Classes¶

RNAsketch.Design¶

Design.py: Class as wrapper for ViennaRNA and Nupack functions to design an RNA molecule This implements the core class which holds all the states of a riboswitch

class RNAsketch.Design.Design(structures, sequence='')[source]¶

Bases: object

Design contains all neccessary information to generate a RNA device or to return a solution. It is used as a container between the different functions.

Parameters:	structures – RNA secondary structure string in dot-bracket notation sequence – RNA sequence string in IUPAC notation [AUGC]

classtype¶

ensemble_defect¶

Returns:	Dict of ensemble defect values of all states with state names as keys

eos¶

Returns:	Dict of energy of structure values of all states with state names as keys

eos_diff_mfe¶

Returns:	Dict of energy of structure to MFE difference values of all states with state names as keys

eos_reached_mfe¶

Returns:	Dict of booleans telling if the energy of struct equals the mfe energy of all states with state names as keys

length¶

Returns:	Length of the designed sequence

mfe_energy¶

Returns:	Dict of mfe values of all states with state names as keys

mfe_structure¶

Returns:	Dict of mfe structures of all states with state names as keys

newState(key, struct, temperature=37.0, ligand=None, constraint=None, enforce_constraint=False)[source]¶

Creates a new state of the given subclass.

Parameters:

Parameters:	key – Name of the state (string) struct – Dot-bracket notation of a structure input temperature – Temperature for the folding predictions of this state (default: 37.0 degree celsius) ligand – List specifying the ligand binding-pocket and energy, e.g. for Theophylline [“GAUACCAG&CCCUUGGCAGC”,”(…((((&)…)))…)”,-9.22] constraint – specify a hard constraint string enforce_constraint – boolean if we should enforce constraints

key – Name of the state (string)
struct – Dot-bracket notation of a structure input
temperature – Temperature for the folding predictions of this state (default: 37.0 degree celsius)
ligand – List specifying the ligand binding-pocket and energy, e.g. for Theophylline [“GAUACCAG&CCCUUGGCAGC”,”(…((((&)…)))…)”,-9.22]
constraint – specify a hard constraint string
enforce_constraint – boolean if we should enforce constraints

number_of_structures¶

Returns:	Number of uniq structures of all states

pf_energy¶

Returns:	Dict of partition function energy values of all states with state names as keys

pf_structure¶

Returns:	Dict of partition function consensus structures of all states with state names as keys

pos¶

Returns:	Dict of probability of structure values of all states with state names as keys

sequence¶

Returns:	Sequence of this design object

structures¶

Returns:	List containing the structures of all states

write_csv(separator=';')[source]¶

Generates a csv version of all values of this design separated by the given separator

Parameters:	separator – separator for the values
Returns:	string containing all values of this design separated by the given separator

write_csv_header(separator=';')[source]¶

Generates a csv header for all values of this design separated by the given separator

Parameters:	separator – separator for the values
Returns:	string containing a csv header for this design separated by the given separator

write_out(score=0)[source]¶

Generates a nice human readable version of all values of this design

Parameters:	score – optimization score for this design
Returns:	string containing a nicely formatted version of all design values

RNAsketch.Design.get_Design(structures, sequence, package, temperature=None)[source]¶

Convenience function to build and return the right Design object

Parameters:	structures – RNA secondary structure string in dot-brackete notation sequence – RNA sequence string in IUPAC notation [AUGC] package – String specifying the folding energy evaluation package (‘nupack’, ‘vrna’, ‘pkiss’, ‘hotknots’) temperature – Temperature for the folding predictions in degree celsius (default: 37.0)

class RNAsketch.Design.hotknotsDesign(structures, sequence='')[source]¶

Bases: RNAsketch.Design.Design

classtype¶

newState(key, struct, temperature=37.0, ligand=None, constraint=None, enforce_constraint=False)[source]¶

Creates a new state of the given subclass.

Parameters:

Parameters:	key – Name of the state (string) struct – Dot-bracket notation of a structure input temperature – Temperature for the folding predictions of this state (default: 37.0 degree celsius) ligand – List specifying the ligand binding-pocket and energy, e.g. for Theophylline [“GAUACCAG&CCCUUGGCAGC”,”(…((((&)…)))…)”,-9.22] constraint – specify a hard constraint string enforce_constraint – boolean if we should enforce constraints

key – Name of the state (string)
struct – Dot-bracket notation of a structure input
temperature – Temperature for the folding predictions of this state (default: 37.0 degree celsius)
ligand – List specifying the ligand binding-pocket and energy, e.g. for Theophylline [“GAUACCAG&CCCUUGGCAGC”,”(…((((&)…)))…)”,-9.22]
constraint – specify a hard constraint string
enforce_constraint – boolean if we should enforce constraints

class RNAsketch.Design.nupackDesign(structures, sequence='')[source]¶

Bases: RNAsketch.Design.Design

classtype¶

newState(key, struct, temperature=37.0, ligand=None, constraint=None, enforce_constraint=False)[source]¶

Creates a new state of the given subclass.

Parameters:

Parameters:	key – Name of the state (string) struct – Dot-bracket notation of a structure input temperature – Temperature for the folding predictions of this state (default: 37.0 degree celsius) ligand – List specifying the ligand binding-pocket and energy, e.g. for Theophylline [“GAUACCAG&CCCUUGGCAGC”,”(…((((&)…)))…)”,-9.22] constraint – specify a hard constraint string enforce_constraint – boolean if we should enforce constraints

key – Name of the state (string)
struct – Dot-bracket notation of a structure input
temperature – Temperature for the folding predictions of this state (default: 37.0 degree celsius)
ligand – List specifying the ligand binding-pocket and energy, e.g. for Theophylline [“GAUACCAG&CCCUUGGCAGC”,”(…((((&)…)))…)”,-9.22]
constraint – specify a hard constraint string
enforce_constraint – boolean if we should enforce constraints

class RNAsketch.Design.pkissDesign(structures, sequence='')[source]¶

Bases: RNAsketch.Design.Design

classtype¶

newState(key, struct, temperature=37.0, ligand=None, constraint=None, enforce_constraint=False)[source]¶

Creates a new state of the given subclass.

Parameters:

Parameters:	key – Name of the state (string) struct – Dot-bracket notation of a structure input temperature – Temperature for the folding predictions of this state (default: 37.0 degree celsius) ligand – List specifying the ligand binding-pocket and energy, e.g. for Theophylline [“GAUACCAG&CCCUUGGCAGC”,”(…((((&)…)))…)”,-9.22] constraint – specify a hard constraint string enforce_constraint – boolean if we should enforce constraints

key – Name of the state (string)
struct – Dot-bracket notation of a structure input
temperature – Temperature for the folding predictions of this state (default: 37.0 degree celsius)
ligand – List specifying the ligand binding-pocket and energy, e.g. for Theophylline [“GAUACCAG&CCCUUGGCAGC”,”(…((((&)…)))…)”,-9.22]
constraint – specify a hard constraint string
enforce_constraint – boolean if we should enforce constraints

class RNAsketch.Design.vrnaDesign(structures, sequence='')[source]¶

Bases: RNAsketch.Design.Design

classtype¶

newState(key, struct, temperature=37.0, ligand=None, constraint=None, enforce_constraint=False)[source]¶

Creates a new state of the given subclass.

Parameters:

Parameters:	key – Name of the state (string) struct – Dot-bracket notation of a structure input temperature – Temperature for the folding predictions of this state (default: 37.0 degree celsius) ligand – List specifying the ligand binding-pocket and energy, e.g. for Theophylline [“GAUACCAG&CCCUUGGCAGC”,”(…((((&)…)))…)”,-9.22] constraint – specify a hard constraint string enforce_constraint – boolean if we should enforce constraints

key – Name of the state (string)
struct – Dot-bracket notation of a structure input
temperature – Temperature for the folding predictions of this state (default: 37.0 degree celsius)
ligand – List specifying the ligand binding-pocket and energy, e.g. for Theophylline [“GAUACCAG&CCCUUGGCAGC”,”(…((((&)…)))…)”,-9.22]
constraint – specify a hard constraint string
enforce_constraint – boolean if we should enforce constraints

RNAsketch.State¶

State.py: Class as wrapper for ViennaRNA and Nupack functions to design an RNA molecule. This implements the various states of a riboswitch.

class RNAsketch.State.State(parent, structure=None, temperature=37.0, ligand=None, constraint=None, enforce_constraint=False)[source]¶

Bases: object

State object holds structure, ligand, constraints and calculates all values for this state.

Parameters:	structure – Dot-bracket structure string parent – Parent Design object

classtype¶

constraint¶

Returns:	Structural constraint of this state (hard constraint)

cut_points¶

Returns:	List containing the positions of the cut points (& or +) in the sequence

enforce_constraint¶

Returns:	Boolean whether to enforce the hard constraint or not

ensemble_defect¶

Returns:	Ensemble defect value given all the properties of this state (constraints, temperature,…)

eos¶

Returns:	Energy of structure given all the properties of this state (constraints, temperature,…)

eos_diff_mfe¶

Returns:	Energy difference of structure to mfe given all the properties of this state (constraints, temperature,…)

eos_reached_mfe¶

Returns:	Boolean defining whether the eos reached the mfe energy

length¶

Returns:	Length of the design sequence if available, otherwise of the stuctural input

ligand¶

Returns:	Ligand binding definitions for this state; List with sequence pattern, structure pattern and binding energy (soft constraint)

mfe_energy¶

Returns:	MFE value given all the properties of this state (constraints, temperature,…)

mfe_structure¶

Returns:	MFE structure given all the properties of this state (constraints, temperature,…)

multifold¶

Returns:	Number of cut points to specify if it is a cofold or multifold problem

pf_energy¶

In case of a dimer cofold calculation with viennarna, the function returns the energy of true hybrid states only.

Returns:	Partition function energy value given all the properties of this state (constraints, temperature,…)

pf_structure¶

Returns:	Partition function consensus structure given all the properties of this state (constraints, temperature,…)

pos¶

Returns:	Probability of structure given all the properties of this state (constraints, temperature,…)

reset()[source]¶

structure¶

Returns:	Dot-bracket structure as constraint for this state

temperature¶

Returns:	Temperature of this state

RNAsketch.State.add_cuts(input, cut_points)[source]¶

Takes a string and add back the cut point characters at the positions stored in the cut points list

Parameters:	input – string without cut point characters
Returns:	string containing cut point characters

RNAsketch.State.create_bp_table(structure)[source]¶

Takes a structure in dot bracket notation and returns a base pair table. Unpaired positions are -1, otherwise the index of the adjacent bracket is listed

Parameters:	structure – string with dot-bracket notation of the strcture
Return bpt:	base pair table

class RNAsketch.State.hotknotsState(parent, structure=None, temperature=37.0, ligand=None, constraint=None, enforce_constraint=False)[source]¶

Bases: RNAsketch.State.State

classtype¶

class RNAsketch.State.nupackState(parent, structure=None, temperature=37.0, ligand=None, constraint=None, enforce_constraint=False)[source]¶

Bases: RNAsketch.State.State

classtype¶

class RNAsketch.State.pKissState(parent, structure=None, temperature=37.0, ligand=None, constraint=None, enforce_constraint=False)[source]¶

Bases: RNAsketch.State.State

classtype¶

RNAsketch.State.remove_cuts(input)[source]¶

Takes a string and removes all cut characters (+&) from this string

Parameters:	input – string containing cut point characters
Returns:	string without cut point characters

class RNAsketch.State.vrnaState(parent, structure=None, temperature=37.0, ligand=None, constraint=None, enforce_constraint=False)[source]¶

Bases: RNAsketch.State.State

classtype¶

RNAsketch.RNAStructure¶

class RNAsketch.Structure.RNAStructure(dotbracket)[source]¶

Bases: object

RNAStructure object to handle RNA secondary structures. Holds a pairtable internally to operate on.

Parameters:	dotbracket – Dot-bracket notation of the RNA secondary structure as string

hasLonelyPairs()[source]¶

Returns a boolean whether the structure has lonely pairs

Returns:	boolean

removeLonelyPairs()[source]¶

Returns a dotbracket string without lonely pairs.

Returns:	structure string in dot-bracket notation without any lonely pairs

resolvePKs()[source]¶

Removes any pseudoknots from the structure. Pseudoknotted base-pairs are missing in the returned structure!

Returns:	list of pseudoknot-free structure strings in dot-bracket notation

RNAsketch.RPSampler¶

class RNAsketch.RNARedPrintSampler.RPSampler(structures, constraint='', model='nussinov', weights=[], gcweight=1, temperature=37.0, stacksize=1000, StopConstruct=False, RedPrintFolder=None, debug=False)[source]¶

Bases: object

RPSampler is a python wrapper for RNARedPrint and implements a similar interface to the RNAblueprint DependencyGraphMT object.

Parameters:

Parameters:	structures – List of Dot-bracket structure strings constraint – Sequence constraints in IUPACK notation model – String specifying the model, can be ‘uniform’, ‘nussinov’, ‘basepairs’ or ‘stacking’ weights – List of integers specifying the boltzmann weight for the target structures, range in ]0, +infinity] gcweight – Integer specifying the GC-weight, ]0, +infinity] temperature – Temperature for the folding predictions (default: 37.0 degree celsius) stacksize – Size of one sequence sampling batch (default: 1000 sequences) StopConstruct – Bool specifying if we want to benchmark the construction time. Measured time can be obtained from construction_time after construction (default: False) RedPrintFolder – Location of the RNARedPrint project folder (default: ‘./RNARedPrint/’) debug – Bool to print debug statements (default: False)

structures – List of Dot-bracket structure strings
constraint – Sequence constraints in IUPACK notation
model – String specifying the model, can be ‘uniform’, ‘nussinov’, ‘basepairs’ or ‘stacking’
weights – List of integers specifying the boltzmann weight for the target structures, range in ]0, +infinity]
gcweight – Integer specifying the GC-weight, ]0, +infinity]
temperature – Temperature for the folding predictions (default: 37.0 degree celsius)
stacksize – Size of one sequence sampling batch (default: 1000 sequences)
StopConstruct – Bool specifying if we want to benchmark the construction time. Measured time can be obtained from construction_time after construction (default: False)
RedPrintFolder – Location of the RNARedPrint project folder (default: ‘./RNARedPrint/’)
debug – Bool to print debug statements (default: False)

dump_new_stack()[source]¶

Draws a sample from RNARedPrint and returns the list of generated sequences at once. The variable stacksize specifies the amount of sequences.

Returns:	List of RNA sequence strings

gcweight¶: Integer specifying the GC-weight, ]0, +infinity]

get_sequence()[source]¶

Get the sampled sequence as a string.

Returns:	RNA Sequence string in IUPACK notation

model¶

String specifying the sampling model.

Returns:	string, can be ‘uniform’, ‘nussinov’, ‘basepairs’ or ‘stacking’

revert_sequence(amount)[source]¶: Compatibility to the DependencyGraphMT object, does nothing internally.

sample()[source]¶

Sample a new sequence.

Returns:	Returns 0 for compatibility to DependencyGraphMT.

sample_clocal()[source]¶: Compatibility to the DependencyGraphMT object, calls sample() internally.

sample_plocal()[source]¶: Compatibility to the DependencyGraphMT object, calls sample() internally.

set_history_size(size)[source]¶: Compatibility to the DependencyGraphMT object, does nothing internally.

set_sequence(seq)[source]¶: Compatibility to the DependencyGraphMT object, does nothing internally.

weights¶: List of integers specifying the boltzmann weight for the target structures, range in ]0, +infinity]