Merge pull request #21 from softnanolab/feature-translate

Feature translate

.github/workflows/coverage.yml

@@ -2,10 +2,7 @@
 
 name: Coverage
 
-on: 
-  push:
-    branches:
-      [master]
+on: push
 
 jobs:
   coverage:

drawNA/oxdna/nucleotide.py

@@ -3,8 +3,9 @@
 """
 import numpy as np
 import pandas as pd
+from scipy.spatial.transform import Rotation
 
-from typing import List
+from typing import List, Union
 import warnings
 
 from .utils import get_rotation_matrix
@@ -304,4 +305,62 @@ def make_across(self) -> "Nucleotide":
         self.across = nucleotide
         return nucleotide
 
+    def transform(self, matrix: np.ndarray):
 
+        vecs = [self.pos_com, self._a1, self._a3, self._v, self._L]
+
+        if matrix.shape == (3, 3):
+            for vec in vecs:
+                vec = np.dot(matrix, vec.T)
+
+
+        elif matrix.shape == (3, 4):
+            for vec in vecs:
+                vec = np.dot(matrix, np.hstack([vec, [1]]))
+
+        else:
+            raise TypeError(
+                f'Transformation Matrix must have shape (3, 3) '
+                f'or (3, 4) but has shape {matrix.shape}'
+            )
+
+        return
+
+    def translate(self, translation_vector: np.ndarray):
+
+        if isinstance(translation_vector, list):
+            translation_vector = np.array(translation_vector)
+
+        if not (translation_vector.shape == (1, 3) or 
+                translation_vector.shape == (3, )):
+                raise TypeError(
+                    f'Translation vector has the wrong shape '
+                    f'({translation_vector.shape})'
+                )
+        self.pos_com += translation_vector
+        return
+
+    def rotate(self, rotator: np.ndarray):
+
+        if isinstance(rotator, list):
+            rotator = np.array(rotator)
+
+        # if 1d array with length 3 -> euler angles
+        if rotator.shape == (1, 3) or rotator.shape == (3, ):
+            matrix = Rotation.from_euler('xyz', rotator).as_matrix()
+
+        # if 1d array with length 4 -> quaternion
+        elif rotator.shape == (1, 4) or rotator.shape == (4, ):
+            matrix = Rotation(rotator).as_matrix()
+
+        # if 2d array use transform
+        elif rotator.shape == (3, 3):
+            matrix = rotator
+
+        else:
+            raise TypeError(
+                f'Rotator was passed that is not valid:\n{rotator}'
+            )
+
+        self.transform(matrix)
+        return

drawNA/oxdna/strand.py

@@ -153,6 +153,21 @@ def sequence(self, seq: str):
     def copy(self):
         return deepcopy(Strand(self._nucleotides))
 
+    def transform(self, matrix: np.ndarray):
+        for nucleotide in self._nucleotides:
+            nucleotide.transform(matrix)
+        return
+
+    def translate(self, translation_vector: np.ndarray):
+        for nucleotide in self._nucleotides:
+            nucleotide.translate(translation_vector)
+        return
+
+    def rotate(self, rotator: np.ndarray):
+        for nucleotide in self._nucleotides:
+            nucleotide.rotate(rotator)
+        return
+
 
 def generate_helix(
     n: int = None,

drawNA/oxdna/system.py

@@ -265,3 +265,21 @@ def add_strands(self, strand_obj: (list or dict) = None, index: int = None):
             raise TypeError(
                 "add_strands() requires ONE of a list or dictionary of strands"
             )
+
+    def transform(self, matrix: np.ndarray):
+        for strand in self._strands:
+            for nucleotide in strand._nucleotides:
+                nucleotide.transform(matrix)
+        return
+
+    def translate(self, translation_vector: np.ndarray):
+        for strand in self._strands:
+            for nucleotide in strand._nucleotides:
+                nucleotide.translate(translation_vector)
+        return
+
+    def rotate(self, rotator: np.ndarray):
+        for strand in self._strands:
+            for nucleotide in strand._nucleotides:
+                nucleotide.rotate(rotator)
+        return

drawNA/polygons.py

@@ -2,7 +2,6 @@
 from typing import List
 
 import numpy as np
-import meshio
 import matplotlib.pyplot as plt
 import matplotlib.tri as tri
 
@@ -89,7 +88,7 @@ def write_STL(self, fout: str):
         triangulation = tri.Triangulation(self.vertices[:, 0], self.vertices[:, 1])
         triangles = triangulation.get_masked_triangles()
         cells = [("triangle", triangles)]
-        meshio.write_points_cells(fout, self.vertices, cells)
+        #meshio.write_points_cells(fout, self.vertices, cells)
 
     def write_PLY(self, fout: str, comments: List[str] = []):
         """

setup.py

@@ -5,7 +5,7 @@
 
 setuptools.setup(
     name="drawNA",
-    version="1.1.0",
+    version="1.0.1",
     author="Shanil Panara & Debesh Mandal",
     description="Package for creating origami",
     long_description=long_description,

test/test_oxdna/test_nucleotide.py

@@ -51,6 +51,35 @@ def test_Nucleotide_across():
     new_2.index = 1
     assert nucleotide.across == new_2.index
     assert new_2.across == nucleotide.index   
+
+def test_Nucleotide_transform():
+    nucleotide = Nucleotide(
+        "A",
+        np.array([1.0, 0.0, 0.0]),
+        np.array([1.0, 0.0, 0.0]),
+        np.array([0.0, 0.0, 1.0]),
+    )
+
+    nucleotide.translate(np.array([10., 0., 0.]))
+    assert all(nucleotide.pos_com == [11., 0., 0.])
+
+    nucleotide.rotate([0., 0., 0., 1.])
+    nucleotide.rotate([0., 0., 0.])
+    nucleotide.rotate(
+        np.array([
+            [1., 0., 0.],
+            [0., 1., 0.],
+            [0., 0., 0.],
+        ])
+    )
+
+    nucleotide.transform(np.array([
+        [1., 0., 0., 0.],
+        [0., 1., 0., 0.],
+        [0., 0., 1., 0.],
+    ]))
+
+    return
 
 if __name__ == "__main__":
     test_Nucleotide()

test/test_oxdna/test_strand.py

@@ -106,6 +106,67 @@ def test_generate_helix_seq():
     assert len(strand.nucleotides) == 10
     assert strand.sequence[0:11] == long_seq[0:10]
 
+def test_strand_transform():
+    strand = Strand(
+        [
+            Nucleotide(
+                "A",
+                np.array([1.0, 0.0, 0.0]),
+                np.array([1.0, 0.0, 0.0]),
+                np.array([0, 0.0, 1.0]),
+            ),
+            Nucleotide(
+                "A",
+                np.array([2.0, 0.0, 0.0]),
+                np.array([1.0, 0.0, 0.0]),
+                np.array([0, 0.0, 1.0]),
+            ),
+            Nucleotide(
+                "A",
+                np.array([3.0, 0.0, 0.0]),
+                np.array([1.0, 0.0, 0.0]),
+                np.array([0, 0.0, 1.0]),
+            ),
+            Nucleotide(
+                "A",
+                np.array([4.0, 0.0, 0.0]),
+                np.array([1.0, 0.0, 0.0]),
+                np.array([0, 0.0, 1.0]),
+            ),
+            Nucleotide(
+                "A",
+                np.array([5.0, 0.0, 0.0]),
+                np.array([1.0, 0.0, 0.0]),
+                np.array([0, 0.0, 1.0]),
+            ),
+            Nucleotide(
+                "A",
+                np.array([6.0, 0.0, 0.0]),
+                np.array([1.0, 0.0, 0.0]),
+                np.array([0, 0.0, 1.0]),
+            ),
+        ]
+    )
+    strand.translate(np.array([10., 0., 0.]))
+
+
+    strand.rotate([0., 0., 0., 1.])
+    strand.rotate([0., 0., 0.])
+    strand.rotate(
+        np.array([
+            [1., 0., 0.],
+            [0., 1., 0.],
+            [0., 0., 0.],
+        ])
+    )
+
+    strand.transform(np.array([
+        [1., 0., 0., 0.],
+        [0., 1., 0., 0.],
+        [0., 0., 1., 0.],
+    ]))
+    return
+
 
 if __name__ == "__main__":
 

test/test_oxdna/test_system.py

@@ -125,6 +125,25 @@ def test_System():
     print(system)
     print(system.dataframe)
     # system.write_oxDNA()
+
+    system.translate(np.array([10., 0., 0.]))
+
+
+    system.rotate([0., 0., 0., 1.])
+    system.rotate([0., 0., 0.])
+    system.rotate(
+        np.array([
+            [1., 0., 0.],
+            [0., 1., 0.],
+            [0., 0., 0.],
+        ])
+    )
+
+    system.transform(np.array([
+        [1., 0., 0., 0.],
+        [0., 1., 0., 0.],
+        [0., 0., 1., 0.],
+    ]))
     return
 
 

test/test_polygons.py

@@ -34,7 +34,7 @@ def test_BoundaryPolygon():
     assert isinstance(square.edges[0], Edge)
 
     # square.plot2D(show=False)
-    square.write_STL(f"{ROOT}/square.stl")
+    # square.write_STL(f"{ROOT}/square.stl")
     square.write_PLY(f"{ROOT}/square.ply")