Merge pull request #112 from UC-Davis-molecular-computing/dev

Dev
UC-Davis-molecular-computing · Jul 11, 2020 · 87997c0 · 87997c0
2 parents 7b1161b + 054a8bf
commit 87997c0
Show file tree

Hide file tree

Showing 61 changed files with 1,802 additions and 139 deletions.
diff --git a/.gitignore b/.gitignore
@@ -22,3 +22,4 @@ __pycache__/
 tests_outputs/
 .vscode/
 dist/
+.mypy_cache/
diff --git a/README.md b/README.md
@@ -8,7 +8,7 @@ The scadnano Python module is a library for describing synthetic DNA nanostructu
 
 If you find scadnano useful in a scientific project, please cite its associated paper:
 
-> <ins>scadnano: A browser-based, scriptable tool for designing DNA nanostructures</ins>.  
+> scadnano: A browser-based, scriptable tool for designing DNA nanostructures.  
   David Doty, Benjamin L Lee, and Tristan Stérin.  
   DNA 2020: *Proceedings of the 26th International Conference on DNA Computing and Molecular Programming*  
   [ [paper](https://arxiv.org/abs/2005.11841) | [BibTeX](https://web.cs.ucdavis.edu/~doty/papers/scadnano.bib) ]
@@ -37,9 +37,17 @@ Please report issues in the web interface at the [scadnano web interface GitHub
 
 ## Installation
 
-The scadnano Python package requires Python version 3.7 or later. If you do not have that version (or later) of Python installed, follow [this link](https://www.python.org/downloads/) to install it.
+The scadnano Python package requires Python version 3.7 or later. If you do not have that version (or later) of Python installed, follow [this link](https://www.python.org/downloads/) to install it. 
 
-Once Python is installed, there are two ways you can install the scadnano Python package:
+If you are using Python 3.6 and do not wish to upgrade, with some effort you can install a package that give the required features.
+The Python 3.7 module that is not present in 3.6 is the 
+[dataclasses](https://docs.python.org/3/library/dataclasses.html) module.
+You can install a backported library for it: 
+[dataclasses backport](https://pypi.org/project/dataclasses/) (this library appears to require at least Python version 3.6)
+
+Furthermore, the [typing](https://docs.python.org/3/library/typing.html) module was present in Python 3.5, but scadnano requires at least version Python 3.6.2.
+
+Once Python is installed (and the dataclasses backport if you have Python version 3.6), there are two ways you can install the scadnano Python package:
 
 
 1. pip (recommended)
@@ -58,7 +66,9 @@ Once Python is installed, there are two ways you can install the scadnano Python
 
 2. download
 
-    As a simple alternative (in case you run into trouble using pip), you can download and place the following files (located in the [scadnano/](https://github.com/UC-Davis-molecular-computing/scadnano-python-package/tree/master/scadnano) subfolder) in your PYTHONPATH (e.g., in the same directory as the scripts you are running). To download them, right-click on "Raw" near the top and select (in Chrome or Firefox) "Save link as...)
+    *Note:* If you are reading this on the PyPI website, the links below won't work. They are relative links intended to be read on the [GitHub README page](https://github.com/UC-Davis-molecular-computing/scadnano-python-package#readme).
+
+    As a simple alternative (in case you run into trouble using pip), you can download and place the following files (located in the [scadnano/](scadnano) subfolder) in your PYTHONPATH (e.g., in the same directory as the scripts you are running). To download them, right-click on "Raw" near the top and select (in Chrome or Firefox) "Save link as...". 
 
     * *required*: [scadnano.py](scadnano/scadnano.py) 
     * *optional*: [modifications.py](scadnano/modifications.py); This contains some common DNA modifications such as biotin and Cy3. 

diff --git a/examples/2_staple_2_helix_origami_deletions_insertions_new_geometry.py b/examples/2_staple_2_helix_origami_deletions_insertions_new_geometry.py
@@ -23,7 +23,7 @@ def main():
     scaf = sc.Strand(domains=[scaf_ss1_left, scaf_ss0, loopout, scaf_ss1_right], is_scaffold=True)
 
     # geometry
-    geometry = sc.Geometry(z_step=0.2, helix_radius=1.2, inter_helix_gap=1.0)
+    geometry = sc.Geometry(rise_per_base_pair=0.2, helix_radius=1.2, inter_helix_gap=1.0)
 
     # whole design
     design = sc.DNADesign(helices=helices, strands=[scaf, stap_left, stap_right], grid=sc.square,

diff --git a/examples/output_designs/16_helix_origami_barrel_from_algoSST_paper.dna b/examples/output_designs/16_helix_origami_barrel_from_algoSST_paper.dna
@@ -1,5 +1,5 @@
 {
-  "version": "0.9.1",
+  "version": "0.9.9",
   "grid": "square",
   "helices": [
     {

diff --git a/examples/output_designs/16_helix_origami_rectangle.dna b/examples/output_designs/16_helix_origami_rectangle.dna
@@ -1,5 +1,5 @@
 {
-  "version": "0.9.1",
+  "version": "0.9.9",
   "grid": "square",
   "helices": [
     {"max_offset": 448, "grid_position": [0, 0]},

diff --git a/examples/output_designs/16_helix_origami_rectangle_idt.dna b/examples/output_designs/16_helix_origami_rectangle_idt.dna
@@ -1,5 +1,5 @@
 {
-  "version": "0.9.1",
+  "version": "0.9.9",
   "grid": "square",
   "helices": [
     {"max_offset": 448, "grid_position": [0, 0]},

diff --git a/examples/output_designs/16_helix_origami_rectangle_no_seq.dna b/examples/output_designs/16_helix_origami_rectangle_no_seq.dna
@@ -1,5 +1,5 @@
 {
-  "version": "0.9.1",
+  "version": "0.9.9",
   "grid": "square",
   "helices": [
     {"max_offset": 448, "grid_position": [0, 0]},

diff --git a/examples/output_designs/16_helix_origami_rectangle_no_seq_no_twist.dna b/examples/output_designs/16_helix_origami_rectangle_no_seq_no_twist.dna
@@ -1,5 +1,5 @@
 {
-  "version": "0.9.1",
+  "version": "0.9.9",
   "grid": "square",
   "helices": [
     {"max_offset": 448, "grid_position": [0, 0]},

diff --git a/examples/output_designs/16_helix_origami_rectangle_no_twist.dna b/examples/output_designs/16_helix_origami_rectangle_no_twist.dna
@@ -1,5 +1,5 @@
 {
-  "version": "0.9.1",
+  "version": "0.9.9",
   "grid": "square",
   "helices": [
     {"max_offset": 448, "grid_position": [0, 0]},

diff --git a/examples/output_designs/16_helix_origami_rectangle_seed_tiles_grow_from_top.dna b/examples/output_designs/16_helix_origami_rectangle_seed_tiles_grow_from_top.dna
@@ -1,5 +1,5 @@
 {
-  "version": "0.9.1",
+  "version": "0.9.9",
   "grid": "square",
   "helices": [
     {

diff --git a/examples/output_designs/16_helix_origami_rectangle_shifted_seam_no_seq.dna b/examples/output_designs/16_helix_origami_rectangle_shifted_seam_no_seq.dna
@@ -1,5 +1,5 @@
 {
-  "version": "0.9.1",
+  "version": "0.9.9",
   "grid": "square",
   "helices": [
     {"max_offset": 448, "grid_position": [0, 0]},

diff --git a/examples/output_designs/1_staple_1_helix_origami.dna b/examples/output_designs/1_staple_1_helix_origami.dna
@@ -1,5 +1,5 @@
 {
-  "version": "0.9.1",
+  "version": "0.9.9",
   "grid": "square",
   "helices": [
     {

diff --git a/examples/output_designs/1_staple_1_helix_origami_mismatches.dna b/examples/output_designs/1_staple_1_helix_origami_mismatches.dna
@@ -1,5 +1,5 @@
 {
-  "version": "0.9.1",
+  "version": "0.9.9",
   "grid": "square",
   "helices": [
     {"grid_position": [0, 0]}

diff --git a/examples/output_designs/1_staple_1_helix_origami_position_nondefault.dna b/examples/output_designs/1_staple_1_helix_origami_position_nondefault.dna
@@ -1,5 +1,5 @@
 {
-  "version": "0.9.1",
+  "version": "0.9.9",
   "grid": "square",
   "helices": [
     {

diff --git a/examples/output_designs/1_staple_1_helix_origami_roll.dna b/examples/output_designs/1_staple_1_helix_origami_roll.dna
@@ -1,5 +1,5 @@
 {
-  "version": "0.9.1",
+  "version": "0.9.9",
   "grid": "square",
   "helices": [
     {"grid_position": [0, 0], "roll": 90}

diff --git a/examples/output_designs/24_helix_origami_rectangle_twist_corrected.dna b/examples/output_designs/24_helix_origami_rectangle_twist_corrected.dna
@@ -1,5 +1,5 @@
 {
-  "version": "0.9.1",
+  "version": "0.9.9",
   "grid": "square",
   "helices": [
     {"max_offset": 304, "grid_position": [0, 0]},

diff --git a/examples/output_designs/2_helix_2_strands_multiple_substrands_no_seq.dna b/examples/output_designs/2_helix_2_strands_multiple_substrands_no_seq.dna
@@ -1,5 +1,5 @@
 {
-  "version": "0.9.1",
+  "version": "0.9.9",
   "grid": "square",
   "helices": [
     {"grid_position": [0, 0]},

diff --git a/examples/output_designs/2_staple_2_helix_modifications.dna b/examples/output_designs/2_staple_2_helix_modifications.dna
@@ -1,22 +1,28 @@
 {
-  "version": "0.9.1",
+  "version": "0.9.9",
   "grid": "square",
   "helices": [
     {"grid_position": [0, 0]},
     {"grid_position": [0, 1]}
   ],
   "modifications_in_design": {
-    "/5Cy5/": {
+    "/iCy5/": {
       "display_text": "Cy5",
-      "idt_text": "/5Cy5/",
+      "idt_text": "/iCy5/",
       "display_connector": false,
-      "location": "5'"
+      "location": "internal"
     },
-    "/3Bio/": {
+    "/5Biosg/": {
       "display_text": "B",
-      "idt_text": "/3Bio/",
+      "idt_text": "/5Biosg/",
       "display_connector": false,
-      "location": "3'"
+      "location": "5'"
+    },
+    "/5Cy5/": {
+      "display_text": "Cy5",
+      "idt_text": "/5Cy5/",
+      "display_connector": false,
+      "location": "5'"
     },
     "/iBiodT/": {
       "display_text": "B",
@@ -25,18 +31,6 @@
       "location": "internal",
       "allowed_bases": ["T"]
     },
-    "/iCy5/": {
-      "display_text": "Cy5",
-      "idt_text": "/iCy5/",
-      "display_connector": false,
-      "location": "internal"
-    },
-    "/5Biosg/": {
-      "display_text": "B",
-      "idt_text": "/5Biosg/",
-      "display_connector": false,
-      "location": "5'"
-    },
     "/iCy3/": {
       "display_text": "Cy3",
       "idt_text": "/iCy3/",
@@ -48,6 +42,12 @@
       "idt_text": "/3Cy3Sp/",
       "display_connector": false,
       "location": "3'"
+    },
+    "/3Bio/": {
+      "display_text": "B",
+      "idt_text": "/3Bio/",
+      "display_connector": false,
+      "location": "3'"
     }
   },
   "strands": [

diff --git a/examples/output_designs/2_staple_2_helix_origami_6bases_wide.dna b/examples/output_designs/2_staple_2_helix_origami_6bases_wide.dna
@@ -1,5 +1,5 @@
 {
-  "version": "0.9.1",
+  "version": "0.9.9",
   "grid": "square",
   "helices": [
     {"grid_position": [0, 0]},

diff --git a/examples/output_designs/2_staple_2_helix_origami_deletions.dna b/examples/output_designs/2_staple_2_helix_origami_deletions.dna
@@ -1,5 +1,5 @@
 {
-  "version": "0.9.1",
+  "version": "0.9.9",
   "grid": "square",
   "helices": [
     {"grid_position": [0, 0]},

diff --git a/examples/output_designs/2_staple_2_helix_origami_deletions_insertions.dna b/examples/output_designs/2_staple_2_helix_origami_deletions_insertions.dna
@@ -1,5 +1,5 @@
 {
-  "version": "0.9.1",
+  "version": "0.9.9",
   "grid": "square",
   "helices": [
     {"max_offset": 48, "grid_position": [0, 0]},

diff --git a/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_labels.dna b/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_labels.dna
@@ -1,5 +1,5 @@
 {
-  "version": "0.9.1",
+  "version": "0.9.9",
   "grid": "square",
   "helices": [
     {"max_offset": 48, "grid_position": [0, 0]},

diff --git a/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_mods.dna b/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_mods.dna
@@ -1,5 +1,5 @@
 {
-  "version": "0.9.1",
+  "version": "0.9.9",
   "grid": "square",
   "helices": [
     {"max_offset": 48, "grid_position": [0, 0]},

diff --git a/...les/output_designs/2_staple_2_helix_origami_deletions_insertions_mods_chained_methods.dna b/...les/output_designs/2_staple_2_helix_origami_deletions_insertions_mods_chained_methods.dna
@@ -1,5 +1,5 @@
 {
-  "version": "0.9.1",
+  "version": "0.9.9",
   "grid": "square",
   "helices": [
     {"max_offset": 48, "grid_position": [0, 0]},

diff --git a/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_new_geometry.dna b/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_new_geometry.dna
@@ -1,8 +1,8 @@
 {
-  "version": "0.9.1",
+  "version": "0.9.9",
   "grid": "square",
   "geometry": {
-    "z_step": 0.2,
+    "rise_per_base_pair": 0.2,
     "helix_radius": 1.2,
     "inter_helix_gap": 1.0
   },

diff --git a/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_no_seq.dna b/examples/output_designs/2_staple_2_helix_origami_deletions_insertions_no_seq.dna
@@ -1,5 +1,5 @@
 {
-  "version": "0.9.1",
+  "version": "0.9.9",
   "grid": "square",
   "helices": [
     {"grid_position": [0, 0]},

diff --git a/examples/output_designs/3_helix_deletions_insertions.dna b/examples/output_designs/3_helix_deletions_insertions.dna
@@ -1,5 +1,5 @@
 {
-  "version": "0.9.1",
+  "version": "0.9.9",
   "grid": "square",
   "helices": [
     {"max_offset": 64, "grid_position": [0, 0]},

diff --git a/examples/output_designs/4_helix_grid_none.dna b/examples/output_designs/4_helix_grid_none.dna
@@ -1,5 +1,5 @@
 {
-  "version": "0.9.1",
+  "version": "0.9.9",
   "grid": "none",
   "helices": [
     {

diff --git a/examples/output_designs/4_helix_grid_none_min_offset_position_x_nondefault.dna b/examples/output_designs/4_helix_grid_none_min_offset_position_x_nondefault.dna
@@ -1,5 +1,5 @@
 {
-  "version": "0.9.1",
+  "version": "0.9.9",
   "grid": "none",
   "helices": [
     {

diff --git a/examples/output_designs/4_helix_min_offsets_nonzero.dna b/examples/output_designs/4_helix_min_offsets_nonzero.dna
@@ -1,5 +1,5 @@
 {
-  "version": "0.9.1",
+  "version": "0.9.9",
   "grid": "square",
   "helices": [
     {"max_offset": 30, "grid_position": [0, 0]},

diff --git a/examples/output_designs/56_helix_origami_rectangle.dna b/examples/output_designs/56_helix_origami_rectangle.dna
@@ -1,5 +1,5 @@
 {
-  "version": "0.9.1",
+  "version": "0.9.9",
   "grid": "square",
   "helices": [
     {"max_offset": 160, "grid_position": [0, 0]},

diff --git a/examples/output_designs/64_helix_origami_rectangle.dna b/examples/output_designs/64_helix_origami_rectangle.dna
@@ -1,5 +1,5 @@
 {
-  "version": "0.9.1",
+  "version": "0.9.9",
   "grid": "square",
   "helices": [
     {"max_offset": 128, "grid_position": [0, 0]},

diff --git a/examples/output_designs/6_helix_6_col_origami_rectangle.dna b/examples/output_designs/6_helix_6_col_origami_rectangle.dna
@@ -1,5 +1,5 @@
 {
-  "version": "0.9.1",
+  "version": "0.9.9",
   "grid": "square",
   "helices": [
     {"grid_position": [0, 0]},

diff --git a/examples/output_designs/6_helix_bundle_honeycomb.dna b/examples/output_designs/6_helix_bundle_honeycomb.dna
@@ -1,5 +1,5 @@
 {
-  "version": "0.9.1",
+  "version": "0.9.9",
   "grid": "honeycomb",
   "helices": [
     {"max_offset": 1295, "grid_position": [1, 1, 0]},

diff --git a/examples/output_designs/6_helix_origami_rectangle.dna b/examples/output_designs/6_helix_origami_rectangle.dna
@@ -1,5 +1,5 @@
 {
-  "version": "0.9.1",
+  "version": "0.9.9",
   "grid": "square",
   "helices": [
     {"max_offset": 192, "grid_position": [0, 0]},

diff --git a/examples/output_designs/6_helix_origami_rectangle_helices_out_of_order.dna b/examples/output_designs/6_helix_origami_rectangle_helices_out_of_order.dna
@@ -1,5 +1,5 @@
 {
-  "version": "0.9.1",
+  "version": "0.9.9",
   "grid": "square",
   "helices": [
     {"max_offset": 192, "grid_position": [0, 0]},

diff --git a/examples/output_designs/add_deletions_to_24_helix_rectangle.dna b/examples/output_designs/add_deletions_to_24_helix_rectangle.dna
@@ -1,5 +1,5 @@
 {
-  "version": "0.9.1",
+  "version": "0.9.9",
   "grid": "e",
   "helices": [
     {"max_offset": 304, "grid_position": [0, -3]},

diff --git a/examples/output_designs/empty.dna b/examples/output_designs/empty.dna
@@ -1,5 +1,5 @@
 {
-  "version": "0.9.1",
+  "version": "0.9.9",
   "grid": "square",
   "helices": [],
   "strands": []

diff --git a/examples/output_designs/hairpin.dna b/examples/output_designs/hairpin.dna
@@ -1,5 +1,5 @@
 {
-  "version": "0.9.1",
+  "version": "0.9.9",
   "grid": "square",
   "helices": [
     {"grid_position": [0, 0]}

diff --git a/examples/output_designs/helices_out_of_order_nonconsecutive.dna b/examples/output_designs/helices_out_of_order_nonconsecutive.dna
@@ -1,5 +1,5 @@
 {
-  "version": "0.9.1",
+  "version": "0.9.9",
   "grid": "none",
   "helices": [
     {"max_offset": 20, "grid_position": [0, 2], "idx": 2},

diff --git a/examples/output_designs/hex_lattice_10x10.dna b/examples/output_designs/hex_lattice_10x10.dna
@@ -1,5 +1,5 @@
 {
-  "version": "0.9.1",
+  "version": "0.9.9",
   "grid": "hex",
   "helices": [
     {"max_offset": 16, "grid_position": [0, 0, 0]},

diff --git a/examples/output_designs/hex_lattice_10x10_with_negative.dna b/examples/output_designs/hex_lattice_10x10_with_negative.dna
@@ -1,5 +1,5 @@
 {
-  "version": "0.9.1",
+  "version": "0.9.9",
   "grid": "hex",
   "helices": [
     {"max_offset": 16, "grid_position": [-4, -4, 0]},

diff --git a/examples/output_designs/honeycomb_lattice_10x10.dna b/examples/output_designs/honeycomb_lattice_10x10.dna
@@ -1,5 +1,5 @@
 {
-  "version": "0.9.1",
+  "version": "0.9.9",
   "grid": "honeycomb",
   "helices": [
     {"max_offset": 16, "grid_position": [0, 0, 0]},