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RDKit
Open-source cheminformatics and machine learning.
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Classes | |
struct | EmbedParameters |
Parameter object for controlling embedding. More... | |
Functions | |
RDKIT_DISTGEOMHELPERS_EXPORT void | initBoundsMat (DistGeom::BoundsMatrix *mmat, double defaultMin=0.0, double defaultMax=1000.0) |
Set default upper and lower distance bounds in a distance matrix. More... | |
RDKIT_DISTGEOMHELPERS_EXPORT void | initBoundsMat (DistGeom::BoundsMatPtr mmat, double defaultMin=0.0, double defaultMax=1000.0) |
RDKIT_DISTGEOMHELPERS_EXPORT 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. More... | |
RDKIT_DISTGEOMHELPERS_EXPORT void | setTopolBounds (const ROMol &mol, DistGeom::BoundsMatPtr mmat, std::vector< std::pair< int, int > > &bonds, std::vector< std::vector< int > > &angles, bool set15bounds=true, bool scaleVDW=false) |
RDKIT_DISTGEOMHELPERS_EXPORT void | EmbedMultipleConfs (ROMol &mol, INT_VECT &res, unsigned int numConfs, const EmbedParameters ¶ms) |
INT_VECT | EmbedMultipleConfs (ROMol &mol, unsigned int numConfs, const EmbedParameters ¶ms) |
int | EmbedMolecule (ROMol &mol, const EmbedParameters ¶ms) |
Compute an embedding (in 3D) for the specified molecule using Distance. More... | |
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, bool onlyHeavyAtomsForRMS=false) |
Compute an embedding (in 3D) for the specified molecule using Distance. More... | |
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, bool onlyHeavyAtomsForRMS=false) |
INT_VECT | EmbedMultipleConfs (ROMol &mol, unsigned int numConfs=10, 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, bool onlyHeavyAtomsForRMS=false) |
Variables | |
RDKIT_DISTGEOMHELPERS_EXPORT const EmbedParameters | KDG |
Parameters corresponding to Sereina Riniker's KDG approach. More... | |
RDKIT_DISTGEOMHELPERS_EXPORT const EmbedParameters | ETDG |
Parameters corresponding to Sereina Riniker's ETDG approach. More... | |
RDKIT_DISTGEOMHELPERS_EXPORT const EmbedParameters | ETKDG |
Parameters corresponding to Sereina Riniker's ETKDG approach. More... | |
RDKIT_DISTGEOMHELPERS_EXPORT const EmbedParameters | ETKDGv2 |
Parameters corresponding to Sereina Riniker's ETKDG approach - version 2. More... | |
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Compute an embedding (in 3D) for the specified molecule using Distance.
Definition at line 181 of file Embedder.h.
References EmbedMultipleConfs().
Referenced by EmbedMolecule().
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Compute an embedding (in 3D) for the specified molecule using Distance.
The following operations are performed (in order) here:
Adjust initial coordinates by minimizing a Distance Violation error function
NOTE**: if the molecule has multiple fragments, they will be embedded separately, this means that they will likely occupy the same region of space.
mol | Molecule of interest |
maxIterations | Max. number of times the embedding will be tried if coordinates are not obtained successfully. The default value is 10x the number of atoms. |
seed | provides a seed for the random number generator (so that the same coordinates can be obtained for a molecule on multiple runs). If negative, the RNG will not be seeded. |
clearConfs | Clear all existing conformations on the molecule |
useRandomCoords | Start the embedding from random coordinates instead of using eigenvalues of the distance matrix. |
boxSizeMult | Determines the size of the box that is used for random coordinates. If this is a positive number, the side length will equal the largest element of the distance matrix times boxSizeMult . If this is a negative number, the side length will equal -boxSizeMult (i.e. independent of the elements of the distance matrix). |
randNegEig | Picks coordinates at random when a embedding process produces negative eigenvalues |
numZeroFail | Fail embedding if we find this many or more zero eigenvalues (within a tolerance) |
coordMap | a map of int to Point3D, between atom IDs and their locations their locations. If this container is provided, the coordinates are used to set distance constraints on the embedding. The resulting conformer(s) should have distances between the specified atoms that reproduce those between the points in coordMap . Because the embedding produces a molecule in an arbitrary reference frame, an alignment step is required to actually reproduce the provided coordinates. |
optimizerForceTol | set the tolerance on forces in the distgeom optimizer (this shouldn't normally be altered in client code). |
ignoreSmoothingFailures | try to embed the molecule even if triangle bounds smoothing fails |
enforceChirality | enforce the correct chirality if chiral centers are present |
useExpTorsionAnglePrefs | impose experimental torsion-angle preferences |
useBasicKnowledge | impose "basic knowledge" terms such as flat aromatic rings, ketones, etc. |
verbose | print output of experimental torsion-angle preferences |
basinThresh | set the basin threshold for the DGeom force field, (this shouldn't normally be altered in client code). |
onlyHeavyAtomsForRMS | only use the heavy atoms when doing RMS filtering |
Definition at line 262 of file Embedder.h.
References EmbedMolecule().
RDKIT_DISTGEOMHELPERS_EXPORT void RDKit::DGeomHelpers::EmbedMultipleConfs | ( | ROMol & | mol, |
INT_VECT & | res, | ||
unsigned int | numConfs, | ||
const EmbedParameters & | params | ||
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Referenced by EmbedMolecule(), EmbedMultipleConfs(), and RDKit::DGeomHelpers::EmbedParameters::EmbedParameters().
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Definition at line 172 of file Embedder.h.
References EmbedMultipleConfs().
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This is kind of equivalent to calling EmbedMolecule multiple times - just that the bounds matrix is computed only once from the topology
NOTE**: if the molecule has multiple fragments, they will be embedded separately, this means that they will likely occupy the same region of space.
mol | Molecule of interest |
res | Used to return the resulting conformer ids |
numConfs | Number of conformations to be generated |
numThreads | Sets the number of threads to use (more than one thread will only be used if the RDKit was build with multithread support). If set to zero, the max supported by the system will be used. |
maxIterations | Max. number of times the embedding will be tried if coordinates are not obtained successfully. The default value is 10x the number of atoms. |
seed | provides a seed for the random number generator (so that the same coordinates can be obtained for a molecule on multiple runs). If negative, the RNG will not be seeded. |
clearConfs | Clear all existing conformations on the molecule |
useRandomCoords | Start the embedding from random coordinates instead of using eigenvalues of the distance matrix. |
boxSizeMult | Determines the size of the box that is used for random coordinates. If this is a positive number, the side length will equal the largest element of the distance matrix times boxSizeMult . If this is a negative number, the side length will equal -boxSizeMult (i.e. independent of the elements of the distance matrix). |
randNegEig | Picks coordinates at random when a embedding process produces negative eigenvalues |
numZeroFail | Fail embedding if we find this many or more zero eigenvalues (within a tolerance) |
pruneRmsThresh | Retain only the conformations out of 'numConfs' after embedding that are at least this far apart from each other. RMSD is computed on the heavy atoms. Pruning is greedy; i.e. the first embedded conformation is retained and from then on only those that are at least pruneRmsThresh away from already retained conformations are kept. The pruning is done after embedding and bounds violation minimization. No pruning by default. |
coordMap | a map of int to Point3D, between atom IDs and their locations their locations. If this container is provided, the coordinates are used to set distance constraints on the embedding. The resulting conformer(s) should have distances between the specified atoms that reproduce those between the points in coordMap . Because the embedding produces a molecule in an arbitrary reference frame, an alignment step is required to actually reproduce the provided coordinates. |
optimizerForceTol | set the tolerance on forces in the DGeom optimizer (this shouldn't normally be altered in client code). |
ignoreSmoothingFailures | try to embed the molecule even if triangle bounds smoothing fails |
enforceChirality | enforce the correct chirality if chiral centers are present |
useExpTorsionAnglePrefs | impose experimental torsion-angle preferences |
useBasicKnowledge | impose "basic knowledge" terms such as flat aromatic rings, ketones, etc. |
verbose | print output of experimental torsion-angle preferences |
basinThresh | set the basin threshold for the DGeom force field, (this shouldn't normally be altered in client code). |
onlyHeavyAtomsForRMS | only use the heavy atoms when doing RMS filtering |
Definition at line 354 of file Embedder.h.
References EmbedMultipleConfs().
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This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
Definition at line 374 of file Embedder.h.
References EmbedMultipleConfs(), ETDG, ETKDG, ETKDGv2, KDG, and RDKIT_DISTGEOMHELPERS_EXPORT.
RDKIT_DISTGEOMHELPERS_EXPORT void RDKit::DGeomHelpers::initBoundsMat | ( | DistGeom::BoundsMatrix * | mmat, |
double | defaultMin = 0.0 , |
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double | defaultMax = 1000.0 |
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Set default upper and lower distance bounds in a distance matrix.
mmat | pointer to the bounds matrix to be altered |
defaultMin | default value for the lower distance bounds |
defaultMax | default value for the upper distance bounds |
RDKIT_DISTGEOMHELPERS_EXPORT void RDKit::DGeomHelpers::initBoundsMat | ( | DistGeom::BoundsMatPtr | mmat, |
double | defaultMin = 0.0 , |
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double | defaultMax = 1000.0 |
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RDKIT_DISTGEOMHELPERS_EXPORT void RDKit::DGeomHelpers::setTopolBounds | ( | const ROMol & | mol, |
DistGeom::BoundsMatPtr | mmat, | ||
bool | set15bounds = true , |
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bool | scaleVDW = false |
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Set upper and lower distance bounds between atoms in a molecule based on.
This consists of setting 1-2, 1-3 and 1-4 distance based on bond lengths, bond angles and torsion angle ranges. Optionally 1-5 bounds can also be set, in particular, for path that contain rigid 1-4 paths.
The final step involves setting lower bound to the sum of the vdW radii for the remaining atom pairs.
mol | The molecule of interest |
mmat | Bounds matrix to the bounds are written |
set15bounds | If true try to set 1-5 bounds also based on topology |
scaleVDW | If true scale the sum of the vdW radii while setting lower bounds so that a smaller value (0.7*(vdw1 + vdw2) ) is used for paths that are less five bonds apart. |
Note For some strained systems the bounds matrix resulting from setting 1-5 bounds may fail triangle smoothing. In these cases it is recommended to back out and recompute the bounds matrix with no 1-5 bounds and with vdW scaling.
RDKIT_DISTGEOMHELPERS_EXPORT void RDKit::DGeomHelpers::setTopolBounds | ( | const ROMol & | mol, |
DistGeom::BoundsMatPtr | mmat, | ||
std::vector< std::pair< int, int > > & | bonds, | ||
std::vector< std::vector< int > > & | angles, | ||
bool | set15bounds = true , |
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bool | scaleVDW = false |
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Overload for experimental torsion angle preferences
RDKIT_DISTGEOMHELPERS_EXPORT const EmbedParameters RDKit::DGeomHelpers::ETDG |
Parameters corresponding to Sereina Riniker's ETDG approach.
Referenced by EmbedMultipleConfs().
RDKIT_DISTGEOMHELPERS_EXPORT const EmbedParameters RDKit::DGeomHelpers::ETKDG |
Parameters corresponding to Sereina Riniker's ETKDG approach.
Referenced by EmbedMultipleConfs().
RDKIT_DISTGEOMHELPERS_EXPORT const EmbedParameters RDKit::DGeomHelpers::ETKDGv2 |
Parameters corresponding to Sereina Riniker's ETKDG approach - version 2.
Referenced by EmbedMultipleConfs().
RDKIT_DISTGEOMHELPERS_EXPORT const EmbedParameters RDKit::DGeomHelpers::KDG |
Parameters corresponding to Sereina Riniker's KDG approach.
Referenced by EmbedMultipleConfs().