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

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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", hydrophobicity= 1...

ARGININE = ResidueType("R", "ARG", "Arginine", hydrophobicity=...

ASPARAGINE = ResidueType("N", "ASN", "Asparagine", hydrophobic...

ASPARTIC_ACID = ResidueType("D", "ASP", "Aspartic acid", hydro...

CYSTEINE = ResidueType("C", "CYS", "Cysteine", hydrophobicity=...

GLUTAMIC_ACID = ResidueType("E", "GLU", "Glutamic acid", hydro...

GLUTAMINE = ResidueType("Q", "GLN", "Glutamine", hydrophobicit...

GLYCINE = ResidueType("G", "GLY", "Glycine", hydrophobicity=-0...

HISTIDINE = ResidueType("H", "HIS", "Histidine", hydrophobicit...

ISOLEUCINE = ResidueType("I", "ILE", "Isoleucine", hydrophobic...

LEUCINE = ResidueType("L", "LEU", "Leucine", hydrophobicity= 3...

LYSINE = ResidueType("K", "LYS", "Lysine", hydrophobicity=-3.9...

METHIONINE = ResidueType("M", "MET", "Methionine", hydrophobic...

PHENYLALANINE = ResidueType("F", "PHE", "Phenylalanine", hydro...

PROLINE = ResidueType("P", "PRO", "Proline", hydrophobicity=-1...

SERINE = ResidueType("S", "SER", "Serine", hydrophobicity=-0.8...

THREONINE = ResidueType("T", "THR", "Threonine", hydrophobicit...

TRYPTOPHAN = ResidueType("W", "TRP", "Tryptophan", hydrophobic...

TYROSINE = ResidueType("Y", "TYR", "Tyrosine", hydrophobicity=...

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

VALINE = ResidueType("V", "VAL", "Valine", hydrophobicity= 4.2...

STD_AMINO_ACIDS = [ALANINE, CYSTEINE, ASPARTIC_ACID, GLUTAMIC_...

NON_STD_AMINO_ACIDS = make_non_std_amino_acids()

AMINO_ACIDS = STD_AMINO_ACIDS+ NON_STD_AMINO_ACIDS

AMINO_ACIDS_THREE_LETTER = {res.long_code: res for res in AMIN...

AMINO_ACIDS_ONE_LETTER = {res.short_code: res for res in STD_A...

AMINO_ACIDS_ONE_AND_THREE_LETTER = dict(AMINO_ACIDS_ONE_LETTER...

__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)',
...

ALANINE

Value:

ResidueType("A", "ALA", "Alanine", hydrophobicity= 1.80, hydrophilicit
y=-0.50, helix_propensity= HELIX_PROPENSITY.LIKELY, beta_strand_propen
sity= BETA_STRAND_PROPENSITY.AMBIVALENT, turn_propensity= TURN_PROPENS
ITY.TURN_BREAKING, helix_termination_tendency= HELIX_TERMINATION_TENDE
NCY.AMBIVALENT, exposure_tendency= SOLVENT_EXPOSURE_TENDENCY.AMBIVALEN
T, steric_group= STERIC_GROUP.SMALL, side_chain_chem= SIDE_CHAIN_CHEM.
NEUTRAL_HYDROPHOBIC_ALIPHATIC, isoelectric_point= 6.00)

ARGININE

Value:

ResidueType("R", "ARG", "Arginine", hydrophobicity=-4.50, hydrophilici
ty= 3.00, helix_propensity= HELIX_PROPENSITY.AMBIVALENT, beta_strand_p
ropensity= BETA_STRAND_PROPENSITY.AMBIVALENT, turn_propensity= TURN_PR
OPENSITY.AMBIVALENT, helix_termination_tendency= HELIX_TERMINATION_TEN
DENCY.HELIX_STARTING, exposure_tendency= SOLVENT_EXPOSURE_TENDENCY.SUR
FACE, steric_group= STERIC_GROUP.POLAR, side_chain_chem= SIDE_CHAIN_CH
EM.BASIC_HYDROPHILIC, isoelectric_point= 10.76)

ASPARAGINE

Value:

ResidueType("N", "ASN", "Asparagine", hydrophobicity=-3.50, hydrophili
city= 0.20, helix_propensity= HELIX_PROPENSITY.AMBIVALENT, beta_strand
_propensity= BETA_STRAND_PROPENSITY.AMBIVALENT, turn_propensity= TURN_
PROPENSITY.TURN_FORMING, helix_termination_tendency= HELIX_TERMINATION
_TENDENCY.HELIX_ENDING, exposure_tendency= SOLVENT_EXPOSURE_TENDENCY.S
URFACE, steric_group= STERIC_GROUP.AMBIVALENT, side_chain_chem= SIDE_C
HAIN_CHEM.NEUTRAL_HYDROPHILIC, isoelectric_point= 5.41)

ASPARTIC_ACID

Value:

ResidueType("D", "ASP", "Aspartic acid", hydrophobicity=-3.50, hydroph
ilicity= 3.00, helix_propensity= HELIX_PROPENSITY.AMBIVALENT, beta_str
and_propensity= BETA_STRAND_PROPENSITY.STRAND_FORMING, turn_propensity
= TURN_PROPENSITY.TURN_FORMING, helix_termination_tendency= HELIX_TERM
INATION_TENDENCY.HELIX_ENDING, steric_group= STERIC_GROUP.AMBIVALENT, 
side_chain_chem= SIDE_CHAIN_CHEM.ACIDIC_HYDROPHILIC, isoelectric_point
= 2.77)

CYSTEINE

Value:

ResidueType("C", "CYS", "Cysteine", hydrophobicity= 2.50, hydrophilici
ty=-1.00, helix_propensity= HELIX_PROPENSITY.AMBIVALENT, beta_strand_p
ropensity= BETA_STRAND_PROPENSITY.AMBIVALENT, turn_propensity= TURN_PR
OPENSITY.TURN_BREAKING, helix_termination_tendency= HELIX_TERMINATION_
TENDENCY.AMBIVALENT, exposure_tendency= SOLVENT_EXPOSURE_TENDENCY.AMBI
VALENT, steric_group= STERIC_GROUP.SMALL, side_chain_chem= SIDE_CHAIN_
CHEM.PRIMARY_THIOL, isoelectric_point= 5.07)

GLUTAMIC_ACID

Value:

ResidueType("E", "GLU", "Glutamic acid", hydrophobicity=-3.50, hydroph
ilicity= 3.00, helix_propensity= HELIX_PROPENSITY.LIKELY, beta_strand_
propensity= BETA_STRAND_PROPENSITY.STRAND_FORMING, turn_propensity= TU
RN_PROPENSITY.AMBIVALENT, helix_termination_tendency= HELIX_TERMINATIO
N_TENDENCY.HELIX_ENDING, exposure_tendency= SOLVENT_EXPOSURE_TENDENCY.
SURFACE, steric_group= STERIC_GROUP.POLAR, side_chain_chem= SIDE_CHAIN
_CHEM.ACIDIC_HYDROPHILIC, isoelectric_point= 3.22)

GLUTAMINE

Value:

ResidueType("Q", "GLN", "Glutamine", hydrophobicity=-3.50, hydrophilic
ity= 0.20, helix_propensity= HELIX_PROPENSITY.LIKELY, beta_strand_prop
ensity= BETA_STRAND_PROPENSITY.AMBIVALENT, turn_propensity= TURN_PROPE
NSITY.AMBIVALENT, helix_termination_tendency= HELIX_TERMINATION_TENDEN
CY.AMBIVALENT, exposure_tendency= SOLVENT_EXPOSURE_TENDENCY.SURFACE, s
teric_group= STERIC_GROUP.POLAR, side_chain_chem= SIDE_CHAIN_CHEM.NEUT
RAL_HYDROPHILIC, isoelectric_point= 5.65)

GLYCINE

Value:

ResidueType("G", "GLY", "Glycine", hydrophobicity=-0.40, hydrophilicit
y= 0.00, helix_propensity= HELIX_PROPENSITY.HELIX_BREAKING, beta_stran
d_propensity= BETA_STRAND_PROPENSITY.STRAND_FORMING, turn_propensity= 
TURN_PROPENSITY.TURN_FORMING, helix_termination_tendency= HELIX_TERMIN
ATION_TENDENCY.HELIX_STARTING, exposure_tendency= SOLVENT_EXPOSURE_TEN
DENCY.AMBIVALENT, steric_group= STERIC_GROUP.SMALL, side_chain_chem= S
IDE_CHAIN_CHEM.NEUTRAL_HYDROPHOBIC_ALIPHATIC, isoelectric_point= 5.97)

HISTIDINE

Value:

ResidueType("H", "HIS", "Histidine", hydrophobicity=-3.20, hydrophilic
ity=-0.50, helix_propensity= HELIX_PROPENSITY.AMBIVALENT, beta_strand_
propensity= BETA_STRAND_PROPENSITY.AMBIVALENT, turn_propensity= TURN_P
ROPENSITY.TURN_BREAKING, helix_termination_tendency= HELIX_TERMINATION
_TENDENCY.HELIX_STARTING, exposure_tendency= SOLVENT_EXPOSURE_TENDENCY
.SURFACE, steric_group= STERIC_GROUP.AROMATIC, side_chain_chem= SIDE_C
HAIN_CHEM.BASIC_HYDROPHILIC, isoelectric_point= 7.59)

ISOLEUCINE

Value:

ResidueType("I", "ILE", "Isoleucine", hydrophobicity= 4.50, hydrophili
city=-1.80, helix_propensity= HELIX_PROPENSITY.WEAK, beta_strand_prope
nsity= BETA_STRAND_PROPENSITY.STRAND_BREAKING, turn_propensity= TURN_P
ROPENSITY.TURN_BREAKING, helix_termination_tendency= HELIX_TERMINATION
_TENDENCY.AMBIVALENT, exposure_tendency= SOLVENT_EXPOSURE_TENDENCY.BUR
IED, steric_group= STERIC_GROUP.AMBIVALENT, side_chain_chem= SIDE_CHAI
N_CHEM.NEUTRAL_HYDROPHOBIC_ALIPHATIC, isoelectric_point= 6.02)

LEUCINE

Value:

ResidueType("L", "LEU", "Leucine", hydrophobicity= 3.80, hydrophilicit
y=-1.80, helix_propensity= HELIX_PROPENSITY.LIKELY, beta_strand_propen
sity= BETA_STRAND_PROPENSITY.STRAND_BREAKING, turn_propensity= TURN_PR
OPENSITY.TURN_BREAKING, helix_termination_tendency= HELIX_TERMINATION_
TENDENCY.HELIX_ENDING, exposure_tendency= SOLVENT_EXPOSURE_TENDENCY.BU
RIED, steric_group= STERIC_GROUP.AMBIVALENT, side_chain_chem= SIDE_CHA
IN_CHEM.NEUTRAL_HYDROPHOBIC_ALIPHATIC, isoelectric_point= 5.98)

LYSINE

Value:

ResidueType("K", "LYS", "Lysine", hydrophobicity=-3.90, hydrophilicity
= 3.00, helix_propensity= HELIX_PROPENSITY.LIKELY, beta_strand_propens
ity= BETA_STRAND_PROPENSITY.STRAND_FORMING, turn_propensity= TURN_PROP
ENSITY.AMBIVALENT, helix_termination_tendency= HELIX_TERMINATION_TENDE
NCY.HELIX_STARTING, exposure_tendency= SOLVENT_EXPOSURE_TENDENCY.SURFA
CE, steric_group= STERIC_GROUP.POLAR, side_chain_chem= SIDE_CHAIN_CHEM
.BASIC_HYDROPHILIC, isoelectric_point= 9.74)

METHIONINE

Value:

ResidueType("M", "MET", "Methionine", hydrophobicity= 1.90, hydrophili
city=-1.30, helix_propensity= HELIX_PROPENSITY.LIKELY, beta_strand_pro
pensity= BETA_STRAND_PROPENSITY.STRAND_BREAKING, turn_propensity= TURN
_PROPENSITY.TURN_BREAKING, helix_termination_tendency= HELIX_TERMINATI
ON_TENDENCY.HELIX_STARTING, exposure_tendency= SOLVENT_EXPOSURE_TENDEN
CY.BURIED, steric_group= STERIC_GROUP.AMBIVALENT, side_chain_chem= SID
E_CHAIN_CHEM.NEUTRAL_HYDROPHOBIC_ALIPHATIC, isoelectric_point= 5.74)

PHENYLALANINE

Value:

ResidueType("F", "PHE", "Phenylalanine", hydrophobicity= 2.80, hydroph
ilicity=-2.50, helix_propensity= HELIX_PROPENSITY.WEAK, beta_strand_pr
opensity= BETA_STRAND_PROPENSITY.STRAND_BREAKING, turn_propensity= TUR
N_PROPENSITY.TURN_BREAKING, helix_termination_tendency= HELIX_TERMINAT
ION_TENDENCY.HELIX_STARTING, exposure_tendency= SOLVENT_EXPOSURE_TENDE
NCY.BURIED, steric_group= STERIC_GROUP.AROMATIC, side_chain_chem= SIDE
_CHAIN_CHEM.NEUTRAL_HYDROPHOBIC_AROMATIC, isoelectric_point= 5.48)

PROLINE

Value:

ResidueType("P", "PRO", "Proline", hydrophobicity=-1.60, hydrophilicit
y= 0.00, helix_propensity= HELIX_PROPENSITY.HELIX_BREAKING, beta_stran
d_propensity= BETA_STRAND_PROPENSITY.STRAND_FORMING, turn_propensity= 
TURN_PROPENSITY.TURN_FORMING, helix_termination_tendency= HELIX_TERMIN
ATION_TENDENCY.HELIX_ENDING, exposure_tendency= SOLVENT_EXPOSURE_TENDE
NCY.AMBIVALENT, steric_group= STERIC_GROUP.AMBIVALENT, side_chain_chem
= SIDE_CHAIN_CHEM.IMINO_ACID, isoelectric_point= 6.30)

SERINE

Value:

ResidueType("S", "SER", "Serine", hydrophobicity=-0.80, hydrophilicity
= 0.30, helix_propensity= HELIX_PROPENSITY.AMBIVALENT, beta_strand_pro
pensity= BETA_STRAND_PROPENSITY.AMBIVALENT, turn_propensity= TURN_PROP
ENSITY.TURN_FORMING, helix_termination_tendency= HELIX_TERMINATION_TEN
DENCY.HELIX_ENDING, exposure_tendency= SOLVENT_EXPOSURE_TENDENCY.AMBIV
ALENT, steric_group= STERIC_GROUP.SMALL, side_chain_chem= SIDE_CHAIN_C
HEM.NEUTRAL_HYDROPHILIC, isoelectric_point= 5.58)

THREONINE

Value:

ResidueType("T", "THR", "Threonine", hydrophobicity=-0.70, hydrophilic
ity=-0.40, helix_propensity= HELIX_PROPENSITY.AMBIVALENT, beta_strand_
propensity= BETA_STRAND_PROPENSITY.STRAND_BREAKING, turn_propensity= T
URN_PROPENSITY.AMBIVALENT, helix_termination_tendency= HELIX_TERMINATI
ON_TENDENCY.HELIX_STARTING, exposure_tendency= SOLVENT_EXPOSURE_TENDEN
CY.AMBIVALENT, side_chain_chem= SIDE_CHAIN_CHEM.NEUTRAL_HYDROPHILIC, s
teric_group= STERIC_GROUP.AMBIVALENT, isoelectric_point= 5.60)

TRYPTOPHAN

Value:

ResidueType("W", "TRP", "Tryptophan", hydrophobicity=-0.90, hydrophili
city=-3.40, helix_propensity= HELIX_PROPENSITY.WEAK, beta_strand_prope
nsity= BETA_STRAND_PROPENSITY.STRAND_BREAKING, turn_propensity= TURN_P
ROPENSITY.TURN_BREAKING, helix_termination_tendency= HELIX_TERMINATION
_TENDENCY.HELIX_ENDING, exposure_tendency= SOLVENT_EXPOSURE_TENDENCY.A
MBIVALENT, steric_group= STERIC_GROUP.AROMATIC, side_chain_chem= SIDE_
CHAIN_CHEM.NEUTRAL_HYDROPHOBIC_AROMATIC, isoelectric_point= 5.89)

TYROSINE

Value:

ResidueType("Y", "TYR", "Tyrosine", hydrophobicity=-1.30, hydrophilici
ty=-2.30, helix_propensity= HELIX_PROPENSITY.HELIX_BREAKING, beta_stra
nd_propensity= BETA_STRAND_PROPENSITY.STRAND_BREAKING, turn_propensity
= TURN_PROPENSITY.AMBIVALENT, helix_termination_tendency= HELIX_TERMIN
ATION_TENDENCY.AMBIVALENT, exposure_tendency= SOLVENT_EXPOSURE_TENDENC
Y.AMBIVALENT, steric_group= STERIC_GROUP.AROMATIC, side_chain_chem= SI
DE_CHAIN_CHEM.NEUTRAL_HYDROPHOBIC_AROMATIC, isoelectric_point= 5.66)

VALINE

Value:

ResidueType("V", "VAL", "Valine", hydrophobicity= 4.20, hydrophilicity
=-1.50, helix_propensity= HELIX_PROPENSITY.WEAK, beta_strand_propensit
y= BETA_STRAND_PROPENSITY.STRAND_BREAKING, turn_propensity= TURN_PROPE
NSITY.TURN_BREAKING, helix_termination_tendency= HELIX_TERMINATION_TEN
DENCY.AMBIVALENT, exposure_tendency= SOLVENT_EXPOSURE_TENDENCY.BURIED,
 steric_group= STERIC_GROUP.AMBIVALENT, side_chain_chem= SIDE_CHAIN_CH
EM.NEUTRAL_HYDROPHOBIC_ALIPHATIC, isoelectric_point= 5.96)

STD_AMINO_ACIDS

Value:

[ALANINE, CYSTEINE, ASPARTIC_ACID, GLUTAMIC_ACID, PHENYLALANINE, GLYCI
NE, HISTIDINE, ISOLEUCINE, LYSINE, LEUCINE, METHIONINE, ASPARAGINE, PR
OLINE, GLUTAMINE, ARGININE, SERINE, THREONINE, VALINE, TRYPTOPHAN, TYR
OSINE, UNKNOWN]

AMINO_ACIDS_THREE_LETTER

Value:

{res.long_code: res for res in AMINO_ACIDS}

AMINO_ACIDS_ONE_LETTER

Value:

{res.short_code: res for res in STD_AMINO_ACIDS}

AMINO_ACIDS_ONE_AND_THREE_LETTER

Value:

dict(AMINO_ACIDS_ONE_LETTER.items()+ AMINO_ACIDS_THREE_LETTER.items())