(self)) for accurate signature.
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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:
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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
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__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.
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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:
-
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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
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__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.
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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:
-
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class
schrodinger.protein.residue.
DeoxyribonucleotideType
(short_code, long_code, name, charge=None, hydrophobicity=None, hydrophilicity=None, helix_propensity=None, beta_strand_propensity=None, turn_propensity=None, helix_termination_tendency=None, exposure_tendency=None, steric_group=None, side_chain_chem=None, isoelectric_point=None)¶ Bases:
schrodinger.protein.residue.NucleotideType
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__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.
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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:
-
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class
schrodinger.protein.residue.
RibonucleotideType
(short_code, long_code, name, charge=None, hydrophobicity=None, hydrophilicity=None, helix_propensity=None, beta_strand_propensity=None, turn_propensity=None, helix_termination_tendency=None, exposure_tendency=None, steric_group=None, side_chain_chem=None, isoelectric_point=None)¶ Bases:
schrodinger.protein.residue.NucleotideType
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__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.
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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:
-
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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
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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.
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schrodinger.protein.residue.
make_one_letter_map
(res_list)¶
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schrodinger.protein.residue.
make_three_letter_map
(res_list)¶
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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
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class
schrodinger.protein.residue.
AbstractSequenceElement
¶ Bases:
schrodinger.models.json.JsonableClassMixin
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is_res
¶ Utility function to check whether a residue is not a gap
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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
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hasStructure
()¶ Returns: Whether this element has a structure i.e. whether it has corresponding XYZ coordinates in Maestro. :rtype: bool
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idx_in_seq
¶
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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
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__init__
¶ Initialize self. See help(type(self)) for accurate signature.
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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
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classmethod
fromJsonImplementation
(json_dict)¶ Abstract method that must be defined by all derived classes. Takes in a dictionary and constructs an instance of the derived class.
Parameters: json_dict (dict) – A dictionary loaded from a JSON string or file. Returns: An instance of the derived class. :rtype : cls
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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.
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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
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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
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class
schrodinger.protein.residue.
Gap
¶ Bases:
schrodinger.protein.residue.AbstractSequenceElement
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is_gap
= True¶
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__init__
()¶ Initialize self. See help(type(self)) for accurate signature.
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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
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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
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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
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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
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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
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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.
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hasStructure
()¶ Returns: Whether this element has a structure i.e. whether it has corresponding XYZ coordinates in Maestro. :rtype: bool
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idx_in_seq
¶
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is_res
¶ Utility function to check whether a residue is not a gap
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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
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class
schrodinger.protein.residue.
Residue
(element_type, inscode=None, resnum=None, seqres_only=False)¶ Bases:
schrodinger.protein.residue.AbstractSequenceElement
An amino acid residue.
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is_gap
= False¶
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descriptors
¶
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__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.
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type
¶
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seqres_only
¶
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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
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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
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getChainKey
()¶
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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
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hasSetResNum
() → bool¶ Returns: Whether a specific resnum has been set
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resnum
¶ If resnum is set to None, resnum will be auto-generated from column number.
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inscode
¶ If inscode and rescode are both set to None, the inscode will be ‘+’.
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rescode
¶
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short_code
¶
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long_code
¶
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chain
¶ The name of the sequence chain that this residue belongs to. :rtype: str
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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
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hydrophobicity
¶ Returns: Hydrophobicity for the ResidueType on the Kyte-Doolittle scale, if available; otherwise None. Return type: float
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hydrophilicity
¶ Returns: Hydrophilicity for the ResidueType on the Hopp-Woods scale, if available; otherwise None Return type: float
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charge
¶ Returns: charge of the ResidueType of the residue Return type: RESIDUE_CHARGE
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helix_propensity
¶ Returns: Helix propensity for the ResidueType of the residue Return type: HELIX_PROPENSITY
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beta_strand_propensity
¶ Returns: Beta-strand propensity for the ResidueType of the residue Return type: BETA_STRAND_PROPENSITY
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turn_propensity
¶ Returns: Turn propensity for the ResidueType of the residue Return type: TURN_PROPENSITY
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helix_termination_tendency
¶ Returns: Helix termination tendency for the ResidueType of the residue Return type: HELIX_TERMINATION_TENDENCY
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exposure_tendency
¶ Returns: Solvent exposure tendency for the ResidueType of the residue Return type: SOLVENT_EXPOSURE_TENDENCY
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steric_group
¶ Returns: Steric group for the ResidueType of the residue Return type: STERIC_GROUP
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side_chain_chem
¶ Returns: Side chain chemistry for the ResidueType of the residue Return type: SIDE_CHAIN_CHEM
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ss_prediction_psipred
¶ Returns a DSSP code matching the secondary structure prediction for the residue or None. Value is calculated from thePsiPred backend.
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ss_prediction_sspro
¶ Returns a DSSP code matching the secondary structure prediction for the residue or None. Value is calculated from the SSpro backend.
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isoelectric_point
¶ Returns: A float representing the isoelectric point value for the ResidueType of the residue
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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
- ref_res (
-
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
- ref_res (
-
getIdentity
(ref_res)¶ Return the identity between the residue and a reference residue
Parameters: ref_res ( schrodinger.protein.residue.Residue
) – The reference residueReturns: 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 residueReturns: 1 if the residue and reference residue are have similar side chain chemistry, 0 otherwise. Return type: int
-
getStructureResProperties
()¶ Return all properties for the corresponding structure residue’s alpha carbon. Properties that apply to the whole residue are stored as atom properties on this atom. An empty dictionary will be returned if this residue doesn’t have a corresponding alpha carbon.
Returns: A dictionary-like object containing the properties. Return type: structure._StructureAtomProperty or dict
-
updateDescriptors
(descriptors)¶ Updates the descriptor dicts with new descriptor values
Parameters: descriptors (dict[str, float]) – A dict mapping descriptor names to their values
-
getDescriptorValue
(descriptor_name)¶
-
getDescriptorKeys
()¶
-
getProperty
(seq_prop)¶ Get the residue’s value corresponding to the given SequenceProperty object
Parameters: seq_prop (schrodinger.protein.properties.SequenceProperty) – The object describing the residue property Returns: The value of the sequence property Return type: float or None
-
area
¶
-
b_factor
¶
-
composition
¶
-
disulfide_bond
¶
-
domains
¶
-
classmethod
fromJson
(json_obj)¶ A factory method which constructs a new object from a given dict loaded from a json string or file.
Parameters: json_obj (dict) – A json-loaded dictionary to create an object from. Returns: An instance of this class. :rtype : cls
-
gapless_idx_in_seq
¶ Return the index of this residue within its sequence ignoring gaps
Returns: Index of this residue in its sequence or None if it is not part of a sequence. Return type: int or None
-
get_version
()¶ Method to get the version of a particular object. Defaults to the current version of mmshare. This class can be overridden for custom versioning behavior.
-
hasStructure
()¶ Returns: Whether this element has a structure i.e. whether it has corresponding XYZ coordinates in Maestro. :rtype: bool
-
idx_in_seq
¶
-
is_res
¶ Utility function to check whether a residue is not a gap
-
molecule_number
¶
-
pfam
¶
-
pred_accessibility
¶
-
pred_disordered
¶
-
pred_disulfide_bond
¶
-
pred_domain_arr
¶
-
pred_secondary_structure
¶
-
secondary_structure
¶
-
sequence
¶ The sequence that this element is part of. Will be
None
if this residue is not part of a sequence. Stored as a weakref to avoid circular references. :rtype: sequence.AbstractSingleChainSequence
-
toJson
(_mark_version=True)¶ Create and returns a data structure made up of jsonable items.
Return type: An instance of one the classes from NATIVE_JSON_DATATYPES
-
-
class
schrodinger.protein.residue.
CombinedChainResidueWrapper
(res, combined_chain_seq)¶ Bases:
object
A wrapper for a residue or gap so that res.sequence points to the combined-chain sequence and res.idx_in_seq gives the index within the combined-chain sequence.
Note that these wrappers are generated as needed and the combined-chain sequence does not store any reference to the generated instances. As such, these residues should not be stored using weakrefs and should not be compared using identity. Also note that these residues will not compare equal to the split-chain residues that they wrap.
-
__init__
(res, combined_chain_seq)¶ Parameters: - 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
-
idx_in_seq
¶ This residue’s index in the combined-chain sequence, or None if the residue has been removed from the sequence.
Return type: int or None
-
split_res
¶ The split-chain residue or gap that this residue is wrapping.
Return type: AbstractSequenceElement
-
split_sequence
¶ The split-chain sequence that this residue is part or, or None if the residue has been removed from the sequence.
Return type: sequence.ProteinSequence or None
-
disulfide_bond
¶ The current disulfide bond, if any, that this residue is involved in. :rtype: CombinedChainDisulfideBond or None
-
-
class
schrodinger.protein.residue.
DisulfideBond
(res1, res2)¶ Bases:
object
Representation of a disulfide bond.
-
__init__
(res1, res2)¶ Parameters:
-
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)
-
is_intra_sequence
¶ Check whether the bond is valid and intra-sequence.
Returns: Whether the bond is a valid, intra-sequence bond. Return type: bool Raises: ValueError – If the bond is not valid
-
res_pair
¶
-
is_inter_sequence
¶ Check whether the bond is valid and inter-sequence.
Returns: Whether the bond is a valid, inter-sequence bond. Return type: bool Raises: ValueError – If the bond is not valid
-
-
schrodinger.protein.residue.
add_disulfide_bond
(res1, res2, known=True)¶ Add a disulfide bond between two residues.
Parameters: - res1 (residue.Residue) – A residue to link with a disulfide bond
- res2 (residue.Residue) – Another residue to link with a disulfide bond
- known (bool) – Whether the bond is a known bond or a predicted bond.
-
schrodinger.protein.residue.
remove_disulfide_bond
(bond)¶ Remove a disulfide bond between two residues.
Parameters: bond (residue.DisulfideBond) – The bond to disconnect
-
class
schrodinger.protein.residue.
Nucleotide
(element_type, inscode=None, resnum=None, seqres_only=False)¶ Bases:
schrodinger.protein.residue.Residue
-
__init__
(element_type, inscode=None, resnum=None, seqres_only=False)¶ Parameters: - element_type (ResidueType) – The kind of the residue
- inscode (str) – The insertion code
- resnum (int) – PDB residue number
- seqres_only (bool) – Whether this residue only appears in the SEQRES record of a structure. Only applies to sequences associated with a structure.
-
area
¶
-
b_factor
¶
-
beta_strand_propensity
¶ Returns: Beta-strand propensity for the ResidueType of the residue Return type: BETA_STRAND_PROPENSITY
-
chain
¶ The name of the sequence chain that this residue belongs to. :rtype: str
-
charge
¶ Returns: charge of the ResidueType of the residue Return type: RESIDUE_CHARGE
-
composition
¶
-
descriptors
¶
-
disulfide_bond
¶
-
domains
¶
-
exposure_tendency
¶ Returns: Solvent exposure tendency for the ResidueType of the residue Return type: SOLVENT_EXPOSURE_TENDENCY
-
classmethod
fromJson
(json_obj)¶ A factory method which constructs a new object from a given dict loaded from a json string or file.
Parameters: json_obj (dict) – A json-loaded dictionary to create an object from. Returns: An instance of this class. :rtype : cls
-
classmethod
fromJsonImplementation
(json_obj)¶ Abstract method that must be defined by all derived classes. Takes in a dictionary and constructs an instance of the derived class.
Parameters: json_dict (dict) – A dictionary loaded from a JSON string or file. Returns: An instance of the derived class. :rtype : cls
-
gapless_idx_in_seq
¶ Return the index of this residue within its sequence ignoring gaps
Returns: Index of this residue in its sequence or None if it is not part of a sequence. Return type: int or None
-
getBinarySimilarity
(ref_res, similarity_matrix={('A', 'A'): 4, ('A', 'B'): -2, ('A', 'C'): 0, ('A', 'D'): -2, ('A', 'E'): -1, ('A', 'F'): -2, ('A', 'G'): 0, ('A', 'H'): -2, ('A', 'I'): -1, ('A', 'K'): -1, ('A', 'L'): -1, ('A', 'M'): -1, ('A', 'N'): -2, ('A', 'P'): -1, ('A', 'Q'): -1, ('A', 'R'): -1, ('A', 'S'): 1, ('A', 'T'): 0, ('A', 'V'): 0, ('A', 'W'): -3, ('A', 'X'): 0, ('A', 'Y'): -2, ('A', 'Z'): -1, ('B', 'A'): -2, ('B', 'B'): 4, ('B', 'C'): -3, ('B', 'D'): 4, ('B', 'E'): 1, ('B', 'F'): -3, ('B', 'G'): -1, ('B', 'H'): 0, ('B', 'I'): -3, ('B', 'K'): 0, ('B', 'L'): -4, ('B', 'M'): -3, ('B', 'N'): 3, ('B', 'P'): -2, ('B', 'Q'): 0, ('B', 'R'): -1, ('B', 'S'): 0, ('B', 'T'): -1, ('B', 'V'): -3, ('B', 'W'): -4, ('B', 'X'): -1, ('B', 'Y'): -3, ('B', 'Z'): 1, ('C', 'A'): 0, ('C', 'B'): -3, ('C', 'C'): 9, ('C', 'D'): -3, ('C', 'E'): -4, ('C', 'F'): -2, ('C', 'G'): -3, ('C', 'H'): -3, ('C', 'I'): -1, ('C', 'K'): -3, ('C', 'L'): -1, ('C', 'M'): -1, ('C', 'N'): -3, ('C', 'P'): -3, ('C', 'Q'): -3, ('C', 'R'): -3, ('C', 'S'): -1, ('C', 'T'): -1, ('C', 'V'): -1, ('C', 'W'): -2, ('C', 'X'): -2, ('C', 'Y'): -2, ('C', 'Z'): -3, ('D', 'A'): -2, ('D', 'B'): 4, ('D', 'C'): -3, ('D', 'D'): 6, ('D', 'E'): 2, ('D', 'F'): -3, ('D', 'G'): -1, ('D', 'H'): -1, ('D', 'I'): -3, ('D', 'K'): -1, ('D', 'L'): -4, ('D', 'M'): -3, ('D', 'N'): 1, ('D', 'P'): -1, ('D', 'Q'): 0, ('D', 'R'): -2, ('D', 'S'): 0, ('D', 'T'): -1, ('D', 'V'): -3, ('D', 'W'): -4, ('D', 'X'): -1, ('D', 'Y'): -3, ('D', 'Z'): 1, ('E', 'A'): -1, ('E', 'B'): 1, ('E', 'C'): -4, ('E', 'D'): 2, ('E', 'E'): 5, ('E', 'F'): -3, ('E', 'G'): -2, ('E', 'H'): 0, ('E', 'I'): -3, ('E', 'K'): 1, ('E', 'L'): -3, ('E', 'M'): -2, ('E', 'N'): 0, ('E', 'P'): -1, ('E', 'Q'): 2, ('E', 'R'): 0, ('E', 'S'): 0, ('E', 'T'): -1, ('E', 'V'): -2, ('E', 'W'): -3, ('E', 'X'): -1, ('E', 'Y'): -2, ('E', 'Z'): 4, ('F', 'A'): -2, ('F', 'B'): -3, ('F', 'C'): -2, ('F', 'D'): -3, ('F', 'E'): -3, ('F', 'F'): 6, ('F', 'G'): -3, ('F', 'H'): -1, ('F', 'I'): 0, ('F', 'K'): -3, ('F', 'L'): 0, ('F', 'M'): 0, ('F', 'N'): -3, ('F', 'P'): -4, ('F', 'Q'): -3, ('F', 'R'): -3, ('F', 'S'): -2, ('F', 'T'): -2, ('F', 'V'): -1, ('F', 'W'): 1, ('F', 'X'): -1, ('F', 'Y'): 3, ('F', 'Z'): -3, ('G', 'A'): 0, ('G', 'B'): -1, ('G', 'C'): -3, ('G', 'D'): -1, ('G', 'E'): -2, ('G', 'F'): -3, ('G', 'G'): 6, ('G', 'H'): -2, ('G', 'I'): -4, ('G', 'K'): -2, ('G', 'L'): -4, ('G', 'M'): -3, ('G', 'N'): 0, ('G', 'P'): -2, ('G', 'Q'): -2, ('G', 'R'): -2, ('G', 'S'): 0, ('G', 'T'): -2, ('G', 'V'): -3, ('G', 'W'): -2, ('G', 'X'): -1, ('G', 'Y'): -3, ('G', 'Z'): -2, ('H', 'A'): -2, ('H', 'B'): 0, ('H', 'C'): -3, ('H', 'D'): -1, ('H', 'E'): 0, ('H', 'F'): -1, ('H', 'G'): -2, ('H', 'H'): 8, ('H', 'I'): -3, ('H', 'K'): -1, ('H', 'L'): -3, ('H', 'M'): -2, ('H', 'N'): 1, ('H', 'P'): -2, ('H', 'Q'): 0, ('H', 'R'): 0, ('H', 'S'): -1, ('H', 'T'): -2, ('H', 'V'): -3, ('H', 'W'): -2, ('H', 'X'): -1, ('H', 'Y'): 2, ('H', 'Z'): 0, ('I', 'A'): -1, ('I', 'B'): -3, ('I', 'C'): -1, ('I', 'D'): -3, ('I', 'E'): -3, ('I', 'F'): 0, ('I', 'G'): -4, ('I', 'H'): -3, ('I', 'I'): 4, ('I', 'K'): -3, ('I', 'L'): 2, ('I', 'M'): 1, ('I', 'N'): -3, ('I', 'P'): -3, ('I', 'Q'): -3, ('I', 'R'): -3, ('I', 'S'): -2, ('I', 'T'): -1, ('I', 'V'): 3, ('I', 'W'): -3, ('I', 'X'): -1, ('I', 'Y'): -1, ('I', 'Z'): -3, ('K', 'A'): -1, ('K', 'B'): 0, ('K', 'C'): -3, ('K', 'D'): -1, ('K', 'E'): 1, ('K', 'F'): -3, ('K', 'G'): -2, ('K', 'H'): -1, ('K', 'I'): -3, ('K', 'K'): 5, ('K', 'L'): -2, ('K', 'M'): -1, ('K', 'N'): 0, ('K', 'P'): -1, ('K', 'Q'): 1, ('K', 'R'): 2, ('K', 'S'): 0, ('K', 'T'): -1, ('K', 'V'): -2, ('K', 'W'): -3, ('K', 'X'): -1, ('K', 'Y'): -2, ('K', 'Z'): 1, ('L', 'A'): -1, ('L', 'B'): -4, ('L', 'C'): -1, ('L', 'D'): -4, ('L', 'E'): -3, ('L', 'F'): 0, ('L', 'G'): -4, ('L', 'H'): -3, ('L', 'I'): 2, ('L', 'K'): -2, ('L', 'L'): 4, ('L', 'M'): 2, ('L', 'N'): -3, ('L', 'P'): -3, ('L', 'Q'): -2, ('L', 'R'): -2, ('L', 'S'): -2, ('L', 'T'): -1, ('L', 'V'): 1, ('L', 'W'): -2, ('L', 'X'): -1, ('L', 'Y'): -1, ('L', 'Z'): -3, ('M', 'A'): -1, ('M', 'B'): -3, ('M', 'C'): -1, ('M', 'D'): -3, ('M', 'E'): -2, ('M', 'F'): 0, ('M', 'G'): -3, ('M', 'H'): -2, ('M', 'I'): 1, ('M', 'K'): -1, ('M', 'L'): 2, ('M', 'M'): 5, ('M', 'N'): -2, ('M', 'P'): -2, ('M', 'Q'): 0, ('M', 'R'): -1, ('M', 'S'): -1, ('M', 'T'): -1, ('M', 'V'): 1, ('M', 'W'): -1, ('M', 'X'): -1, ('M', 'Y'): -1, ('M', 'Z'): -1, ('N', 'A'): -2, ('N', 'B'): 3, ('N', 'C'): -3, ('N', 'D'): 1, ('N', 'E'): 0, ('N', 'F'): -3, ('N', 'G'): 0, ('N', 'H'): 1, ('N', 'I'): -3, ('N', 'K'): 0, ('N', 'L'): -3, ('N', 'M'): -2, ('N', 'N'): 6, ('N', 'P'): -2, ('N', 'Q'): 0, ('N', 'R'): 0, ('N', 'S'): 1, ('N', 'T'): 0, ('N', 'V'): -3, ('N', 'W'): -4, ('N', 'X'): -1, ('N', 'Y'): -2, ('N', 'Z'): 0, ('P', 'A'): -1, ('P', 'B'): -2, ('P', 'C'): -3, ('P', 'D'): -1, ('P', 'E'): -1, ('P', 'F'): -4, ('P', 'G'): -2, ('P', 'H'): -2, ('P', 'I'): -3, ('P', 'K'): -1, ('P', 'L'): -3, ('P', 'M'): -2, ('P', 'N'): -2, ('P', 'P'): 7, ('P', 'Q'): -1, ('P', 'R'): -2, ('P', 'S'): -1, ('P', 'T'): -1, ('P', 'V'): -2, ('P', 'W'): -4, ('P', 'X'): -2, ('P', 'Y'): -3, ('P', 'Z'): -1, ('Q', 'A'): -1, ('Q', 'B'): 0, ('Q', 'C'): -3, ('Q', 'D'): 0, ('Q', 'E'): 2, ('Q', 'F'): -3, ('Q', 'G'): -2, ('Q', 'H'): 0, ('Q', 'I'): -3, ('Q', 'K'): 1, ('Q', 'L'): -2, ('Q', 'M'): 0, ('Q', 'N'): 0, ('Q', 'P'): -1, ('Q', 'Q'): 5, ('Q', 'R'): 1, ('Q', 'S'): 0, ('Q', 'T'): -1, ('Q', 'V'): -2, ('Q', 'W'): -2, ('Q', 'X'): -1, ('Q', 'Y'): -1, ('Q', 'Z'): 3, ('R', 'A'): -1, ('R', 'B'): -1, ('R', 'C'): -3, ('R', 'D'): -2, ('R', 'E'): 0, ('R', 'F'): -3, ('R', 'G'): -2, ('R', 'H'): 0, ('R', 'I'): -3, ('R', 'K'): 2, ('R', 'L'): -2, ('R', 'M'): -1, ('R', 'N'): 0, ('R', 'P'): -2, ('R', 'Q'): 1, ('R', 'R'): 5, ('R', 'S'): -1, ('R', 'T'): -1, ('R', 'V'): -3, ('R', 'W'): -3, ('R', 'X'): -1, ('R', 'Y'): -2, ('R', 'Z'): 0, ('S', 'A'): 1, ('S', 'B'): 0, ('S', 'C'): -1, ('S', 'D'): 0, ('S', 'E'): 0, ('S', 'F'): -2, ('S', 'G'): 0, ('S', 'H'): -1, ('S', 'I'): -2, ('S', 'K'): 0, ('S', 'L'): -2, ('S', 'M'): -1, ('S', 'N'): 1, ('S', 'P'): -1, ('S', 'Q'): 0, ('S', 'R'): -1, ('S', 'S'): 4, ('S', 'T'): 1, ('S', 'V'): -2, ('S', 'W'): -3, ('S', 'X'): 0, ('S', 'Y'): -2, ('S', 'Z'): 0, ('T', 'A'): 0, ('T', 'B'): -1, ('T', 'C'): -1, ('T', 'D'): -1, ('T', 'E'): -1, ('T', 'F'): -2, ('T', 'G'): -2, ('T', 'H'): -2, ('T', 'I'): -1, ('T', 'K'): -1, ('T', 'L'): -1, ('T', 'M'): -1, ('T', 'N'): 0, ('T', 'P'): -1, ('T', 'Q'): -1, ('T', 'R'): -1, ('T', 'S'): 1, ('T', 'T'): 5, ('T', 'V'): 0, ('T', 'W'): -2, ('T', 'X'): 0, ('T', 'Y'): -2, ('T', 'Z'): -1, ('V', 'A'): 0, ('V', 'B'): -3, ('V', 'C'): -1, ('V', 'D'): -3, ('V', 'E'): -2, ('V', 'F'): -1, ('V', 'G'): -3, ('V', 'H'): -3, ('V', 'I'): 3, ('V', 'K'): -2, ('V', 'L'): 1, ('V', 'M'): 1, ('V', 'N'): -3, ('V', 'P'): -2, ('V', 'Q'): -2, ('V', 'R'): -3, ('V', 'S'): -2, ('V', 'T'): 0, ('V', 'V'): 4, ('V', 'W'): -3, ('V', 'X'): -1, ('V', 'Y'): -1, ('V', 'Z'): -2, ('W', 'A'): -3, ('W', 'B'): -4, ('W', 'C'): -2, ('W', 'D'): -4, ('W', 'E'): -3, ('W', 'F'): 1, ('W', 'G'): -2, ('W', 'H'): -2, ('W', 'I'): -3, ('W', 'K'): -3, ('W', 'L'): -2, ('W', 'M'): -1, ('W', 'N'): -4, ('W', 'P'): -4, ('W', 'Q'): -2, ('W', 'R'): -3, ('W', 'S'): -3, ('W', 'T'): -2, ('W', 'V'): -3, ('W', 'W'): 11, ('W', 'X'): -2, ('W', 'Y'): 2, ('W', 'Z'): -3, ('X', 'A'): 0, ('X', 'B'): -1, ('X', 'C'): -2, ('X', 'D'): -1, ('X', 'E'): -1, ('X', 'F'): -1, ('X', 'G'): -1, ('X', 'H'): -1, ('X', 'I'): -1, ('X', 'K'): -1, ('X', 'L'): -1, ('X', 'M'): -1, ('X', 'N'): -1, ('X', 'P'): -2, ('X', 'Q'): -1, ('X', 'R'): -1, ('X', 'S'): 0, ('X', 'T'): 0, ('X', 'V'): -1, ('X', 'W'): -2, ('X', 'X'): -1, ('X', 'Y'): -1, ('X', 'Z'): -1, ('Y', 'A'): -2, ('Y', 'B'): -3, ('Y', 'C'): -2, ('Y', 'D'): -3, ('Y', 'E'): -2, ('Y', 'F'): 3, ('Y', 'G'): -3, ('Y', 'H'): 2, ('Y', 'I'): -1, ('Y', 'K'): -2, ('Y', 'L'): -1, ('Y', 'M'): -1, ('Y', 'N'): -2, ('Y', 'P'): -3, ('Y', 'Q'): -1, ('Y', 'R'): -2, ('Y', 'S'): -2, ('Y', 'T'): -2, ('Y', 'V'): -1, ('Y', 'W'): 2, ('Y', 'X'): -1, ('Y', 'Y'): 7, ('Y', 'Z'): -2, ('Z', 'A'): -1, ('Z', 'B'): 1, ('Z', 'C'): -3, ('Z', 'D'): 1, ('Z', 'E'): 4, ('Z', 'F'): -3, ('Z', 'G'): -2, ('Z', 'H'): 0, ('Z', 'I'): -3, ('Z', 'K'): 1, ('Z', 'L'): -3, ('Z', 'M'): -1, ('Z', 'N'): 0, ('Z', 'P'): -1, ('Z', 'Q'): 3, ('Z', 'R'): 0, ('Z', 'S'): 0, ('Z', 'T'): -1, ('Z', 'V'): -2, ('Z', 'W'): -3, ('Z', 'X'): -1, ('Z', 'Y'): -2, ('Z', 'Z'): 4})¶ Returns if the residue and a reference residue are similar
Parameters: - 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
- ref_res (
-
getChainKey
()¶
-
getConservation
(ref_res)¶ Return whether the residue and a reference residue have similar side-chain chemistry.
The similarity criterion is based on “side chain chemistry” descriptor matching.
Parameters: ref_res ( schrodinger.protein.residue.Residue
) – The reference residueReturns: 1 if the residue and reference residue are have similar side chain chemistry, 0 otherwise. Return type: int
-
getDescriptorKeys
()¶
-
getDescriptorValue
(descriptor_name)¶
-
getIdentity
(ref_res)¶ Return the identity between the residue and a reference residue
Parameters: ref_res ( schrodinger.protein.residue.Residue
) – The reference residueReturns: 1 if same as the reference residue, 0 otherwise. Return type: int
-
getKey
()¶ Get a key that uniquely identifies the residue relative to structures.
Returns: Residue key as (entry_id, chain, inscode, resnum, molnum, pdbname), or None if residue is unparented or has no structure Return type: ResidueKey or NoneType
-
getProperty
(seq_prop)¶ Get the residue’s value corresponding to the given SequenceProperty object
Parameters: seq_prop (schrodinger.protein.properties.SequenceProperty) – The object describing the residue property Returns: The value of the sequence property Return type: float or None
-
getSimilarity
(ref_res, similarity_matrix={('A', 'A'): 4, ('A', 'B'): -2, ('A', 'C'): 0, ('A', 'D'): -2, ('A', 'E'): -1, ('A', 'F'): -2, ('A', 'G'): 0, ('A', 'H'): -2, ('A', 'I'): -1, ('A', 'K'): -1, ('A', 'L'): -1, ('A', 'M'): -1, ('A', 'N'): -2, ('A', 'P'): -1, ('A', 'Q'): -1, ('A', 'R'): -1, ('A', 'S'): 1, ('A', 'T'): 0, ('A', 'V'): 0, ('A', 'W'): -3, ('A', 'X'): 0, ('A', 'Y'): -2, ('A', 'Z'): -1, ('B', 'A'): -2, ('B', 'B'): 4, ('B', 'C'): -3, ('B', 'D'): 4, ('B', 'E'): 1, ('B', 'F'): -3, ('B', 'G'): -1, ('B', 'H'): 0, ('B', 'I'): -3, ('B', 'K'): 0, ('B', 'L'): -4, ('B', 'M'): -3, ('B', 'N'): 3, ('B', 'P'): -2, ('B', 'Q'): 0, ('B', 'R'): -1, ('B', 'S'): 0, ('B', 'T'): -1, ('B', 'V'): -3, ('B', 'W'): -4, ('B', 'X'): -1, ('B', 'Y'): -3, ('B', 'Z'): 1, ('C', 'A'): 0, ('C', 'B'): -3, ('C', 'C'): 9, ('C', 'D'): -3, ('C', 'E'): -4, ('C', 'F'): -2, ('C', 'G'): -3, ('C', 'H'): -3, ('C', 'I'): -1, ('C', 'K'): -3, ('C', 'L'): -1, ('C', 'M'): -1, ('C', 'N'): -3, ('C', 'P'): -3, ('C', 'Q'): -3, ('C', 'R'): -3, ('C', 'S'): -1, ('C', 'T'): -1, ('C', 'V'): -1, ('C', 'W'): -2, ('C', 'X'): -2, ('C', 'Y'): -2, ('C', 'Z'): -3, ('D', 'A'): -2, ('D', 'B'): 4, ('D', 'C'): -3, ('D', 'D'): 6, ('D', 'E'): 2, ('D', 'F'): -3, ('D', 'G'): -1, ('D', 'H'): -1, ('D', 'I'): -3, ('D', 'K'): -1, ('D', 'L'): -4, ('D', 'M'): -3, ('D', 'N'): 1, ('D', 'P'): -1, ('D', 'Q'): 0, ('D', 'R'): -2, ('D', 'S'): 0, ('D', 'T'): -1, ('D', 'V'): -3, ('D', 'W'): -4, ('D', 'X'): -1, ('D', 'Y'): -3, ('D', 'Z'): 1, ('E', 'A'): -1, ('E', 'B'): 1, ('E', 'C'): -4, ('E', 'D'): 2, ('E', 'E'): 5, ('E', 'F'): -3, ('E', 'G'): -2, ('E', 'H'): 0, ('E', 'I'): -3, ('E', 'K'): 1, ('E', 'L'): -3, ('E', 'M'): -2, ('E', 'N'): 0, ('E', 'P'): -1, ('E', 'Q'): 2, ('E', 'R'): 0, ('E', 'S'): 0, ('E', 'T'): -1, ('E', 'V'): -2, ('E', 'W'): -3, ('E', 'X'): -1, ('E', 'Y'): -2, ('E', 'Z'): 4, ('F', 'A'): -2, ('F', 'B'): -3, ('F', 'C'): -2, ('F', 'D'): -3, ('F', 'E'): -3, ('F', 'F'): 6, ('F', 'G'): -3, ('F', 'H'): -1, ('F', 'I'): 0, ('F', 'K'): -3, ('F', 'L'): 0, ('F', 'M'): 0, ('F', 'N'): -3, ('F', 'P'): -4, ('F', 'Q'): -3, ('F', 'R'): -3, ('F', 'S'): -2, ('F', 'T'): -2, ('F', 'V'): -1, ('F', 'W'): 1, ('F', 'X'): -1, ('F', 'Y'): 3, ('F', 'Z'): -3, ('G', 'A'): 0, ('G', 'B'): -1, ('G', 'C'): -3, ('G', 'D'): -1, ('G', 'E'): -2, ('G', 'F'): -3, ('G', 'G'): 6, ('G', 'H'): -2, ('G', 'I'): -4, ('G', 'K'): -2, ('G', 'L'): -4, ('G', 'M'): -3, ('G', 'N'): 0, ('G', 'P'): -2, ('G', 'Q'): -2, ('G', 'R'): -2, ('G', 'S'): 0, ('G', 'T'): -2, ('G', 'V'): -3, ('G', 'W'): -2, ('G', 'X'): -1, ('G', 'Y'): -3, ('G', 'Z'): -2, ('H', 'A'): -2, ('H', 'B'): 0, ('H', 'C'): -3, ('H', 'D'): -1, ('H', 'E'): 0, ('H', 'F'): -1, ('H', 'G'): -2, ('H', 'H'): 8, ('H', 'I'): -3, ('H', 'K'): -1, ('H', 'L'): -3, ('H', 'M'): -2, ('H', 'N'): 1, ('H', 'P'): -2, ('H', 'Q'): 0, ('H', 'R'): 0, ('H', 'S'): -1, ('H', 'T'): -2, ('H', 'V'): -3, ('H', 'W'): -2, ('H', 'X'): -1, ('H', 'Y'): 2, ('H', 'Z'): 0, ('I', 'A'): -1, ('I', 'B'): -3, ('I', 'C'): -1, ('I', 'D'): -3, ('I', 'E'): -3, ('I', 'F'): 0, ('I', 'G'): -4, ('I', 'H'): -3, ('I', 'I'): 4, ('I', 'K'): -3, ('I', 'L'): 2, ('I', 'M'): 1, ('I', 'N'): -3, ('I', 'P'): -3, ('I', 'Q'): -3, ('I', 'R'): -3, ('I', 'S'): -2, ('I', 'T'): -1, ('I', 'V'): 3, ('I', 'W'): -3, ('I', 'X'): -1, ('I', 'Y'): -1, ('I', 'Z'): -3, ('K', 'A'): -1, ('K', 'B'): 0, ('K', 'C'): -3, ('K', 'D'): -1, ('K', 'E'): 1, ('K', 'F'): -3, ('K', 'G'): -2, ('K', 'H'): -1, ('K', 'I'): -3, ('K', 'K'): 5, ('K', 'L'): -2, ('K', 'M'): -1, ('K', 'N'): 0, ('K', 'P'): -1, ('K', 'Q'): 1, ('K', 'R'): 2, ('K', 'S'): 0, ('K', 'T'): -1, ('K', 'V'): -2, ('K', 'W'): -3, ('K', 'X'): -1, ('K', 'Y'): -2, ('K', 'Z'): 1, ('L', 'A'): -1, ('L', 'B'): -4, ('L', 'C'): -1, ('L', 'D'): -4, ('L', 'E'): -3, ('L', 'F'): 0, ('L', 'G'): -4, ('L', 'H'): -3, ('L', 'I'): 2, ('L', 'K'): -2, ('L', 'L'): 4, ('L', 'M'): 2, ('L', 'N'): -3, ('L', 'P'): -3, ('L', 'Q'): -2, ('L', 'R'): -2, ('L', 'S'): -2, ('L', 'T'): -1, ('L', 'V'): 1, ('L', 'W'): -2, ('L', 'X'): -1, ('L', 'Y'): -1, ('L', 'Z'): -3, ('M', 'A'): -1, ('M', 'B'): -3, ('M', 'C'): -1, ('M', 'D'): -3, ('M', 'E'): -2, ('M', 'F'): 0, ('M', 'G'): -3, ('M', 'H'): -2, ('M', 'I'): 1, ('M', 'K'): -1, ('M', 'L'): 2, ('M', 'M'): 5, ('M', 'N'): -2, ('M', 'P'): -2, ('M', 'Q'): 0, ('M', 'R'): -1, ('M', 'S'): -1, ('M', 'T'): -1, ('M', 'V'): 1, ('M', 'W'): -1, ('M', 'X'): -1, ('M', 'Y'): -1, ('M', 'Z'): -1, ('N', 'A'): -2, ('N', 'B'): 3, ('N', 'C'): -3, ('N', 'D'): 1, ('N', 'E'): 0, ('N', 'F'): -3, ('N', 'G'): 0, ('N', 'H'): 1, ('N', 'I'): -3, ('N', 'K'): 0, ('N', 'L'): -3, ('N', 'M'): -2, ('N', 'N'): 6, ('N', 'P'): -2, ('N', 'Q'): 0, ('N', 'R'): 0, ('N', 'S'): 1, ('N', 'T'): 0, ('N', 'V'): -3, ('N', 'W'): -4, ('N', 'X'): -1, ('N', 'Y'): -2, ('N', 'Z'): 0, ('P', 'A'): -1, ('P', 'B'): -2, ('P', 'C'): -3, ('P', 'D'): -1, ('P', 'E'): -1, ('P', 'F'): -4, ('P', 'G'): -2, ('P', 'H'): -2, ('P', 'I'): -3, ('P', 'K'): -1, ('P', 'L'): -3, ('P', 'M'): -2, ('P', 'N'): -2, ('P', 'P'): 7, ('P', 'Q'): -1, ('P', 'R'): -2, ('P', 'S'): -1, ('P', 'T'): -1, ('P', 'V'): -2, ('P', 'W'): -4, ('P', 'X'): -2, ('P', 'Y'): -3, ('P', 'Z'): -1, ('Q', 'A'): -1, ('Q', 'B'): 0, ('Q', 'C'): -3, ('Q', 'D'): 0, ('Q', 'E'): 2, ('Q', 'F'): -3, ('Q', 'G'): -2, ('Q', 'H'): 0, ('Q', 'I'): -3, ('Q', 'K'): 1, ('Q', 'L'): -2, ('Q', 'M'): 0, ('Q', 'N'): 0, ('Q', 'P'): -1, ('Q', 'Q'): 5, ('Q', 'R'): 1, ('Q', 'S'): 0, ('Q', 'T'): -1, ('Q', 'V'): -2, ('Q', 'W'): -2, ('Q', 'X'): -1, ('Q', 'Y'): -1, ('Q', 'Z'): 3, ('R', 'A'): -1, ('R', 'B'): -1, ('R', 'C'): -3, ('R', 'D'): -2, ('R', 'E'): 0, ('R', 'F'): -3, ('R', 'G'): -2, ('R', 'H'): 0, ('R', 'I'): -3, ('R', 'K'): 2, ('R', 'L'): -2, ('R', 'M'): -1, ('R', 'N'): 0, ('R', 'P'): -2, ('R', 'Q'): 1, ('R', 'R'): 5, ('R', 'S'): -1, ('R', 'T'): -1, ('R', 'V'): -3, ('R', 'W'): -3, ('R', 'X'): -1, ('R', 'Y'): -2, ('R', 'Z'): 0, ('S', 'A'): 1, ('S', 'B'): 0, ('S', 'C'): -1, ('S', 'D'): 0, ('S', 'E'): 0, ('S', 'F'): -2, ('S', 'G'): 0, ('S', 'H'): -1, ('S', 'I'): -2, ('S', 'K'): 0, ('S', 'L'): -2, ('S', 'M'): -1, ('S', 'N'): 1, ('S', 'P'): -1, ('S', 'Q'): 0, ('S', 'R'): -1, ('S', 'S'): 4, ('S', 'T'): 1, ('S', 'V'): -2, ('S', 'W'): -3, ('S', 'X'): 0, ('S', 'Y'): -2, ('S', 'Z'): 0, ('T', 'A'): 0, ('T', 'B'): -1, ('T', 'C'): -1, ('T', 'D'): -1, ('T', 'E'): -1, ('T', 'F'): -2, ('T', 'G'): -2, ('T', 'H'): -2, ('T', 'I'): -1, ('T', 'K'): -1, ('T', 'L'): -1, ('T', 'M'): -1, ('T', 'N'): 0, ('T', 'P'): -1, ('T', 'Q'): -1, ('T', 'R'): -1, ('T', 'S'): 1, ('T', 'T'): 5, ('T', 'V'): 0, ('T', 'W'): -2, ('T', 'X'): 0, ('T', 'Y'): -2, ('T', 'Z'): -1, ('V', 'A'): 0, ('V', 'B'): -3, ('V', 'C'): -1, ('V', 'D'): -3, ('V', 'E'): -2, ('V', 'F'): -1, ('V', 'G'): -3, ('V', 'H'): -3, ('V', 'I'): 3, ('V', 'K'): -2, ('V', 'L'): 1, ('V', 'M'): 1, ('V', 'N'): -3, ('V', 'P'): -2, ('V', 'Q'): -2, ('V', 'R'): -3, ('V', 'S'): -2, ('V', 'T'): 0, ('V', 'V'): 4, ('V', 'W'): -3, ('V', 'X'): -1, ('V', 'Y'): -1, ('V', 'Z'): -2, ('W', 'A'): -3, ('W', 'B'): -4, ('W', 'C'): -2, ('W', 'D'): -4, ('W', 'E'): -3, ('W', 'F'): 1, ('W', 'G'): -2, ('W', 'H'): -2, ('W', 'I'): -3, ('W', 'K'): -3, ('W', 'L'): -2, ('W', 'M'): -1, ('W', 'N'): -4, ('W', 'P'): -4, ('W', 'Q'): -2, ('W', 'R'): -3, ('W', 'S'): -3, ('W', 'T'): -2, ('W', 'V'): -3, ('W', 'W'): 11, ('W', 'X'): -2, ('W', 'Y'): 2, ('W', 'Z'): -3, ('X', 'A'): 0, ('X', 'B'): -1, ('X', 'C'): -2, ('X', 'D'): -1, ('X', 'E'): -1, ('X', 'F'): -1, ('X', 'G'): -1, ('X', 'H'): -1, ('X', 'I'): -1, ('X', 'K'): -1, ('X', 'L'): -1, ('X', 'M'): -1, ('X', 'N'): -1, ('X', 'P'): -2, ('X', 'Q'): -1, ('X', 'R'): -1, ('X', 'S'): 0, ('X', 'T'): 0, ('X', 'V'): -1, ('X', 'W'): -2, ('X', 'X'): -1, ('X', 'Y'): -1, ('X', 'Z'): -1, ('Y', 'A'): -2, ('Y', 'B'): -3, ('Y', 'C'): -2, ('Y', 'D'): -3, ('Y', 'E'): -2, ('Y', 'F'): 3, ('Y', 'G'): -3, ('Y', 'H'): 2, ('Y', 'I'): -1, ('Y', 'K'): -2, ('Y', 'L'): -1, ('Y', 'M'): -1, ('Y', 'N'): -2, ('Y', 'P'): -3, ('Y', 'Q'): -1, ('Y', 'R'): -2, ('Y', 'S'): -2, ('Y', 'T'): -2, ('Y', 'V'): -1, ('Y', 'W'): 2, ('Y', 'X'): -1, ('Y', 'Y'): 7, ('Y', 'Z'): -2, ('Z', 'A'): -1, ('Z', 'B'): 1, ('Z', 'C'): -3, ('Z', 'D'): 1, ('Z', 'E'): 4, ('Z', 'F'): -3, ('Z', 'G'): -2, ('Z', 'H'): 0, ('Z', 'I'): -3, ('Z', 'K'): 1, ('Z', 'L'): -3, ('Z', 'M'): -1, ('Z', 'N'): 0, ('Z', 'P'): -1, ('Z', 'Q'): 3, ('Z', 'R'): 0, ('Z', 'S'): 0, ('Z', 'T'): -1, ('Z', 'V'): -2, ('Z', 'W'): -3, ('Z', 'X'): -1, ('Z', 'Y'): -2, ('Z', 'Z'): 4})¶ Returns the similarity between the residue and a reference residue
Parameters: - 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
- ref_res (
-
getStructureResProperties
()¶ Return all properties for the corresponding structure residue’s alpha carbon. Properties that apply to the whole residue are stored as atom properties on this atom. An empty dictionary will be returned if this residue doesn’t have a corresponding alpha carbon.
Returns: A dictionary-like object containing the properties. Return type: structure._StructureAtomProperty or dict
-
get_version
()¶ Method to get the version of a particular object. Defaults to the current version of mmshare. This class can be overridden for custom versioning behavior.
-
hasSetResNum
() → bool¶ Returns: Whether a specific resnum has been set
-
hasStructure
()¶ Returns: Whether this element has a structure i.e. whether it has corresponding XYZ coordinates in Maestro. :rtype: bool
-
helix_propensity
¶ Returns: Helix propensity for the ResidueType of the residue Return type: HELIX_PROPENSITY
-
helix_termination_tendency
¶ Returns: Helix termination tendency for the ResidueType of the residue Return type: HELIX_TERMINATION_TENDENCY
-
hydrophilicity
¶ Returns: Hydrophilicity for the ResidueType on the Hopp-Woods scale, if available; otherwise None Return type: float
-
hydrophobicity
¶ Returns: Hydrophobicity for the ResidueType on the Kyte-Doolittle scale, if available; otherwise None. Return type: float
-
idx_in_seq
¶
-
inscode
¶ If inscode and rescode are both set to None, the inscode will be ‘+’.
-
is_gap
= False¶
-
is_res
¶ Utility function to check whether a residue is not a gap
-
isoelectric_point
¶ Returns: A float representing the isoelectric point value for the ResidueType of the residue
-
long_code
¶
-
molecule_number
¶
-
pfam
¶
-
pred_accessibility
¶
-
pred_disordered
¶
-
pred_disulfide_bond
¶
-
pred_domain_arr
¶
-
pred_secondary_structure
¶
-
rescode
¶
-
resnum
¶ If resnum is set to None, resnum will be auto-generated from column number.
-
secondary_structure
¶
-
seqres_only
¶
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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
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short_code
¶
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side_chain_chem
¶ Returns: Side chain chemistry for the ResidueType of the residue Return type: SIDE_CHAIN_CHEM
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ss_prediction_psipred
¶ Returns a DSSP code matching the secondary structure prediction for the residue or None. Value is calculated from thePsiPred backend.
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ss_prediction_sspro
¶ Returns a DSSP code matching the secondary structure prediction for the residue or None. Value is calculated from the SSpro backend.
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steric_group
¶ Returns: Steric group for the ResidueType of the residue Return type: STERIC_GROUP
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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
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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
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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
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turn_propensity
¶ Returns: Turn propensity for the ResidueType of the residue Return type: TURN_PROPENSITY
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type
¶
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updateDescriptors
(descriptors)¶ Updates the descriptor dicts with new descriptor values
Parameters: descriptors (dict[str, float]) – A dict mapping descriptor names to their values
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