Skip to content

Description formatting for pre-packaged constraints (example for #195) #196

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Draft
cgevans wants to merge 4 commits into
base: dev
Choose a base branch
from
Draft

Description formatting for pre-packaged constraints (example for #195) #196

Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
2604c2d
description formatting example
cgevans Jul 4, 2022
571b8a0
change to rna_duplex_strand_pairs_constraint
cgevans Jul 4, 2022
490798a
add format_description, docstring, error handling
cgevans Jul 4, 2022
2d1a64d
format_description for more constraints
cgevans Jul 20, 2022
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
158 changes: 134 additions & 24 deletions nuad/constraints.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4457,9 +4457,10 @@ def nupack_domain_complex_free_energy_constraint(
weight: float = 1.0,
score_transfer_function: Callable[[float], float] = default_score_transfer_function,
parallel: bool = False,
description: Optional[str] = None,
description: str = 'NUPACK secondary structure of domain exceeds {threshold} kcal/mol',
short_description: str = 'strand_ss_nupack',
domains: Optional[Iterable[Domain]] = None) -> DomainConstraint:
domains: Optional[Iterable[Domain]] = None,
format_description: bool = True) -> DomainConstraint:
"""
Returns constraint that checks individual :any:`Domain`'s for excessive interaction using
NUPACK's pfunc.
Expand Down Expand Up @@ -4501,8 +4502,22 @@ def evaluate(seqs: Tuple[str], _: Optional[Domain]) -> Tuple[float, str]:
excess = threshold - energy
return max(0.0, excess), f'{energy:6.2f} kcal/mol'

if description is None:
description = f'NUPACK secondary structure of domain exceeds {threshold} kcal/mol'
if format_description:
try:
description = description.format(threshold=threshold,
temperature=temperature,
sodium=sodium,
magnesium=magnesium,
weight=weight,
parallel=parallel,
short_description=short_description,
domains=domains)
except KeyError as e:
print(f"In parsing the description, I couldn't find key {e}; if you didn't intend to use formatting in" +
" your description, set the parameter format_description to False, or avoid using curly braces {}" +
" in your description.")
except ValueError as e:
print(f'I tried parsing the description and it failed; to avoid this warning, please set the parameter format_description to False, or avoid using curly braces {{}} in your description. (ValueError: {e}.)')

if domains is not None:
domains = tuple(domains)
Expand All @@ -4524,9 +4539,10 @@ def nupack_strand_complex_free_energy_constraint(
weight: float = 1.0,
score_transfer_function: Callable[[float], float] = default_score_transfer_function,
parallel: bool = False,
description: Optional[str] = None,
description: str = 'NUPACK secondary structure of strand exceeds {threshold} kcal/mol',
short_description: str = 'strand_ss_nupack',
strands: Optional[Iterable[Strand]] = None) -> StrandConstraint:
strands: Optional[Iterable[Strand]] = None,
format_description: bool = True) -> StrandConstraint:
"""
Returns constraint that checks individual :any:`Strand`'s for excessive interaction using
NUPACK's pfunc.
Expand Down Expand Up @@ -4568,8 +4584,22 @@ def evaluate(seqs: Tuple[str], _: Optional[Strand]) -> Tuple[float, str]:
excess = threshold - energy
return max(0.0, excess), f'{energy:6.2f} kcal/mol'

if description is None:
description = f'NUPACK secondary structure of strand exceeds {threshold} kcal/mol'
if format_description:
try:
description = description.format(threshold=threshold,
temperature=temperature,
sodium=sodium,
magnesium=magnesium,
weight=weight,
parallel=parallel,
short_description=short_description,
strands=strands)
except KeyError as e:
print(f"In parsing the description, I couldn't find key {e}; if you didn't intend to use formatting in" +
" your description, set the parameter format_description to False, or avoid using curly braces {}" +
" in your description.")
except ValueError as e:
print(f'I tried parsing the description and it failed; to avoid this warning, please set the parameter format_description to False, or avoid using curly braces {{}} in your description. (ValueError: {e}.)')

if strands is not None:
strands = tuple(strands)
Expand All @@ -4594,6 +4624,7 @@ def nupack_domain_pair_constraint(
description: Optional[str] = None,
short_description: str = 'dom_pair_nupack',
pairs: Optional[Iterable[Tuple[Domain, Domain]]] = None,
format_description: bool = True
) -> DomainPairConstraint:
"""
Returns constraint that checks given pairs of :any:`Domain`'s for excessive interaction using
Expand Down Expand Up @@ -4641,6 +4672,24 @@ def nupack_domain_pair_constraint(
raise ValueError(f'threshold = {threshold} must be one of float or dict, '
f'but it is {type(threshold)}')

if format_description:
try:
description = description.format(threshold=threshold,
temperature=temperature,
sodium=sodium,
magnesium=magnesium,
weight=weight,
parallel=parallel,
short_description=short_description,
pairs=pairs)
except KeyError as e:
print(f"In parsing the description, I couldn't find key {e}; if you didn't intend to use formatting in" +
" your description, set the parameter format_description to False, or avoid using curly braces {}" +
" in your description.")
except ValueError as e:
print(f'I tried parsing the description and it failed; to avoid this warning, please set the parameter format_description to False, or avoid using curly braces {{}} in your description. (ValueError: {e}.)')


def binding_closure(seq_pair: Tuple[str, str]) -> float:
return dv.binding(seq_pair[0], seq_pair[1], temperature=temperature,
sodium=sodium, magnesium=magnesium)
Expand Down Expand Up @@ -4712,10 +4761,11 @@ def nupack_strand_pairs_constraint(
magnesium: float = dv.default_magnesium,
weight: float = 1.0,
score_transfer_function: Callable[[float], float] = default_score_transfer_function,
description: Optional[str] = None,
description: str = 'NUPACK binding energy of strand pair exceeds {threshold} kcal/mol',
short_description: str = 'strand_pair_nupack',
parallel: bool = False,
pairs: Optional[Iterable[Tuple[Strand, Strand]]] = None,
format_description: bool = True
) -> StrandPairConstraint:
"""
Returns constraint that checks given pairs of :any:`Strand`'s for excessive interaction using
Expand Down Expand Up @@ -4751,8 +4801,23 @@ def nupack_strand_pairs_constraint(
"""
_check_nupack_installed()

if description is None:
description = f'NUPACK binding energy of strand pair exceeds {threshold} kcal/mol'
if format_description:
try:
description = description.format(threshold=threshold,
temperature=temperature,
sodium=sodium,
magnesium=magnesium,
weight=weight,
parallel=parallel,
short_description=short_description,
pairs=pairs)
except KeyError as e:
print(f"In parsing the description, I couldn't find key {e}; if you didn't intend to use formatting in" +
" your description, set the parameter format_description to False, or avoid using curly braces {}" +
" in your description.")
except ValueError as e:
print(f'I tried parsing the description and it failed; to avoid this warning, please set the parameter format_description to False, or avoid using curly braces {{}} in your description. (ValueError: {e}.)')


def evaluate(seqs: Tuple[str, ...], _: Optional[StrandPair]) -> Tuple[float, str]:
seq1, seq2 = seqs
Expand Down Expand Up @@ -4857,10 +4922,11 @@ def rna_duplex_domain_pairs_constraint(
temperature: float = dv.default_temperature,
weight: float = 1.0,
score_transfer_function: Callable[[float], float] = lambda x: x,
description: Optional[str] = None,
description: str = 'RNAduplex energy for some domain pairs exceeds {threshold} kcal/mol',
short_description: str = 'rna_dup_dom_pairs',
pairs: Optional[Iterable[Tuple[Domain, Domain]]] = None,
parameters_filename: str = dv.default_vienna_rna_parameter_filename) \
parameters_filename: str = dv.default_vienna_rna_parameter_filename,
format_description: bool = True) \
-> DomainPairsConstraint:
"""
Returns constraint that checks given pairs of :any:`Domain`'s for excessive interaction using
Expand Down Expand Up @@ -4888,8 +4954,23 @@ def rna_duplex_domain_pairs_constraint(
"""
_check_vienna_rna_installed()

if description is None:
description = f'RNAduplex energy for some domain pairs exceeds {threshold} kcal/mol'
if format_description:
try:
description = description.format(
threshold=threshold,
temperature=temperature,
weight=weight,
short_description=short_description,
pairs=pairs,
parameters_filename=parameters_filename
)
except KeyError as e:
print(f"In parsing the description, I couldn't find key {e}; if you didn't intend to use formatting in" +
" your description, set the parameter format_description to False, or avoid using curly braces {}" +
" in your description.")
except ValueError as e:
print(f'I tried parsing the description and it failed; to avoid this warning, please set the parameter format_description to False, or avoid using curly braces {{}} in your description. (ValueError: {e}.)')


def evaluate_bulk(domain_pairs: Iterable[DomainPair]) -> List[Tuple[DomainPair, float, str]]:
sequence_pairs, _, _ = _all_pairs_domain_sequences_complements_names_from_domains(domain_pairs)
Expand Down Expand Up @@ -5148,7 +5229,8 @@ def rna_duplex_strand_pairs_constraints_by_number_matching_domains(
parallel: bool = False,
strands: Optional[Iterable[Strand]] = None,
pairs: Optional[Iterable[Tuple[Strand, Strand]]] = None,
parameters_filename: str = dv.default_vienna_rna_parameter_filename) \
parameters_filename: str = dv.default_vienna_rna_parameter_filename,
format_descriptions: bool = True) \
-> List[StrandPairsConstraint]:
"""
Convenience function for creating many constraints as returned by
Expand Down Expand Up @@ -5198,6 +5280,7 @@ def rna_duplex_strand_pairs_constraints_by_number_matching_domains(
strands=strands,
pairs=pairs,
parameters_filename=parameters_filename,
format_descriptions=format_descriptions
)


Expand All @@ -5206,11 +5289,12 @@ def rna_duplex_strand_pairs_constraint(
temperature: float = dv.default_temperature,
weight: float = 1.0,
score_transfer_function: Callable[[float], float] = default_score_transfer_function,
description: Optional[str] = None,
description: str = 'RNAduplex energy for some strand pairs exceeds {threshold} kcal/mol',
short_description: str = 'rna_dup_strand_pairs',
parallel: bool = False,
pairs: Optional[Iterable[Tuple[Strand, Strand]]] = None,
parameters_filename: str = dv.default_vienna_rna_parameter_filename) \
parameters_filename: str = dv.default_vienna_rna_parameter_filename,
format_description: bool = True) \
-> StrandPairsConstraint:
"""
Returns constraint that checks given pairs of :any:`Strand`'s for excessive interaction using
Expand Down Expand Up @@ -5241,14 +5325,32 @@ def rna_duplex_strand_pairs_constraint(
:param parameters_filename:
Name of parameters file for ViennaRNA;
default is same as :py:meth:`vienna_nupack.rna_duplex_multiple`
:param format_description:
Whether to format the description with {} string formatting; if True constraint
parameters other than score_transfer_function and format_description can be included
in the description by adding them between {}, eg, "{threshold}".
:return:
The :any:`StrandPairsConstraint`.
"""
_check_vienna_rna_installed()

if description is None:
description = f'RNAduplex energy for some strand pairs exceeds ' \
f'{threshold} kcal/mol at {temperature} C'
if format_description:
try:
description = description.format(
threshold=threshold,
temperature=temperature,
weight=weight,
short_description=short_description,
parallel=parallel,
pairs=pairs,
parameters_filename=parameters_filename
)
except KeyError as e:
print(f"In parsing the description, I couldn't find key {e}; if you didn't intend to use formatting in" +
" your description, set the parameter format_description to False, or avoid using curly braces {}" +
" in your description.")
except ValueError as e:
print(f'I tried parsing the description and it failed; to avoid this warning, please set the parameter format_description to False, or avoid using curly braces {{}} in your description. (ValueError: {e}.)')

num_threads = max(cpu_count() - 1, 1) # this seems to be slightly faster than using all cores

Expand Down Expand Up @@ -5314,7 +5416,7 @@ def rna_cofold_strand_pairs_constraint(
temperature: float = dv.default_temperature,
weight: float = 1.0,
score_transfer_function: Callable[[float], float] = default_score_transfer_function,
description: Optional[str] = None,
description: str = 'RNAcofold energy for some strand pairs exceeds {threshold} kcal/mol',
short_description: str = 'rna_dup_strand_pairs',
parallel: bool = False,
pairs: Optional[Iterable[Tuple[Strand, Strand]]] = None,
Expand Down Expand Up @@ -5348,8 +5450,16 @@ def rna_cofold_strand_pairs_constraint(
"""
_check_vienna_rna_installed()

if description is None:
description = f'RNAcofold energy for some strand pairs exceeds {threshold} kcal/mol'
description = description.format(
threshold=threshold,
temperature=temperature,
weight=weight,
description=description,
short_description=short_description,
parallel=parallel,
pairs=pairs,
parameters_filename=parameters_filename
)

num_threads = max(cpu_count() - 1, 1) # this seems to be slightly faster than using all cores

Expand Down