From bf7263de30d61975ed2a42659ac1d6c2bb28404c Mon Sep 17 00:00:00 2001 From: Rohitthakan <110251143+Rohitthakan@users.noreply.github.com> Date: Wed, 29 May 2024 12:03:18 +0530 Subject: [PATCH 1/2] fixed the warning of array to scalar deprecation --- package/MDAnalysis/analysis/nuclinfo.py | 175 +++++------------------- 1 file changed, 35 insertions(+), 140 deletions(-) diff --git a/package/MDAnalysis/analysis/nuclinfo.py b/package/MDAnalysis/analysis/nuclinfo.py index 4baa0ba5bf7..7c765590bf6 100644 --- a/package/MDAnalysis/analysis/nuclinfo.py +++ b/package/MDAnalysis/analysis/nuclinfo.py @@ -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"]: @@ -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"]: @@ -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" @@ -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 @@ -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 ---------- @@ -325,50 +235,35 @@ 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)) + + phase_ang = (atan2(q3_norm.item(), q2_norm.item())) * 180. / pi + return phase_ang % 360 From 4956f3defb1b60df13857d202efc03e89ec0eb5f Mon Sep 17 00:00:00 2001 From: Rohitthakan <110251143+Rohitthakan@users.noreply.github.com> Date: Wed, 29 May 2024 12:20:58 +0530 Subject: [PATCH 2/2] Update nuclinfo.py --- package/MDAnalysis/analysis/nuclinfo.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/package/MDAnalysis/analysis/nuclinfo.py b/package/MDAnalysis/analysis/nuclinfo.py index 7c765590bf6..b6bea2f74c3 100644 --- a/package/MDAnalysis/analysis/nuclinfo.py +++ b/package/MDAnalysis/analysis/nuclinfo.py @@ -262,7 +262,10 @@ def phase_as(universe, seg, i): 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)) - phase_ang = (atan2(q3_norm.item(), q2_norm.item())) * 180. / pi + B = q3_norm.item() + A = q2_norm.item() + + phase_ang = (atan2(B, A)) * 180. / pi return phase_ang % 360