1 //
2 // Copyright (C) 2003-2006 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 #include <RDGeneral/export.h>
11 #ifndef _RD_MOLTRANSFORMS_H_
12 #define _RD_MOLTRANSFORMS_H_
13
14 #include <Geometry/point.h>
15 #include <Numerics/SymmMatrix.h>
16
17 #ifdef RDK_HAS_EIGEN3
18 #include <Eigen/Dense>
19 #endif
20
21 namespace RDKit {
22 class ROMol;
23 class Atom;
24 class Conformer;
25 } // namespace RDKit
26
27 namespace RDGeom {
28 class Transform3D;
29 }
30
31 namespace MolTransforms {
32 RDKIT_MOLTRANSFORMS_EXPORT void transformMolsAtoms(RDKit::ROMol *mol,
33 RDGeom::Transform3D &tform);
34 RDKIT_MOLTRANSFORMS_EXPORT void transformAtom(RDKit::Atom *atom,
35 RDGeom::Transform3D &tform);
36
37 //! Compute the centroid of a conformer
38 /*!
39 This is simple the average of the heavy atom locations in the conformer,
40 not attention is paid to hydrogens or the differences in atomic radii
41
42 \param conf Conformer of interest
43 \param ignoreHs If true, ignore hydrogen atoms
44 */
45 RDKIT_MOLTRANSFORMS_EXPORT RDGeom::Point3D computeCentroid(
46 const RDKit::Conformer &conf, bool ignoreHs = true);
47
48 #ifdef RDK_HAS_EIGEN3
49 //! Compute principal axes and moments of inertia for a conformer
50 /*!
51 These values are calculated from the inertia tensor:
52 Iij = - sum_{s=1..N}(w_s * r_{si} * r_{sj}) i != j
53 Iii = sum_{s=1..N} sum_{j!=i} (w_s * r_{sj} * r_{sj})
54 where the coordinates are relative to the center of mass.
55
56
57 \param conf Conformer of interest
58 \param axes used to return the principal axes
59 \param moments used to return the principal moments
60 \param ignoreHs If true, ignore hydrogen atoms
61 \param force If true, the calculation will be carried out even if a
62 cached value is present
63 \param weights If present used to weight the atomic coordinates
64
65 \returns whether or not the calculation was successful
66 */
67 RDKIT_MOLTRANSFORMS_EXPORT bool computePrincipalAxesAndMoments(
68 const RDKit::Conformer &conf, Eigen::Matrix3d &axes,
69 Eigen::Vector3d &moments, bool ignoreHs = false, bool force = false,
70 const std::vector<double> *weights = nullptr);
71 //! Compute principal axes and moments from the gyration matrix of a conformer
72 /*!
73
74 These values are calculated from the gyration matrix/tensor:
75 Iij = sum_{s=1..N}(w_s * r_{si} * r_{sj}) i != j
76 Iii = sum_{s=1..N} sum_{t!=s}(w_s * r_{si} * r_{ti})
77 where the coordinates are relative to the center of mass.
78
79 \param conf Conformer of interest
80 \param axes used to return the principal axes
81 \param moments used to return the principal moments
82 \param ignoreHs If true, ignore hydrogen atoms
83 \param force If true, the calculation will be carried out even if a
84 cached value is present
85 \param weights If present used to weight the atomic coordinates
86
87 \returns whether or not the calculation was successful
88 */
89 RDKIT_MOLTRANSFORMS_EXPORT bool
90 computePrincipalAxesAndMomentsFromGyrationMatrix(
91 const RDKit::Conformer &conf, Eigen::Matrix3d &axes,
92 Eigen::Vector3d &moments, bool ignoreHs = false, bool force = false,
93 const std::vector<double> *weights = nullptr);
94 #endif
95
96 //! Compute the transformation require to orient the conformation
97 //! along the principal axes about the center; i.e. center is made to coincide
98 // with the
99 //! origin, the largest principal axis with the x-axis, the next largest with
100 // the y-axis
101 //! and the smallest with the z-axis
102 /*!
103 If center is not specified the centroid of the conformer will be used
104 \param conf Conformer of interest
105 \param center Center to be used for canonicalization, defaults to
106 the centroid of the
107 conformation
108 \param normalizeCovar Normalize the covariance matrix with the number of
109 atoms
110 \param ignoreHs Optionally ignore hydrogens
111 */
112 RDKIT_MOLTRANSFORMS_EXPORT RDGeom::Transform3D *computeCanonicalTransform(
113 const RDKit::Conformer &conf, const RDGeom::Point3D *center = nullptr,
114 bool normalizeCovar = false, bool ignoreHs = true);
115
116 //! Transform the conformation using the specified transformation
117 RDKIT_MOLTRANSFORMS_EXPORT void transformConformer(
118 RDKit::Conformer &conf, const RDGeom::Transform3D &trans);
119
120 //! Transforms coordinates in a molecule's substance groups
121 RDKIT_MOLTRANSFORMS_EXPORT void transformMolSubstanceGroups(
122 RDKit::ROMol &mol, const RDGeom::Transform3D &trans);
123
124 //! Canonicalize the orientation of a conformer so that its principal axes
125 //! around the specified center point coincide with the x, y, z axes
126 /*!
127 \param conf The conformer of interest
128 \param center Optional center point about which the principal axes are
129 computed
130 if not specified the centroid of the conformer will be
131 used
132 \param normalizeCovar Optionally normalize the covariance matrix by the number
133 of atoms
134 \param ignoreHs If true, ignore hydrogen atoms
135
136 */
137 RDKIT_MOLTRANSFORMS_EXPORT void canonicalizeConformer(
138 RDKit::Conformer &conf, const RDGeom::Point3D *center = nullptr,
139 bool normalizeCovar = false, bool ignoreHs = true);
140
141 //! Canonicalize all the conformations in a molecule
142 /*!
143 \param mol the molecule of interest
144 \param normalizeCovar Optionally normalize the covariance matrix by the number
145 of atoms
146 \param ignoreHs If true, ignore hydrogens
147 */
148 RDKIT_MOLTRANSFORMS_EXPORT void canonicalizeMol(RDKit::ROMol &mol,
149 bool normalizeCovar = false,
150 bool ignoreHs = true);
151
152 //! Get the bond length between the specified atoms i, j
153 RDKIT_MOLTRANSFORMS_EXPORT double getBondLength(const RDKit::Conformer &conf,
154 unsigned int iAtomId,
155 unsigned int jAtomId);
156
157 //! Set the bond length between the specified atoms i, j
158 //! (all atoms bonded to atom j are moved)
159 RDKIT_MOLTRANSFORMS_EXPORT void setBondLength(RDKit::Conformer &conf,
160 unsigned int iAtomId,
161 unsigned int jAtomId,
162 double value);
163
164 //! Get the angle in radians among the specified atoms i, j, k
165 RDKIT_MOLTRANSFORMS_EXPORT double getAngleRad(const RDKit::Conformer &conf,
166 unsigned int iAtomId,
167 unsigned int jAtomId,
168 unsigned int kAtomId);
169
170 //! Get the angle in degrees among the specified atoms i, j, k
getAngleDeg(const RDKit::Conformer & conf,unsigned int iAtomId,unsigned int jAtomId,unsigned int kAtomId)171 inline double getAngleDeg(const RDKit::Conformer &conf, unsigned int iAtomId,
172 unsigned int jAtomId, unsigned int kAtomId) {
173 return (180. / M_PI * getAngleRad(conf, iAtomId, jAtomId, kAtomId));
174 }
175
176 //! Set the angle in radians among the specified atoms i, j, k
177 //! (all atoms bonded to atom k are moved)
178 RDKIT_MOLTRANSFORMS_EXPORT void setAngleRad(RDKit::Conformer &conf,
179 unsigned int iAtomId,
180 unsigned int jAtomId,
181 unsigned int kAtomId, double value);
182
183 //! Set the angle in degrees among the specified atoms i, j, k
184 //! (all atoms bonded to atom k are moved)
setAngleDeg(RDKit::Conformer & conf,unsigned int iAtomId,unsigned int jAtomId,unsigned int kAtomId,double value)185 inline void setAngleDeg(RDKit::Conformer &conf, unsigned int iAtomId,
186 unsigned int jAtomId, unsigned int kAtomId,
187 double value) {
188 setAngleRad(conf, iAtomId, jAtomId, kAtomId, value / 180. * M_PI);
189 }
190
191 //! Get the dihedral angle in radians among the specified atoms i, j, k, l
192 RDKIT_MOLTRANSFORMS_EXPORT double getDihedralRad(const RDKit::Conformer &conf,
193 unsigned int iAtomId,
194 unsigned int jAtomId,
195 unsigned int kAtomId,
196 unsigned int lAtomId);
197
198 //! Get the dihedral angle in degrees among the specified atoms i, j, k, l
getDihedralDeg(const RDKit::Conformer & conf,unsigned int iAtomId,unsigned int jAtomId,unsigned int kAtomId,unsigned int lAtomId)199 inline double getDihedralDeg(const RDKit::Conformer &conf, unsigned int iAtomId,
200 unsigned int jAtomId, unsigned int kAtomId,
201 unsigned int lAtomId) {
202 return (180. / M_PI *
203 getDihedralRad(conf, iAtomId, jAtomId, kAtomId, lAtomId));
204 }
205
206 //! Set the dihedral angle in radians among the specified atoms i, j, k, l
207 //! (all atoms bonded to atom l are moved)
208 RDKIT_MOLTRANSFORMS_EXPORT void setDihedralRad(
209 RDKit::Conformer &conf, unsigned int iAtomId, unsigned int jAtomId,
210 unsigned int kAtomId, unsigned int lAtomId, double value);
211
212 //! Set the dihedral angle in degrees among the specified atoms i, j, k, l
213 //! (all atoms bonded to atom l are moved)
setDihedralDeg(RDKit::Conformer & conf,unsigned int iAtomId,unsigned int jAtomId,unsigned int kAtomId,unsigned int lAtomId,double value)214 inline void setDihedralDeg(RDKit::Conformer &conf, unsigned int iAtomId,
215 unsigned int jAtomId, unsigned int kAtomId,
216 unsigned int lAtomId, double value) {
217 setDihedralRad(conf, iAtomId, jAtomId, kAtomId, lAtomId, value / 180. * M_PI);
218 }
219 } // namespace MolTransforms
220 #endif
221