Merge pull request #161 from UC-Davis-molecular-computing/dev

Dev
UC-Davis-molecular-computing · Jan 14, 2021 · e0cd9c8 · e0cd9c8
2 parents 434ccc4 + cfb2ffd
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diff --git a/README.md b/README.md
@@ -39,6 +39,14 @@ Please report issues in the web interface at the [scadnano web interface GitHub
 
 ## Installation
 
+Short version: type this at the command line:
+
+```console
+pip install scadnano
+```
+
+Read below for troubleshooting suggestions if that didn't work.
+
 ### Getting Python
 The scadnano Python package requires Python version 3.7 or later (with a workaround available for version 3.6, but not for any lower version). 
 
@@ -73,6 +81,17 @@ Once Python is installed (and the dataclasses backport if you have Python versio
     pip install scadnano
     ```
 
+    If it worked, you should be able to open a Python interpreter and import the scadnano module:
+
+    ```console
+    Python 3.7.9 (default, Aug 31 2020, 17:10:11) [MSC v.1916 64 bit (AMD64)] :: Anaconda, Inc. on win32
+    Type "help", "copyright", "credits" or "license" for more information.
+    >>> import scadnano as sc
+    >>> print(sc.Domain(helix=1, forward=True, start=0, end=8))
+    Domain(, helix=1, forward=True, start=0, end=8)
+    >>>
+    ```
+
     ### Troubleshooting
     If the above does not work for you, here are some things to try.
 
@@ -193,7 +212,7 @@ def create_design():
     helices = [sc.Helix(max_offset=48), sc.Helix(max_offset=48)]
 
     # whole design
-    design = sc.Design(helices=helices, strands=[], grid=sc.square)
+    design = sc.Design(helices=helices, grid=sc.square)
 
     # for absolute offsets, call method "to"
     # left staple

diff --git a/examples/16_helix_origami_barrel_from_algoSST_paper.py b/examples/16_helix_origami_barrel_from_algoSST_paper.py
@@ -107,12 +107,11 @@ def add_adapters(design: sc.Design) -> None:
     for bot_helix in range(2, 18, 2):
         top_helix = bot_helix - 1 if bot_helix != 2 else 17
         dom_top = sc.Domain(helix=top_helix, forward=True,
-                           start=left_outside_seed, end=left_inside_seed)
+                            start=left_outside_seed, end=left_inside_seed)
         dom_bot = sc.Domain(helix=bot_helix, forward=False,
-                           start=left_outside_seed, end=left_inside_seed)
-        idt = sc.IDTFields(name=f'adap-left-{top_helix}-{bot_helix}',
-                           scale='25nm', purification='STD')
-        adapter = sc.Strand(domains=[dom_bot, dom_top], idt=idt)
+                            start=left_outside_seed, end=left_inside_seed)
+        idt = sc.IDTFields(scale='25nm', purification='STD')
+        adapter = sc.Strand(domains=[dom_bot, dom_top], name=f'adap-left-{top_helix}-{bot_helix}', idt=idt)
         design.add_strand(adapter)
 
     # right adapters
@@ -121,12 +120,11 @@ def add_adapters(design: sc.Design) -> None:
     for bot_helix in range(2, 18, 2):
         top_helix = bot_helix - 1 if bot_helix != 2 else 17
         dom_top = sc.Domain(helix=top_helix, forward=True,
-                           start=right_inside_seed, end=right_outside_seed)
+                            start=right_inside_seed, end=right_outside_seed)
         dom_bot = sc.Domain(helix=bot_helix, forward=False,
-                           start=right_inside_seed, end=right_outside_seed)
-        idt = sc.IDTFields(name=f'adap-right-{top_helix}-{bot_helix}',
-                           scale='25nm', purification='STD')
-        adapter = sc.Strand(domains=[dom_top, dom_bot], idt=idt)
+                            start=right_inside_seed, end=right_outside_seed)
+        idt = sc.IDTFields(scale='25nm', purification='STD')
+        adapter = sc.Strand(domains=[dom_top, dom_bot], name=f'adap-right-{top_helix}-{bot_helix}', idt=idt)
         design.add_strand(adapter)
 
 
@@ -163,9 +161,9 @@ def add_tiles_and_assign_dna(design: sc.Design) -> None:
                            start=left_left, end=left_right)
         ss_bot = sc.Domain(helix=bot_helix, forward=False,
                            start=left_left, end=left_right)
-        idt = sc.IDTFields(name=f'tile-left-{top_helix}-{bot_helix}',
-                           scale='25nm', purification='STD')
-        tile = sc.Strand(domains=[ss_bot, ss_top], color=sc.Color(0, 0, 0), idt=idt)
+        idt = sc.IDTFields(scale='25nm', purification='STD')
+        tile = sc.Strand(domains=[ss_bot, ss_top], name=f'tile-left-{top_helix}-{bot_helix}',
+                         color=sc.Color(0, 0, 0), idt=idt)
         design.add_strand(tile)
         design.assign_dna(tile, seq)
 
@@ -178,9 +176,9 @@ def add_tiles_and_assign_dna(design: sc.Design) -> None:
                            start=right_left, end=right_right)
         ss_bot = sc.Domain(helix=bot_helix, forward=False,
                            start=right_left, end=right_right)
-        idt = sc.IDTFields(name=f'tile-right-{top_helix}-{bot_helix}',
-                           scale='25nm', purification='STD')
-        tile = sc.Strand(domains=[ss_bot, ss_top], color=sc.Color(0, 0, 0), idt=idt)
+        idt = sc.IDTFields(scale='25nm', purification='STD')
+        tile = sc.Strand(domains=[ss_bot, ss_top], name=f'tile-right-{top_helix}-{bot_helix}',
+                         color=sc.Color(0, 0, 0), idt=idt)
         design.add_strand(tile)
         design.assign_dna(tile, seq)
 

diff --git a/examples/16_helix_origami_rectangle_seed_tiles_grow_from_top.py b/examples/16_helix_origami_rectangle_seed_tiles_grow_from_top.py
@@ -73,9 +73,8 @@ def add_adapters(design: sc.Design) -> None:
                            start=left_outside_seed, end=left_inside_seed)
         ss_bot = sc.Domain(helix=bot_helix, forward=False,
                            start=left_outside_seed, end=left_inside_seed)
-        idt = sc.IDTFields(name=f'adap-left-{top_helix}-{bot_helix}',
-                           scale='25nm', purification='STD')
-        adapter = sc.Strand(domains=[ss_bot, ss_top], idt=idt)
+        idt = sc.IDTFields(scale='25nm', purification='STD')
+        adapter = sc.Strand(domains=[ss_bot, ss_top], name=f'adap-left-{top_helix}-{bot_helix}', idt=idt)
         design.add_strand(adapter)
 
     # right adapters
@@ -87,9 +86,8 @@ def add_adapters(design: sc.Design) -> None:
                            start=right_inside_seed, end=right_outside_seed)
         ss_bot = sc.Domain(helix=bot_helix, forward=False,
                            start=right_inside_seed, end=right_outside_seed)
-        idt = sc.IDTFields(name=f'adap-right-{top_helix}-{bot_helix}',
-                           scale='25nm', purification='STD')
-        adapter = sc.Strand(domains=[ss_top, ss_bot], idt=idt)
+        idt = sc.IDTFields(scale='25nm', purification='STD')
+        adapter = sc.Strand(domains=[ss_top, ss_bot], name=f'adap-right-{top_helix}-{bot_helix}', idt=idt)
         design.add_strand(adapter)
 
 

diff --git a/examples/1_staple_1_helix_origami_idt_duplicate_names.py b/examples/1_staple_1_helix_origami_idt_duplicate_names.py
@@ -6,10 +6,10 @@ def create_design() -> sc.Design:
     ss3_r = sc.Domain(0, True, 8, 12)
     ss_l = sc.Domain(0, False, 0, 12)
 
-    s1_r = sc.Strand([ss1_r], idt=sc.IDTFields('s1_r'))
-    s2_r = sc.Strand([ss2_r], idt=sc.IDTFields('s1_r'))
-    s3_r = sc.Strand([ss3_r], idt=sc.IDTFields('s1_r'))
-    s_l = sc.Strand([ss_l], idt=sc.IDTFields('s_l'))
+    s1_r = sc.Strand([ss1_r], idt=sc.IDTFields(), name='s1_r')
+    s2_r = sc.Strand([ss2_r], idt=sc.IDTFields(), name='s1_r')
+    s3_r = sc.Strand([ss3_r], idt=sc.IDTFields(), name='s1_r')
+    s_l = sc.Strand([ss_l], idt=sc.IDTFields(), name='s_l')
 
     strands = [s1_r, s2_r, s3_r, s_l]
 

diff --git a/examples/idt-plates-explicit.py b/examples/idt-plates-explicit.py
@@ -18,9 +18,9 @@ def create_design() -> sc.Design:
         row = ROWS[row_idx]
         col = COLS[col_idx]
         well = f'{row}{col}'
-        idt = sc.IDTFields(name=f"staple{s}", plate=f'plate{plate}', well=well)
+        idt = sc.IDTFields(plate=f'plate{plate}', well=well)
 
-        strand = sc.Strand(domains=[ss_f, ss_r], idt=idt)
+        strand = sc.Strand(domains=[ss_f, ss_r], idt=idt, name=f'staple{s}')
         strands.append(strand)
         row_idx += 1
         if row_idx == len(ROWS):