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// $Id$
//
// Copyright (C) 2005-2006 Rational Discovery LLC
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
#define PY_ARRAY_UNIQUE_SYMBOL rdshapehelpers_array_API
#include <RDBoost/python.h>
#include <GraphMol/ROMol.h>
#include <RDBoost/Wrap.h>
#include <RDBoost/import_array.h>
#include <Geometry/Transform3D.h>
#include <Geometry/UniformGrid3D.h>
#include <GraphMol/ShapeHelpers/ShapeEncoder.h>
#include <GraphMol/ShapeHelpers/ShapeUtils.h>
#include <DataStructs/DiscreteValueVect.h>
#include <Geometry/point.h>
namespace python = boost::python;
namespace RDKit {
void _copyTransform(const PyArrayObject *transMat, RDGeom::Transform3D &trans) {
unsigned int nrows = PyArray_DIM(transMat, 0);
unsigned int ncols = PyArray_DIM(transMat, 1);
if ((nrows != 4) || (ncols != 4)) {
throw_value_error("The transform has to be square matrix, of size 4x4");
}
if (PyArray_DESCR(const_cast<PyArrayObject *>(transMat))->type_num !=
NPY_DOUBLE)
throw_value_error("Only double arrays allowed for transform object ");
unsigned int dSize = nrows * nrows;
const double *inData = reinterpret_cast<const double *>(
PyArray_DATA(const_cast<PyArrayObject *>(transMat)));
double *tData = trans.getData();
memcpy(static_cast<void *>(tData), static_cast<const void *>(inData),
dSize * sizeof(double));
}
python::tuple getConformerDimsAndOffset(const Conformer &conf,
python::object trans = python::object(),
double padding = 2.5) {
RDGeom::Point3D dims, offSet;
PyObject *transObj = trans.ptr();
if (PyArray_Check(transObj)) {
PyArrayObject *transMat = reinterpret_cast<PyArrayObject *>(transObj);
RDGeom::Transform3D ctrans;
_copyTransform(transMat, ctrans);
MolShapes::computeConfDimsAndOffset(conf, dims, offSet, &ctrans, padding);
} else {
MolShapes::computeConfDimsAndOffset(conf, dims, offSet, nullptr, padding);
}
python::tuple res = python::make_tuple(dims, offSet);
return res;
}
python::tuple getConfBox(const Conformer &conf,
python::object trans = python::object(),
double padding = 2.5) {
RDGeom::Point3D lowerCorner, upperCorner;
PyObject *transObj = trans.ptr();
if (PyArray_Check(transObj)) {
PyArrayObject *transMat = reinterpret_cast<PyArrayObject *>(transObj);
RDGeom::Transform3D ctrans;
_copyTransform(transMat, ctrans);
MolShapes::computeConfBox(conf, lowerCorner, upperCorner, &ctrans, padding);
} else {
MolShapes::computeConfBox(conf, lowerCorner, upperCorner, nullptr, padding);
}
python::tuple res = python::make_tuple(lowerCorner, upperCorner);
return res;
}
python::tuple getUnionOfTwoBox(python::tuple box1, python::tuple box2) {
unsigned int len1 = python::extract<unsigned int>(box1.attr("__len__")());
unsigned int len2 = python::extract<unsigned int>(box2.attr("__len__")());
if ((len1 != 2) || (len2 != 2)) {
throw_value_error(
"In correct format for one of the box: expecting a tuple of two "
"Point3D");
}
RDGeom::Point3D lC1 =
python::extract<RDGeom::Point3D>(box1.attr("__getitem__")(0));
RDGeom::Point3D uC1 =
python::extract<RDGeom::Point3D>(box1.attr("__getitem__")(1));
RDGeom::Point3D lC2 =
python::extract<RDGeom::Point3D>(box2.attr("__getitem__")(0));
RDGeom::Point3D uC2 =
python::extract<RDGeom::Point3D>(box2.attr("__getitem__")(1));
RDGeom::Point3D lowerCorner, upperCorner;
MolShapes::computeUnionBox(lC1, uC1, lC2, uC2, lowerCorner, upperCorner);
python::tuple res = python::make_tuple(lowerCorner, upperCorner);
return res;
}
void EncodeMolShape(
const ROMol &mol, RDGeom::UniformGrid3D &grid, int confId = -1,
python::object trans = python::object(), // PyObject *trans=0,
double vdwScale = 0.8, double stepSize = 0.25, int maxLayers = -1,
bool ignoreHs = true) {
PyObject *transObj = trans.ptr();
if (PyArray_Check(transObj)) {
PyArrayObject *transMat = reinterpret_cast<PyArrayObject *>(transObj);
RDGeom::Transform3D ctrans;
_copyTransform(transMat, ctrans);
MolShapes::EncodeShape(mol, grid, confId, &ctrans, vdwScale, stepSize,
maxLayers, ignoreHs);
} else {
MolShapes::EncodeShape(mol, grid, confId, nullptr, vdwScale, stepSize,
maxLayers, ignoreHs);
}
}
double tverskyMolShapes(const ROMol &mol1, const ROMol &mol2, double alpha, double beta, int confId1 = -1,
int confId2 = -1, double gridSpacing = 0.5,
DiscreteValueVect::DiscreteValueType bitsPerPoint =
DiscreteValueVect::TWOBITVALUE,
double vdwScale = 0.8, double stepSize = 0.25,
int maxLayers = -1, bool ignoreHs = true) {
return MolShapes::tverskyIndex(mol1, mol2, alpha, beta, confId1, confId2, gridSpacing,
bitsPerPoint, vdwScale, stepSize,
maxLayers, ignoreHs);
}
double tanimotoMolShapes(const ROMol &mol1, const ROMol &mol2, int confId1 = -1,
int confId2 = -1, double gridSpacing = 0.5,
DiscreteValueVect::DiscreteValueType bitsPerPoint =
DiscreteValueVect::TWOBITVALUE,
double vdwScale = 0.8, double stepSize = 0.25,
int maxLayers = -1, bool ignoreHs = true) {
return MolShapes::tanimotoDistance(mol1, mol2, confId1, confId2, gridSpacing,
bitsPerPoint, vdwScale, stepSize,
maxLayers, ignoreHs);
}
double protrudeMolShapes(const ROMol &mol1, const ROMol &mol2, int confId1 = -1,
int confId2 = -1, double gridSpacing = 0.5,
DiscreteValueVect::DiscreteValueType bitsPerPoint =
DiscreteValueVect::TWOBITVALUE,
double vdwScale = 0.8, double stepSize = 0.25,
int maxLayers = -1, bool ignoreHs = true,
bool allowReordering = true) {
return MolShapes::protrudeDistance(mol1, mol2, confId1, confId2, gridSpacing,
bitsPerPoint, vdwScale, stepSize,
maxLayers, ignoreHs, allowReordering);
}
}
BOOST_PYTHON_MODULE(rdShapeHelpers) {
python::scope().attr("__doc__") =
"Module containing functions to encode and compare the shapes of "
"molecules";
rdkit_import_array();
// RegisterListConverter<RDKit::Atom*>();
std::string docString =
"Encode the shape of a molecule (one of its conformer) onto a grid\n\n\
\n\
ARGUMENTS:\n\n\
- mol : the molecule of interest\n\
- grid : grid onto which the encoding is written \n\
- confId : id of the conformation of interest on mol (defaults to the first one) \n\
- trans : any transformation that needs to be used to encode onto the grid (note the molecule remains unchanged) \n\
- vdwScale : Scaling factor for the radius of the atoms to determine the base radius \n\
used in the encoding - grid points inside this sphere carry the maximum occupancy \n\
- setpSize : thickness of the layers outside the base radius, the occupancy value is decreased \n\
from layer to layer from the maximum value \n\
- maxLayers : the maximum number of layers - defaults to the number of bits \n\
used per grid point - e.g. two bits per grid point will allow 3 layers\n\
- ignoreHs : when set, the contribution of Hs to the shape will be ignored\n";
python::def(
"EncodeShape", RDKit::EncodeMolShape,
(python::arg("mol"), python::arg("grid"), python::arg("confId") = -1,
python::arg("trans") = python::object(), python::arg("vdwScale") = 0.8,
python::arg("stepSize") = 0.25, python::arg("maxLayers") = -1,
python::arg("ignoreHs") = true),
docString.c_str());
docString =
"Compute the shape tanimoto distance between two molecule based on a predefined alignment\n\
\n\
ARGUMENTS:\n\
- mol1 : The first molecule of interest \n\
- mol2 : The second molecule of interest \n\
- confId1 : Conformer in the first molecule (defaults to first conformer) \n\
- confId2 : Conformer in the second molecule (defaults to first conformer) \n\
- gridSpacing : resolution of the grid used to encode the molecular shapes \n\
- bitsPerPoint : number of bits used to encode the occupancy at each grid point \n\
defaults to two bits per grid point \n\
- vdwScale : Scaling factor for the radius of the atoms to determine the base radius \n\
used in the encoding - grid points inside this sphere carry the maximum occupancy \n\
- stepSize : thickness of the each layer outside the base radius, the occupancy value is decreased \n\
from layer to layer from the maximum value \n\
- maxLayers : the maximum number of layers - defaults to the number of bits \n\
used per grid point - e.g. two bits per grid point will allow 3 layers \n\
- ignoreHs : when set, the contribution of Hs to the shape will be ignored\n";
python::def(
"ShapeTanimotoDist", RDKit::tanimotoMolShapes,
(python::arg("mol1"), python::arg("mol2"), python::arg("confId1") = -1,
python::arg("confId2") = -1, python::arg("gridSpacing") = 0.5,
python::arg("bitsPerPoint") = RDKit::DiscreteValueVect::TWOBITVALUE,
python::arg("vdwScale") = 0.8, python::arg("stepSize") = 0.25,
python::arg("maxLayers") = -1, python::arg("ignoreHs") = true),
docString.c_str());
docString =
"Compute the shape protrude distance between two molecule based on a predefined alignment\n\
\n\
ARGUMENTS:\n\
- mol1 : The first molecule of interest \n\
- mol2 : The second molecule of interest \n\
- confId1 : Conformer in the first molecule (defaults to first conformer) \n\
- confId2 : Conformer in the second molecule (defaults to first conformer) \n\
- gridSpacing : resolution of the grid used to encode the molecular shapes \n\
- bitsPerPoint : number of bit used to encode the occupancy at each grid point \n\
defaults to two bits per grid point \n\
- vdwScale : Scaling factor for the radius of the atoms to determine the base radius \n\
used in the encoding - grid points inside this sphere carry the maximum occupancy \n\
- stepSize : thickness of the each layer outside the base radius, the occupancy value is decreased \n\
from layer to layer from the maximum value \n\
- maxLayers : the maximum number of layers - defaults to the number of bits \n\
used per grid point - e.g. two bits per grid point will allow 3 layers \n\
- ignoreHs : when set, the contribution of Hs to the shape will be ignored\n\
- allowReordering : when set, the order will be automatically updated so that the value calculated\n\
is the protrusion of the smaller shape from the larger one.\n";
python::def(
"ShapeProtrudeDist", RDKit::protrudeMolShapes,
(python::arg("mol1"), python::arg("mol2"), python::arg("confId1") = -1,
python::arg("confId2") = -1, python::arg("gridSpacing") = 0.5,
python::arg("bitsPerPoint") = RDKit::DiscreteValueVect::TWOBITVALUE,
python::arg("vdwScale") = 0.8, python::arg("stepSize") = 0.25,
python::arg("maxLayers") = -1, python::arg("ignoreHs") = true,
python::arg("allowReordering") = true),
docString.c_str());
docString =
"Compute the size of the box that can fit the conformations, and offset \n\
of the box from the origin\n";
python::def("ComputeConfDimsAndOffset", RDKit::getConformerDimsAndOffset,
(python::arg("conf"), python::arg("trans") = python::object(),
python::arg("padding") = 2.0),
docString.c_str());
docString =
"Compute the lower and upper corners of a cuboid that will fit the "
"conformer";
python::def("ComputeConfBox", RDKit::getConfBox,
(python::arg("conf"), python::arg("trans") = python::object(),
python::arg("padding") = 2.0),
docString.c_str());
docString =
"Compute the union of two boxes, so that all the points in both boxes are \n\
contained in the new box";
python::def("ComputeUnionBox", RDKit::getUnionOfTwoBox, docString.c_str());
}
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