public class ROMol extends RDProps
This is the primary class for most molecule operations.
If you need to be manipulating the molecule (e.g. adding or deleting atoms or bonds, use an RWMol instead.
Modifier | Constructor and Description |
---|---|
|
ROMol() |
protected |
ROMol(long cPtr,
boolean cMemoryOwn) |
|
ROMol(ROMol other) |
|
ROMol(ROMol other,
boolean quickCopy) |
|
ROMol(ROMol other,
boolean quickCopy,
int confId) |
|
ROMol(java.lang.String binStr) |
Modifier and Type | Method and Description |
---|---|
long |
addConformer(Conformer ownedConf) |
long |
addConformer(Conformer ownedConf,
boolean assignId) |
ROMol |
addHs(boolean explicitOnly) |
ROMol |
addHs(boolean explicitOnly,
boolean addCoords) |
double |
alignMol(ROMol refMol) |
double |
alignMol(ROMol refMol,
int prbCid) |
double |
alignMol(ROMol refMol,
int prbCid,
int refCid) |
double |
alignMol(ROMol refMol,
int prbCid,
int refCid,
Match_Vect atomMap) |
double |
alignMol(ROMol refMol,
int prbCid,
int refCid,
Match_Vect atomMap,
SWIGTYPE_p_RDNumeric__VectorT_double_t weights) |
double |
alignMol(ROMol refMol,
int prbCid,
int refCid,
Match_Vect atomMap,
SWIGTYPE_p_RDNumeric__VectorT_double_t weights,
boolean reflect) |
double |
alignMol(ROMol refMol,
int prbCid,
int refCid,
Match_Vect atomMap,
SWIGTYPE_p_RDNumeric__VectorT_double_t weights,
boolean reflect,
long maxIters) |
void |
alignMolConformers(ROMol mol) |
void |
alignMolConformers(ROMol mol,
UInt_Vect atomIds) |
void |
alignMolConformers(ROMol mol,
UInt_Vect atomIds,
UInt_Vect confIds) |
void |
alignMolConformers(ROMol mol,
UInt_Vect atomIds,
UInt_Vect confIds,
SWIGTYPE_p_RDNumeric__VectorT_double_t weights) |
void |
alignMolConformers(ROMol mol,
UInt_Vect atomIds,
UInt_Vect confIds,
SWIGTYPE_p_RDNumeric__VectorT_double_t weights,
boolean reflect) |
void |
alignMolConformers(ROMol mol,
UInt_Vect atomIds,
UInt_Vect confIds,
SWIGTYPE_p_RDNumeric__VectorT_double_t weights,
boolean reflect,
long maxIters) |
SWIGTYPE_p_RDKit__CXXAtomIteratorT_boost__adjacency_listT_boost__vecS_boost__vecS_boost__undirectedS_RDKit__Atom_p_RDKit__Bond_p_t_RDKit__Atom_p_t |
atoms() |
AromaticAtomIterator |
beginAromaticAtoms() |
AtomIterator |
beginAtoms() |
BondIterator |
beginBonds() |
SWIGTYPE_p_std__listT_boost__shared_ptrT_RDKit__Conformer_t_t__iterator |
beginConformers() |
HeteroatomIterator |
beginHeteros() |
SWIGTYPE_p_RDKit__MatchingAtomIterator_T_RDKit__Atom_const_RDKit__ROMol_const_t |
beginMatchingAtoms(SWIGTYPE_p_f_p_q_const__RDKit__Atom__bool query) |
SWIGTYPE_p_RDKit__MatchingAtomIterator_T_RDKit__Atom_RDKit__ROMol_t |
beginMatchingAtoms(SWIGTYPE_p_f_p_RDKit__Atom__bool query) |
QueryAtomIterator |
beginQueryAtoms(QueryAtom query) |
SWIGTYPE_p_RDKit__CXXBondIteratorT_boost__adjacency_listT_boost__vecS_boost__vecS_boost__undirectedS_RDKit__Atom_p_RDKit__Bond_p_t_RDKit__Bond_p_t |
bonds() |
void |
canonicalizeMol() |
void |
canonicalizeMol(boolean normalizeCovar) |
void |
canonicalizeMol(boolean normalizeCovar,
boolean ignoreHs) |
void |
clearAllAtomBookmarks() |
void |
clearAllBondBookmarks() |
void |
clearAtomBookmark(int mark) |
void |
clearAtomBookmark(int mark,
Atom atom) |
void |
clearBondBookmark(int mark) |
void |
clearBondBookmark(int mark,
Bond bond) |
void |
clearComputedProps() |
void |
clearComputedProps(boolean includeRings) |
void |
clearConformers() |
void |
ClearSingleBondDirFlags() |
long |
compute2DCoords() |
long |
compute2DCoords(Int_Point2D_Map coordMap) |
long |
compute2DCoords(Int_Point2D_Map coordMap,
boolean canonOrient) |
long |
compute2DCoords(Int_Point2D_Map coordMap,
boolean canonOrient,
boolean clearConfs) |
long |
compute2DCoords(Int_Point2D_Map coordMap,
boolean canonOrient,
boolean clearConfs,
long nFlipsPerSample) |
long |
compute2DCoords(Int_Point2D_Map coordMap,
boolean canonOrient,
boolean clearConfs,
long nFlipsPerSample,
long nSamples) |
long |
compute2DCoords(Int_Point2D_Map coordMap,
boolean canonOrient,
boolean clearConfs,
long nFlipsPerSample,
long nSamples,
int sampleSeed) |
long |
compute2DCoords(Int_Point2D_Map coordMap,
boolean canonOrient,
boolean clearConfs,
long nFlipsPerSample,
long nSamples,
int sampleSeed,
boolean permuteDeg4Nodes) |
long |
compute2DCoords(Int_Point2D_Map coordMap,
boolean canonOrient,
boolean clearConfs,
long nFlipsPerSample,
long nSamples,
int sampleSeed,
boolean permuteDeg4Nodes,
boolean forceRDKit) |
long |
compute2DCoords(ROMol templ) |
long |
compute2DCoordsMimicDistMat() |
long |
compute2DCoordsMimicDistMat(SWIGTYPE_p_RDDepict__DOUBLE_SMART_PTR dmat) |
long |
compute2DCoordsMimicDistMat(SWIGTYPE_p_RDDepict__DOUBLE_SMART_PTR dmat,
boolean canonOrient) |
long |
compute2DCoordsMimicDistMat(SWIGTYPE_p_RDDepict__DOUBLE_SMART_PTR dmat,
boolean canonOrient,
boolean clearConfs) |
long |
compute2DCoordsMimicDistMat(SWIGTYPE_p_RDDepict__DOUBLE_SMART_PTR dmat,
boolean canonOrient,
boolean clearConfs,
double weightDistMat) |
long |
compute2DCoordsMimicDistMat(SWIGTYPE_p_RDDepict__DOUBLE_SMART_PTR dmat,
boolean canonOrient,
boolean clearConfs,
double weightDistMat,
long nFlipsPerSample) |
long |
compute2DCoordsMimicDistMat(SWIGTYPE_p_RDDepict__DOUBLE_SMART_PTR dmat,
boolean canonOrient,
boolean clearConfs,
double weightDistMat,
long nFlipsPerSample,
long nSamples) |
long |
compute2DCoordsMimicDistMat(SWIGTYPE_p_RDDepict__DOUBLE_SMART_PTR dmat,
boolean canonOrient,
boolean clearConfs,
double weightDistMat,
long nFlipsPerSample,
long nSamples,
int sampleSeed) |
long |
compute2DCoordsMimicDistMat(SWIGTYPE_p_RDDepict__DOUBLE_SMART_PTR dmat,
boolean canonOrient,
boolean clearConfs,
double weightDistMat,
long nFlipsPerSample,
long nSamples,
int sampleSeed,
boolean permuteDeg4Nodes) |
long |
compute2DCoordsMimicDistMat(SWIGTYPE_p_RDDepict__DOUBLE_SMART_PTR dmat,
boolean canonOrient,
boolean clearConfs,
double weightDistMat,
long nFlipsPerSample,
long nSamples,
int sampleSeed,
boolean permuteDeg4Nodes,
boolean forceRDKit) |
void |
computeGasteigerCharges(ROMol mol) |
void |
computeGasteigerCharges(ROMol mol,
Double_Vect charges) |
void |
computeGasteigerCharges(ROMol mol,
Double_Vect charges,
int nIter) |
void |
computeGasteigerCharges(ROMol mol,
Double_Vect charges,
int nIter,
boolean throwOnParamFailure) |
void |
computeGasteigerCharges(ROMol mol,
int nIter) |
void |
computeGasteigerCharges(ROMol mol,
int nIter,
boolean throwOnParamFailure) |
void |
debugMol(SWIGTYPE_p_std__ostream str) |
void |
delete() |
ROMol |
deleteSubstructs(ROMol query,
boolean replaceAll) |
void |
DetectBondStereoChemistry(Conformer conf) |
AromaticAtomIterator |
endAromaticAtoms() |
AtomIterator |
endAtoms() |
BondIterator |
endBonds() |
SWIGTYPE_p_std__listT_boost__shared_ptrT_RDKit__Conformer_t_t__iterator |
endConformers() |
HeteroatomIterator |
endHeteros() |
SWIGTYPE_p_RDKit__MatchingAtomIterator_T_RDKit__Atom_RDKit__ROMol_t |
endMatchingAtoms() |
QueryAtomIterator |
endQueryAtoms() |
protected void |
finalize() |
int |
findSSSR() |
int |
findSSSR(Int_Vect_Vect res) |
void |
generateDepictionMatching2DStructure(ROMol reference) |
void |
generateDepictionMatching2DStructure(ROMol reference,
int confId) |
void |
generateDepictionMatching2DStructure(ROMol reference,
int confId,
boolean acceptFailure) |
void |
generateDepictionMatching2DStructure(ROMol reference,
int confId,
boolean acceptFailure,
boolean forceRDKit) |
void |
generateDepictionMatching2DStructure(ROMol reference,
int confId,
ROMol referencePattern) |
void |
generateDepictionMatching2DStructure(ROMol reference,
int confId,
ROMol referencePattern,
boolean acceptFailure) |
void |
generateDepictionMatching2DStructure(ROMol reference,
int confId,
ROMol referencePattern,
boolean acceptFailure,
boolean forceRDKit) |
SWIGTYPE_p_double |
getAdjacencyMatrix() |
SWIGTYPE_p_double |
getAdjacencyMatrix(boolean useBO) |
SWIGTYPE_p_double |
getAdjacencyMatrix(boolean useBO,
int emptyVal) |
SWIGTYPE_p_double |
getAdjacencyMatrix(boolean useBO,
int emptyVal,
boolean force) |
SWIGTYPE_p_double |
getAdjacencyMatrix(boolean useBO,
int emptyVal,
boolean force,
java.lang.String propNamePrefix) |
double |
getAlignmentTransform(ROMol refMol,
Transform3D trans) |
double |
getAlignmentTransform(ROMol refMol,
Transform3D trans,
int prbCid) |
double |
getAlignmentTransform(ROMol refMol,
Transform3D trans,
int prbCid,
int refCid) |
double |
getAlignmentTransform(ROMol refMol,
Transform3D trans,
int prbCid,
int refCid,
Match_Vect atomMap) |
double |
getAlignmentTransform(ROMol refMol,
Transform3D trans,
int prbCid,
int refCid,
Match_Vect atomMap,
SWIGTYPE_p_RDNumeric__VectorT_double_t weights) |
double |
getAlignmentTransform(ROMol refMol,
Transform3D trans,
int prbCid,
int refCid,
Match_Vect atomMap,
SWIGTYPE_p_RDNumeric__VectorT_double_t weights,
boolean reflect) |
double |
getAlignmentTransform(ROMol refMol,
Transform3D trans,
int prbCid,
int refCid,
Match_Vect atomMap,
SWIGTYPE_p_RDNumeric__VectorT_double_t weights,
boolean reflect,
long maxIters) |
SWIGTYPE_p_std__listT_RDKit__Atom_p_t |
getAllAtomsWithBookmark(int mark) |
SWIGTYPE_p_std__listT_RDKit__Bond_p_t |
getAllBondsWithBookmark(int mark) |
Bond_Vect |
getAtomBonds(Atom at) |
SWIGTYPE_p_std__mapT_int_std__listT_RDKit__Atom_p_t_t |
getAtomBookmarks() |
long |
getAtomDegree(Atom at) |
Atom_Vect |
getAtomNeighbors(Atom at) |
Atom_Vect |
getAtoms() |
Atom |
getAtomWithBookmark(int mark) |
Atom |
getAtomWithIdx(long idx) |
Bond |
getBondBetweenAtoms(long idx1,
long idx2) |
SWIGTYPE_p_std__mapT_int_std__listT_RDKit__Bond_p_t_t |
getBondBookmarks() |
Bond |
getBondWithBookmark(int mark) |
Bond |
getBondWithIdx(long idx) |
Conformer |
getConformer()
return the conformer with a specified ID if the ID is negative the first conformation will be returned
|
Conformer |
getConformer(int id)
return the conformer with a specified ID if the ID is negative the first conformation will be returned
|
protected static long |
getCPtr(ROMol obj) |
SWIGTYPE_p_double |
getDistanceMat() |
SWIGTYPE_p_double |
getDistanceMat(boolean useBO) |
SWIGTYPE_p_double |
getDistanceMat(boolean useBO,
boolean useAtomWts) |
SWIGTYPE_p_double |
getDistanceMat(boolean useBO,
boolean useAtomWts,
boolean force) |
SWIGTYPE_p_double |
getDistanceMat(boolean useBO,
boolean useAtomWts,
boolean force,
java.lang.String propNamePrefix) |
SWIGTYPE_p_double |
getDistanceMat(Int_Vect activeAtoms,
SWIGTYPE_p_std__vectorT_RDKit__Bond_const_p_t bonds) |
SWIGTYPE_p_double |
getDistanceMat(Int_Vect activeAtoms,
SWIGTYPE_p_std__vectorT_RDKit__Bond_const_p_t bonds,
boolean useBO) |
SWIGTYPE_p_double |
getDistanceMat(Int_Vect activeAtoms,
SWIGTYPE_p_std__vectorT_RDKit__Bond_const_p_t bonds,
boolean useBO,
boolean useAtomWts) |
long |
getNumAtoms() |
long |
getNumAtoms(boolean onlyExplicit) |
long |
getNumBonds() |
long |
getNumBonds(boolean onlyHeavy) |
long |
getNumConformers() |
long |
getNumHeavyAtoms() |
java.lang.String |
getProp(java.lang.String key) |
RingInfo |
getRingInfo() |
Int_List |
getShortestPath(int aid1,
int aid2) |
StereoGroup_Vect |
getStereoGroups() |
Match_Vect |
getSubstructMatch(ROMol query) |
Match_Vect |
getSubstructMatch(ROMol query,
boolean useChirality) |
Match_Vect |
getSubstructMatch(ROMol query,
SubstructMatchParameters ps) |
Match_Vect_Vect |
getSubstructMatches(ROMol query) |
Match_Vect_Vect |
getSubstructMatches(ROMol query,
boolean uniquify) |
Match_Vect_Vect |
getSubstructMatches(ROMol query,
boolean uniquify,
boolean useChirality) |
Match_Vect_Vect |
getSubstructMatches(ROMol query,
SubstructMatchParameters ps) |
Atom |
getUniqueAtomWithBookmark(int mark) |
Bond |
getUniqueBondWithBookmark(int mark) |
boolean |
hasAtomBookmark(int mark) |
boolean |
hasBondBookmark(int mark) |
boolean |
hasSubstructMatch(ROMol query) |
boolean |
hasSubstructMatch(ROMol query,
boolean useChirality) |
boolean |
hasSubstructMatch(ROMol query,
SubstructMatchParameters ps) |
ROMol |
mergeQueryHs() |
static ROMol |
MolFromBinary(Int_Vect pkl) |
java.lang.String |
MolToFASTA() |
java.lang.String |
MolToHELM() |
java.lang.String |
MolToMolBlock() |
java.lang.String |
MolToMolBlock(boolean includeStereo) |
java.lang.String |
MolToMolBlock(boolean includeStereo,
int confId) |
void |
MolToMolFile(java.lang.String fName) |
void |
MolToMolFile(java.lang.String fName,
boolean includeStereo) |
void |
MolToMolFile(java.lang.String fName,
boolean includeStereo,
int confId) |
void |
MolToMolFile(java.lang.String fName,
boolean includeStereo,
int confId,
boolean kekulize) |
java.lang.String |
MolToPDBBlock() |
java.lang.String |
MolToPDBBlock(int confId) |
java.lang.String |
MolToPDBBlock(int confId,
long flavor) |
void |
MolToPDBFile(java.lang.String fName) |
void |
MolToPDBFile(java.lang.String fName,
int confId) |
void |
MolToPDBFile(java.lang.String fName,
int confId,
long flavor) |
java.lang.String |
MolToSequence() |
java.lang.String |
MolToSmiles() |
java.lang.String |
MolToSmiles(boolean doIsomericSmiles) |
java.lang.String |
MolToSmiles(boolean doIsomericSmiles,
boolean doKekule) |
java.lang.String |
MolToSmiles(boolean doIsomericSmiles,
boolean doKekule,
int rootedAtAtom) |
void |
MolToTPLFile(java.lang.String fName) |
void |
MolToTPLFile(java.lang.String fName,
java.lang.String partialChargeProp) |
void |
MolToTPLFile(java.lang.String fName,
java.lang.String partialChargeProp,
boolean writeFirstConfTwice) |
java.lang.String |
MolToTPLText() |
java.lang.String |
MolToTPLText(java.lang.String partialChargeProp) |
java.lang.String |
MolToTPLText(java.lang.String partialChargeProp,
boolean writeFirstConfTwice) |
java.lang.String |
MolToXYZBlock() |
java.lang.String |
MolToXYZBlock(int confId) |
void |
MolToXYZFile(java.lang.String fName) |
void |
MolToXYZFile(java.lang.String fName,
int confId) |
boolean |
needsUpdatePropertyCache() |
Double_Pair |
O3AAlignMol(ROMol refMol) |
Double_Pair |
O3AAlignMol(ROMol refMol,
int prbCid) |
Double_Pair |
O3AAlignMol(ROMol refMol,
int prbCid,
int refCid) |
Double_Pair |
O3AAlignMol(ROMol refMol,
int prbCid,
int refCid,
boolean reflect) |
Double_Pair |
O3AAlignMol(ROMol refMol,
int prbCid,
int refCid,
boolean reflect,
long maxIters) |
Double_Pair |
O3AAlignMol(ROMol refMol,
int prbCid,
int refCid,
boolean reflect,
long maxIters,
long accuracy) |
void |
pickBondsToWedge() |
void |
rankMolAtoms(UInt_Vect ranks) |
void |
rankMolAtoms(UInt_Vect ranks,
boolean breakTies) |
void |
rankMolAtoms(UInt_Vect ranks,
boolean breakTies,
boolean includeChirality) |
void |
rankMolAtoms(UInt_Vect ranks,
boolean breakTies,
boolean includeChirality,
boolean includeIsotopes) |
void |
removeConformer(long id) |
ROMol |
removeHs(boolean implicitOnly) |
ROMol |
removeHs(boolean implicitOnly,
boolean updateExplicitCount) |
ROMol |
removeHs(boolean implicitOnly,
boolean updateExplicitCount,
boolean sanitize) |
void |
replaceAtomBookmark(Atom at,
int mark) |
ROMol |
replaceCore(ROMol coreQuery) |
ROMol |
replaceCore(ROMol coreQuery,
boolean replaceDummies) |
ROMol |
replaceCore(ROMol coreQuery,
boolean replaceDummies,
boolean labelByIndex) |
ROMol |
replaceSidechains(ROMol coreQuery) |
ROMol_Vect |
replaceSubstructs(ROMol query,
ROMol replacement) |
ROMol_Vect |
replaceSubstructs(ROMol query,
ROMol replacement,
boolean replaceAll) |
void |
setAtomBookmark(Atom at,
int mark)
This is an overloaded member function, provided for convenience.
|
void |
setBondBookmark(Bond bond,
int mark)
This is an overloaded member function, provided for convenience.
|
void |
setConjugation() |
void |
setHybridization() |
int |
symmetrizeSSSR() |
int |
symmetrizeSSSR(Int_Vect_Vect res) |
Int_Vect |
ToBinary() |
java.lang.String |
ToSVG() |
java.lang.String |
ToSVG(Int_Vect highlightAtoms) |
java.lang.String |
ToSVG(Int_Vect highlightAtoms,
int lineWidthMult) |
java.lang.String |
ToSVG(Int_Vect highlightAtoms,
int lineWidthMult,
int fontSize) |
java.lang.String |
ToSVG(int lineWidthMult) |
java.lang.String |
ToSVG(int lineWidthMult,
int fontSize) |
void |
transformMolsAtoms(Transform3D tform) |
void |
updatePropertyCache()
calculates any of our lazy properties
|
void |
updatePropertyCache(boolean strict)
calculates any of our lazy properties
|
void |
WedgeMolBonds(Conformer conf) |
clear, clearProp, getCPtr, getDict, getPropList, getPropList, getPropList, hasProp, setProp, setProp, updateProps, updateProps
protected ROMol(long cPtr, boolean cMemoryOwn)
public ROMol()
public ROMol(ROMol other, boolean quickCopy, int confId)
public ROMol(ROMol other, boolean quickCopy)
public ROMol(ROMol other)
public ROMol(java.lang.String binStr)
protected static long getCPtr(ROMol obj)
public SWIGTYPE_p_RDKit__CXXAtomIteratorT_boost__adjacency_listT_boost__vecS_boost__vecS_boost__undirectedS_RDKit__Atom_p_RDKit__Bond_p_t_RDKit__Atom_p_t atoms()
public SWIGTYPE_p_RDKit__CXXBondIteratorT_boost__adjacency_listT_boost__vecS_boost__vecS_boost__undirectedS_RDKit__Atom_p_RDKit__Bond_p_t_RDKit__Bond_p_t bonds()
public long getNumAtoms(boolean onlyExplicit)
public long getNumAtoms()
public long getNumHeavyAtoms()
public Atom getAtomWithIdx(long idx)
public long getAtomDegree(Atom at)
public long getNumBonds(boolean onlyHeavy)
public long getNumBonds()
public Bond getBondWithIdx(long idx)
public Bond getBondBetweenAtoms(long idx1, long idx2)
public void setAtomBookmark(Atom at, int mark)
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
public void replaceAtomBookmark(Atom at, int mark)
public Atom getAtomWithBookmark(int mark)
public Atom getUniqueAtomWithBookmark(int mark)
public SWIGTYPE_p_std__listT_RDKit__Atom_p_t getAllAtomsWithBookmark(int mark)
public void clearAtomBookmark(int mark)
public void clearAtomBookmark(int mark, Atom atom)
public void clearAllAtomBookmarks()
public boolean hasAtomBookmark(int mark)
public SWIGTYPE_p_std__mapT_int_std__listT_RDKit__Atom_p_t_t getAtomBookmarks()
public void setBondBookmark(Bond bond, int mark)
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
template
public Bond getBondWithBookmark(int mark)
public Bond getUniqueBondWithBookmark(int mark)
public SWIGTYPE_p_std__listT_RDKit__Bond_p_t getAllBondsWithBookmark(int mark)
public void clearBondBookmark(int mark)
public void clearBondBookmark(int mark, Bond bond)
public void clearAllBondBookmarks()
public boolean hasBondBookmark(int mark)
public SWIGTYPE_p_std__mapT_int_std__listT_RDKit__Bond_p_t_t getBondBookmarks()
public Conformer getConformer(int id)
return the conformer with a specified ID if the ID is negative the first conformation will be returned
public Conformer getConformer()
return the conformer with a specified ID if the ID is negative the first conformation will be returned
public void removeConformer(long id)
public void clearConformers()
public long getNumConformers()
public RingInfo getRingInfo()
public AtomIterator beginAtoms()
public AtomIterator endAtoms()
public BondIterator beginBonds()
public BondIterator endBonds()
public AromaticAtomIterator beginAromaticAtoms()
public AromaticAtomIterator endAromaticAtoms()
public HeteroatomIterator beginHeteros()
public HeteroatomIterator endHeteros()
public QueryAtomIterator beginQueryAtoms(QueryAtom query)
public QueryAtomIterator endQueryAtoms()
public SWIGTYPE_p_RDKit__MatchingAtomIterator_T_RDKit__Atom_RDKit__ROMol_t beginMatchingAtoms(SWIGTYPE_p_f_p_RDKit__Atom__bool query)
public SWIGTYPE_p_RDKit__MatchingAtomIterator_T_RDKit__Atom_const_RDKit__ROMol_const_t beginMatchingAtoms(SWIGTYPE_p_f_p_q_const__RDKit__Atom__bool query)
public SWIGTYPE_p_RDKit__MatchingAtomIterator_T_RDKit__Atom_RDKit__ROMol_t endMatchingAtoms()
public SWIGTYPE_p_std__listT_boost__shared_ptrT_RDKit__Conformer_t_t__iterator beginConformers()
public SWIGTYPE_p_std__listT_boost__shared_ptrT_RDKit__Conformer_t_t__iterator endConformers()
public void clearComputedProps(boolean includeRings)
public void clearComputedProps()
clearComputedProps
in class RDProps
public void updatePropertyCache(boolean strict)
calculates any of our lazy properties
public void updatePropertyCache()
calculates any of our lazy properties
public boolean needsUpdatePropertyCache()
public void debugMol(SWIGTYPE_p_std__ostream str)
public StereoGroup_Vect getStereoGroups()
public java.lang.String getProp(java.lang.String key)
public long addConformer(Conformer ownedConf, boolean assignId)
public long addConformer(Conformer ownedConf)
public java.lang.String MolToSmiles(boolean doIsomericSmiles, boolean doKekule, int rootedAtAtom)
public java.lang.String MolToSmiles(boolean doIsomericSmiles, boolean doKekule)
public java.lang.String MolToSmiles(boolean doIsomericSmiles)
public java.lang.String MolToSmiles()
public java.lang.String MolToMolBlock(boolean includeStereo, int confId)
public java.lang.String MolToMolBlock(boolean includeStereo)
public java.lang.String MolToMolBlock()
public void MolToMolFile(java.lang.String fName, boolean includeStereo, int confId, boolean kekulize)
public void MolToMolFile(java.lang.String fName, boolean includeStereo, int confId)
public void MolToMolFile(java.lang.String fName, boolean includeStereo)
public void MolToMolFile(java.lang.String fName)
public java.lang.String MolToTPLText(java.lang.String partialChargeProp, boolean writeFirstConfTwice)
public java.lang.String MolToTPLText(java.lang.String partialChargeProp)
public java.lang.String MolToTPLText()
public void MolToTPLFile(java.lang.String fName, java.lang.String partialChargeProp, boolean writeFirstConfTwice)
public void MolToTPLFile(java.lang.String fName, java.lang.String partialChargeProp)
public void MolToTPLFile(java.lang.String fName)
public java.lang.String MolToPDBBlock(int confId, long flavor)
public java.lang.String MolToPDBBlock(int confId)
public java.lang.String MolToPDBBlock()
public void MolToPDBFile(java.lang.String fName, int confId, long flavor)
public void MolToPDBFile(java.lang.String fName, int confId)
public void MolToPDBFile(java.lang.String fName)
public java.lang.String MolToSequence()
public java.lang.String MolToFASTA()
public java.lang.String MolToHELM()
public java.lang.String MolToXYZBlock(int confId)
public java.lang.String MolToXYZBlock()
public void MolToXYZFile(java.lang.String fName, int confId)
public void MolToXYZFile(java.lang.String fName)
public boolean hasSubstructMatch(ROMol query, boolean useChirality)
public boolean hasSubstructMatch(ROMol query)
public boolean hasSubstructMatch(ROMol query, SubstructMatchParameters ps)
public Match_Vect getSubstructMatch(ROMol query, SubstructMatchParameters ps)
public Match_Vect_Vect getSubstructMatches(ROMol query, SubstructMatchParameters ps)
public Match_Vect getSubstructMatch(ROMol query, boolean useChirality)
public Match_Vect getSubstructMatch(ROMol query)
public Match_Vect_Vect getSubstructMatches(ROMol query, boolean uniquify, boolean useChirality)
public Match_Vect_Vect getSubstructMatches(ROMol query, boolean uniquify)
public Match_Vect_Vect getSubstructMatches(ROMol query)
public ROMol_Vect replaceSubstructs(ROMol query, ROMol replacement, boolean replaceAll)
public ROMol_Vect replaceSubstructs(ROMol query, ROMol replacement)
public void DetectBondStereoChemistry(Conformer conf)
public void WedgeMolBonds(Conformer conf)
public void pickBondsToWedge()
public void ClearSingleBondDirFlags()
public void setConjugation()
public void setHybridization()
public long compute2DCoords(Int_Point2D_Map coordMap, boolean canonOrient, boolean clearConfs, long nFlipsPerSample, long nSamples, int sampleSeed, boolean permuteDeg4Nodes, boolean forceRDKit)
public long compute2DCoords(Int_Point2D_Map coordMap, boolean canonOrient, boolean clearConfs, long nFlipsPerSample, long nSamples, int sampleSeed, boolean permuteDeg4Nodes)
public long compute2DCoords(Int_Point2D_Map coordMap, boolean canonOrient, boolean clearConfs, long nFlipsPerSample, long nSamples, int sampleSeed)
public long compute2DCoords(Int_Point2D_Map coordMap, boolean canonOrient, boolean clearConfs, long nFlipsPerSample, long nSamples)
public long compute2DCoords(Int_Point2D_Map coordMap, boolean canonOrient, boolean clearConfs, long nFlipsPerSample)
public long compute2DCoords(Int_Point2D_Map coordMap, boolean canonOrient, boolean clearConfs)
public long compute2DCoords(Int_Point2D_Map coordMap, boolean canonOrient)
public long compute2DCoords(Int_Point2D_Map coordMap)
public long compute2DCoords()
public long compute2DCoords(ROMol templ)
public long compute2DCoordsMimicDistMat(SWIGTYPE_p_RDDepict__DOUBLE_SMART_PTR dmat, boolean canonOrient, boolean clearConfs, double weightDistMat, long nFlipsPerSample, long nSamples, int sampleSeed, boolean permuteDeg4Nodes, boolean forceRDKit)
public long compute2DCoordsMimicDistMat(SWIGTYPE_p_RDDepict__DOUBLE_SMART_PTR dmat, boolean canonOrient, boolean clearConfs, double weightDistMat, long nFlipsPerSample, long nSamples, int sampleSeed, boolean permuteDeg4Nodes)
public long compute2DCoordsMimicDistMat(SWIGTYPE_p_RDDepict__DOUBLE_SMART_PTR dmat, boolean canonOrient, boolean clearConfs, double weightDistMat, long nFlipsPerSample, long nSamples, int sampleSeed)
public long compute2DCoordsMimicDistMat(SWIGTYPE_p_RDDepict__DOUBLE_SMART_PTR dmat, boolean canonOrient, boolean clearConfs, double weightDistMat, long nFlipsPerSample, long nSamples)
public long compute2DCoordsMimicDistMat(SWIGTYPE_p_RDDepict__DOUBLE_SMART_PTR dmat, boolean canonOrient, boolean clearConfs, double weightDistMat, long nFlipsPerSample)
public long compute2DCoordsMimicDistMat(SWIGTYPE_p_RDDepict__DOUBLE_SMART_PTR dmat, boolean canonOrient, boolean clearConfs, double weightDistMat)
public long compute2DCoordsMimicDistMat(SWIGTYPE_p_RDDepict__DOUBLE_SMART_PTR dmat, boolean canonOrient, boolean clearConfs)
public long compute2DCoordsMimicDistMat(SWIGTYPE_p_RDDepict__DOUBLE_SMART_PTR dmat, boolean canonOrient)
public long compute2DCoordsMimicDistMat(SWIGTYPE_p_RDDepict__DOUBLE_SMART_PTR dmat)
public long compute2DCoordsMimicDistMat()
public void generateDepictionMatching2DStructure(ROMol reference, int confId, boolean acceptFailure, boolean forceRDKit)
public void generateDepictionMatching2DStructure(ROMol reference, int confId, boolean acceptFailure)
public void generateDepictionMatching2DStructure(ROMol reference, int confId)
public void generateDepictionMatching2DStructure(ROMol reference)
public void generateDepictionMatching2DStructure(ROMol reference, int confId, ROMol referencePattern, boolean acceptFailure, boolean forceRDKit)
public void generateDepictionMatching2DStructure(ROMol reference, int confId, ROMol referencePattern, boolean acceptFailure)
public void generateDepictionMatching2DStructure(ROMol reference, int confId, ROMol referencePattern)
public int findSSSR(Int_Vect_Vect res)
public int findSSSR()
public int symmetrizeSSSR(Int_Vect_Vect res)
public int symmetrizeSSSR()
public SWIGTYPE_p_double getDistanceMat(boolean useBO, boolean useAtomWts, boolean force, java.lang.String propNamePrefix)
public SWIGTYPE_p_double getDistanceMat(boolean useBO, boolean useAtomWts, boolean force)
public SWIGTYPE_p_double getDistanceMat(boolean useBO, boolean useAtomWts)
public SWIGTYPE_p_double getDistanceMat(boolean useBO)
public SWIGTYPE_p_double getDistanceMat()
public SWIGTYPE_p_double getDistanceMat(Int_Vect activeAtoms, SWIGTYPE_p_std__vectorT_RDKit__Bond_const_p_t bonds, boolean useBO, boolean useAtomWts)
public SWIGTYPE_p_double getDistanceMat(Int_Vect activeAtoms, SWIGTYPE_p_std__vectorT_RDKit__Bond_const_p_t bonds, boolean useBO)
public SWIGTYPE_p_double getDistanceMat(Int_Vect activeAtoms, SWIGTYPE_p_std__vectorT_RDKit__Bond_const_p_t bonds)
public SWIGTYPE_p_double getAdjacencyMatrix(boolean useBO, int emptyVal, boolean force, java.lang.String propNamePrefix)
public SWIGTYPE_p_double getAdjacencyMatrix(boolean useBO, int emptyVal, boolean force)
public SWIGTYPE_p_double getAdjacencyMatrix(boolean useBO, int emptyVal)
public SWIGTYPE_p_double getAdjacencyMatrix(boolean useBO)
public SWIGTYPE_p_double getAdjacencyMatrix()
public Int_List getShortestPath(int aid1, int aid2)
public void transformMolsAtoms(Transform3D tform)
public void canonicalizeMol(boolean normalizeCovar, boolean ignoreHs)
public void canonicalizeMol(boolean normalizeCovar)
public void canonicalizeMol()
public Atom_Vect getAtoms()
public Int_Vect ToBinary()
public ROMol addHs(boolean explicitOnly, boolean addCoords)
public ROMol addHs(boolean explicitOnly)
public ROMol removeHs(boolean implicitOnly, boolean updateExplicitCount, boolean sanitize)
public ROMol removeHs(boolean implicitOnly, boolean updateExplicitCount)
public ROMol removeHs(boolean implicitOnly)
public ROMol mergeQueryHs()
public double alignMol(ROMol refMol, int prbCid, int refCid, Match_Vect atomMap, SWIGTYPE_p_RDNumeric__VectorT_double_t weights, boolean reflect, long maxIters)
public double alignMol(ROMol refMol, int prbCid, int refCid, Match_Vect atomMap, SWIGTYPE_p_RDNumeric__VectorT_double_t weights, boolean reflect)
public double alignMol(ROMol refMol, int prbCid, int refCid, Match_Vect atomMap, SWIGTYPE_p_RDNumeric__VectorT_double_t weights)
public double alignMol(ROMol refMol, int prbCid, int refCid, Match_Vect atomMap)
public double alignMol(ROMol refMol, int prbCid, int refCid)
public double alignMol(ROMol refMol, int prbCid)
public double alignMol(ROMol refMol)
public void alignMolConformers(ROMol mol, UInt_Vect atomIds, UInt_Vect confIds, SWIGTYPE_p_RDNumeric__VectorT_double_t weights, boolean reflect, long maxIters)
public void alignMolConformers(ROMol mol, UInt_Vect atomIds, UInt_Vect confIds, SWIGTYPE_p_RDNumeric__VectorT_double_t weights, boolean reflect)
public void alignMolConformers(ROMol mol, UInt_Vect atomIds, UInt_Vect confIds, SWIGTYPE_p_RDNumeric__VectorT_double_t weights)
public void alignMolConformers(ROMol mol)
public double getAlignmentTransform(ROMol refMol, Transform3D trans, int prbCid, int refCid, Match_Vect atomMap, SWIGTYPE_p_RDNumeric__VectorT_double_t weights, boolean reflect, long maxIters)
public double getAlignmentTransform(ROMol refMol, Transform3D trans, int prbCid, int refCid, Match_Vect atomMap, SWIGTYPE_p_RDNumeric__VectorT_double_t weights, boolean reflect)
public double getAlignmentTransform(ROMol refMol, Transform3D trans, int prbCid, int refCid, Match_Vect atomMap, SWIGTYPE_p_RDNumeric__VectorT_double_t weights)
public double getAlignmentTransform(ROMol refMol, Transform3D trans, int prbCid, int refCid, Match_Vect atomMap)
public double getAlignmentTransform(ROMol refMol, Transform3D trans, int prbCid, int refCid)
public double getAlignmentTransform(ROMol refMol, Transform3D trans, int prbCid)
public double getAlignmentTransform(ROMol refMol, Transform3D trans)
public Double_Pair O3AAlignMol(ROMol refMol, int prbCid, int refCid, boolean reflect, long maxIters, long accuracy)
public Double_Pair O3AAlignMol(ROMol refMol, int prbCid, int refCid, boolean reflect, long maxIters)
public Double_Pair O3AAlignMol(ROMol refMol, int prbCid, int refCid, boolean reflect)
public Double_Pair O3AAlignMol(ROMol refMol, int prbCid, int refCid)
public Double_Pair O3AAlignMol(ROMol refMol, int prbCid)
public Double_Pair O3AAlignMol(ROMol refMol)
public void computeGasteigerCharges(ROMol mol, int nIter, boolean throwOnParamFailure)
public void computeGasteigerCharges(ROMol mol, int nIter)
public void computeGasteigerCharges(ROMol mol)
public void computeGasteigerCharges(ROMol mol, Double_Vect charges, int nIter, boolean throwOnParamFailure)
public void computeGasteigerCharges(ROMol mol, Double_Vect charges, int nIter)
public void computeGasteigerCharges(ROMol mol, Double_Vect charges)
public void rankMolAtoms(UInt_Vect ranks, boolean breakTies, boolean includeChirality, boolean includeIsotopes)
public void rankMolAtoms(UInt_Vect ranks, boolean breakTies, boolean includeChirality)
public void rankMolAtoms(UInt_Vect ranks, boolean breakTies)
public void rankMolAtoms(UInt_Vect ranks)
public java.lang.String ToSVG(Int_Vect highlightAtoms, int lineWidthMult, int fontSize)
public java.lang.String ToSVG(Int_Vect highlightAtoms, int lineWidthMult)
public java.lang.String ToSVG(Int_Vect highlightAtoms)
public java.lang.String ToSVG(int lineWidthMult, int fontSize)
public java.lang.String ToSVG(int lineWidthMult)
public java.lang.String ToSVG()