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2016-4 Schrodinger Python API
Package schrodinger :: Package application :: Package msv :: Package domain :: Module residue :: Class Residue
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Class Residue

object --+
         |
        Residue
Instance Methods [hide private]
 
__init__(self, residue_type, inscode='', resum=None, origin=None)
x.__init__(...) initializes x; see help(type(x)) for signature
 
__str__(self)
Returns the short code for the residue
 
__repr__(self)
repr(x)
 
setStructureInformation(self, struct_res)
Extract any structural information from a structure._Residue object and set it on the instance
float
getSimilarity(self, ref_res, similarity_matrix={('A', 'A'): 4, ('B', 'A'): -2, ('B', 'B'): 4, ('B', 'C'): -3,...)
Returns the similarity between the residue and a reference residue
int
getBinarySimilarity(self, ref_res, similarity_matrix={('A', 'A'): 4, ('B', 'A'): -2, ('B', 'B'): 4, ('B', 'C'): -3,...)
Returns if the residue and a reference residue are similar
int
getIdentity(self, ref_res)
Return the identity between the residue and a reference residue
int
getHomology(self, ref_res)
Return a float scoring the homology between the sequence and a reference sequence, assuming that they're already aligned

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __setattr__, __sizeof__, __subclasshook__

Properties [hide private]
  rescode
  short_code
  long_code
float hydrophobicity
float hydrophilicity
HELIX_PROPENSITY helix_propensity
BETA_STRAND_PROPENSITY beta_strand_propensity
TURN_PROPENSITY turn_propensity
HELIX_TERMINATION_TENDENCY helix_termination_tendency
SOLVENT_EXPOSURE_TENDENCY exposure_tendency
STERIC_GROUP steric_group
SIDE_CHAIN_CHEM side_chain_chem
  ss_prediction_psipred
Returns a DSSP code matching the secondary structure prediction for the residue or None.
  ss_prediction_sspro
Returns a DSSP code matching the secondary structure prediction for the residue or None.
  isoelectric_point

Inherited from object: __class__

Method Details [hide private]

__init__(self, residue_type, inscode='', resum=None, origin=None)
(Constructor)

 

x.__init__(...) initializes x; see help(type(x)) for signature

Parameters:
  • residue_type (ResidueType) - The kind of the residue
  • inscode (str) - The insertion code
  • resnum (int) - PDB residue number
  • origin (object) - Optional code indicating the provenance of the residue
Overrides: object.__init__

__str__(self)
(Informal representation operator)

 

Returns the short code for the residue

Overrides: object.__str__

__repr__(self)
(Representation operator)

 

repr(x)

Overrides: object.__repr__
(inherited documentation)

setStructureInformation(self, struct_res)

 

Extract any structural information from a structure._Residue object and set it on the instance

Parameters:

getSimilarity(self, ref_res, similarity_matrix={('A', 'A'): 4, ('B', 'A'): -2, ('B', 'B'): 4, ('B', 'C'): -3,...)

 

Returns the similarity between the residue and a reference residue

Parameters:
Returns: float
similarity score based on the similarity matrix

getBinarySimilarity(self, ref_res, similarity_matrix={('A', 'A'): 4, ('B', 'A'): -2, ('B', 'B'): 4, ('B', 'C'): -3,...)

 

Returns if the residue and a reference residue are similar

Parameters:
Returns: int
1 if the similarity score is positive, otherwise 0.

getIdentity(self, ref_res)

 

Return the identity between the residue and a reference residue

Parameters:
Returns: int
1 if same as the reference residue, 0 otherwise.

getHomology(self, ref_res)

 

Return a float scoring the homology between the sequence and a reference sequence, assuming that they're already aligned

The homology criterion is based on "side chain chemistry" descriptor matching.

Parameters:
Returns: int
1 if the residue and reference residue are homologous, 0 otherwise.

Property Details [hide private]

rescode

Get Method:
unreachable.rescode(self)

short_code

Get Method:
unreachable.short_code(self)

long_code

Get Method:
unreachable.long_code(self)

hydrophobicity

Get Method:
unreachable.hydrophobicity(self) - Returns: Hydrophobicity for the ResidueType on the Kyte-Doolittle scale, if available; otherwise None.
Type:
float

hydrophilicity

Get Method:
unreachable.hydrophilicity(self) - Returns: Hydrophilicity for the ResidueType on the Hopp-Woods scale, if available; otherwise None
Type:
float

helix_propensity

Get Method:
unreachable.helix_propensity(self) - Returns: Helix propensity for the ResidueType of the residue
Type:
HELIX_PROPENSITY

beta_strand_propensity

Get Method:
unreachable.beta_strand_propensity(self) - Returns: Beta-strand propensity for the ResidueType of the residue
Type:
BETA_STRAND_PROPENSITY

turn_propensity

Get Method:
unreachable.turn_propensity(self) - Returns: Turn propensity for the ResidueType of the residue
Type:
TURN_PROPENSITY

helix_termination_tendency

Get Method:
unreachable.helix_termination_tendency(self) - Returns: Helix termination tendency for the ResidueType of the residue
Type:
HELIX_TERMINATION_TENDENCY

exposure_tendency

Get Method:
unreachable.exposure_tendency(self) - Returns: Solvent exposure tendency for the ResidueType of the residue
Type:
SOLVENT_EXPOSURE_TENDENCY

steric_group

Get Method:
unreachable.steric_group(self) - Returns: Steric group for the ResidueType of the residue
Type:
STERIC_GROUP

side_chain_chem

Get Method:
unreachable.side_chain_chem(self) - Returns: Side chain chemistry for the ResidueType of the residue
Type:
SIDE_CHAIN_CHEM

ss_prediction_psipred

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

Get Method:
unreachable.ss_prediction_psipred(self) - Returns a DSSP code matching the secondary structure prediction for the residue or None.
Set Method:
unreachable.ss_prediction_psipred(self, value)

ss_prediction_sspro

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

Get Method:
unreachable.ss_prediction_sspro(self) - Returns a DSSP code matching the secondary structure prediction for the residue or None.
Set Method:
unreachable.ss_prediction_sspro(self, value)

isoelectric_point

Get Method:
unreachable.isoelectric_point(self) - Returns: A float representing the isoelectric point value for the ResidueType of the residue

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2016-4 Schrodinger Python API
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