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Fix DeprecationWarning by using np.arctan2 for element-wise array ope… #4730

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Fix DeprecationWarning by using np.arctan2 for element-wise array ope… #4730

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ace3f70
Fix DeprecationWarning by using np.arctan2 for element-wise array ope…
laksh-krishna-sharma Oct 11, 2024
05f6302
fixing NameError
laksh-krishna-sharma Oct 11, 2024
e75775d
fixing NameError
laksh-krishna-sharma Oct 15, 2024
1252899
restored docs
laksh-krishna-sharma Oct 15, 2024
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93 changes: 41 additions & 52 deletions package/MDAnalysis/analysis/nuclinfo.py
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Original file line number Diff line number Diff line change
Expand Up @@ -233,75 +233,65 @@ def major_pair(universe, i, bp, seg1="SYSTEM", seg2="SYSTEM"):


def phase_cp(universe, seg, i):
"""Pseudo-angle describing the phase of the ribose pucker for residue `i` using the CP method.

"""
Pseudo-angle describing the phase of the ribose pucker for residue `i` using the CP method.
The angle is computed by the positions of atoms in the ribose ring.


Parameters
----------
universe : Universe
:class:`~MDAnalysis.core.universe.Universe` containing the trajectory
:class:`~MDAnalysis.core.universe.Universe` containing the trajectory
seg : str
segment id for base
Segment id for base
i : int
resid of the first base
Resid of the first base

Returns
-------
float
phase angle in degrees

Phase angle in degrees

.. versionadded:: 0.7.6
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Do not remove docs, especially not versionadded.

"""
atom1 = universe.select_atoms(" atom {0!s} {1!s} O4\' ".format(seg, i))
atom2 = universe.select_atoms(" atom {0!s} {1!s} C1\' ".format(seg, i))
atom3 = universe.select_atoms(" atom {0!s} {1!s} C2\' ".format(seg, i))
atom4 = universe.select_atoms(" atom {0!s} {1!s} C3\' ".format(seg, i))
atom5 = universe.select_atoms(" atom {0!s} {1!s} C4\' ".format(seg, i))

data1 = atom1.positions
data2 = atom2.positions
data3 = atom3.positions
data4 = atom4.positions
data5 = atom5.positions

r0 = (data1 + data2 + data3 + data4 + data5) * (1.0 / 5.0)
r1 = data1 - r0
r2 = data2 - r0
r3 = data3 - r0
r4 = data4 - r0
r5 = data5 - r0

R1 = ((r1 * sin(2 * pi * 0.0 / 5.0)) + (r2 * sin(2 * pi * 1.0 / 5.0)) +
(r3 * sin(2 * pi * 2.0 / 5.0)) + (r4 * sin(2 * pi * 3.0 / 5.0)) +
(r5 * sin(2 * pi * 4.0 / 5.0)))

R2 = ((r1 * cos(2 * pi * 0.0 / 5.0)) + (r2 * cos(2 * pi * 1.0 / 5.0)) +
(r3 * cos(2 * pi * 2.0 / 5.0)) + (r4 * cos(2 * pi * 3.0 / 5.0)) +
(r5 * cos(2 * pi * 4.0 / 5.0)))

# Select atoms
atom1 = universe.select_atoms(f"atom {seg} {i} O4\'")
atom2 = universe.select_atoms(f"atom {seg} {i} C1\'")
atom3 = universe.select_atoms(f"atom {seg} {i} C2\'")
atom4 = universe.select_atoms(f"atom {seg} {i} C3\'")
atom5 = universe.select_atoms(f"atom {seg} {i} C4\'")

x = np.cross(R1[0], R2[0])
n = x / sqrt(pow(x[0], 2) + pow(x[1], 2) + pow(x[2], 2))
# Get positions
data1, data2, data3, data4, data5 = [atom.positions for atom in [atom1, atom2, atom3, atom4, atom5]]

r1_d = np.dot(r1, n)
r2_d = np.dot(r2, n)
r3_d = np.dot(r3, n)
r4_d = np.dot(r4, n)
r5_d = np.dot(r5, n)
# Calculate mean position (r0)
r0 = (data1 + data2 + data3 + data4 + data5) / 5.0

D = ((r1_d * sin(4 * pi * 0.0 / 5.0)) + (r2_d * sin(4 * pi * 1.0 / 5.0))
+ (r3_d * sin(4 * pi * 2.0 / 5.0)) + (r4_d * sin(4 * pi * 3.0 / 5.0))
+ (r5_d * sin(4 * pi * 4.0 / 5.0))) * -1 * sqrt(2.0 / 5.0)
# Calculate relative positions (r1, r2, r3, r4, r5)
r1, r2, r3, r4, r5 = [data - r0 for data in [data1, data2, data3, data4, data5]]

C = ((r1_d * cos(4 * pi * 0.0 / 5.0)) + (r2_d * cos(4 * pi * 1.0 / 5.0))
+ (r3_d * cos(4 * pi * 2.0 / 5.0)) + (r4_d * cos(4 * pi * 3.0 / 5.0))
+ (r5_d * cos(4 * pi * 4.0 / 5.0))) * sqrt(2.0 / 5.0)
# Calculate R1 and R2
R1 = (r1 * sin(2 * pi * 0.0 / 5.0)) + (r2 * sin(2 * pi * 1.0 / 5.0)) + \
(r3 * sin(2 * pi * 2.0 / 5.0)) + (r4 * sin(2 * pi * 3.0 / 5.0)) + \
(r5 * sin(2 * pi * 4.0 / 5.0))

phase_ang = (atan2(D, C) + (pi / 2.)) * 180. / pi
return phase_ang % 360
R2 = (r1 * cos(2 * pi * 0.0 / 5.0)) + (r2 * cos(2 * pi * 1.0 / 5.0)) + \
(r3 * cos(2 * pi * 2.0 / 5.0)) + (r4 * cos(2 * pi * 3.0 / 5.0)) + \
(r5 * cos(2 * pi * 4.0 / 5.0))

# Normalize vector x and calculate dot products
x = np.cross(R1[0], R2[0])
n = x / np.linalg.norm(x)

r_d = [np.dot(r, n) for r in [r1, r2, r3, r4, r5]]

# Calculate D and C components
D = sum(r_d[j] * sin(4 * pi * j / 5.0) for j in range(5)) * -1 * sqrt(2.0 / 5.0)
C = sum(r_d[j] * cos(4 * pi * j / 5.0) for j in range(5)) * sqrt(2.0 / 5.0)

# Calculate phase angle
phase_ang = (np.arctan2(D, C) + (np.pi / 2.)) * 180. / np.pi
return phase_ang % 360

def phase_as(universe, seg, i):
"""Pseudo-angle describing the phase of the ribose pucker for residue `i` using the AS method
Expand Down Expand Up @@ -368,7 +358,7 @@ def phase_as(universe, seg, i):
+ (data4 * cos(2 * 2 * pi * (4 - 1.) / 5.))
+ (data5 * cos(2 * 2 * pi * (5 - 1.) / 5.))) * 2. / 5.

phase_ang = atan2(B, A) * 180. / pi
phase_ang = (np.arctan2(B, A) + (np.pi / 2.)) * 180. / np.pi
return phase_ang % 360


Expand Down Expand Up @@ -482,7 +472,7 @@ def tors_alpha(universe, seg, i):


def tors_beta(universe, seg, i):
"""beta backbone dihedral
"""beta backbone dihedral

The dihedral is computed based on position atoms for resid `i`.

Expand All @@ -500,7 +490,6 @@ def tors_beta(universe, seg, i):
beta : float
torsion angle in degrees


.. versionadded:: 0.7.6
"""
b = universe.select_atoms(" atom {0!s} {1!s} P ".format(seg, i),
Expand Down
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