RDKit: RDDepictor.h Source File

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RDDepictor.h
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1 //
2 // Copyright (C) 2003-2010 Greg Landrum and 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
11 #ifndef _RDDEPICTOR_H_
12 #define _RDDEPICTOR_H_
13
14 #include <RDGeneral/types.h>
15 #include <list>
16 #include <GraphMol/ROMol.h>
17 #include "EmbeddedFrag.h"
18
19 namespace RDKit {
20 class ROMol;
21 }
22
23 namespace RDDepict {
24
25 //! \brief Generate 2D coordinates (a depiction) for a molecule
26 /*!
27
28 \param mol the molecule were are interested in
29
30 \param coordMap a map of int to Point2D, between atom IDs and
31 their locations. This is the container the user needs to fill if
32 he/she wants to specify coordinates for a portion of the molecule,
33 defaults to 0
34
35 \param canonOrient canonicalize the orientation so that the long
36 axes align with the x-axis etc.
37
38 \param clearConfs clear all existing conformations on the molecule
39 before adding the 2D coordinates instead of simply adding to the
40 list
41
42 \param nFlipsPerSample - the number of rotatable bonds that are
43 flipped at random for each sample
44
45 \param nSamples - the number of samples
46
47 \param sampleSeed - seed for the random sampling process
48
49 \param permuteDeg4Nodes - try permuting the drawing order of bonds around
50 atoms with four neighbors in order to improve the depiction
51
52 \return ID of the conformation added to the molecule cotaining the
53 2D coordinates
54
55 */
56 unsigned int compute2DCoords(RDKit::ROMol &mol,
57 const RDGeom::INT_POINT2D_MAP *coordMap = 0,
58 bool canonOrient = false, bool clearConfs = true,
59 unsigned int nFlipsPerSample = 0,
60 unsigned int nSamples = 0, int sampleSeed = 0,
61 bool permuteDeg4Nodes = false);
62
63 //! \brief Compute the 2D coordinates such the interatom distances
64 // mimic those in a distance matrix
65 /*!
66
67 This function generates 2D coordinates such that the inter-atom
68 distances mimic those specified via dmat. This is done by randomly
69 sampling(flipping) the rotatable bonds in the molecule and
70 evaluating a cost function which contains two components. The
71 first component is the sum of inverse of the squared inter-atom
72 distances, this helps in spreading the atoms far from each
73 other. The second component is the sum of squares of the
74 difference in distance between those in dmat and the generated
75 structure. The user can adjust the relative importance of the two
76 components via a adjustable paramter (see below)
77
78 ARGUMENTS:
79
80 \param mol - molecule to generate coordinates for
81
82 \param dmat - the distance matrix we want to mimic, this is a
83 symmetric N by N matrix where N is the number of atoms in mol. All
84 negative entries in dmat are ignored.
85
86 \param canonOrient - canonicalize the orientation after the 2D
87 embedding is done
88
89 \param clearConfs - clear any previously existing conformations on
90 mol before adding a conformation
91
92 \param weightDistMat - A value between 0.0 and 1.0, this
93 determines the importance of mimicing the the inter atoms
94 distances in dmat. (1.0 - weightDistMat) is the weight associated
95 to spreading out the structure (density) in the cost function
96
97 \param nFlipsPerSample - the number of rotatable bonds that are
98 flipped at random for each sample
99
100 \param nSamples - the number of samples
101
102 \param sampleSeed - seed for the random sampling process
103
104 \param permuteDeg4Nodes - try permuting the drawing order of bonds around
105 atoms with four neighbors in order to improve the depiction
106
107 \return ID of the conformation added to the molecule cotaining the
108 2D coordinates
109
110
111 */
112 unsigned int compute2DCoordsMimicDistMat(
113 RDKit::ROMol &mol, const DOUBLE_SMART_PTR *dmat = 0,
114 bool canonOrient = true, bool clearConfs = true, double weightDistMat = 0.5,
115 unsigned int nFlipsPerSample = 3, unsigned int nSamples = 100,
116 int sampleSeed = 25, bool permuteDeg4Nodes = true);
117 };
118
119 #endif
RDDepict::DOUBLE_SMART_PTR
boost::shared_array< double > DOUBLE_SMART_PTR
Definition: EmbeddedFrag.h:25
RDDepict::compute2DCoordsMimicDistMat
unsigned int compute2DCoordsMimicDistMat(RDKit::ROMol &mol, const DOUBLE_SMART_PTR *dmat=0, bool canonOrient=true, bool clearConfs=true, double weightDistMat=0.5, unsigned int nFlipsPerSample=3, unsigned int nSamples=100, int sampleSeed=25, bool permuteDeg4Nodes=true)
Compute the 2D coordinates such the interatom distances.
types.h
EmbeddedFrag.h
ROMol.h
Defines the primary molecule class ROMol as well as associated typedefs.
RDKit::ROMol
ROMol is a molecule class that is intended to have a fixed topology.
Definition: ROMol.h:102
RDGeom::INT_POINT2D_MAP
std::map< int, Point2D > INT_POINT2D_MAP
Definition: point.h:511
RDDepict
Definition: Reaction.h:422
RDKit
Includes a bunch of functionality for handling Atom and Bond queries.
Definition: Atom.h:28
RDDepict::compute2DCoords
unsigned int compute2DCoords(RDKit::ROMol &mol, const RDGeom::INT_POINT2D_MAP *coordMap=0, bool canonOrient=false, bool clearConfs=true, unsigned int nFlipsPerSample=0, unsigned int nSamples=0, int sampleSeed=0, bool permuteDeg4Nodes=false)
Generate 2D coordinates (a depiction) for a molecule.