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
31 // topology
32 /*!
33  This consists of setting 1-2, 1-3 and 1-4 distance based on bond lengths,
34  bond angles and torsion angle ranges. Optionally 1-5 bounds can also be set,
35  in particular, for path that contain rigid 1-4 paths.
36 
37  The final step involves setting lower bound to the sum of the vdW radii for
38  the remaining atom pairs.
39 
40  \param mol The molecule of interest
41  \param mmat Bounds matrix to the bounds are written
42  \param set15bounds If true try to set 1-5 bounds also based on topology
43  \param scaleVDW If true scale the sum of the vdW radii while setting lower
44  bounds
45  so that a smaller value (0.7*(vdw1 + vdw2) ) is used for
46  paths
47  that are less five bonds apart.
48 
49  <b>Note</b>
50  For some strained systems the bounds matrix resulting from setting 1-5 bounds
51  may
52  fail triangle smoothing. In these cases it is recommended to back out and
53  recompute the bounds matrix with no 1-5 bounds and with vdW scaling.
54 */
55 void setTopolBounds(const ROMol &mol, DistGeom::BoundsMatPtr mmat,
56  bool set15bounds = true, bool scaleVDW = false);
57 
58 /*! Overload for experimental torsion angle preferences */
59 void setTopolBounds(const ROMol &mol, DistGeom::BoundsMatPtr mmat,
60  std::vector<std::pair<int, int> > &bonds,
61  std::vector<std::vector<int> > &angles,
62  bool set15bounds = true, bool scaleVDW = false);
63 }
64 }
65 #endif
boost::shared_ptr< BoundsMatrix > BoundsMatPtr
Definition: BoundsMatrix.h:116
ROMol is a molecule class that is intended to have a fixed topology.
Definition: ROMol.h:103
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.
Std stuff.
Definition: Atom.h:29
Class to store the distance bound.
Definition: BoundsMatrix.h:26