11 #ifndef _RD_EMBEDDER_H_ 12 #define _RD_EMBEDDER_H_ 19 namespace DGeomHelpers {
72 int EmbedMolecule(ROMol &mol,
unsigned int maxIterations=0,
int seed=-1,
74 bool useRandomCoords=
false,
double boxSizeMult=2.0,
76 unsigned int numZeroFail=1,
77 const std::map<int,RDGeom::Point3D> *coordMap=0,
78 double optimizerForceTol=1e-3,
79 bool ignoreSmoothingFailures=
false,
80 double basinThresh=5.0
143 unsigned int numConfs=10,
145 unsigned int maxIterations=30,
146 int seed=-1,
bool clearConfs=
true,
147 bool useRandomCoords=
false,
double boxSizeMult=2.0,
148 bool randNegEig=
true,
unsigned int numZeroFail=1,
149 double pruneRmsThresh=-1.0,
150 const std::map<int,RDGeom::Point3D> *coordMap=0,
151 double optimizerForceTol=1e-3,
152 bool ignoreSmoothingFailures=
false,
153 double basinThresh=5.0);
156 unsigned int maxIterations=30,
157 int seed=-1,
bool clearConfs=
true,
158 bool useRandomCoords=
false,
double boxSizeMult=2.0,
159 bool randNegEig=
true,
unsigned int numZeroFail=1,
160 double pruneRmsThresh=-1.0,
161 const std::map<int,RDGeom::Point3D> *coordMap=0,
162 double optimizerForceTol=1e-3,
163 bool ignoreSmoothingFailures=
false,
164 double basinThresh=5.0);
Defines the primary molecule class ROMol as well as associated typedefs.
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)
Compute an embedding (in 3D) for the specified molecule using Distance Geometry.
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)
std::vector< int > INT_VECT
Includes a bunch of functionality for handling Atom and Bond queries.