schrodinger.ui.sequencealignment.residue module¶

Implementation of sequence viewer Residue class.

class schrodinger.ui.sequencealignment.residue.Residue(sequence=None, code=' ', ss_code='-', name='UNK', inverted=True, color=(255, 255, 255))[source]¶

Bases: object

This class implements a Residue, a basic sequence element. The Residue object can correspond to an actual amino acid, nucleotide, or a single plot point. It also stores associated Maestro metadata (such as atom number or residue color).

__init__(sequence=None, code=' ', ss_code='-', name='UNK', inverted=True, color=(255, 255, 255))[source]¶

copy()[source]¶

Creates a copy of self.

Return type: Residue
Returns: a copy of self

id()[source]¶

Returns a residue ID. The residue ID is a string concatenating the residue number and insertion code.

Return type: string
Returns: residue ID (number + insertion code)

makeName()[source]¶

colorTaylor()[source]¶

Returns a color according to Taylor scheme.

Return type: (int, int, int)
Returns: color according to Taylor scheme

colorType()[source]¶

Returns a color according to the residue type.

Return type: (int, int, int)
Returns: color according to residue type

colorKD()[source]¶

Returns a color according to Kyte-Doolittle hydrophobicity scale.

Return type: (int, int, int)
Returns: color according to hydrophobicity scale

colorHW()[source]¶

Returns a color according to Hopp-Woods hydrophilicity scale.

Return type: (int, int, int)
Returns: color according to hydrophilicity scale

colorHelixPropensity()[source]¶

Returns a color according to helix propensity.

Return type: (int, int, int)
Returns: color according to helix propensity

colorStrandPropensity()[source]¶

Returns a color according to beta strand propensity.

Return type: (int, int, int)
Returns: color according to beta strand propensity

colorTurnPropensity()[source]¶

Returns a color according to turn propensity.

Return type: (int, int, int)
Returns: color according to turn propensity

colorHelixTerminators()[source]¶

Returns a color according to helix terminating tendency.

Return type: (int, int, int)
Returns: color according to helix terminating tendency

colorStericGroup()[source]¶

Returns a color according to steric group classification.

Return type: (int, int, int)
Returns: color according to steric group classification

colorExposureTendency()[source]¶

Returns a color according to solvent exposure tendency.

Return type: (int, int, int)
Returns: color according to solvent exposure tendency

colorSidechainChemistry()[source]¶

Returns a color according to sidechain chemistry.

Return type: (int, int, int)
Returns: color according to sidechain chemistry

repair()[source]¶: Repairs the residue by adding missing attributes (using default values) to the residue.

getSignature()[source]¶

This function returns residue signature.

Return type: str
Returns: Signature consisting of residue name, space, chain_id, colon and residue number. If chain_id is not available, space character is used instead.