Package schrodinger :: Package application :: Package msv :: Package domain :: Module residue

[frames] | no frames]

Module residue

Classes

[hide private]

ResidueOrigin
ResidueOrigin(entry_id, number_by_entry)

HELIX_PROPENSITY

BETA_STRAND_PROPENSITY

TURN_PROPENSITY

HELIX_TERMINATION_TENDENCY

SOLVENT_EXPOSURE_TENDENCY

STERIC_GROUP

SIDE_CHAIN_CHEM

ResidueType

Residue

Functions

[hide private]

tuple of (str, int)

get_origin(struct_res)
Takes a _Residue object and returns a tuple allowing it to be reidentified in the ct

bool

is_alpha_carbon(atom)
Takes an atom and returns a bool indicating whether it is an alpha carbon

schrodinger.structure._Atom or None

get_alpha_carbon_for_residue(res)
Returns the alpha carbon of a _Residue object or None if not available

float or None

get_b_factor(res)
Returns: b-factor value for a given structure.Residue or None if no temperature factor is available

get_matrix_value(matrix, first, second)
Return a similarity matrix value for a specified pair of residues.

make_non_std_amino_acids()

Variables

[hide private]

CB_TT_MAP = {0: 'Loop', 1: 'Helix', 2: 'Strand', <SIDE_CHAIN_C...

DSSP_CODES = {'B': 'residue in isolated Beta-bridge', 'C': 'co...

ALANINE = ResidueType('A', 'ALA', 'Alanine')

ARGININE = ResidueType('R', 'ARG', 'Arginine')

ASPARAGINE = ResidueType('N', 'ASN', 'Asparagine')

ASPARTIC_ACID = ResidueType('D', 'ASP', 'Aspartic acid')

CYSTEINE = ResidueType('C', 'CYS', 'Cysteine')

GLUTAMIC_ACID = ResidueType('E', 'GLU', 'Glutamic acid')

GLUTAMINE = ResidueType('Q', 'GLN', 'Glutamine')

GLYCINE = ResidueType('G', 'GLY', 'Glycine')

HISTIDINE = ResidueType('H', 'HIS', 'Histidine')

ISOLEUCINE = ResidueType('I', 'ILE', 'Isoleucine')

LEUCINE = ResidueType('L', 'LEU', 'Leucine')

LYSINE = ResidueType('K', 'LYS', 'Lysine')

METHIONINE = ResidueType('M', 'MET', 'Methionine')

PHENYLALANINE = ResidueType('F', 'PHE', 'Phenylalanine')

PROLINE = ResidueType('P', 'PRO', 'Proline')

SERINE = ResidueType('S', 'SER', 'Serine')

THREONINE = ResidueType('T', 'THR', 'Threonine')

TRYPTOPHAN = ResidueType('W', 'TRP', 'Tryptophan')

TYROSINE = ResidueType('Y', 'TYR', 'Tyrosine')

UNKNOWN = ResidueType('X', 'UNK', 'Unknown')

VALINE = ResidueType('V', 'VAL', 'Valine')

STD_AMINO_ACIDS = [ResidueType('A', 'ALA', 'Alanine'), Residue...

NON_STD_AMINO_ACIDS = [ResidueType('A', 'AIB', 'Alanine'), Res...

AMINO_ACIDS = [ResidueType('A', 'ALA', 'Alanine'), ResidueType...

AMINO_ACIDS_THREE_LETTER = {'2AS': ResidueType('D', '2AS', 'As...

AMINO_ACIDS_ONE_LETTER = {'A': ResidueType('A', 'ALA', 'Alanin...

AMINO_ACIDS_ONE_AND_THREE_LETTER = {'2AS': ResidueType('D', '2...

__package__ = 'schrodinger.application.msv.domain'

Function Details

[hide private]

get_origin(struct_res)

Takes a _Residue object and returns a tuple allowing it to be reidentified in the ct

Parameters:

struct_res (schrodinger.structure._Residue or None) - The residue to extract structural information from

Returns: tuple of (str, int)

A tuple that can be used to identify the residue in the ct

is_alpha_carbon(atom)

Takes an atom and returns a bool indicating whether it is an alpha carbon

Parameters:

atom (schrodinger.structure._StructureAtom) - An atom to inspect

Returns: bool

Whether the atom is an alpha carbon

get_alpha_carbon_for_residue(res)

Returns the alpha carbon of a _Residue object or None if not available

Parameters:

res (schrodinger.structure._Residue) - The residue to inspect for an alpha carbon

Returns: schrodinger.structure._Atom or None

An atom in the residue or None

get_b_factor(res)

Parameters:

res (schrodinger.structure._Residue) - The residue to examine

Returns: float or None

b-factor value for a given structure.Residue or None if no temperature factor is available

Variables Details

[hide private]

CB_TT_MAP

Value:

{0: 'Loop',
 1: 'Helix',
 2: 'Strand',
 <SIDE_CHAIN_CHEM.BASIC_HYDROPHILIC: 3>: 'basic, hydrophilic',
 <SIDE_CHAIN_CHEM.NEUTRAL_HYDROPHOBIC_AROMATIC: 5>: 'neitral, hydropho
bic, aromatic',
 <BETA_STRAND_PROPENSITY.STRAND_FORMING: 4>: 'strand-forming',
 <HELIX_PROPENSITY.HELIX_BREAKING: 5>: 'helix-breaking',
...

DSSP_CODES

Value:

{'B': 'residue in isolated Beta-bridge',
 'C': 'coil',
 'E': 'extended strand in parallel and/or anti-parallel Beta sheet con
formation',
 'G': '3-turn helix',
 'H': '4-turn helix',
 'I': '5-turn helix',
 'S': 'bend (non-hydrogen-bond based)',
...

STD_AMINO_ACIDS

Value:

[ResidueType('A', 'ALA', 'Alanine'),
 ResidueType('C', 'CYS', 'Cysteine'),
 ResidueType('D', 'ASP', 'Aspartic acid'),
 ResidueType('E', 'GLU', 'Glutamic acid'),
 ResidueType('F', 'PHE', 'Phenylalanine'),
 ResidueType('G', 'GLY', 'Glycine'),
 ResidueType('H', 'HIS', 'Histidine'),
 ResidueType('I', 'ILE', 'Isoleucine'),
...

NON_STD_AMINO_ACIDS

Value:

[ResidueType('A', 'AIB', 'Alanine'),
 ResidueType('A', 'ALA', 'Alanine'),
 ResidueType('A', 'ALM', 'Alanine'),
 ResidueType('A', 'AYA', 'Alanine'),
 ResidueType('A', 'BNN', 'Alanine'),
 ResidueType('A', 'CHG', 'Alanine'),
 ResidueType('A', 'CSD', 'Alanine'),
 ResidueType('X', 'DAL', 'Alanine'),
...

AMINO_ACIDS

Value:

[ResidueType('A', 'ALA', 'Alanine'),
 ResidueType('C', 'CYS', 'Cysteine'),
 ResidueType('D', 'ASP', 'Aspartic acid'),
 ResidueType('E', 'GLU', 'Glutamic acid'),
 ResidueType('F', 'PHE', 'Phenylalanine'),
 ResidueType('G', 'GLY', 'Glycine'),
 ResidueType('H', 'HIS', 'Histidine'),
 ResidueType('I', 'ILE', 'Isoleucine'),
...

AMINO_ACIDS_THREE_LETTER

Value:

{'2AS': ResidueType('D', '2AS', 'Aspartic acid'),
 '3AH': ResidueType('H', '3AH', 'Histidine'),
 '5HP': ResidueType('E', '5HP', 'Glutamic acid'),
 'ACL': ResidueType('R', 'ACL', 'Arginine'),
 'AGM': ResidueType('R', 'AGM', 'Arginine'),
 'AIB': ResidueType('A', 'AIB', 'Alanine'),
 'ALA': ResidueType('A', 'ALA', 'Alanine'),
 'ALM': ResidueType('A', 'ALM', 'Alanine'),
...

AMINO_ACIDS_ONE_LETTER

Value:

{'A': ResidueType('A', 'ALA', 'Alanine'),
 'C': ResidueType('C', 'CYS', 'Cysteine'),
 'D': ResidueType('D', 'ASP', 'Aspartic acid'),
 'E': ResidueType('E', 'GLU', 'Glutamic acid'),
 'F': ResidueType('F', 'PHE', 'Phenylalanine'),
 'G': ResidueType('G', 'GLY', 'Glycine'),
 'H': ResidueType('H', 'HIS', 'Histidine'),
 'I': ResidueType('I', 'ILE', 'Isoleucine'),
...

AMINO_ACIDS_ONE_AND_THREE_LETTER

Value:

{'2AS': ResidueType('D', '2AS', 'Aspartic acid'),
 '3AH': ResidueType('H', '3AH', 'Histidine'),
 '5HP': ResidueType('E', '5HP', 'Glutamic acid'),
 'A': ResidueType('A', 'ALA', 'Alanine'),
 'ACL': ResidueType('R', 'ACL', 'Arginine'),
 'AGM': ResidueType('R', 'AGM', 'Arginine'),
 'AIB': ResidueType('A', 'AIB', 'Alanine'),
 'ALA': ResidueType('A', 'ALA', 'Alanine'),
...