Merge pull request #105 from UC-Davis-molecular-computing/dev

Dev

CODEOWNERS

@@ -0,0 +1 @@
+* @dave-doty

README.md

@@ -10,7 +10,7 @@ If you find scadnano useful in a scientific project, please cite its associated
 
 > <ins>scadnano: A browser-based, scriptable tool for designing DNA nanostructures</ins>.  
   David Doty, Benjamin L Lee, and Tristan Stérin.  
-  DNA 2020: *Proceedings of the 26th International Conference on DNA Computing and Molecular Programming*
+  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) ]
 
 
@@ -58,13 +58,12 @@ 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):
+    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...)
 
-    * *required*: [scadnano.py](https://raw.githubusercontent.com/UC-Davis-molecular-computing/scadnano-python-package/master/scadnano/scadnano.py) 
-    * *optional*: [modifications.py](https://raw.githubusercontent.com/UC-Davis-molecular-computing/scadnano-python-package/master/scadnano/modifications.py); This contains some common DNA modifications such as biotin and Cy3. 
-    * *optional*: [origami_rectangle.py](https://raw.githubusercontent.com/UC-Davis-molecular-computing/scadnano-python-package/master/scadnano/origami_rectangle.py); This can help create origami rectangles, but it is not necessary to use scadnano.
-    * *optional*: [_version.py](https://raw.githubusercontent.com/UC-Davis-molecular-computing/scadnano-python-package/master/scadnano/_version.py) This ensures that the current version number is written into any `.dna` files written by the library; otherwise it may be out of date. (Which should not matter for the most part.)
+    * *required*: [scadnano.py](scadnano/scadnano.py) 
+    * *optional*: [modifications.py](scadnano/modifications.py); This contains some common DNA modifications such as biotin and Cy3. 
+    * *optional*: [origami_rectangle.py](scadnano/origami_rectangle.py); This can help create origami rectangles, but it is not necessary to use scadnano.
+    * *optional*: [_version.py](scadnano/_version.py) This ensures that the current version number is written into any `.dna` files written by the library; otherwise it may be out of date. (Which should not matter for the most part.)
     
     The scadnano package uses the Python package [xlwt](https://pypi.org/project/xlwt/) to write Excel files, so in order to call the method [`DNADesign.write_idt_plate_excel_file()`](https://scadnano-python-package.readthedocs.io/#scadnano.DNADesign.write_idt_plate_excel_file) to export an Excel file with DNA sequences, xlwt must be installed. To install, type `pip install xlwt` at the command line.
 
@@ -161,7 +160,7 @@ def main():
     design.add_insertion(helix=0, offset=26, length=2)
 
     # also assigns complement to strands other than scaf bound to it
-    design.assign_dna(scaf, 'AACGT' * 18)
+    design.assign_dna(design.scaffold, 'AACGT' * 18)
 
     return design
 

examples/very_large_origami.py

@@ -0,0 +1,15 @@
+import origami_rectangle as rect
+import scadnano as sc
+
+
+def main():
+    # this is a very large origami (taking ~25,000 bases). It is useful for testing the performance of
+    # rendering code, since at the time it was created, it is very janky to update, particularly for
+    # things that edit strands such as adding a strand or adding a nick in a strand
+    design = rect.create(num_helices=40, num_cols=40)
+    return design
+
+
+if not sc.in_browser() and __name__ == '__main__':
+    design = main()
+    design.write_scadnano_file(directory='output_designs')

scadnano/origami_rectangle.py

@@ -216,6 +216,8 @@ def create(*, num_helices: int, num_cols: int, assign_seq: bool = True, seam_lef
               f'greater than the 7249 available in standard M13.')
     if seam_left_column < 0:
         seam_left_column = num_cols // 2 - 1
+        if seam_left_column % 2 == 1:
+            seam_left_column += 1
     if seam_left_column % 2 == 1:
         raise ValueError(f'seam_left_column must be even but is {seam_left_column}')
 

scadnano/scadnano.py

@@ -2741,7 +2741,7 @@ class Geometry(_JSONSerializable):
     """Parameters controlling some geometric visualization/physical aspects of Design."""
 
     rise_per_base_pair: float = 0.332
-    """The distance in nanometers between two adjacent base pairs along the length of a DNA double helix."""
+    """Distance in nanometers between two adjacent base pairs along the length of a DNA double helix."""
 
     helix_radius: float = 1.0
     """Radius of a DNA helix in nanometers."""