schrodinger.application.bioluminate.protein module

Module to gather residue property data for proteins.

Copyright (c) Schrodinger, LLC. All rights reserved

class schrodinger.application.bioluminate.protein.Consensus(asl_map, minimum_number, dist_cutoff=2.0)

Access the atoms, residues, and molecules (or just their indices) that are considered to be consensus objects for a template structure and query structure. All properties are returned as an OrderedDict that maps the template objects to their consensus objects from the query structure.

Here is an example of how to get all the consensus waters between two protein structures. We define the cutoff here at 2 Angstroms:

from schrodinger.structure import StructureReader
from schrodinger.application.bioluminate import protein

pt = maestro.project_table_get()

# Create an ASL map for all ligands in the WS
asl_map = []
for row in pt.included_rows:
    st = row.getStructure()
    ligands = analyze.find_ligands(st)
    if not ligands:
        continue
    indices = []
    for ligand in ligands:
        indices.extend([str(i) for i in ligand.atom_indexes])

    asl = 'atom.n %s' % ','.join(indices)

    asl_map.append((st, asl))

# Create a consensus of all ligands, specifying that at least three
# structures must have a ligand atom within 2A from one another.
consensus = protein.Consensus(asl_map, 3, dist_cutoff=2)

# To get the atom objects
consensus_atoms = consensus.atoms

# To get the molecule objects
molecules = consensus.molecules
ASL_IONS = 'ions'
ASL_LIGAND = '(((m.atoms 5-130)) and not ((ions) or (res.pt ACE ACT ACY BCT BME BOG CAC CIT CO3 DMS EDO EGL EPE FES FMT FS3 FS4 GOL HEC HED HEM IOD IPA MES MO6 MPD MYR NAG NCO NH2 NH3 NO3 PG4 PO4 POP SEO SO4 SPD SPM SUC SUL TRS )))'
ASL_WATER = 'water and NOT (atom.ele H)'
atom_indices

Get the map of atom indices of consensus atoms.

Returns:Atom indices of consensus atoms
Return type:OrderedDict of ints where the keys are the template atom indices and their values are the consensus atom indices from the query.
atoms

Get the map of atom objects of consensus atoms.

Returns:Atoms of consensus atoms
Return type:OrderedDict of atom objects where the keys are the template atoms and their values are the consensus atoms from the query.
getClosest(ref_atom, mob_atoms)

Gets the closest atom to the ref_atom from mob_atoms.

molecule_indices

Get the map of molecule indices of consensus atoms.

Returns:Molecule indices of consensus atoms
Return type:list of unique consensus molecule indices for each structure in self.asl_map. (Order is maintained)
molecules

Get the map of molecule objects of consensus atoms.

Returns:Molecules of consensus atoms
Return type:list of unique consensus molecule objects for each structure in self.asl_map. (Order is maintained)
residue_indices

Get the map of residue indices of consensus atoms.

Returns:Residue indices of consensus atoms
Return type:list of unique consensus residue indices for each structure in self.asl_map. (Order is maintained)
residues

Get the list of residue objects of consensus atoms for each structure in self.asl_map.

Returns:Residues of consensus atoms
Return type:list of unique consensus residue objects for each structure in self.asl_map. (Order is maintained)
class schrodinger.application.bioluminate.protein.Mutation(ref_struct, struct, residue_map)

Helper class for Mutator. This will store a mutated structure and the resides that were mutated.

class schrodinger.application.bioluminate.protein.Mutator(ref_struct, mutations, concurrent=1, sequential=False, idealize=True)

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.

Here is an example of a mutation of a Ser residue to: Asp, Glu, Asn, & Gln (one-letter codes are D, E, N, & Q respectively). The Ser residue is in chain A and has a residue number of 22. This example will write a file named ‘mutated_structures.maegz’ that has the reference structure as the first CT and each mutation CT after that. Five total structures will be in the output file:

from schrodinger import structure
from schrodinger.application.bioluminate import protein

# Get the input structure
reference_st = structure.StructureReader('receptor.maegz').next()

# Create the writer for the output file and append the reference
writer = structure.StructureWriter('mutated_structures.maegz')
writer.append(reference_st)

# Define the residues and mutations
residues = ['A:22']
muts     = 'DENQ'

# Get a compatible list of mutations. The above turns into
# [('A', 22, 'DENQ')]
mutations = protein.Mutator.convert_residue_list(residues, muts)

# Construct the mutator
mutator = protein.Mutator(st, mutations)

# Loop over each mutation
for mutation in mutator.generate():
    #
    mutated_structure = mutation.struct
    residue_map       = mutation.residue_map

    res_str = ", ".join(str(res) for res in residue_map.values())
    print 'Residues affected by this mutation: %s' % res_str

    # Do something with the mutated structure (refine maybe)

    writer.append(mutated_structure)

@todo: Add logging

GXG_DATA = {'GLH': -143.536, 'ILE': -84.13, 'GLN': -136.183, 'GLY': -105.658, 'TYR': -101.858, 'GLU': -143.536, 'CYS': -100.845, 'ASP': -149.255, 'SER': -96.365, 'LYS': -110.759, 'PRO': -66.763, 'HID': -104.977, 'HIE': -104.977, 'LYN': -110.759, 'ASH': -149.255, 'ASN': -137.153, 'HIP': -104.977, 'VAL': -93.493, 'THR': -98.156, 'HIS': -104.977, 'TRP': -105.114, 'PHE': -96.483, 'ALA': -100.736, 'MET': -99.708, 'LEU': -92.4, 'ARG': -118.478, 'ARN': -118.478}
GXG_DATA_PRIME = {'GLH': -141.673, 'ILE': -97.541, 'GLN': -152.611, 'GLY': -116.263, 'TYR': -123.497, 'GLU': -141.673, 'CYS': -113.747, 'ASP': -154.559, 'SER': -112.693, 'LYS': -123.751, 'PRO': -81.734, 'HID': -121.6, 'HIE': -121.6, 'LYN': -123.751, 'ASH': -154.559, 'ASN': -156.375, 'HIP': -121.6, 'VAL': -109.017, 'THR': -116.048, 'HIS': -121.6, 'TRP': -122.407, 'PHE': -113.719, 'ALA': -112.635, 'MET': -112.643, 'LEU': -107.106, 'ARG': -142.467, 'ARN': -142.467}
MUTATIONS_PROPERTY = 's_bioluminate_Mutations'
SUPPORTED_BUILD_RESIDUES = ['ALA', 'ARG', 'ASN', 'ASP', 'CYS', 'GLN', 'GLU', 'GLY', 'HIS', 'HIP', 'HIE', 'ILE', 'LEU', 'LYS', 'MET', 'PHE', 'PRO', 'SER', 'THR', 'TRP', 'TYR', 'VAL']
UNFOLDED_PROPERTY = 'r_bioluminate_Unfolded_Contribution'
UNFOLDED_PROPERTY_PRIME = 'r_bioluminate_Unfolded_Contribution_Prime'
calculateMutationsList()

Calculate the mutations that will be performed, based on the input residues and their mutations, and the “concurrent” and “sequential” settings.

static convert_muts_file(muts_file, regex=<_sre.SRE_Pattern object at 0x3427b00>)

Converts lines in filename into a list of mutations to use. Returns a list of tuples where each tuple is ( “chain”, “resnum”, “inscode”, “three-letter resnames for mutation”).

Also supports loop insertion and deletion.

Each line is one mutation (could be multiple residues)

classmethod convert_res_file(filename, regex=<_sre.SRE_Pattern object at 0x3426e60>)

Converts lines in filename into a list of mutations to use. Returns a list of tuples where each tuple is ( “chain”, “resnum”, “inscode”, “three-letter resnames for mutation”).

Each line could be multiple mutations (one residue to multiple mutation states)

Parameters:
  • filename (str) – Name of file containing the list of mutations.
  • regex (regular expression object) – Regular expression for matching residues
Raises:

RuntimeError – If any of chain, resnum or mutation is missing
Returns:

List of mutations with valid syntax for the class
Return type:

list of tuples
classmethod convert_res_list(reslist, regex=<_sre.SRE_Pattern object at 0x3426e60>)

Converts list of residues into a list of mutations to use. Returns a list of tuples where each tuple is ( “chain”, “resnum”, “inscode”, “three-letter resnames for mutation”).

Each residue string could be multiple mutations (one residue to multiple mutation states)

Parameters:
  • reslist (list of str) – List of residues to convert to mutations
  • regex (regular expression object) – Regular expression for matching residues
Returns:

List of mutations with valid syntax for the class or None if any item in the list is not valid
Return type:

list of tuples or None
static convert_res_to_muts(res_str, regex=<_sre.SRE_Pattern object at 0x3426e60>, validate=True)
Converts a residue string into a list of mutations to use. Returns a list of tuples of (“chain”, “resnum”, “inscode”, “three-letter resnames for mutation”). Will return None if any item

in the list is not a valid residue string.

A residue string could be multiple mutations (one residue to multiple mutation states)

param res_str:Residue string to convert to mutations
type res_str:str
param regex:Regular expression for matching residues
type regex:regular expression object
param validate:Whether to run validation on the mutation
type validate:bool
return:List of mutations with valid syntax for the class or None if the res_str is not valid.
rtype:list tuples or None
static convert_residue_list(residues, mutations, regex=<_sre.SRE_Pattern object at 0x3426e60>)

Convert a list of residues and mutations to a standard list of mutations. Returns a list of tuples where each tuple is ( “chain”, “resnum”, “inscode”, “three-letter resnames for mutation”).

Parameters:residues (list of strings (Syntax: <chain>:<resnum> if no chain use "_")) – Residues that will be mutated.
:param mutations : The three-letter names for the residues that will be
used in mutation.
Raises:RuntimeError – If any of chain, resnum or mutation is missing or if there is an invalid residue name
Returns:List of mutations with valid syntax for the class
Return type:list of tuples
generate()

Used to loop over all mutations. Each mutation consists of the mutated structure and a residue mapping dict. The structure is raw, that is, unrefined in any way.

Returns:Generator for all mutations defined in self.mutations Each step of generator yields a mutation.
Return type:generator
getLoopMutation(mutated_st, res_str, new_resname)

build loop insertion or deletion

getMutationFromChanges(changes)
mutations

The list of mutations that will be carried out

total_mutations

Total number of mutations that will be generated

static validate_mutated_residues(residues)

Method for validating the residues used in mutations passed in to the MutateProtein class.

Raises:ValueError – If the 3-letter residue name is not supported by the build,mutate method.
@todo: Convert the return to raise a custom MutateProteinError.
This will help in letting front-end know why it fails.

@todo: Add validation for assuring chain and resnum are in self.struct

static validate_mutations(mutations)

Private method for validating the mutations passed in to the MutateProtein class.

Raises:ValueError – If the mutations passed in is not a list, if each item in the list is not a tuple, if the tuple is not of length 4 (chain, resnum idx, inscode, mutation resnames), if the resnum is not an integer, or any of the 3-letter residue names in “mutation resnames” is not supported by the build,mutate method.
@todo: Convert the return to raise a custom MutateProteinError.
This will help in letting front-end know why it fails.

@todo: Add validation for assuring chain and resnum are in self.struct

class schrodinger.application.bioluminate.protein.OrderedResidueDict(residues, default_value=None)

Bases: collections.OrderedDict

Creates an ordered dictionary for residues in a structure

class schrodinger.application.bioluminate.protein.PrimeConfig(st_filename, set_defaults=True, **kwargs)

Bases: schrodinger.application.prime.input.Prime

Class containing the methods to write Prime input files. NOTE THAT THIS ALWAYS USES OPLS2005

ALL_RESIDUES = 'all'
addResidues(residues=None)

Adds residues to consider for refinement. The passed in argument can take the form of:

prepActive(lig_id, residues=None)
prepAntibodyLoop(start_res=None, end_res=None, cpus=1, residues=None)
prepBldStruct(jobname, dirname)
prepEnergy()
prepLoop(start_res=None, end_res=None, res_sphere=7.5, maxcalpha=None, protocol='LOOP_BLD', loop2=None, max_jobs=0, residues=None)
Parameters:
  • start_res (string) – loop start residue, e.g. A:15
  • end_res (string) – loop start residue, e.g. A:20
  • res_sphere (float) – radius of nearby residue refinement
  • maxcalpha (float) – CA atom movement constraint
  • protocol (string) – loop refinement protocol
  • loop2 (list) – the definition of the second loop, e.g. [‘A:4’,’A:6’]
  • residues (None) – Unused, kept for API compatibility
  • max_jobs (int) – how many processes will be run simultaneously
prepMinimize(residues=None)
prepResidue(residues=None)
prepSidechain(residues=None)
prepSidechainBB(residues=None)
prepSidechainCBeta(residues=None)
class schrodinger.application.bioluminate.protein.PrimeStructure(jobname)
createAlignFile(reference_seq, template_seq, filename=None)

Writes an alignment file for the template. If no filename is supplied the file will be named <jobname>.aln.

Parameters:
  • reference_seq (sequence) – The reference sequence
  • template_seq (sequence) – The template sequence
createTemplateFile(template_seq, filename=None)

Writes a template PDB file as .ent

class schrodinger.application.bioluminate.protein.PropertyCalculator(struct, jobname, cleanup=True, nbcutoff=14.0, residues=None, lig_asl=None)

Bases: object

Class for calculating properties of proteins and protein residues.

Here is an example of how to calculate properties for a protein:

from schrodinger import structure
from schrodinger.application.bioluminate import protein

# Get the input structure
st = structure.StructureReader('receptor.maegz').next()

# Define the properties to calculate
calculations = [ 'e_pot', 'e_internal', 'e_interaction', 'prime_energy',
                 'pka', 'sasa_polar', 'sasa_nonpolar', 'sasa_total']

# Create the calculator
calculator = protein.PropertyCalculator(st, "my_calculator_jobname")

# Calculate the properties
properties = calculator.calculate(*calculations)

In the example above the properties output would look something like this:

properties = {
    'e_pot'         : 1573.4,
    'e_internal'    : 624.7,
    'e_interaction' : 994.8,
    'prime_energy'  : 744.2,
    'pka'           : 124.1,
    'sasa_polar',   : 3122.3,
    'sasa_nonpolar' : 271.1,
    'sasa_total'    : 3393.4
}
AGGREGATE_CALCULATIONS = ['e_pot', 'prime_energy', 'pka', 'sasa_polar', 'sasa_nonpolar', 'sasa_total', 'hydropathy', 'rotatable', 'vdw_surf_comp']
RESIDUE_CALCULATIONS = ['e_pot', 'e_internal', 'e_interaction', 'pka', 'sasa_polar', 'sasa_nonpolar', 'sasa_total', 'hydropathy', 'rotatable', 'vdw_surf_comp']
calculate(*properties)

Helper method to calculate multiple properties for self.struct. All results will be returned in a dict where the keys are each of the properties in properties, and their values are the values returned from their corresponding method. Here is a list of valid properties to calculate:

  • e_pot
  • sasa_polar
  • sasa_nonpolar
  • sasa_total
  • prime_energy
  • pka
  • hydropathy
  • rotatable
  • vdw_surf_comp
Parameters:properties (str (see PropertyCalculator.AGGREGATE_CALCULATIONS)) – Properties to calculate
Raises:KeyError – If a property passed in is invalid
Returns:Dict where keys are properties passed in and values are the total value of the property for the protein. e.g {‘e_pot’: 1324.3, ‘sasa_total’: 1846.9}
Return type:dict
calculateOverResidues(*properties)

Helper method that returns a generator which will calculate multiple properties for self.struct. All results will be returned in a tuple with the form ( structure._Residue, calc dict ). Here is a list of valid properties to calculate:

  • e_pot
  • e_internal
  • e_interaction
  • pka
  • sasa_polar
  • sasa_nonpolar
  • sasa_total
  • hydropathy
  • rotatable
  • vdw_surf_comp
Parameters:properties (str (see PropertyCalculator.RESIDUE_CALCULATIONS)) – Properties to calculate
Raises:KeyError – If a property passed in is invalid
Returns:Generator that yields structure._Residue and dict where keys are properties passed in and values are the total value of the property for the protein. e.g (_Residue, {‘e_pot’:1324.3})
Return type:generator
getAtomicNonPolarSASAGenerator(sidechain=False)

Returns a generator that yields the schrodinger.structure._Residue object and its calculated SASA for only the nonpolar atoms in each residue in self.struct.

Parameters:sidechain (bool) – Only consider sidechain atoms when calculating SASA
Return type:generator
getAtomicPolarSASAGenerator(sidechain=False)

Returns a generator that yields the schrodinger.structure._Residue object and its calculated SASA for only the polar atoms in each residue in self.struct.

Parameters:sidechain (bool) – Only consider sidechain atoms when calculating SASA
Return type:generator
getHydropathyGenerator(sidechain=False)

Returns a generator that yields the schrodinger.structure._Residue object and its calculated hydropathy for each residue in self.struct.

Parameters:sidechain (bool) – Only consider sidechain atoms when calculating SASA
Return type:generator
getInteractionEnergyGenerator()

Return a generator that iterates over each residue in self.struct. This yields the schrodinger.structure._Residue object and it’s interaction energy.

Return type:generator
See:schrodinger.structutils.minimize.Minimizer.getInteractionEnergy
getInternalEnergyGenerator()

Return a generator that iterates over each residue in self.struct. This yields the schrodinger.structure._Residue object and it’s internal energy.

Return type:generator
See:schrodinger.structutils.minimize.Minimizer.getSelfEnergy
getPotentialEnergyGenerator()

Return a generator that iterates over each residue in self.struct yielding the schrodinger.structure._Residue object and it’s potential energy.

Return type:generator
See:schrodinger.structutils.minimize.Minimizer.getSelfEnergy
See:schrodinger.structutils.minimize.Minimizer.getInteractionEnergy
getPrimeEnergyByResidues(residues)

Run Prime Minimization on self.struct only minimizing the residues in residues. This will launch a job using job control. After the job completes the total energy will be taken from the first CT using the “r_psp_Prime_Energy” property.

Parameters:residues (list of residues) – Residues to minimize
Returns:Prime energy of protein
Return type:float
getResidueAtomicNonPolarSASA(residue, sidechain=False)

Returns SASA for only the nonpolar atoms in residue

Parameters:
  • residue (structure._Residue) – Residue to get atomic nonpolar SASA contribution for
  • sidechain (bool) – Only consider sidechain atoms when calculating SASA
Return type:

float
getResidueAtomicPolarSASA(residue, sidechain=False)

Returns SASA for all polar atoms in residue

Parameters:
  • residue (structure._Residue) – Residue to get atomic polar SASA contribution for
  • sidechain (bool) – Only consider sidechain atoms when calculating SASA
Return type:

float
getResidueHydropathy(residue, sidechain=False)

Returns hydropathy value for residue

Parameters:
  • residue (structure._Residue) – Residue to get hydropathy value for
  • sidechain (bool) – Only consider sidechain atoms when calculating SASA
Return type:

float
getResidueInteractionEnergy(residue)

Return the residue’s interaction energy.

Parameters:residue (structure._Residue) – Residue to get interaction energy for
Return type:float
See:schrodinger.structutils.minimize.Minimizer.getInteractionEnergy
getResidueInternalEnergy(residue)

Return the residue’s internal energy.

Parameters:residue (structure._Residue) – Residue to get internal energy for
Return type:float
See:schrodinger.structutils.minimize.Minimizer.getSelfEnergy
getResiduePotentialEnergy(residue)

Return the potential energy for a residue.

Parameters:residue (structure._Residue) – Residue to get potential energy for
Return type:float
getResidueRotatableBonds(residue)

Return the number of rotors for a residue.

Parameters:residue (structure._Residue) – Residue to get rotor count for
Return type:int
getResidueSASA(residue, sidechain=False)

Returns the SASA for residue.

Parameters:
  • residue (structure._Residue) – Residue to get SASA for
  • sidechain (bool) – Only consider sidechain atoms when calculating SASA
Return type:

float
getResidueSurfComp(residue)
Returns:Median of vdW surface complementarity values for all accounted points on the surface of this residue.
Return type:float
Parameters:residue (structure._Residue) – Residue to get the value for
getResiduepKa(residue)

Returns the pKa for specified residue

Parameters:residue (structure._Residue) – Residue to get internal energy for
Return type:float
getRotatableBondsGenerator()

Returns a generator that yields the schrodinger.structure._Residue object and its number of rotors for each residue in self.struct.

Return type:generator
getSASAGenerator(sidechain=False)

Returns a generator that yields the schrodinger.structure._Residue object and its calculated SASA for each residue in self.struct.

Parameters:sidechain (bool) – Only consider sidechain atoms when calculating SASA
Return type:generator
getSASANonPolarGenerator(sidechain=False)

Returns a generator that yields the schrodinger.structure._Residue object and its calculated SASA for each nonpolar residue in self.struct.

Parameters:sidechain (bool) – Only consider sidechain atoms when calculating SASA
Return type:generator
getSASAPolarGenerator(sidechain=False)

Returns a generator that yields the schrodinger.structure._Residue object and its calculated SASA for each polar residue in self.struct.

Parameters:sidechain (bool) – Only consider sidechain atoms when calculating SASA
Return type:generator
getTotalAggregation()
getTotalComplementarity()
getTotalHydropathy(sidechain=False)

Returns the total calculated hydropathy value for all residues.

Parameters:sidechain (bool) – Only consider sidechain atoms when calculating SASA
Return type:float
getTotalPotentialEnergy()

Get the potential energy of self.struct which is calculated using schrodinger.structutils.minimize.Minimizer. The potential energy is the sum of the internal energies and the interaction energies.

Returns:Total potential energy of all the residues
Return type:float
See:schrodinger.structutils.minimize.Minimizer.getSelfEnergy
See:schrodinger.structutils.minimize.Minimizer.getInteractionEnergy
getTotalPrimeEnergy()

Run Prime Minimization on self.struct. This will launch a job using job control. After the job completes the total energy will be taken from the first CT using the “r_psp_Prime_Energy” property.

Returns:Prime energy of protein
Return type:float
getTotalRotatableBonds()
Returns:Sum of rotors for all residues.
Return type:float
getTotalSASA(sidechain=False)

Returns the total approximate solvent accessible surface area for all residues.

Parameters:sidechain (bool) – Only consider sidechain atoms when calculating SASA
Return type:float
getTotalSASANonPolar(sidechain=False)

Returns the total approximate solvent accessible surface area for all non-polar residues.

Parameters:sidechain (bool) – Only consider sidechain atoms when calculating SASA
Return type:float
getTotalSASAPolar(sidechain=False)

Returns the total approximate solvent accessible surface area for all polar residues.

Parameters:sidechain (bool) – Only consider sidechain atoms when calculating SASA
Return type:float
getTotalSolubility()
getTotalSurfComp()
Returns:Median of vdW surface complementarity values for all surface points for all residues.
Return type:float
getTotalpKa()

Gets the sum of the pKa values for the protein.

Return type:float
minimizer

The minimizer used in energy calculations.

progress = None

Variable that can be used to get the progress of calculations. This variable is only set in C{self.calculateOverResidues}. Since that method returns a generator, each step can query C{self.progress} to get a description of the progress. This variable is a tuple with the form ( step, total steps ).

runpKa()

Runs PROPKA to get the pKa of all residues in the self.struct, then sets self.pka_data.

setpKaData(summary, renum_map=None)

Compares residues from the PROPKA summary with the residues in self.residues and when matches are found the summary’s pKa is set for that residue in self.pka_data

exception schrodinger.application.bioluminate.protein.PropkaError

Bases: exceptions.Exception

A custom exception for any propka failures

class schrodinger.application.bioluminate.protein.Refiner(struct, residues=None, local=False)

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

Here is an example of how to refine a protein that just had a residue mutated. In this example only the residues within 7.0 angstroms of the mutated residue will be refined:

from schrodinger.structure import StructureReader
from schrodinger.structutils import build
from schrodinger.application.bioluminate import protein

# Get the structure
st = StructureReader('receptor.maegz')

# Atom number 30 is the alpha carbon of a GLU
ca = st.atom[30]

# Mutate GLU -> ASP
renum_map = build.mutate(st, ca.index, "ASP")

# Get the residue that was mutated
mutated_residue = None
for res in st.residue:
    ca_keys  = (ca.chain,  ca.resnum,  ca.inscode)
    res_keys = (res.chain, res.resnum, res.inscode)
    if ca_keys == res_keys:
        mutated_residue = res
        break

# We want to use the reference to gather the residues to refine
refine_residues = protein.get_residues_within(
    st,
    [mutated_residue],
    within = 7.0
)

# Create the refiner
refiner = protein.Refiner(st, residues=refine_residues)

# Run Prime minimization which returns the refined structure
refined_struct = refiner.runPrimeMinimization('my_refinement_jobname')
PRIME_ANTIB_LOOP_PRED = 'prime_antibody_loop_prediction'
PRIME_LOOP_PRED = 'prime_loop_prediction'
PRIME_MINIMIZE = 'prime_minimize'
PRIME_RESIDUE = 'prime_residue'
PRIME_SIDECHAIN = 'prime_sidechain'
PRIME_SIDECHAIN_BB = 'prime_sidechain_bb'
PRIME_SIDECHAIN_CBETA = 'prime_sidechain_cbeta'
PYTHON_MINIMIZE = 'python_minimize'
clean()

Remove all files created from the refinement job

refinePrime(refine_type, jobname, wait=True, **kwargs)

Run a Prime refinement job through job control and return the refined output structure.

Parameters:
  • refine_type (str) – The type of Prime refinement to run (see class variables)
  • jobname (str) – Jobname to use
Raises:
  • RuntimeError – If refine_type is not supported
  • RuntimeError – If launching the refinement job fails
  • RuntimeError – If the refinement job fails
Returns:

Refined structure
Return type:

schrodinger.structure.Structure object
runPrimeLoopPrediction(jobname, start_res=None, end_res=None)

Shortcut to run a Prime loop prediction refinement job..

See:Refiner.refinePrime documentation
runPrimeMinimization(jobname)

Shortcut to run a Prime minimization job

See:Refiner.refinePrime documentation
runPrimeResidue(jobname)

Shortcut to run a Prime residue refinement job

See:Refiner.refinePrime documentation
runPrimeSidechain(jobname)

Shortcut to run a Prime sidechain refinement job

See:Refiner.refinePrime documentation
runPrimeSidechainBB(jobname)

Shortcut to run a Prime sidechain refinement job with backbone sampling. This will sample the backbone by running a loop prediction on a set of 3 residues centered on the residue for which the side chain is being refined.

See:Refiner.refinePrime documentation
runPrimeSidechainCBeta(jobname)

Shortcut to run a Prime sidechain refinement job with CA-CB vector sampling. This will vary the orientation of the CA-CB bond by up to 30 degrees from the initial direction.

See:Refiner.refinePrime documentation
runPythonMinimize(jobname)

Shortcut to run a schrodinger.structutils.minimize.Minimizer job.

Parameters:jobname (str) – Jobname to use
Returns:Minimized structure
Return type:schrodinger.structure.Structure object
runRefinement(refine_type, jobname, **kwargs)

Shortcut to run any of the available refinement jobs.

Parameters:
  • refine_type (str) – The type of Prime refinement to run (see class variables)
  • jobname (str) – Jobname to use
Raises:
  • RuntimeError – If refine_type is not supported
  • RuntimeError – If the refinement job fails
Returns:

Refined structure
Return type:

schrodinger.structure.Structure object
setResidues(residues)

Set the residues to refine. This is a list of integers refering to the residue indices for the structure.

writePrimeInput(refine_type, input_file, st_filename, **kwargs)

Writes the input file for a Prime refinement job.

Parameters:
  • refine_type (str) – The type of Prime refinement to run (see class variables)
  • input_file (str) – Name of the input file for the refinement job
  • st_filename (str) – Filename of the structure to be refined
Raises:

RuntimeError – If refine_type is not supported
Return type:

None
schrodinger.application.bioluminate.protein.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
schrodinger.application.bioluminate.protein.find_residue_atom(st, chain, resnum, inscode)
schrodinger.application.bioluminate.protein.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
Raises:RuntimeError – If the passed in residue is incorrect type
Returns:ASL expression for residue
Return type:str
schrodinger.application.bioluminate.protein.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._Residue`s) – The residues to create an ASL for
Raises:
  • RuntimeError – If residues are not a list or tuple
  • RuntimeError – If any passed in residues are incorrect type
Returns:

ASL expression for all residues
Return type:

str
schrodinger.application.bioluminate.protein.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._Residue`s) – 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 of schrodinger.structure._Residue objects
Return type:

list
schrodinger.application.bioluminate.protein.residue_is_nonpolar(residue)

Tests whether a residue is nonpolar

Parameters:residue (structure._Residue) – Residue to test
Return type:bool
schrodinger.application.bioluminate.protein.residue_is_polar(residue)

Tests whether a residue is polar

Parameters:residue (structure._Residue) – Residue to test
Return type:bool
schrodinger.application.bioluminate.protein.valid_asl(st, asl)

Returns True/False depending on whether the asl is a valid expression or not.