{% if 'expected_end' in status %}
The optimization is in progress.
This report is updated every {{ args.report_interval }}
minute{{ args.report_interval | pluralize('', 's') }}.
- Estimated completion time: {{ status['expected_end'] | localtime }}
- Current Speed: {{ "%.2f"|format(status['speed']) }} s/it
{% endif %}
Task information
- Sequence name: {{ seq.description | e }}
- Sequence length: {{ seq.seq | length }} nt
- Mutation space: {{ metainfo['mutation_space']['singles'] }} types
of mutations, {{ metainfo['mutation_space']['total'] | format_power_html }}
combinations
- Started: {{ status['time'][0] | localtime }}
- Finished: {{ status['time'][-1] | localtime }}
- Command line: {{ exec.command_line }}
{% if 'expected_end' in status -%}
Current Best Sequence
{%- else -%}
Optimized Sequence
{%- endif %}
Sequence optimality metrics
{% set metrics = checkpoints.filter(regex='^metric:').columns %}
| Metric |
Initial |
Optimized |
Metric |
Initial |
Optimized |
{% for names in metrics|batch(2, '') %}
{%- for name in names %}
| {{ name.replace('metric:', '') }} |
{{ checkpoints.iloc[0][name] | format_number }} |
{{ checkpoints.iloc[-1][name] | format_number }} |
{%- endfor %}
{% endfor %}
Local sequence metrics
{{ plotters.sequence_evaluation_curves() }}
Predicted secondary structure
- MFE: {{ status['evaluations']['optimized']['mfe'] | format_number }} kcal/mol
- Total loop length (≥{{ scoring['loop']['threshold'] }}):
{{ status['evaluations']['optimized']['loop'] }}
{% if exec['n_iterations'] > 0 %}
Optimization Process
{{ plotters.fitness_curve() }}
{{ plotters.metric_curves() }}
Parameters
Program Options
| Random seed |
{{ exec.seed }} |
Processes |
{{ exec.processes }} |
Initialization |
{% if exec.lineardesign_lambda is not none -%}
LinearDesign (λ = {{ exec.lineardesign_lambda }})
{%- elif exec.random_initialization or exec.protein -%}
random
{%- else -%}
as-is
{%- endif -%}
|
| Conservative start |
{%- if exec.conservative_start is none -%}
off
{%- else -%}
{{ exec.conservative_start }}
{%- endif -%}
| Species |
{{ exec.species }} |
Codon table |
{{ exec.codon_table }} |
{% endif %}
Optimization
| Iterations |
{{ exec.n_iterations }} |
Population size |
{{ exec.n_population }} |
Survivors |
{{ exec.n_survivors}} |
| Initial mutation rate |
{{ exec.initial_mutation_rate }} |
Wind-down trigger |
{{ exec.winddown_trigger }} |
Wind-down rate |
{{ exec.winddown_rate }} |
Fitness Scoring
{% for name, opts in scoring.items() %}
{% set fun = scorefuncs[name] %}
{{ fun.description | e }}
{% set optlen = opts|length %}
{% set bwidth = [optlen, 3]|min %}
{% for items in opts.items()|batch(bwidth, ('-', '-')) %}
{%- for key, val in items %}
| {{ key | replace('_', ' ') }} |
{{ val }} |
{%- endfor %}
{% endfor %}
{% endfor %}