schrodinger.application.bioluminate.protein.protein module¶
Module to gather residue property data for proteins.
Copyright (c) Schrodinger, LLC. All rights reserved
- schrodinger.application.bioluminate.protein.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.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
) – 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.protein.valid_asl(st, asl)¶
Returns True/False depending on whether the asl is a valid expression or not.
- schrodinger.application.bioluminate.protein.protein.get_residues_within(st, residues, within=0.0, ca=False)¶
Returns a list of residues for
st
that are withinwithin
angstroms of each residue. If theca
keyword is True the within calculation will only look for alpha carbon inresidues
. This means that ifwithin
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 allresidues
correspondresidues (list or tuple of
schrodinger.structure._Residue
) – All residues targeted for refinementwithin (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.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.protein.residue_is_nonpolar(residue)¶
Tests whether a residue is nonpolar (for SASA)
- Parameters
residue (
structure._Residue
) – Residue to test- Return type
bool
- schrodinger.application.bioluminate.protein.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
- class schrodinger.application.bioluminate.protein.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'¶
- __init__(st_filename, set_defaults=True, **kwargs)¶
Accepts one argument which is either a path or a keyword dictionary.
- addResidues(residues=None)¶
Adds residues to consider for refinement. The passed in argument can take the form of:
ASL expression
List of
schrodinger.structure._Residue
objects‘all’
None
- prepEnergy()¶
- prepMinimize(residues=None)¶
- prepResidue(residues=None)¶
- prepSidechain(residues=None)¶
- prepSidechainCBeta(residues=None)¶
- prepSidechainBB(residues=None)¶
- prepActive(lig_id, residues=None)¶
- 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
- prepAntibodyLoop(start_res=None, end_res=None, cpus=1, residues=None)¶
- prepBldStruct(jobname, dirname)¶
- class schrodinger.application.bioluminate.protein.protein.PrimeStructure(jobname)¶
Bases:
object
- __init__(jobname)¶
- createTemplateFile(template_seq, filename=None)¶
Writes a template PDB file as .ent
- 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 sequencetemplate_seq (
sequence
) – The template sequence
- exception schrodinger.application.bioluminate.protein.protein.PropkaError¶
Bases:
Exception
A custom exception for any propka failures
- class schrodinger.application.bioluminate.protein.protein.OrderedResidueDict(residues, default_value=None)¶
Bases:
collections.OrderedDict
Creates an ordered dictionary for residues in a structure
- __init__(residues, default_value=None)¶
- class schrodinger.application.bioluminate.protein.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.Structure.read('receptor.maegz') # 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']¶
- __init__(struct, jobname, cleanup=True, nbcutoff=14.0, residues=None, lig_asl=None)¶
Construct a
ProteinCalculator
class from a structure file and a jobname.- Parameters
struct (
schrodinger.structure.Structure
object) – The protein structure or protein/ligand structuresjobname – The jobname that will be used for all calculations that require output files.
residues (Iterable of
schrodinger.structure._Residue
objects.) – An iterable of _Residue objects to analyze. If not specified, all residues in the structure are considered.lig_asl (str) – The ASL for the ligand substructure. Used for calculating the vdW surface complementarity.
- progress¶
Variable that can be used to get the progress of calculations. This variable is only set in
self.calculateOverResidues
. Since that method returns a generator, each step can queryself.progress
to get a description of the progress. This variable is a tuple with the form ( step, total steps ).
- property minimizer¶
The minimizer used in energy calculations.
- runpKa()¶
Runs PROPKA to get the pKa of all residues in the
self.struct
, then setsself.pka_data
.
- getResiduepKa(residue)¶
Returns the pKa for specified residue
- Parameters
residue (
structure._Residue
) – Residue to get internal energy for- Return type
float
- getTotalpKa()¶
Gets the sum of the pKa values for the protein.
- Return type
float
- 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 inself.pka_data
- 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
- getPrimeEnergyByResidues(residues)¶
Run Prime Minimization on
self.struct
only minimizing the residues inresidues
. 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
- getResiduePotentialEnergy(residue)¶
Return the potential energy for a residue.
- Parameters
residue (
structure._Residue
) – Residue to get potential energy for- Return type
float
- getPotentialEnergyGenerator()¶
Return a generator that iterates over each residue in
self.struct
yielding theschrodinger.structure._Residue
object and it’s potential energy.- Return type
generator
- See
- See
schrodinger.structutils.minimize.Minimizer.getInteractionEnergy
- getTotalPotentialEnergy()¶
Get the potential energy of
self.struct
which is calculated usingschrodinger.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
- 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
- getInternalEnergyGenerator()¶
Return a generator that iterates over each residue in
self.struct
. This yields theschrodinger.structure._Residue
object and it’s internal energy.- Return type
generator
- See
- 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
- getInteractionEnergyGenerator()¶
Return a generator that iterates over each residue in
self.struct
. This yields theschrodinger.structure._Residue
object and it’s interaction energy.- Return type
generator
- See
schrodinger.structutils.minimize.Minimizer.getInteractionEnergy
- getResidueAtomicPolarSASA(residue, sidechain=False)¶
Returns SASA for all polar atoms in residue
- Parameters
residue (
structure._Residue
) – Residue to get atomic polar SASA contribution forsidechain (bool) – Only consider sidechain atoms when calculating SASA
- Return type
float
- 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 inself.struct
.- Parameters
sidechain (bool) – Only consider sidechain atoms when calculating SASA
- Return type
generator
- getResidueAtomicNonPolarSASA(residue, sidechain=False)¶
Returns SASA for only the nonpolar atoms in residue
- Parameters
residue (
structure._Residue
) – Residue to get atomic nonpolar SASA contribution forsidechain (bool) – Only consider sidechain atoms when calculating SASA
- Return type
float
- 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 inself.struct
.- Parameters
sidechain (bool) – Only consider sidechain atoms when calculating SASA
- Return type
generator
- getResidueSASA(residue, sidechain=False)¶
Returns the SASA for residue.
- Parameters
residue (
structure._Residue
) – Residue to get SASA forsidechain (bool) – Only consider sidechain atoms when calculating SASA
- Return type
float
- getSASAPolarGenerator(sidechain=False)¶
Returns a generator that yields the
schrodinger.structure._Residue
object and its calculated SASA for each polar residue inself.struct
.- Parameters
sidechain (bool) – Only consider sidechain atoms when calculating SASA
- Return type
generator
- 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
- getSASANonPolarGenerator(sidechain=False)¶
Returns a generator that yields the
schrodinger.structure._Residue
object and its calculated SASA for each nonpolar residue inself.struct
.- Parameters
sidechain (bool) – Only consider sidechain atoms when calculating SASA
- Return type
generator
- 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
- getSASAGenerator(sidechain=False)¶
Returns a generator that yields the
schrodinger.structure._Residue
object and its calculated SASA for each residue inself.struct
.- Parameters
sidechain (bool) – Only consider sidechain atoms when calculating SASA
- Return type
generator
- 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
- getResidueHydropathy(residue, sidechain=False)¶
Returns hydropathy value for residue
- Parameters
residue (
structure._Residue
) – Residue to get hydropathy value forsidechain (bool) – Only consider sidechain atoms when calculating SASA
- Return type
float
- getHydropathyGenerator(sidechain=False)¶
Returns a generator that yields the
schrodinger.structure._Residue
object and its calculated hydropathy for each residue inself.struct
.- Parameters
sidechain (bool) – Only consider sidechain atoms when calculating SASA
- Return type
generator
- 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
- getResidueRotatableBonds(residue)¶
Return the number of rotors for a residue.
- Parameters
residue (
structure._Residue
) – Residue to get rotor count for- Return type
int
- getRotatableBondsGenerator()¶
Returns a generator that yields the
schrodinger.structure._Residue
object and its number of rotors for each residue inself.struct
.- Return type
generator
- getTotalRotatableBonds()¶
- Returns
Sum of rotors for all residues.
- Return type
float
- getTotalSurfComp()¶
- Returns
Median of vdW surface complementarity values for all surface points for all residues.
- 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
- 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
- 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 inproperties
, 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
- getTotalAggregation()¶
- getTotalSolubility()¶
- getTotalComplementarity()¶
- class schrodinger.application.bioluminate.protein.protein.Refiner(struct, residues=None)¶
Bases:
object
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')
- PYTHON_MINIMIZE = 'python_minimize'¶
- PRIME_MINIMIZE = 'prime_minimize'¶
- PRIME_RESIDUE = 'prime_residue'¶
- PRIME_SIDECHAIN = 'prime_sidechain'¶
- PRIME_SIDECHAIN_CBETA = 'prime_sidechain_cbeta'¶
- PRIME_SIDECHAIN_BB = 'prime_sidechain_bb'¶
- PRIME_LOOP_PRED = 'prime_loop_prediction'¶
- PRIME_ANTIB_LOOP_PRED = 'prime_antibody_loop_prediction'¶
- __init__(struct, residues=None)¶
- Parameters
struct (
schrodinger.structure.Structure
) – The structure being refinedresidues (None or list/tuple of
structure.structure._Residue
) – Residues to consider for refinement
- setResidues(residues)¶
Set the residues to refine. This is a list of integers refering to the residue indices for the structure.
- clean()¶
Remove all files created from the refinement job
- 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
- refinePrime(refine_type, jobname, completed_callback=None, **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
completed_callback (callable) – Whether to start the job and wait, or call given function with Job object is parameter on completion.
- Raises
RuntimeError – If
refine_type
is not supportedRuntimeError – If launching the refinement job fails
RuntimeError – If the refinement job fails
- Returns
Refined structure
- Return type
schrodinger.structure.Structure
object orschrodinger.job.jobcontrol.Job
- 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
- 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
- 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
- runPrimeLoopPrediction(jobname, start_res=None, end_res=None)¶
Shortcut to run a Prime loop prediction refinement job..
- 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
- 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 supportedRuntimeError – If the refinement job fails
- Returns
Refined structure
- Return type
- class schrodinger.application.bioluminate.protein.protein.Consensus(asl_map, minimum_number, dist_cutoff=2.0)¶
Bases:
object
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_WATER = 'water and NOT (atom.ele H)'¶
- ASL_WATER_NOZOB = 'water and NOT (atom.ele H) and NOT (withinbonds 1 (not water))'¶
- 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 )))'¶
- __init__(asl_map, minimum_number, dist_cutoff=2.0)¶
- Parameters
asl_map (tuple of (
structure
, ASL)) – List of structures and the ASL used to limit the atoms used when calculating the consensusminimum_number (int) – The minimum number of matches within structures. An atom will be considered a “consensus” atom if it is within the
dist_cutoff
of at leastminimum_number
of structures in the list of passed in structures.dist_cutoff (float) – Distance in Angstroms used to define a consensus match
- Attention
The list of consensus atoms (or molecules, residues, indices, etc. depending on the property called, i.e.
self.molecules
) will all be unique and will depend on the ASL passed in. If the ASL is not specific enough you may end up with poor results.
- getClosest(ref_atom, mob_atoms)¶
Gets the closest atom to the
ref_atom
frommob_atoms
.
- property atoms¶
Get the map of
atom objects
of consensus atoms.- Returns
Atoms of consensus atoms
- Return type
OrderedDict
ofatom objects
where the keys are the template atoms and their values are the consensus atoms from the query.
- property 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.
- property residues¶
Get the list of
residue objects
of consensus atoms for each structure inself.asl_map
.- Returns
Residues of consensus atoms
- Return type
list of unique consensus
residue objects
for each structure inself.asl_map
. (Order is maintained)
- property 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)
- property 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 inself.asl_map
. (Order is maintained)
- property 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)