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Remove the deprecated Bio.PDB.QCPSuperimposer module (#4511)

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mdehoon
2023-11-28 05:34:00 +09:00
committed by GitHub
parent eee4589d20
commit b2e99382a5
5 changed files with 5 additions and 430 deletions
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174
Bio/PDB/QCPSuperimposer/__init__.py
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@ -1,174 +0,0 @@
# Copyright (C) 2015, Anuj Sharma (anuj.sharma80@gmail.com)
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Structural alignment using Quaternion Characteristic Polynomial (QCP).
QCPSuperimposer finds the best rotation and translation to put
two point sets on top of each other (minimizing the RMSD). This is
eg. useful to superimpose crystal structures. QCP stands for
Quaternion Characteristic Polynomial, which is used in the algorithm.
"""
import numpy as np
from .qcprotmodule import FastCalcRMSDAndRotation
import warnings
from Bio import BiopythonDeprecationWarning
warnings.warn(
"The QCPSuperimposer module will be removed soon in favor of qcprot. The "
"API will remain largely the same.",
BiopythonDeprecationWarning,
)
class QCPSuperimposer:
"""Quaternion Characteristic Polynomial (QCP) Superimposer.
QCPSuperimposer finds the best rotation and translation to put
two point sets on top of each other (minimizing the RMSD). This is
eg. useful to superimposing 3D structures of proteins.
QCP stands for Quaternion Characteristic Polynomial, which is used
in the algorithm.
Reference:
Douglas L Theobald (2005), "Rapid calculation of RMSDs using a
quaternion-based characteristic polynomial.", Acta Crystallogr
A 61(4):478-480
"""
def __init__(self):
"""Initialize the class."""
self._clear()
# Private methods
def _clear(self):
self.reference_coords = None
self.coords = None
self.transformed_coords = None
self.rot = None
self.tran = None
self.rms = None
self.init_rms = None
def _rms(self, coords1, coords2):
"""Return rms deviations between coords1 and coords2 (PRIVATE)."""
diff = coords1 - coords2
return np.sqrt(sum(np.dot(diff, diff.T)) / coords1.shape[0])
def _inner_product(self, coords1, coords2):
G1 = np.inner(coords1, coords1).diagonal().sum()
G2 = np.inner(coords2, coords2).diagonal().sum()
A = np.dot(coords1.T, coords2)
return ((G1 + G2) / 2, A)
def _align(self, centered_coords1, centered_coords2):
(E0, A) = self._inner_product(centered_coords1, centered_coords2)
(
rmsd,
r0,
r1,
r2,
r3,
r4,
r5,
r6,
r7,
r8,
q1,
q2,
q3,
q4,
) = FastCalcRMSDAndRotation(
A[0][0],
A[0][1],
A[0][2],
A[1][0],
A[1][1],
A[1][2],
A[2][0],
A[2][1],
A[2][2],
E0,
len(centered_coords1),
-1.0,
)
rot = np.array([r0, r1, r2, r3, r4, r5, r6, r7, r8]).reshape(3, 3)
return (rmsd, rot, [q1, q2, q3, q4])
# Public methods
def set(self, reference_coords, coords):
"""Set the coordinates to be superimposed.
coords will be put on top of reference_coords.
- reference_coords: an NxDIM array
- coords: an NxDIM array
DIM is the dimension of the points, N is the number
of points to be superimposed.
"""
# clear everything from previous runs
self._clear()
# store coordinates
self.reference_coords = reference_coords
self.coords = coords
n = reference_coords.shape
m = coords.shape
if n != m or n[1] != 3 or m[1] != 3:
raise Exception("Coordinate number/dimension mismatch.")
self.n = n[0]
def run(self):
"""Superimpose the coordinate sets."""
if self.coords is None or self.reference_coords is None:
raise Exception("No coordinates set.")
coords = self.coords
reference_coords = self.reference_coords
# center on centroid
av1 = sum(coords) / self.n
av2 = sum(reference_coords) / self.n
coords = coords - av1
reference_coords = reference_coords - av2
#
(self.rms, self.rot, self.lquart) = self._align(coords, reference_coords)
self.tran = av2 - np.dot(av1, self.rot)
def get_transformed(self):
"""Get the transformed coordinate set."""
if self.coords is None or self.reference_coords is None:
raise Exception("No coordinates set.")
if self.rot is None:
raise Exception("Nothing superimposed yet.")
if self.transformed_coords is None:
self.transformed_coords = np.dot(self.coords, self.rot) + self.tran
return self.transformed_coords
def get_rotran(self):
"""Right multiplying rotation matrix and translation."""
if self.rot is None:
raise Exception("Nothing superimposed yet.")
return self.rot, self.tran
def get_init_rms(self):
"""Root mean square deviation of untransformed coordinates."""
if self.coords is None:
raise Exception("No coordinates set yet.")
if self.init_rms is None:
self.init_rms = self._rms(self.coords, self.reference_coords)
return self.init_rms
def get_rms(self):
"""Root mean square deviation of superimposed coordinates."""
if self.rms is None:
raise Exception("Nothing superimposed yet.")
return self.rms

250
Bio/PDB/QCPSuperimposer/qcprotmodule.c
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@ -1,250 +0,0 @@
/**
* The file contains implementation of the fast rmsd calculation method. The
* sources is a marginally modified version of the implementation available
* at theobald.brandeis.edu/qcp/ (qcprot.c).
*
*********************************************************************************
* NOTE: following changes have been made to the original (qcprot.c):
* - introduced python bindings: change in method signature and return types
* - removed methods that are not used by this module (only one method retained)
*********************************************************************************
*
* Copyright (c) 2009-2013 Pu Liu and Douglas L. Theobald
* All rights reserved.
*
* Redistribution and use in source and binary forms, with or without modification, are permitted
* provided that the following conditions are met:
*
* * Redistributions of source code must retain the above copyright notice, this list of
* conditions and the following disclaimer.
* * Redistributions in binary form must reproduce the above copyright notice, this list
* of conditions and the following disclaimer in the documentation and/or other materials
* provided with the distribution.
* * Neither the name of the <ORGANIZATION> nor the names of its contributors may be used to
* endorse or promote products derived from this software without specific prior written
* permission.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
* "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
* LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
* PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
* HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
* SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
* LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
* DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
* THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
* OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*
*/
#include <math.h>
#include <Python.h>
static PyObject* py_FastCalcRMSDAndRotation(PyObject* self, PyObject* args) {
double Sxx, Sxy, Sxz, Syx, Syy, Syz, Szx, Szy, Szz;
double E0;
double len;
double minScore;
double Szz2, Syy2, Sxx2, Sxy2, Syz2, Sxz2, Syx2, Szy2, Szx2, SyzSzymSyySzz2,
Sxx2Syy2Szz2Syz2Szy2, Sxy2Sxz2Syx2Szx2, SxzpSzx, SyzpSzy, SxypSyx,
SyzmSzy, SxzmSzx, SxymSyx, SxxpSyy, SxxmSyy;
double C[4], rot[9];
int i;
double mxEigenV, rmsd;
double oldg = 0.0;
double b, a, delta, rms, qsqr;
double q1, q2, q3, q4, normq;
double a11, a12, a13, a14, a21, a22, a23, a24;
double a31, a32, a33, a34, a41, a42, a43, a44;
double a2, x2, y2, z2;
double xy, az, zx, ay, yz, ax;
double a3344_4334, a3244_4234, a3243_4233, a3143_4133, a3144_4134,
a3142_4132;
double evecprec = 1e-6;
double evalprec = 1e-11;
/* parse the arguments */
PyArg_ParseTuple(args, "dddddddddddd", &Sxx, &Sxy, &Sxz, &Syx, &Syy, &Syz, &Szx, &Szy, &Szz, &E0, &len, &minScore);
Sxx2 = Sxx * Sxx;
Syy2 = Syy * Syy;
Szz2 = Szz * Szz;
Sxy2 = Sxy * Sxy;
Syz2 = Syz * Syz;
Sxz2 = Sxz * Sxz;
Syx2 = Syx * Syx;
Szy2 = Szy * Szy;
Szx2 = Szx * Szx;
SyzSzymSyySzz2 = 2.0 * (Syz * Szy - Syy * Szz);
Sxx2Syy2Szz2Syz2Szy2 = Syy2 + Szz2 - Sxx2 + Syz2 + Szy2;
C[2] = -2.0
* (Sxx2 + Syy2 + Szz2 + Sxy2 + Syx2 + Sxz2 + Szx2 + Syz2 + Szy2);
C[1] = 8.0
* (Sxx * Syz * Szy + Syy * Szx * Sxz + Szz * Sxy * Syx
- Sxx * Syy * Szz - Syz * Szx * Sxy - Szy * Syx * Sxz);
SxzpSzx = Sxz + Szx;
SyzpSzy = Syz + Szy;
SxypSyx = Sxy + Syx;
SyzmSzy = Syz - Szy;
SxzmSzx = Sxz - Szx;
SxymSyx = Sxy - Syx;
SxxpSyy = Sxx + Syy;
SxxmSyy = Sxx - Syy;
Sxy2Sxz2Syx2Szx2 = Sxy2 + Sxz2 - Syx2 - Szx2;
C[0] = Sxy2Sxz2Syx2Szx2 * Sxy2Sxz2Syx2Szx2
+ (Sxx2Syy2Szz2Syz2Szy2 + SyzSzymSyySzz2)
* (Sxx2Syy2Szz2Syz2Szy2 - SyzSzymSyySzz2)
+ (-(SxzpSzx) * (SyzmSzy) + (SxymSyx) * (SxxmSyy - Szz))
* (-(SxzmSzx) * (SyzpSzy) + (SxymSyx) * (SxxmSyy + Szz))
+ (-(SxzpSzx) * (SyzpSzy) - (SxypSyx) * (SxxpSyy - Szz))
* (-(SxzmSzx) * (SyzmSzy) - (SxypSyx) * (SxxpSyy + Szz))
+ (+(SxypSyx) * (SyzpSzy) + (SxzpSzx) * (SxxmSyy + Szz))
* (-(SxymSyx) * (SyzmSzy) + (SxzpSzx) * (SxxpSyy + Szz))
+ (+(SxypSyx) * (SyzmSzy) + (SxzmSzx) * (SxxmSyy - Szz))
* (-(SxymSyx) * (SyzpSzy) + (SxzmSzx) * (SxxpSyy - Szz));
mxEigenV = E0;
for (i = 0; i < 50; ++i) {
oldg = mxEigenV;
x2 = mxEigenV * mxEigenV;
b = (x2 + C[2]) * mxEigenV;
a = b + C[1];
delta = ((a * mxEigenV + C[0]) / (2.0 * x2 * mxEigenV + b + a));
mxEigenV -= delta;
/* printf("\n diff[%3d]: %16g %16g %16g", i, mxEigenV - oldg, evalprec*mxEigenV, mxEigenV); */
if (fabs(mxEigenV - oldg) < fabs(evalprec * mxEigenV))
break;
}
if (i == 50)
PySys_WriteStderr("\nMore than %d iterations needed!\n", i);
/* the fabs() is to guard against extremely small, but *negative* numbers due to floating point error */
rms = sqrt(fabs(2.0 * (E0 - mxEigenV) / len));
rmsd = rms;
/* printf("\n\n %16g %16g %16g \n", rms, E0, 2.0 * (E0 - mxEigenV)/len); */
if (minScore > 0) {
if (rms < minScore) {
return Py_BuildValue("dddddddddddddd", -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1);
}
}
a11 = SxxpSyy + Szz - mxEigenV;
a12 = SyzmSzy;
a13 = -SxzmSzx;
a14 = SxymSyx;
a21 = SyzmSzy;
a22 = SxxmSyy - Szz - mxEigenV;
a23 = SxypSyx;
a24 = SxzpSzx;
a31 = a13;
a32 = a23;
a33 = Syy - Sxx - Szz - mxEigenV;
a34 = SyzpSzy;
a41 = a14;
a42 = a24;
a43 = a34;
a44 = Szz - SxxpSyy - mxEigenV;
a3344_4334 = a33 * a44 - a43 * a34;
a3244_4234 = a32 * a44 - a42 * a34;
a3243_4233 = a32 * a43 - a42 * a33;
a3143_4133 = a31 * a43 - a41 * a33;
a3144_4134 = a31 * a44 - a41 * a34;
a3142_4132 = a31 * a42 - a41 * a32;
q1 = a22 * a3344_4334 - a23 * a3244_4234 + a24 * a3243_4233;
q2 = -a21 * a3344_4334 + a23 * a3144_4134 - a24 * a3143_4133;
q3 = a21 * a3244_4234 - a22 * a3144_4134 + a24 * a3142_4132;
q4 = -a21 * a3243_4233 + a22 * a3143_4133 - a23 * a3142_4132;
qsqr = q1 * q1 + q2 * q2 + q3 * q3 + q4 * q4;
if (qsqr < evecprec) {
q1 = a12 * a3344_4334 - a13 * a3244_4234 + a14 * a3243_4233;
q2 = -a11 * a3344_4334 + a13 * a3144_4134 - a14 * a3143_4133;
q3 = a11 * a3244_4234 - a12 * a3144_4134 + a14 * a3142_4132;
q4 = -a11 * a3243_4233 + a12 * a3143_4133 - a13 * a3142_4132;
qsqr = q1 * q1 + q2 * q2 + q3 * q3 + q4 * q4;
if (qsqr < evecprec) {
double a1324_1423 = a13 * a24 - a14 * a23, a1224_1422 = a12 * a24
- a14 * a22;
double a1223_1322 = a12 * a23 - a13 * a22, a1124_1421 = a11 * a24
- a14 * a21;
double a1123_1321 = a11 * a23 - a13 * a21, a1122_1221 = a11 * a22
- a12 * a21;
q1 = a42 * a1324_1423 - a43 * a1224_1422 + a44 * a1223_1322;
q2 = -a41 * a1324_1423 + a43 * a1124_1421 - a44 * a1123_1321;
q3 = a41 * a1224_1422 - a42 * a1124_1421 + a44 * a1122_1221;
q4 = -a41 * a1223_1322 + a42 * a1123_1321 - a43 * a1122_1221;
qsqr = q1 * q1 + q2 * q2 + q3 * q3 + q4 * q4;
if (qsqr < evecprec) {
q1 = a32 * a1324_1423 - a33 * a1224_1422 + a34 * a1223_1322;
q2 = -a31 * a1324_1423 + a33 * a1124_1421 - a34 * a1123_1321;
q3 = a31 * a1224_1422 - a32 * a1124_1421 + a34 * a1122_1221;
q4 = -a31 * a1223_1322 + a32 * a1123_1321 - a33 * a1122_1221;
qsqr = q1 * q1 + q2 * q2 + q3 * q3 + q4 * q4;
if (qsqr < evecprec) {
rot[0] = rot[4] = rot[8] = 1.0;
rot[1] = rot[2] = rot[3] = rot[5] = rot[6] = rot[7] = 0.0;
return Py_BuildValue("dddddddddddddd", rmsd, rot[0], rot[1], rot[2], rot[3], rot[4], rot[5], rot[6], rot[7], rot[8], q1, q2, q3, q4);
}
}
}
}
normq = sqrt(qsqr);
q1 /= normq;
q2 /= normq;
q3 /= normq;
q4 /= normq;
a2 = q1 * q1;
x2 = q2 * q2;
y2 = q3 * q3;
z2 = q4 * q4;
xy = q2 * q3;
az = q1 * q4;
zx = q4 * q2;
ay = q1 * q3;
yz = q3 * q4;
ax = q1 * q2;
rot[0] = a2 + x2 - y2 - z2;
rot[1] = 2 * (xy + az);
rot[2] = 2 * (zx - ay);
rot[3] = 2 * (xy - az);
rot[4] = a2 - x2 + y2 - z2;
rot[5] = 2 * (yz + ax);
rot[6] = 2 * (zx + ay);
rot[7] = 2 * (yz - ax);
rot[8] = a2 - x2 - y2 + z2;
return Py_BuildValue("dddddddddddddd", rmsd, rot[0], rot[1], rot[2], rot[3], rot[4], rot[5], rot[6], rot[7], rot[8], q1, q2, q3, q4);
}
static PyMethodDef qcprot_methods[] = {
{"FastCalcRMSDAndRotation", (PyCFunction)py_FastCalcRMSDAndRotation, METH_VARARGS, "The method calculates the RMSD by solving for the most positive eigenvalue using the Newton-Raphson method. The rotation matrix is given by the corresponding eigenvector and is calculated by finding roots of the characteristic polynomial of the matrix. The method returns the rmsd, the rotation matrix and the 4 quaternions."},
{NULL, NULL, 0, NULL}
};
static struct PyModuleDef moduledef = {
PyModuleDef_HEAD_INIT, "qcprotmodule", NULL,
-1, qcprot_methods, NULL, NULL, NULL, NULL};
PyObject * PyInit_qcprotmodule(void) {
return PyModule_Create(&moduledef);
}

5
DEPRECATED.rst
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@ -283,6 +283,11 @@ Bio.PDB.ResidueDepth
Use of the ``PDB_TO_XYZR`` bash script was removed from ``get_surface`` in
Release 1.79.
Bio.PDB.QCPSuperimposer
-----------------------
The ``Bio.PDB.QCPSuperimposer`` module was deprecated in release 1.80, and
removed in release 1.82. Please use the ``Bio.PDB.qcprot`` module instead.
Bio.SeqFeature
--------------
With the introduction of the CompoundLocation in Release 1.62, the SeqFeature

1
Tests/run_tests.py
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@ -95,7 +95,6 @@ if np is None:
"Bio.PDB.PDBParser",
"Bio.PDB.Polypeptide",
"Bio.PDB.PSEA",
"Bio.PDB.QCPSuperimposer",
"Bio.PDB.Residue",
"Bio.PDB.Selection",
"Bio.PDB.StructureAlignment",

5
setup.py
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@ -170,7 +170,6 @@ PACKAGES = [
"Bio.Sequencing",
"Bio.Sequencing.Applications",
"Bio.SVDSuperimposer",
"Bio.PDB.QCPSuperimposer",
"Bio.SwissProt",
"Bio.TogoWS",
"Bio.Phylo",
@ -187,10 +186,6 @@ EXTENSIONS = [
Extension("Bio.Align._pairwisealigner", ["Bio/Align/_pairwisealigner.c"]),
Extension("Bio.cpairwise2", ["Bio/cpairwise2module.c"]),
Extension("Bio.Nexus.cnexus", ["Bio/Nexus/cnexus.c"]),
Extension(
"Bio.PDB.QCPSuperimposer.qcprotmodule",
["Bio/PDB/QCPSuperimposer/qcprotmodule.c"],
),
Extension("Bio.motifs._pwm", ["Bio/motifs/_pwm.c"]),
Extension(
"Bio.Cluster._cluster", ["Bio/Cluster/cluster.c", "Bio/Cluster/clustermodule.c"]