11 #ifndef _RD_EMBEDDER_H_ 12 #define _RD_EMBEDDER_H_ 19 namespace DGeomHelpers {
100 int EmbedMolecule(ROMol &mol,
unsigned int maxIterations = 0,
int seed = -1,
101 bool clearConfs =
true,
bool useRandomCoords =
false,
102 double boxSizeMult = 2.0,
bool randNegEig =
true,
103 unsigned int numZeroFail = 1,
104 const std::map<int, RDGeom::Point3D> *coordMap = 0,
105 double optimizerForceTol = 1e-3,
106 bool ignoreSmoothingFailures =
false,
107 bool enforceChirality =
true,
108 bool useExpTorsionAnglePrefs =
false,
109 bool useBasicKnowledge =
false,
bool verbose =
false,
110 double basinThresh = 5.0);
201 int numThreads = 1,
unsigned int maxIterations = 30,
202 int seed = -1,
bool clearConfs =
true,
203 bool useRandomCoords =
false,
double boxSizeMult = 2.0,
204 bool randNegEig =
true,
unsigned int numZeroFail = 1,
205 double pruneRmsThresh = -1.0,
206 const std::map<int, RDGeom::Point3D> *coordMap = 0,
207 double optimizerForceTol = 1e-3,
208 bool ignoreSmoothingFailures =
false,
209 bool enforceChirality =
true,
210 bool useExpTorsionAnglePrefs =
false,
211 bool useBasicKnowledge =
false,
bool verbose =
false,
212 double basinThresh = 5.0);
215 ROMol &mol,
unsigned int numConfs = 10,
unsigned int maxIterations = 30,
216 int seed = -1,
bool clearConfs =
true,
bool useRandomCoords =
false,
217 double boxSizeMult = 2.0,
bool randNegEig =
true,
218 unsigned int numZeroFail = 1,
double pruneRmsThresh = -1.0,
219 const std::map<int, RDGeom::Point3D> *coordMap = 0,
220 double optimizerForceTol = 1e-3,
bool ignoreSmoothingFailures =
false,
221 bool enforceChirality =
true,
bool useExpTorsionAnglePrefs =
false,
222 bool useBasicKnowledge =
false,
bool verbose =
false,
223 double basinThresh = 5.0);
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, bool enforceChirality=true, bool useExpTorsionAnglePrefs=false, bool useBasicKnowledge=false, bool verbose=false, double basinThresh=5.0)
Compute an embedding (in 3D) for the specified molecule using Distance.
Defines the primary molecule class ROMol as well as associated typedefs.
std::vector< int > INT_VECT
Includes a bunch of functionality for handling Atom and Bond queries.
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, bool enforceChirality=true, bool useExpTorsionAnglePrefs=false, bool useBasicKnowledge=false, bool verbose=false, double basinThresh=5.0)