/usr/include/rdkit/GraphMol/DistGeomHelpers/Embedder.h is in librdkit-dev 201503-3.
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// Copyright (C) 2004-2012 Greg Landrum and 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.
//
#ifndef _RD_EMBEDDER_H_
#define _RD_EMBEDDER_H_
#include <map>
#include <Geometry/point.h>
#include <GraphMol/ROMol.h>
namespace RDKit {
namespace DGeomHelpers {
//! Compute an embedding (in 3D) for the specified molecule using Distance Geometry
/*!
The following operations are performed (in order) here:
-# Build a distance bounds matrix based on the topology, including 1-5
distances but not VDW scaling
-# Triangle smooth this bounds matrix
-# If step 2 fails - repeat step 1, this time without 1-5 bounds and with vdW
scaling, and repeat step 2
-# Pick a distance matrix at random using the bounds matrix
-# Compute initial coordinates from the distance matrix
-# Repeat steps 3 and 4 until maxIterations is reached or embedding is successful
-# Adjust initial coordinates by minimizing a Distance Violation error function
**NOTE**: if the molecule has multiple fragments, they will be embedded separately,
this means that they will likely occupy the same region of space.
\param mol Molecule of interest
\param maxIterations Max. number of times the embedding will be tried if coordinates are
not obtained successfully. The default value is 10x the number of atoms.
\param seed provides a seed for the random number generator (so that the same
coordinates can be obtained for a molecule on multiple runs)
If negative, the RNG will not be seeded.
\param clearConfs Clear all existing conformations on the molecule
\param useRandomCoords Start the embedding from random coordinates instead of
using eigenvalues of the distance matrix.
\param boxSizeMult Determines the size of the box that is used for
random coordinates. If this is a positive number, the
side length will equal the largest element of the distance
matrix times \c boxSizeMult. If this is a negative number,
the side length will equal \c -boxSizeMult (i.e. independent
of the elements of the distance matrix).
\param randNegEig Picks coordinates at random when a embedding process produces
negative eigenvalues
\param numZeroFail Fail embedding if we find this many or more zero eigenvalues
(within a tolerance)
\param coordMap a map of int to Point3D, between atom IDs and their locations
their locations. If this container is provided, the coordinates
are used to set distance constraints on the embedding. The resulting
conformer(s) should have distances between the specified atoms that
reproduce those between the points in \c coordMap. Because the embedding
produces a molecule in an arbitrary reference frame, an alignment step
is required to actually reproduce the provided coordinates.
\param optimizerForceTol set the tolerance on forces in the distgeom optimizer
(this shouldn't normally be altered in client code).
\param ignoreSmoothingFailures try to embed the molecule even if triangle bounds
smoothing fails
\param basinThresh set the basin threshold for the DGeom force field,
(this shouldn't normally be altered in client code).
\return ID of the conformations added to the molecule, -1 if the emdedding failed
*/
int EmbedMolecule(ROMol &mol, unsigned int maxIterations=0, int seed=-1,
bool clearConfs=true,
bool useRandomCoords=false,double boxSizeMult=2.0,
bool randNegEig=true,
unsigned int numZeroFail=1,
const std::map<int,RDGeom::Point3D> *coordMap=0,
double optimizerForceTol=1e-3,
bool ignoreSmoothingFailures=false,
double basinThresh=5.0
);
//*! Embed multiple conformations for a molecule
/*!
This is kind of equivalent to calling EmbedMolecule multiple times - just that the bounds
matrix is computed only once from the topology
**NOTE**: if the molecule has multiple fragments, they will be embedded separately,
this means that they will likely occupy the same region of space.
\param mol Molecule of interest
\param res Used to return the resulting conformer ids
\param numConfs Number of conformations to be generated
\param numThreads Sets the number of threads to use (more than one thread will only
be used if the RDKit was build with multithread support)
\param maxIterations Max. number of times the embedding will be tried if coordinates are
not obtained successfully. The default value is 10x the number of atoms.
\param seed provides a seed for the random number generator (so that the same
coordinates can be obtained for a molecule on multiple runs).
If negative, the RNG will not be seeded.
\param clearConfs Clear all existing conformations on the molecule
\param useRandomCoords Start the embedding from random coordinates instead of
using eigenvalues of the distance matrix.
\param boxSizeMult Determines the size of the box that is used for
random coordinates. If this is a positive number, the
side length will equal the largest element of the distance
matrix times \c boxSizeMult. If this is a negative number,
the side length will equal \c -boxSizeMult (i.e. independent
of the elements of the distance matrix).
\param randNegEig Picks coordinates at random when a embedding process produces
negative eigenvalues
\param numZeroFail Fail embedding if we find this many or more zero eigenvalues
(within a tolerance)
\param pruneRmsThresh Retain only the conformations out of 'numConfs' after embedding that are
at least this far apart from each other. RMSD is computed on the heavy atoms.
Prunining is greedy; i.e. the first embedded conformation is retained and from
then on only those that are atleast pruneRmsThresh away from already
retained conformations are kept. The pruning is done after embedding and
bounds violation minimization. No pruning by default.
\param coordMap a map of int to Point3D, between atom IDs and their locations
their locations. If this container is provided, the coordinates
are used to set distance constraints on the embedding. The resulting
conformer(s) should have distances between the specified atoms that
reproduce those between the points in \c coordMap. Because the embedding
produces a molecule in an arbitrary reference frame, an alignment step
is required to actually reproduce the provided coordinates.
\param optimizerForceTol set the tolerance on forces in the DGeom optimizer
(this shouldn't normally be altered in client code).
\param ignoreSmoothingFailures try to embed the molecule even if triangle bounds
smoothing fails
\param basinThresh set the basin threshold for the DGeom force field,
(this shouldn't normally be altered in client code).
*/
void EmbedMultipleConfs(ROMol &mol,
INT_VECT &res,
unsigned int numConfs=10,
int numThreads=1,
unsigned int maxIterations=30,
int seed=-1, bool clearConfs=true,
bool useRandomCoords=false,double boxSizeMult=2.0,
bool randNegEig=true, unsigned int numZeroFail=1,
double pruneRmsThresh=-1.0,
const std::map<int,RDGeom::Point3D> *coordMap=0,
double optimizerForceTol=1e-3,
bool ignoreSmoothingFailures=false,
double basinThresh=5.0);
//! \overload
INT_VECT EmbedMultipleConfs(ROMol &mol, unsigned int numConfs=10,
unsigned int maxIterations=30,
int seed=-1, bool clearConfs=true,
bool useRandomCoords=false,double boxSizeMult=2.0,
bool randNegEig=true, unsigned int numZeroFail=1,
double pruneRmsThresh=-1.0,
const std::map<int,RDGeom::Point3D> *coordMap=0,
double optimizerForceTol=1e-3,
bool ignoreSmoothingFailures=false,
double basinThresh=5.0);
}
}
#endif
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