mirror of
https://github.com/rdkit/rdkit.git
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c046d9abaa
- flattened out the structure (cpp and h files are in one directory), - changed includes to be #include <Shape/xxx.h>, - removed openbabel dependancies
139 lines
4.4 KiB
C++
139 lines
4.4 KiB
C++
/*******************************************************************************
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moleculeRotation.cpp - Shape-it
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Copyright 2012 by Silicos-it, a division of Imacosi BVBA
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This file is part of Shape-it.
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Shape-it is free software: you can redistribute it and/or modify
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it under the terms of the GNU Lesser General Public License as published
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by the Free Software Foundation, either version 3 of the License, or
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(at your option) any later version.
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Shape-it is distributed in the hope that it will be useful,
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but WITHOUT ANY WARRANTY; without even the implied warranty of
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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GNU Lesser General Public License for more details.
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You should have received a copy of the GNU Lesser General Public License
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along with Shape-it. If not, see <http://www.gnu.org/licenses/>.
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Shape-it is linked against OpenBabel version 2.
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OpenBabel is free software; you can redistribute it and/or modify
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it under the terms of the GNU General Public License as published by
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the Free Software Foundation version 2 of the License.
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***********************************************************************/
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#include <Shape/moleculeRotation.h>
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void
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positionMolecule(RDKit::ROMol& m, Coordinate& centroid, SiMath::Matrix& rotation)
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{
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RDKit::ROMol::AtomIterator ai;
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RDKit::Conformer conf = m.getConformer(0);
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for (ai=m.beginAtoms(); ai!=m.endAtoms(); ai++)
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{
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RDKit::Atom *a = *ai;
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int idx = a->getIdx();
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// Get coordinates
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double x = conf.getAtomPos(idx).x - centroid.x;
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double y = conf.getAtomPos(idx).y - centroid.y;
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double z = conf.getAtomPos(idx).z - centroid.z;
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// Rotate according to eigenvectors SVD
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RDGeom::Point3D point;
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point.x = rotation[0][0] * x + rotation[1][0] * y + rotation[2][0] * z;
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point.y = rotation[0][1] * x + rotation[1][1] * y + rotation[2][1] * z;
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point.z = rotation[0][2] * x + rotation[1][2] * y + rotation[2][2] * z;
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m.getConformer(0).setAtomPos(idx, point);
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}
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return;
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}
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void
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repositionMolecule(RDKit::ROMol& m, SiMath::Matrix& rotation, Coordinate& centroid)
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{
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RDKit::ROMol::AtomIterator ai;
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RDKit::Conformer conf = m.getConformer(0);
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for (ai=m.beginAtoms(); ai!=m.endAtoms(); ai++)
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{
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RDKit::Atom *a = *ai;
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int idx = a->getIdx();
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// Get coordinates
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double x = conf.getAtomPos(idx).x;
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double y = conf.getAtomPos(idx).y;
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double z = conf.getAtomPos(idx).z;
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// Rotate according to eigenvectors SVD
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double xx = rotation[0][0] * x + rotation[0][1] * y + rotation[0][2] * z;
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double yy = rotation[1][0] * x + rotation[1][1] * y + rotation[1][2] * z;
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double zz = rotation[2][0] * x + rotation[2][1] * y + rotation[2][2] * z;
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RDGeom::Point3D point;
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point.x = xx + centroid.x;
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point.y = yy + centroid.y;
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point.z = zz + centroid.z;
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m.getConformer(0).setAtomPos(idx, point);
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}
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return;
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}
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void
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rotateMolecule(RDKit::ROMol& m, SiMath::Vector& rotor)
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{
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// Build rotation matrix
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SiMath::Matrix rot(3,3,0.0);
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double r1 = rotor[1] * rotor[1];
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double r2 = rotor[2] * rotor[2];
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double r3 = rotor[3] * rotor[3];
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rot[0][0] = 1.0 - 2.0*r2 - 2.0*r3;
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rot[0][1] = 2.0 * (rotor[1]*rotor[2] - rotor[0]*rotor[3]);
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rot[0][2] = 2.0 * (rotor[1]*rotor[3] + rotor[0]*rotor[2]);
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rot[1][0] = 2.0 * (rotor[1]*rotor[2] + rotor[0]*rotor[3]);
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rot[1][1] = 1.0 - 2*r3 - 2*r1;
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rot[1][2] = 2.0 * (rotor[2]*rotor[3] - rotor[0]*rotor[1]);
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rot[2][0] = 2.0 * (rotor[1]*rotor[3] - rotor[0]*rotor[2]);
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rot[2][1] = 2.0 * (rotor[2]*rotor[3] + rotor[0]*rotor[1]);
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rot[2][2] = 1.0 - 2*r2 - 2*r1;
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RDKit::ROMol::AtomIterator ai;
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RDKit::Conformer conf = m.getConformer(0);
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for (ai=m.beginAtoms(); ai!=m.endAtoms(); ai++)
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{
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RDKit::Atom *a = *ai;
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int idx = a->getIdx();
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if (idx == 0) {
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//std::cerr << conf.getAtomPos(0).x << " " << m.getConformer(-1).getAtomPos(0).x << std::endl;
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}
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// Get coordinates
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double x = conf.getAtomPos(idx).x;
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double y = conf.getAtomPos(idx).y;
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double z = conf.getAtomPos(idx).z;
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// rotate according to eigenvectors SVD
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RDGeom::Point3D point;
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point.x = rot[0][0] * x + rot[0][1] * y + rot[0][2] * z;
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point.y = rot[1][0] * x + rot[1][1] * y + rot[1][2] * z;
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point.z = rot[2][0] * x + rot[2][1] * y + rot[2][2] * z;
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m.getConformer(0).setAtomPos(idx, point);
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}
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return;
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}
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