Merge pull request #10 from DeepRank/unit_test

Add unit test for transform

Author: CunliangGeng

pdb2sql/5hvd.pdb

@@ -51,6 +51,7 @@ def __init__(self,decoy,ref,verbose=False):
         self.decoy = decoy
         self.ref = ref
         self.verbose = verbose
+        self.origin = [0., 0., 0.]
 
 
     ################################################################################################
@@ -155,7 +156,7 @@ def compute_lrmsd_fast(self,lzone=None,method='svd',check=True):
         U = self.get_rotation_matrix(xyz_decoy_long,xyz_ref_long,method=method)
 
         # rotate the entire fragment
-        xyz_decoy_short = transform.rotation_matrix(xyz_decoy_short,U,center=False)
+        xyz_decoy_short = transform.rotate(xyz_decoy_short,U, center=self.origin)
 
         # compute the RMSD
         return self.get_rmsd(xyz_decoy_short,xyz_ref_short)
@@ -293,7 +294,7 @@ def compute_irmsd_fast(self,izone=None,method='svd',cutoff=10,check=True):
         U = self.get_rotation_matrix(xyz_contact_decoy,xyz_contact_ref,method=method)
 
         # rotate the entire fragment
-        xyz_contact_decoy = transform.rotation_matrix(xyz_contact_decoy,U,center=False)
+        xyz_contact_decoy = transform.rotate(xyz_contact_decoy,U,center=self.origin)
 
         # return the RMSD
         return self.get_rmsd(xyz_contact_decoy,xyz_contact_ref)
@@ -551,7 +552,7 @@ def compute_lrmsd_pdb2sql(self,exportpath=None,method='svd'):
         U = self.get_rotation_matrix(xyz_decoy_long,xyz_ref_long,method=method)
 
         # rotate the entire fragment
-        xyz_decoy_short = transform.rotation_matrix(xyz_decoy_short,U,center=False)
+        xyz_decoy_short = transform.rotate(xyz_decoy_short, U, center=self.origin)
 
 
         # compute the RMSD
@@ -569,7 +570,7 @@ def compute_lrmsd_pdb2sql(self,exportpath=None,method='svd'):
             xyz_decoy += tr_decoy
 
             # rotate decoy
-            xyz_decoy = transform.rotation_matrix(xyz_decoy,U,center=False)
+            xyz_decoy = transform.rotate(xyz_decoy, U, center=self.origin)
 
             # update the sql database
             sql_decoy.update_column('x',xyz_decoy[:,0])
@@ -726,7 +727,7 @@ def compute_irmsd_pdb2sql(self,cutoff=10,method='svd',izone=None,exportpath=None
         U = self.get_rotation_matrix(xyz_contact_decoy,xyz_contact_ref,method=method)
 
         # rotate the entire fragment
-        xyz_contact_decoy = transform.rotation_matrix(xyz_contact_decoy,U,center=False)
+        xyz_contact_decoy = transform.rotate(xyz_contact_decoy, U, center=self.origin)
 
         # compute the RMSD
         irmsd = self.get_rmsd(xyz_contact_decoy,xyz_contact_ref)

pdb2sql/StructureSimilarity.py

@@ -1 +1 @@
-__version__ = '0.2.0'
+__version__ = '0.2.1'

pdb2sql/__version__.py

@@ -8,73 +8,51 @@
 definition of the data set.
 '''
 
-def get_rot_axis_angle(seed=None):
-    """Get the rotation angle/axis.
-
-    Args:
-        seed(int): random seed for numpy
-
-    Returns:
-        list(float): axis of rotation
-        float: angle of rotation
-    """
-    # define the axis
-    # uniform distribution on a sphere
-    # http://mathworld.wolfram.com/SpherePointPicking.html
-    if seed != None:
-        np.random.seed(seed)
-
-    u1, u2 = np.random.rand(), np.random.rand()
-    teta, phi = np.arccos(2 * u1 - 1), 2 * np.pi * u2
-    axis = [np.sin(teta) * np.cos(phi),
-            np.sin(teta) * np.sin(phi),
-            np.cos(teta)]
-
-    # and the rotation angle
-    angle = -np.pi + np.pi * np.random.rand()
-
-    return axis, angle
-
-
+########################################################################
+# Translation
+########################################################################
 def translation(db, vect, **kwargs):
     xyz = _get_xyz(db, **kwargs)
     xyz += vect
     _update(db, xyz, **kwargs)
 
-
+########################################################################
+# Rotation using axis–angle presentation
+# see https://en.wikipedia.org/wiki/Rotation_matrix#Rotation_matrix_from_axis_and_angle
+########################################################################
 def rot_axis(db, axis, angle, **kwargs):
     xyz = _get_xyz(db, **kwargs)
     xyz = rot_xyz_around_axis(xyz, axis, angle)
     _update(db, xyz, **kwargs)
 
-
-def rot_euler(db, alpha, beta, gamma, **kwargs):
-    """Rotate molecule from Euler rotation axis.
+def get_rot_axis_angle(seed=None):
+    """Get the rotation angle and axis.
 
     Args:
-        alpha (float): angle of rotation around the x axis
-        beta (float): angle of rotation around the y axis
-        gamma (float): angle of rotation around the z axis
-        **kwargs: keyword argument to select the atoms.
-            See pdb2sql.get()
-    """
-    xyz = _get_xyz(db, **kwargs)
-    xyz = _rotation_euler(xyz, alpha, beta, gamma)
-    _update(db, xyz, **kwargs)
+        seed(int): random seed for numpy
 
+    Returns:
+        list(float): axis of rotation
+        float: angle of rotation
+    """
+    if seed is not None:
+        np.random.seed(seed)
 
-def rot_mat(db, mat, **kwargs):
-    """Rotate molecule from a rotation matrix.
+    # define the rotation axis
+    # uniform distribution on a sphere
+    # eq1,2 in http://mathworld.wolfram.com/SpherePointPicking.html
+    u1, u2 = np.random.rand(), np.random.rand()
+    theta = 2 * np.pi * u1      # [0, 2*pi)
+    phi = np.arccos(2 * u2 - 1) # [0, pi]
+    # eq19 in http://mathworld.wolfram.com/SphericalCoordinates.html
+    axis = [np.sin(phi) * np.cos(theta),
+            np.sin(phi) * np.sin(theta),
+            np.cos(phi)]
 
-    Args:
-        mat (np.array): 3x3 rotation matrix
-        **kwargs: keyword argument to select the atoms.
-            See pdb2sql.get()
-    """
-    xyz = _get_xyz(db, **kwargs)
-    xyz = _rotation_matrix(xyz, mat)
-    _update(db, xyz, **kwargs)
+    # define the rotation angle
+    angle =  2 * np.pi * np.random.rand()
 
+    return axis, angle
 
 def rot_xyz_around_axis(xyz, axis, angle, center=None):
     """Get the rotated xyz.
@@ -89,17 +67,11 @@ def rot_xyz_around_axis(xyz, axis, angle, center=None):
     Returns:
         np.array: rotated xyz coordinates
     """
-
-    # check center
-    if center is None:
-        center = np.mean(xyz, 0)
-
     # get the data
     ct, st = np.cos(angle), np.sin(angle)
     ux, uy, uz = axis
 
     # definition of the rotation matrix
-    # see https://en.wikipedia.org/wiki/Rotation_matrix
     rot_mat = np.array([[ct + ux**2 * (1 - ct),
                          ux * uy * (1 - ct) - uz * st,
                          ux * uz * (1 - ct) + uy * st],
@@ -111,51 +83,91 @@ def rot_xyz_around_axis(xyz, axis, angle, center=None):
                          ct + uz**2 * (1 - ct)]])
 
     # apply the rotation
-    return np.dot(rot_mat, (xyz - center).T).T + center
+    return rotate(xyz, rot_mat, center)
 
+########################################################################
+# Rotation using Euler anlges
+# see https://en.wikipedia.org/wiki/Rotation_matrix#General_rotations
+########################################################################
 
-def _rotation_euler(xyz, alpha, beta, gamma):
+def rot_euler(db, alpha, beta, gamma, **kwargs):
+    """Rotate molecule from Euler rotation axis.
+
+    Args:
+        alpha (float): angle of rotation around the x axis
+        beta (float): angle of rotation around the y axis
+        gamma (float): angle of rotation around the z axis
+        **kwargs: keyword argument to select the atoms.
+            See pdb2sql.get()
+    """
+    xyz = _get_xyz(db, **kwargs)
+    xyz = rotation_euler(xyz, alpha, beta, gamma)
+    _update(db, xyz, **kwargs)
+
+def rotation_euler(xyz, alpha, beta, gamma, center=None):
 
     # precomte the trig
     ca, sa = np.cos(alpha), np.sin(alpha)
     cb, sb = np.cos(beta), np.sin(beta)
     cg, sg = np.cos(gamma), np.sin(gamma)
 
-    # get the center of the molecule
-    xyz0 = np.mean(xyz, 0)
-
     # rotation matrices
     rx = np.array([[1, 0, 0], [0, ca, -sa], [0, sa, ca]])
     ry = np.array([[cb, 0, sb], [0, 1, 0], [-sb, 0, cb]])
-    rz = np.array([[cg, -sg, 0], [sg, cs, 0], [0, 0, 1]])
+    rz = np.array([[cg, -sg, 0], [sg, cg, 0], [0, 0, 1]])
 
-    rot_mat = np.dot(rz, np.dot(ry, rz))
+    # get rotation matrix
+    rot_mat = np.dot(rz, np.dot(ry, rx))
 
     # apply the rotation
-    return np.dot(rot_mat, (xyz - xyz0).T).T + xyz0
+    return rotate(xyz, rot_mat, center)
 
+########################################################################
+# Rotation using provided rotation matrix
+########################################################################
 
-def rotation_matrix(xyz, rot_mat, center=True):
-    if center:
-        xyz0 = np.mean(xyz)
-        return np.dot(rot_mat, (xyz - xyz0).T).T + xyz0
-    else:
-        return np.dot(rot_mat, (xyz).T).T
+def rot_mat(db, mat, **kwargs):
+    """Rotate molecule from a rotation matrix.
 
+    Args:
+        mat (np.array): 3x3 rotation matrix
+        **kwargs: keyword argument to select the atoms.
+            See pdb2sql.get()
+    """
+    xyz = _get_xyz(db, **kwargs)
+    xyz = rotate(xyz, mat)
+    _update(db, xyz, **kwargs)
 
-def _get_xyz(db, **kwargs):
-    return np.array(db.get('x,y,z', **kwargs))
+def rotate(xyz, rot_mat, center=None):
+    """[summary]
 
+    Args:
+        xyz(np.ndarray): x,y,z coordinates
+        rot_mat(np.ndarray): rotation matrix
+        center (list or np.ndarray, optional): rotation center.
+            Defaults to None, i.e. using molecule center as rotation
+            center.
 
-def _update(db, xyz, **kwargs):
-    db.update('x,y,z', xyz, **kwargs)
+    Raises:
+        TypeError: Rotation center must be list or 1D np.ndarray.
 
+    Returns:
+        np.ndarray: x,y,z coordinates after rotation
+    """
+    # the default rotation center is the center of molecule itself.
+    if center is None:
+        center = np.mean(xyz, 0)
 
-if __name__ == "__main__":
+    if not isinstance(center, (list, np.ndarray)):
+        raise TypeError("Rotation center must be list or 1D np.ndarray")
 
-    t0 = time()
-    db = pdb2sql('5hvd.pdb')
-    print('SQL %f' % (time() - t0))
+    return np.dot(rot_mat, (xyz - center).T).T + center
 
-    tr = np.array([1, 2, 3])
-    translation(db, tr, chainID='A')
+########################################################################
+# helper functions
+########################################################################
+def _get_xyz(db, **kwargs):
+    return np.array(db.get('x,y,z', **kwargs))
+
+def _update(db, xyz, **kwargs):
+    db.update('x,y,z', xyz, **kwargs)

pdb2sql/transform.py

@@ -0,0 +1,6 @@
+ATOM      1  N   THR A   1       1.000   0.000   0.000  1.00  0.69           N
+ATOM      2  CA  THR A   1      -1.000   0.000   0.000  1.00  0.50           C
+ATOM      3  C   THR A   1       0.000   1.000   0.000  1.00  0.45           C
+ATOM      4  O   THR A   1       0.000  -1.000   0.000  1.00  0.69           O
+ATOM      5  CB  THR A   1       0.000   0.000   1.000  1.00  0.50           C
+ATOM      6  H1  THR A   1       0.000   0.000  -1.000  1.00  0.45           H