Merge pull request #243 from UC-Davis-molecular-computing/dev

Dev

examples/nonorthogonal_domains.py

@@ -0,0 +1,126 @@
+from __future__ import annotations
+
+import itertools
+from typing import NamedTuple
+import argparse
+import os
+import logging
+
+import nuad.constraints as nc  # type: ignore
+import nuad.vienna_nupack as nv  # type: ignore
+import nuad.search as ns  # type: ignore
+
+
+def main() -> None:
+    args: CLArgs = parse_command_line_arguments()
+
+    # dc.logger.setLevel(logging.DEBUG)
+    nc.logger.setLevel(logging.INFO)
+
+    random_seed = 1
+
+    domain_length = 20
+
+    # many 1-domain strands with no common domains, every domain length = 20
+
+    # num_strands = 3
+    # num_strands = 5
+    num_strands = 10
+    # num_strands = 11
+    # num_strands = 50
+    # num_strands = 100
+    # num_strands = 355
+
+    design = nc.Design()
+    #                         di
+    # strand i is    [------------------>
+    for i in range(num_strands):
+        design.add_strand([f'd{i}'])
+
+    some_fixed = False
+    # some_fixed = True
+    if some_fixed:
+        # fix domain of strand 0
+        for domain in design.strands[0].domains:
+            domain.set_fixed_sequence('A' * domain_length)
+
+    domain_pool_20 = nc.DomainPool(f'length-20_domains', domain_length)
+
+    for i, strand in enumerate(design.strands):
+        if some_fixed and i == 0:
+            continue
+        for domain in strand.domains:
+            domain.pool = domain_pool_20
+
+    min_energy = -domain_length / 4
+    max_distance = num_strands
+
+    epsilon = 1.0
+    thresholds = {}
+    # for d1, d2 in itertools.combinations_with_replacement(design.domains, 2):
+    for d1, d2 in itertools.combinations(design.domains, 2):
+        if d1.name > d2.name:
+            d1, d2 = d2, d1
+        name1 = d1.name
+        name2 = d2.name
+        idx1 = int(name1[1:])
+        idx2 = int(name2[1:])
+        target_distance = abs(idx1 - idx2) if idx1 != idx2 else -min_energy + 4
+        target_energy = (target_distance / max_distance) * min_energy
+        energy_low = target_energy - epsilon
+        energy_high = target_energy
+        thresholds[(d1, d2)] = (energy_low, energy_high)
+
+    domain_nupack_pair_nonorth_constraint = nc.nupack_domain_pairs_nonorthogonal_constraint(
+        thresholds=thresholds, temperature=37, short_description='dom pairs nonorth nupack')
+
+    domain_rna_plex_pair_nonorth_constraint = nc.rna_plex_domain_pairs_nonorthogonal_constraint(
+        thresholds=thresholds, temperature=37, short_description='dom pairs nonorth plex')
+
+    params = ns.SearchParameters(constraints=[
+        domain_nupack_pair_nonorth_constraint,
+        # domain_rna_plex_pair_nonorth_constraint,
+    ],
+        out_directory=args.directory,
+        restart=args.restart,
+        random_seed=random_seed,
+        max_iterations=None,
+        # save_sequences_for_all_updates=True,
+        save_report_for_all_updates=True,
+        # save_design_for_all_updates=True,
+        force_overwrite=True,
+        # log_time=True,
+        scrolling_output=False,
+    )
+    ns.search_for_sequences(design, params)
+
+
+# command-line arguments
+class CLArgs(NamedTuple):
+    directory: str
+    restart: bool
+
+
+def parse_command_line_arguments() -> CLArgs:
+    default_directory = os.path.join('output', ns.script_name_no_ext())
+
+    parser = argparse.ArgumentParser(  # noqa
+        description='Small example using nonorthogonal domains.',
+        formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+    parser.add_argument('-o', '--output-dir', type=str, default=default_directory,
+                        help='directory in which to place output files')
+    parser.add_argument('-r', '--restart', action='store_true',
+                        help='If true, then assumes output directory contains output of search that was '
+                             'cancelled, to restart '
+                             'from. Similar to -i option, but will automatically find the most recent design '
+                             '(assuming they are numbered with a number such as -84), and will start the '
+                             'numbering from there (i.e., the next files to be written upon improving the '
+                             'design will have -85).')
+
+    args = parser.parse_args()
+
+    return CLArgs(directory=args.output_dir, restart=args.restart)
+
+
+if __name__ == '__main__':
+    main()

nuad/__version__.py

@@ -1 +1 @@
-version = '0.4.4'  # version line; WARNING: do not remove or change this line or comment
+version = '0.4.5'  # version line; WARNING: do not remove or change this line or comment