RDKit
Open-source cheminformatics and machine learning.
BoundsMatrixBuilder.h
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1 //
2 // Copyright (C) 2004-2006 Rational Discovery LLC
3 //
4 // @@ All Rights Reserved @@
5 // This file is part of the RDKit.
6 // The contents are covered by the terms of the BSD license
7 // which is included in the file license.txt, found at the root
8 // of the RDKit source tree.
9 //
10 #ifndef _RD_BOUNDS_MATRIX_BUILDER_H_
11 #define _RD_BOUNDS_MATRIX_BUILDER_H_
12 
13 #include <DistGeom/BoundsMatrix.h>
14 
15 namespace RDKit {
16  class ROMol;
17  namespace DGeomHelpers {
18  //! Set default upper and lower distance bounds in a distance matrix
19  /*!
20  \param mmat pointer to the bounds matrix to be altered
21  \param defaultMin default value for the lower distance bounds
22  \param defaultMax default value for the upper distance bounds
23 
24  */
25  void initBoundsMat(DistGeom::BoundsMatrix *mmat,double defaultMin=0.0,
26  double defaultMax=1000.0);
27  void initBoundsMat(DistGeom::BoundsMatPtr mmat,double defaultMin=0.0,
28  double defaultMax=1000.0);
29 
30  //! Set upper and lower distance bounds between atoms in a molecule based on topology
31  /*!
32  This consists of setting 1-2, 1-3 and 1-4 distance based on bond lengths,
33  bond angles and torsion angle ranges. Optionally 1-5 bounds can also be set,
34  in particular, for path that contain rigid 1-4 paths.
35 
36  The final step involves setting lower bound to the sum of the vdW radii for
37  the remaining atom pairs.
38 
39  \param mol The molecule of interest
40  \param mmat Bounds matrix to the bounds are written
41  \param set15bounds If true try to set 1-5 bounds also based on topology
42  \param scaleVDW If true scale the sum of the vdW radii while setting lower bounds
43  so that a smaller value (0.7*(vdw1 + vdw2) ) is used for paths
44  that are less five bonds apart.
45 
46  <b>Note</b>
47  For some strained systems the bounds matrix resulting from setting 1-5 bounds may
48  fail triangle smoothing. In these cases it is recommended to back out and
49  recompute the bounds matrix with no 1-5 bounds and with vdW scaling.
50  */
51  void setTopolBounds(const ROMol &mol, DistGeom::BoundsMatPtr mmat,
52  bool set15bounds=true, bool scaleVDW=false);
53  }
54 }
55 #endif
boost::shared_ptr< BoundsMatrix > BoundsMatPtr
Definition: BoundsMatrix.h:113
ROMol is a molecule class that is intended to have a fixed topology.
Definition: ROMol.h:105
void initBoundsMat(DistGeom::BoundsMatrix *mmat, double defaultMin=0.0, double defaultMax=1000.0)
Set default upper and lower distance bounds in a distance matrix.
void setTopolBounds(const ROMol &mol, DistGeom::BoundsMatPtr mmat, bool set15bounds=true, bool scaleVDW=false)
Set upper and lower distance bounds between atoms in a molecule based on topology.
Includes a bunch of functionality for handling Atom and Bond queries.
Definition: Atom.h:28
Class to store the distance bound.
Definition: BoundsMatrix.h:26