Package schrodinger :: Package application :: Package bioluminate :: Module protein

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Module protein

Module to gather residue property data for proteins.

Classes

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PrimeConfig
Class containing the methods to write Prime input files.

PrimeStructure

PropkaError
A custom exception for any propka failures

OrderedResidueDict
Creates an ordered dictionary for residues in a structure

PropertyCalculator
Class for calculating properties of proteins and protein residues.

Mutation
Helper class for Mutator.

Mutator
Mutates a set of residues in a protein structure allowing concurrent mutations as well as the option to limit concurrent mutations to sequential residues only.

Refiner
Creates input files and runs calculations for protein refinement jobs using Prime and our schrodinger.structutils.minimize.Minimizer class.

Consensus
Access the atoms, residues, and molecules (or just their indices) that are considered to be consensus objects for a template structure and query structure.

Functions

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find_residue_atom(st, chain, resnum, inscode)

str

get_residue_asl(residue, ca=False)
Creates an ASL based on a residue's chain, residue number and inscode.

str

get_residues_asl(residues, ca=False)
Creates an ASL based on a list of residue's chains, residue numbers and inscodes.

valid_asl(st, asl)
Returns True/False depending on whether the asl is a valid expression or not.

list

get_residues_within(st, residues, within=0.0, ca=False)
Returns a list of residues for st that are within within angstroms of each residue.

bool

residue_is_polar(residue)
Tests whether a residue is polar

bool

residue_is_nonpolar(residue)
Tests whether a residue is nonpolar

atom_is_nonpolar(atom)
Returns true if the atom is considered non-polar.

Variables

[hide private]

_version = '$Revision: 0.0 $'

NONPOLAR_HEAVY_ELEMENTS = ['C', 'S']

ALL_RESIDUES = ['ALA', 'ARG', 'ASN', 'ASP', 'CYS', 'GLN', 'GLU...

SUPPORTED_RESIDUES = ['ALA', 'ARG', 'ASN', 'ASP', 'CYS', 'GLN'...

AA_3_LETTER_MAP = {'ALA': 'A', 'ARG': 'R', 'ARN': 'R', 'ASH': ...

AA_1_LETTER_MAP = {'A': 'ALA', 'C': 'CYS', 'D': 'ASP', 'E': 'G...

POLAR_RESIDUES = ['ARG', 'ASP', 'GLU', 'HIS', 'ASN', 'GLN', 'L...

NONPOLAR_RESIDUES = ['PHE', 'LEU', 'ILE', 'TRP', 'VAL', 'MET',...

AROMATIC_RESIDUES = ['PHE', 'TYR', 'TRP', 'HIS', 'HIE', 'HIP']

BASIC_RESIDUES = ['ARG', 'LYS', 'HIS']

ACIDIC_RESIDUES = ['ASP', 'GLU']

CHARGED_RESIDUES = ['ARG', 'LYS', 'HIS', 'ASP', 'GLU']

NEUTRAL_RESIDUES = ['ALA', 'ASN', 'CYS', 'GLN', 'GLY', 'HIE', ...

RESIDUE_ROTOR_COUNT = {'ALA': 0, 'ARG': 4, 'ARN': 4, 'ASH': 2,...

HYDROPATHY_SCALE = {'ALA': 1.8, 'ARG': -4.5, 'ARN': -4.5, 'ASH...

MUTATION_1_LETTER_RE = re.compile(r'(?x)(?P<chain>[a-zA-Z_]{1}...

MUTATION_3_LETTER_RE = re.compile(r'(?x)(?P<chain>[a-zA-Z_]{1}...

MUTATION_RE = re.compile(r'(?x)(?P<chain>[a-zA-Z_]{1}):(?P<res...

PROP_CONVERSIONS = {'affinity_coulomb': 'Affinity_Coulomb', 'a...

__package__ = 'schrodinger.application.bioluminate'

Function Details

[hide private]

get_residue_asl(residue, ca=False)

Creates an ASL based on a residue's chain, residue number and inscode. The ASL can optionally only include the alpha carbon of the residue.

Parameters:

residue (schrodinger.structure._Residue) - The residue to create an ASL for

Returns: str

ASL expression for residue

Raises:

RuntimeError - If the passed in residue is incorrect type

get_residues_asl(residues, ca=False)

Creates an ASL based on a list of residue's chains, residue numbers and inscodes. The ASL can optionally only include the alpha carbon of the residue.

Parameters:

residue (list or tuple of schrodinger.structure._Residues) - The residues to create an ASL for

Returns: str

ASL expression for all residues

Raises:

RuntimeError - If residues are not a list or tuple
RuntimeError - If any passed in residues are incorrect type

get_residues_within(st, residues, within=0.0, ca=False)

Returns a list of residues for st that are within within angstroms of each residue. If the ca keyword is True the within calculation will only look for alpha carbon in residues. This means that if within is set to 5.5 angstroms and there is only a single atom that belongs to a residue at that cutoff, the residue that the atom belongs to will be refined.

Parameters:

st (schrodinger.structure.Structure) - Structure to evaluate and which all residues correspond
residues (list or tuple of schrodinger.structure._Residues) - All residues targeted for refinement
within (float) - Distance (angstroms) of residues to include in refinement
ca (bool) - Use only alpha carbons to find residues within

Returns: list

List of schrodinger.structure._Residue objects

residue_is_polar(residue)

Tests whether a residue is polar

Parameters:

residue (structure._Residue) - Residue to test

Returns: bool

residue_is_nonpolar(residue)

Tests whether a residue is nonpolar

Parameters:

residue (structure._Residue) - Residue to test

Returns: bool

atom_is_nonpolar(atom)

Returns true if the atom is considered non-polar. Here are the rules for non-polar atoms:

The atom's element is a C or S
The atom's element is a H and one bonded atom's element is C or S

Parameters:

atom (schrodinger.structure._StructureAtom)

Variables Details

[hide private]

ALL_RESIDUES

Value:

['ALA',
 'ARG',
 'ASN',
 'ASP',
 'CYS',
 'GLN',
 'GLU',
 'GLY',
...

SUPPORTED_RESIDUES

Value:

['ALA',
 'ARG',
 'ASN',
 'ASP',
 'CYS',
 'GLN',
 'GLU',
 'GLY',
...

AA_3_LETTER_MAP

Value:

{'ALA': 'A',
 'ARG': 'R',
 'ARN': 'R',
 'ASH': 'D',
 'ASN': 'N',
 'ASP': 'D',
 'CYS': 'C',
 'GLH': 'E',
...

AA_1_LETTER_MAP

Value:

{'A': 'ALA',
 'C': 'CYS',
 'D': 'ASP',
 'E': 'GLU',
 'F': 'PHE',
 'G': 'GLY',
 'H': 'HIS',
 'I': 'ILE',
...

POLAR_RESIDUES

Value:

['ARG',
 'ASP',
 'GLU',
 'HIS',
 'ASN',
 'GLN',
 'LYS',
 'SER',
...

NONPOLAR_RESIDUES

Value:

['PHE', 'LEU', 'ILE', 'TRP', 'VAL', 'MET', 'PRO', 'CYS', 'ALA']

NEUTRAL_RESIDUES

Value:

['ALA',
 'ASN',
 'CYS',
 'GLN',
 'GLY',
 'HIE',
 'ILE',
 'LEU',
...

RESIDUE_ROTOR_COUNT

Value:

{'ALA': 0,
 'ARG': 4,
 'ARN': 4,
 'ASH': 2,
 'ASN': 2,
 'ASP': 2,
 'CYS': 2,
 'GLH': 3,
...

HYDROPATHY_SCALE

Value:

{'ALA': 1.8,
 'ARG': -4.5,
 'ARN': -4.5,
 'ASH': -3.5,
 'ASN': -3.5,
 'ASP': -3.5,
 'CYS': 2.5,
 'CYT': 2.5,
...

MUTATION_1_LETTER_RE

Value:

re.compile(r'(?x)(?P<chain>[a-zA-Z_]{1}):(?P<resnum>-?\d+)(?P<inscode>
[a-zA-Z]{1})?\s?(?P<mutations>[ACEDGFIHKMLNQPSRTWVY]+)?')

MUTATION_3_LETTER_RE

Value:

re.compile(r'(?x)(?P<chain>[a-zA-Z_]{1}):(?P<resnum>-?\d+)(?P<inscode>
[a-zA-Z]{1})?\s?(?P<mutations>(ALA|ARG|ASN|ASP|CYS|GLN|GLU|GLY|HIS|HIP
|HIE|ILE|LEU|LYS|MET|PHE|PRO|SER|THR|TRP|TYR|VAL|ARN|ASH|GLH|HID|LYN)(
,ALA|ARG|ASN|ASP|CYS|GLN|GLU|GLY|HIS|HIP|HIE|ILE|LEU|LYS|MET|PHE|PRO|S
ER|THR|TRP|TYR|VAL|ARN|ASH|GLH|HID|LYN)*)?')

MUTATION_RE

Value:

re.compile(r'(?x)(?P<chain>[a-zA-Z_]{1}):(?P<resnum>-?\d+)(?P<inscode>
[a-zA-Z]{1})?->(?P<new_resname>(ALA|ARG|ASN|ASP|CYS|GLN|GLU|GLY|HIS|HI
P|HIE|ILE|LEU|LYS|MET|PHE|PRO|SER|THR|TRP|TYR|VAL|ARN|ASH|GLH|HID|LYN)
)')

PROP_CONVERSIONS

Value:

{'affinity_coulomb': 'Affinity_Coulomb',
 'affinity_cov': 'Affinity_Covalent',
 'affinity_gb': 'Affinity_Solv_GB',
 'affinity_hbond': 'Affinity_Hbond',
 'affinity_lipo': 'Affinity_Lipo',
 'affinity_packing': 'Affinity_Packing',
 'affinity_sa': 'Affinity_Solv_SA',
 'affinity_selfcont': 'Affinity_SelfCont',
...