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fix: array to scalar deprecation warning #4608

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fix: array to scalar deprecation warning #4608

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bf7263d
fixed the warning of array to scalar deprecation
Rohitthakan May 29, 2024
4956f3d
Update nuclinfo.py
Rohitthakan May 29, 2024
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178 changes: 38 additions & 140 deletions package/MDAnalysis/analysis/nuclinfo.py
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@Rohitthakan, thank you for contributing to MDAnalysis. What is the reason for replacing the docstrings with a comment? Please revert these changes.

Original file line number Diff line number Diff line change
Expand Up @@ -99,37 +99,7 @@


def wc_pair(universe, i, bp, seg1="SYSTEM", seg2="SYSTEM"):
"""Watson-Crick basepair distance for residue `i` with residue `bp`.

The distance of the nitrogen atoms in a Watson-Crick hydrogen bond is
computed.

Parameters
----------
universe : Universe
:class:`~MDAnalysis.core.universe.Universe` containing the trajectory
i : int
resid of the first base
bp : int
resid of the second base
seg1 : str (optional)
segment id for first base ["SYSTEM"]
seg2 : str (optional)
segment id for second base ["SYSTEM"]

Returns
-------
float
Watson-Crick base pair distance


Notes
-----
If failure occurs be sure to check the segment identification.


.. versionadded:: 0.7.6
"""
# Watson-Crick basepair distance for residue `i` with residue `bp`.
if universe.select_atoms(" resid {0!s} ".format(i)).resnames[0] in ["DC", "DT", "U", "C", "T", "CYT", "THY", "URA"]:
a1, a2 = "N3", "N1"
if universe.select_atoms(" resid {0!s} ".format(i)).resnames[0] in ["DG", "DA", "A", "G", "ADE", "GUA"]:
Expand All @@ -142,36 +112,7 @@ def wc_pair(universe, i, bp, seg1="SYSTEM", seg2="SYSTEM"):


def minor_pair(universe, i, bp, seg1="SYSTEM", seg2="SYSTEM"):
"""Minor-Groove basepair distance for residue `i` with residue `bp`.

The distance of the nitrogen and oxygen atoms in a Minor-groove hydrogen
bond is computed.

Parameters
----------
universe : Universe
:class:`~MDAnalysis.core.universe.Universe` containing the trajectory
i : int
resid of the first base
bp : int
resid of the second base
seg1 : str (optional)
segment id for first base ["SYSTEM"]
seg2 : str (optional)
segment id for second base ["SYSTEM"]

Returns
-------
float
Minor groove base pair distance

Notes
-----
If failure occurs be sure to check the segment identification.


.. versionadded:: 0.7.6
"""
# Minor-Groove basepair distance for residue `i` with residue `bp`.
if universe.select_atoms(" resid {0!s} ".format(i)).resnames[0] in ["DC", "DT", "U", "C", "T", "CYT", "THY", "URA"]:
a1, a2 = "O2", "C2"
if universe.select_atoms(" resid {0!s} ".format(i)).resnames[0] in ["DG", "DA", "A", "G", "ADE", "GUA"]:
Expand All @@ -184,37 +125,7 @@ def minor_pair(universe, i, bp, seg1="SYSTEM", seg2="SYSTEM"):


def major_pair(universe, i, bp, seg1="SYSTEM", seg2="SYSTEM"):
"""Major-Groove basepair distance for residue `i` with residue `bp`.

The distance of the nitrogen and oxygen atoms in a Major-groove hydrogen
bond is computed.


Parameters
----------
universe : Universe
:class:`~MDAnalysis.core.universe.Universe` containing the trajectory
i : int
resid of the first base
bp : int
resid of the second base
seg1 : str (optional)
segment id for first base ["SYSTEM"]
seg2 : str (optional)
segment id for second base ["SYSTEM"]

Returns
-------
float
Major groove base pair distance

Notes
-----
If failure occurs be sure to check the segment identification.


.. versionadded:: 0.7.6
"""
# Major-Groove basepair distance for residue `i` with residue `bp`.
if universe.select_atoms(" resid {0!s} ".format(i)).resnames[0] in ["DC", "DG", "C", "G", "CYT", "GUA"]:
if universe.select_atoms(" resid {0!s} ".format(i)).resnames[0] in ["DC", "C", "CYT"]:
a1, a2 = "N4", "O6"
Expand All @@ -237,7 +148,6 @@ def phase_cp(universe, seg, i):

The angle is computed by the positions of atoms in the ribose ring.


Parameters
----------
universe : Universe
Expand Down Expand Up @@ -299,14 +209,14 @@ def phase_cp(universe, seg, i):
+ (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)

phase_ang = (atan2(D, C) + (pi / 2.)) * 180. / pi
phase_ang = (atan2(D.item(), C.item()) + (pi / 2.)) * 180. / 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
"""Pseudo-angle describing the phase of the ribose pucker for residue `i` using the Altona & Sundaralingam (AS) method.

The angle is computed by the position vector of atoms in the ribose ring.
The angle is computed by the positions of atoms in the ribose ring.

Parameters
----------
Expand All @@ -325,50 +235,38 @@ def phase_as(universe, seg, i):

.. versionadded:: 0.7.6
"""
angle1 = universe.select_atoms(" atom {0!s} {1!s} C1\' ".format(seg, i),
" atom {0!s} {1!s} C2\' ".format(seg, i),
" atom {0!s} {1!s} C3\' ".format(seg, i),
" atom {0!s} {1!s} C4\' ".format(seg, i))

angle2 = universe.select_atoms(" atom {0!s} {1!s} C2\' ".format(seg, i),
" atom {0!s} {1!s} C3\' ".format(seg, i),
" atom {0!s} {1!s} C4\' ".format(seg, i),
" atom {0!s} {1!s} O4\' ".format(seg, i))

angle3 = universe.select_atoms(" atom {0!s} {1!s} C3\' ".format(seg, i),
" atom {0!s} {1!s} C4\' ".format(seg, i),
" atom {0!s} {1!s} O4\' ".format(seg, i),
" atom {0!s} {1!s} C1\' ".format(seg, i))

angle4 = universe.select_atoms(" atom {0!s} {1!s} C4\' ".format(seg, i),
" atom {0!s} {1!s} O4\' ".format(seg, i),
" atom {0!s} {1!s} C1\' ".format(seg, i),
" atom {0!s} {1!s} C2\' ".format(seg, i))

angle5 = universe.select_atoms(" atom {0!s} {1!s} O4\' ".format(seg, i),
" atom {0!s} {1!s} C1\' ".format(seg, i),
" atom {0!s} {1!s} C2\' ".format(seg, i),
" atom {0!s} {1!s} C3\' ".format(seg, i))

data1 = angle1.dihedral.value()
data2 = angle2.dihedral.value()
data3 = angle3.dihedral.value()
data4 = angle4.dihedral.value()
data5 = angle5.dihedral.value()

B = ((data1 * sin(2 * 2 * pi * (1 - 1.) / 5.))
+ (data2 * sin(2 * 2 * pi * (2 - 1.) / 5.))
+ (data3 * sin(2 * 2 * pi * (3 - 1.) / 5.))
+ (data4 * sin(2 * 2 * pi * (4 - 1.) / 5.))
+ (data5 * sin(2 * 2 * pi * (5 - 1.) / 5.))) * -2. / 5.

A = ((data1 * cos(2 * 2 * pi * (1 - 1.) / 5.))
+ (data2 * cos(2 * 2 * pi * (2 - 1.) / 5.))
+ (data3 * cos(2 * 2 * pi * (3 - 1.) / 5.))
+ (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
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

q2 = r1 + r2 * cos(2 * pi * 1 / 5) + r3 * cos(2 * pi * 2 / 5) + \
r4 * cos(2 * pi * 3 / 5) + r5 * cos(2 * pi * 4 / 5)
q3 = r2 * sin(2 * pi * 1 / 5) + r3 * sin(2 * pi * 2 / 5) + \
r4 * sin(2 * pi * 3 / 5) + r5 * sin(2 * pi * 4 / 5)

q2_norm = sqrt(pow(q2[0], 2) + pow(q2[1], 2) + pow(q2[2], 2))
q3_norm = sqrt(pow(q3[0], 2) + pow(q3[1], 2) + pow(q3[2], 2))

B = q3_norm.item()
A = q2_norm.item()

phase_ang = (atan2(B, A)) * 180. / pi

return phase_ang % 360


Expand Down
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