public class RWMol extends ROMol
See documentation for ROMol for general remarks
Modifier | Constructor and Description |
---|---|
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RWMol() |
protected |
RWMol(long cPtr,
boolean cMemoryOwn) |
|
RWMol(ROMol other) |
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RWMol(ROMol other,
boolean quickCopy) |
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RWMol(ROMol other,
boolean quickCopy,
int confId) |
|
RWMol(RWMol other) |
Modifier and Type | Method and Description |
---|---|
long |
addAtom()
adds an empty Atom to our collection
|
long |
addAtom(Atom atom)
adds an Atom to our collection
|
long |
addAtom(Atom atom,
boolean updateLabel)
adds an Atom to our collection
|
long |
addAtom(boolean updateLabel)
adds an empty Atom to our collection
|
long |
addBond(Atom beginAtom,
Atom endAtom)
This is an overloaded member function, provided for convenience.
|
long |
addBond(Atom beginAtom,
Atom endAtom,
Bond.BondType order)
This is an overloaded member function, provided for convenience.
|
long |
addBond(Bond bond)
adds a Bond to our collection
|
long |
addBond(long beginAtomIdx,
long endAtomIdx)
adds a Bond between the indicated Atoms
|
long |
addBond(long beginAtomIdx,
long endAtomIdx,
Bond.BondType order)
adds a Bond between the indicated Atoms
|
void |
clear() |
Bond |
createPartialBond(long beginAtomIdx)
starts a Bond and sets its beginAtomIdx
|
Bond |
createPartialBond(long beginAtomIdx,
Bond.BondType order)
starts a Bond and sets its beginAtomIdx
|
void |
delete() |
void |
DetectAtomStereoChemistry(Conformer conf) |
protected void |
finalize() |
long |
finishPartialBond(long endAtomIdx,
int bondBookmark)
finishes a partially constructed bond
|
long |
finishPartialBond(long endAtomIdx,
int bondBookmark,
Bond.BondType order)
finishes a partially constructed bond
|
Atom |
getActiveAtom() |
protected static long |
getCPtr(RWMol obj) |
Atom |
getLastAtom() |
void |
insertMol(ROMol other) |
void |
Kekulize() |
void |
Kekulize(boolean markAtomsBonds) |
void |
Kekulize(boolean markAtomsBonds,
long maxBackTracks) |
static RWMol |
MolFromFASTA(java.lang.String text) |
static RWMol |
MolFromFASTA(java.lang.String text,
boolean sanitize) |
static RWMol |
MolFromFASTA(java.lang.String text,
boolean sanitize,
int flavor) |
static RWMol |
MolFromHELM(java.lang.String text) |
static RWMol |
MolFromHELM(java.lang.String text,
boolean sanitize) |
static RWMol |
MolFromMol2Block(java.lang.String molBlock) |
static RWMol |
MolFromMol2Block(java.lang.String molBlock,
boolean sanitize) |
static RWMol |
MolFromMol2Block(java.lang.String molBlock,
boolean sanitize,
boolean removeHs) |
static RWMol |
MolFromMol2Block(java.lang.String molBlock,
boolean sanitize,
boolean removeHs,
Mol2Type variant) |
static RWMol |
MolFromMol2Block(java.lang.String molBlock,
boolean sanitize,
boolean removeHs,
Mol2Type variant,
boolean cleanupSubstructures) |
static RWMol |
MolFromMol2File(java.lang.String fName) |
static RWMol |
MolFromMol2File(java.lang.String fName,
boolean sanitize) |
static RWMol |
MolFromMol2File(java.lang.String fName,
boolean sanitize,
boolean removeHs) |
static RWMol |
MolFromMol2File(java.lang.String fName,
boolean sanitize,
boolean removeHs,
Mol2Type variant) |
static RWMol |
MolFromMol2File(java.lang.String fName,
boolean sanitize,
boolean removeHs,
Mol2Type variant,
boolean cleanupSubstructures) |
static RWMol |
MolFromMolBlock(java.lang.String molB) |
static RWMol |
MolFromMolBlock(java.lang.String molB,
boolean sanitize) |
static RWMol |
MolFromMolBlock(java.lang.String molB,
boolean sanitize,
boolean removeHs) |
static RWMol |
MolFromMolFile(java.lang.String filename) |
static RWMol |
MolFromMolFile(java.lang.String filename,
boolean sanitize) |
static RWMol |
MolFromMolFile(java.lang.String filename,
boolean sanitize,
boolean removeHs) |
static RWMol |
MolFromPDBBlock(java.lang.String molB) |
static RWMol |
MolFromPDBBlock(java.lang.String molB,
boolean sanitize) |
static RWMol |
MolFromPDBBlock(java.lang.String molB,
boolean sanitize,
boolean removeHs) |
static RWMol |
MolFromPDBBlock(java.lang.String molB,
boolean sanitize,
boolean removeHs,
long flavor) |
static RWMol |
MolFromPDBBlock(java.lang.String molB,
boolean sanitize,
boolean removeHs,
long flavor,
boolean proximityBonding) |
static RWMol |
MolFromPDBFile(java.lang.String fName) |
static RWMol |
MolFromPDBFile(java.lang.String fName,
boolean sanitize) |
static RWMol |
MolFromPDBFile(java.lang.String fName,
boolean sanitize,
boolean removeHs) |
static RWMol |
MolFromPDBFile(java.lang.String fName,
boolean sanitize,
boolean removeHs,
long flavor) |
static RWMol |
MolFromPDBFile(java.lang.String fName,
boolean sanitize,
boolean removeHs,
long flavor,
boolean proximityBonding) |
static RWMol |
MolFromSequence(java.lang.String text) |
static RWMol |
MolFromSequence(java.lang.String text,
boolean sanitize) |
static RWMol |
MolFromSequence(java.lang.String text,
boolean sanitize,
int flavor) |
static RWMol |
MolFromSmarts(java.lang.String sma) |
static RWMol |
MolFromSmarts(java.lang.String sma,
int debugParse) |
static RWMol |
MolFromSmarts(java.lang.String sma,
int debugParse,
boolean mergeHs) |
static RWMol |
MolFromSmarts(java.lang.String sma,
int debugParse,
boolean mergeHs,
String_String_Map replacements) |
static RWMol |
MolFromSmiles(java.lang.String smi) |
static RWMol |
MolFromSmiles(java.lang.String smi,
int debugParse) |
static RWMol |
MolFromSmiles(java.lang.String smi,
int debugParse,
boolean sanitize) |
static RWMol |
MolFromSmiles(java.lang.String smi,
int debugParse,
boolean sanitize,
String_String_Map replacements) |
static RWMol |
MolFromTPLFile(java.lang.String fName) |
static RWMol |
MolFromTPLFile(java.lang.String fName,
boolean sanitize) |
static RWMol |
MolFromTPLFile(java.lang.String fName,
boolean sanitize,
boolean skipFirstConf) |
void |
removeAtom(Atom atom)
This is an overloaded member function, provided for convenience.
|
void |
removeAtom(long idx) |
void |
removeBond(long beginAtomIdx,
long endAtomIdx) |
void |
replaceAtom(long idx,
Atom atom)
replaces a particular Atom
|
void |
replaceAtom(long idx,
Atom atom,
boolean updateLabel)
replaces a particular Atom
|
void |
replaceAtom(long idx,
Atom atom,
boolean updateLabel,
boolean preserveProps) |
void |
replaceBond(long idx,
Bond bond) |
void |
replaceBond(long idx,
Bond bond,
boolean preserveProps) |
void |
sanitizeMol() |
void |
setActiveAtom(Atom atom) |
void |
setActiveAtom(long idx)
This is an overloaded member function, provided for convenience.
|
void |
setStereoGroups(StereoGroup_Vect stereo_groups) |
addConformer, addConformer, addHs, addHs, alignMol, alignMol, alignMol, alignMol, alignMol, alignMol, alignMol, alignMolConformers, alignMolConformers, alignMolConformers, alignMolConformers, alignMolConformers, alignMolConformers, atoms, beginAromaticAtoms, beginAtoms, beginBonds, beginConformers, beginHeteros, beginMatchingAtoms, beginMatchingAtoms, beginQueryAtoms, bonds, canonicalizeMol, canonicalizeMol, canonicalizeMol, clearAllAtomBookmarks, clearAllBondBookmarks, clearAtomBookmark, clearAtomBookmark, clearBondBookmark, clearBondBookmark, clearComputedProps, clearComputedProps, clearConformers, ClearSingleBondDirFlags, compute2DCoords, compute2DCoords, compute2DCoords, compute2DCoords, compute2DCoords, compute2DCoords, compute2DCoords, compute2DCoords, compute2DCoords, compute2DCoords, compute2DCoordsMimicDistMat, compute2DCoordsMimicDistMat, compute2DCoordsMimicDistMat, compute2DCoordsMimicDistMat, compute2DCoordsMimicDistMat, compute2DCoordsMimicDistMat, compute2DCoordsMimicDistMat, compute2DCoordsMimicDistMat, compute2DCoordsMimicDistMat, compute2DCoordsMimicDistMat, computeGasteigerCharges, computeGasteigerCharges, computeGasteigerCharges, computeGasteigerCharges, computeGasteigerCharges, computeGasteigerCharges, debugMol, deleteSubstructs, DetectBondStereoChemistry, endAromaticAtoms, endAtoms, endBonds, endConformers, endHeteros, endMatchingAtoms, endQueryAtoms, findSSSR, findSSSR, generateDepictionMatching2DStructure, generateDepictionMatching2DStructure, generateDepictionMatching2DStructure, generateDepictionMatching2DStructure, generateDepictionMatching2DStructure, generateDepictionMatching2DStructure, generateDepictionMatching2DStructure, getAdjacencyMatrix, getAdjacencyMatrix, getAdjacencyMatrix, getAdjacencyMatrix, getAdjacencyMatrix, getAlignmentTransform, getAlignmentTransform, getAlignmentTransform, getAlignmentTransform, getAlignmentTransform, getAlignmentTransform, getAlignmentTransform, getAllAtomsWithBookmark, getAllBondsWithBookmark, getAtomBonds, getAtomBookmarks, getAtomDegree, getAtomNeighbors, getAtoms, getAtomWithBookmark, getAtomWithIdx, getBondBetweenAtoms, getBondBookmarks, getBondWithBookmark, getBondWithIdx, getConformer, getConformer, getCPtr, getDistanceMat, getDistanceMat, getDistanceMat, getDistanceMat, getDistanceMat, getDistanceMat, getDistanceMat, getDistanceMat, getNumAtoms, getNumAtoms, getNumBonds, getNumBonds, getNumConformers, getNumHeavyAtoms, getProp, getRingInfo, getShortestPath, getStereoGroups, getSubstructMatch, getSubstructMatch, getSubstructMatch, getSubstructMatches, getSubstructMatches, getSubstructMatches, getSubstructMatches, getUniqueAtomWithBookmark, getUniqueBondWithBookmark, hasAtomBookmark, hasBondBookmark, hasSubstructMatch, hasSubstructMatch, hasSubstructMatch, mergeQueryHs, MolFromBinary, MolToFASTA, MolToHELM, MolToMolBlock, MolToMolBlock, MolToMolBlock, MolToMolFile, MolToMolFile, MolToMolFile, MolToMolFile, MolToPDBBlock, MolToPDBBlock, MolToPDBBlock, MolToPDBFile, MolToPDBFile, MolToPDBFile, MolToSequence, MolToSmiles, MolToSmiles, MolToSmiles, MolToSmiles, MolToTPLFile, MolToTPLFile, MolToTPLFile, MolToTPLText, MolToTPLText, MolToTPLText, MolToXYZBlock, MolToXYZBlock, MolToXYZFile, MolToXYZFile, needsUpdatePropertyCache, O3AAlignMol, O3AAlignMol, O3AAlignMol, O3AAlignMol, O3AAlignMol, O3AAlignMol, pickBondsToWedge, rankMolAtoms, rankMolAtoms, rankMolAtoms, rankMolAtoms, removeConformer, removeHs, removeHs, removeHs, replaceAtomBookmark, replaceCore, replaceCore, replaceCore, replaceSidechains, replaceSubstructs, replaceSubstructs, setAtomBookmark, setBondBookmark, setConjugation, setHybridization, symmetrizeSSSR, symmetrizeSSSR, ToBinary, ToSVG, ToSVG, ToSVG, ToSVG, ToSVG, ToSVG, transformMolsAtoms, updatePropertyCache, updatePropertyCache, WedgeMolBonds
clearProp, getCPtr, getDict, getPropList, getPropList, getPropList, hasProp, setProp, setProp, updateProps, updateProps
protected RWMol(long cPtr, boolean cMemoryOwn)
public RWMol()
public RWMol(ROMol other, boolean quickCopy, int confId)
public RWMol(ROMol other, boolean quickCopy)
public RWMol(ROMol other)
public RWMol(RWMol other)
protected static long getCPtr(RWMol obj)
public void insertMol(ROMol other)
public long addAtom(boolean updateLabel)
adds an empty Atom to our collection
updateLabel
- (optional) if this is true, the new Atom will be our activeAtom
public long addAtom()
adds an empty Atom to our collection
updateLabel
- (optional) if this is true, the new Atom will be our activeAtom
public long addAtom(Atom atom, boolean updateLabel)
adds an Atom to our collection
atom
- pointer to the Atom to add
updateLabel (optional) if this is true, the new Atom will be our activeAtom
takeOwnership (optional) if this is true, we take ownership of atom instead of copying it.
public long addAtom(Atom atom)
adds an Atom to our collection
atom
- pointer to the Atom to add
updateLabel (optional) if this is true, the new Atom will be our activeAtom
takeOwnership (optional) if this is true, we take ownership of atom instead of copying it.
public void replaceAtom(long idx, Atom atom, boolean updateLabel, boolean preserveProps)
public void replaceAtom(long idx, Atom atom, boolean updateLabel)
replaces a particular Atom
idx
- the index of the Atom to replace
atom the new atom, which will be copied.
updateLabel (optional) if this is true, the new Atom will be our activeAtompublic void replaceAtom(long idx, Atom atom)
replaces a particular Atom
idx
- the index of the Atom to replace
atom the new atom, which will be copied.
updateLabel (optional) if this is true, the new Atom will be our activeAtompublic Atom getLastAtom()
public Atom getActiveAtom()
public void setActiveAtom(Atom atom)
public void setActiveAtom(long idx)
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
public void removeAtom(long idx)
public void removeAtom(Atom atom)
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
public long addBond(long beginAtomIdx, long endAtomIdx, Bond.BondType order)
adds a Bond between the indicated Atoms
public long addBond(long beginAtomIdx, long endAtomIdx)
adds a Bond between the indicated Atoms
public long addBond(Atom beginAtom, Atom endAtom, Bond.BondType order)
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
public long addBond(Atom beginAtom, Atom endAtom)
This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
public long addBond(Bond bond)
adds a Bond to our collection
bond
- pointer to the Bond to add
takeOwnership (optional) if this is true, we take ownership of bond instead of copying it.
public Bond createPartialBond(long beginAtomIdx, Bond.BondType order)
starts a Bond and sets its beginAtomIdx
Bond *pBond = mol->createPartialBond(1); mol->setBondBookmark(pBond,666); ... do some other stuff ... mol->finishPartialBond(2,666,Bond::SINGLE); mol->clearBondBookmark(666,pBond);
or, if we want to set the BondType initially:
Bond *pBond = mol->createPartialBond(1,Bond::DOUBLE); mol->setBondBookmark(pBond,666); ... do some other stuff ... mol->finishPartialBond(2,666); mol->clearBondBookmark(666,pBond);
the call to finishPartialBond() will take priority if you set the BondType in both calls.
public Bond createPartialBond(long beginAtomIdx)
starts a Bond and sets its beginAtomIdx
Bond *pBond = mol->createPartialBond(1); mol->setBondBookmark(pBond,666); ... do some other stuff ... mol->finishPartialBond(2,666,Bond::SINGLE); mol->clearBondBookmark(666,pBond);
or, if we want to set the BondType initially:
Bond *pBond = mol->createPartialBond(1,Bond::DOUBLE); mol->setBondBookmark(pBond,666); ... do some other stuff ... mol->finishPartialBond(2,666); mol->clearBondBookmark(666,pBond);
the call to finishPartialBond() will take priority if you set the BondType in both calls.
public long finishPartialBond(long endAtomIdx, int bondBookmark, Bond.BondType order)
finishes a partially constructed bond
public long finishPartialBond(long endAtomIdx, int bondBookmark)
finishes a partially constructed bond
public void removeBond(long beginAtomIdx, long endAtomIdx)
public void replaceBond(long idx, Bond bond, boolean preserveProps)
public void replaceBond(long idx, Bond bond)
public void setStereoGroups(StereoGroup_Vect stereo_groups)
public static RWMol MolFromSmiles(java.lang.String smi, int debugParse, boolean sanitize, String_String_Map replacements)
public static RWMol MolFromSmiles(java.lang.String smi, int debugParse, boolean sanitize)
public static RWMol MolFromSmiles(java.lang.String smi, int debugParse)
public static RWMol MolFromSmiles(java.lang.String smi)
public static RWMol MolFromSmarts(java.lang.String sma, int debugParse, boolean mergeHs, String_String_Map replacements)
public static RWMol MolFromSmarts(java.lang.String sma, int debugParse, boolean mergeHs)
public static RWMol MolFromSmarts(java.lang.String sma, int debugParse)
public static RWMol MolFromSmarts(java.lang.String sma)
public static RWMol MolFromMolBlock(java.lang.String molB, boolean sanitize, boolean removeHs)
public static RWMol MolFromMolBlock(java.lang.String molB, boolean sanitize)
public static RWMol MolFromMolBlock(java.lang.String molB)
public static RWMol MolFromMolFile(java.lang.String filename, boolean sanitize, boolean removeHs)
public static RWMol MolFromMolFile(java.lang.String filename, boolean sanitize)
public static RWMol MolFromMolFile(java.lang.String filename)
public static RWMol MolFromTPLFile(java.lang.String fName, boolean sanitize, boolean skipFirstConf)
public static RWMol MolFromTPLFile(java.lang.String fName, boolean sanitize)
public static RWMol MolFromTPLFile(java.lang.String fName)
public static RWMol MolFromMol2File(java.lang.String fName, boolean sanitize, boolean removeHs, Mol2Type variant, boolean cleanupSubstructures)
public static RWMol MolFromMol2File(java.lang.String fName, boolean sanitize, boolean removeHs, Mol2Type variant)
public static RWMol MolFromMol2File(java.lang.String fName, boolean sanitize, boolean removeHs)
public static RWMol MolFromMol2File(java.lang.String fName, boolean sanitize)
public static RWMol MolFromMol2File(java.lang.String fName)
public static RWMol MolFromMol2Block(java.lang.String molBlock, boolean sanitize, boolean removeHs, Mol2Type variant, boolean cleanupSubstructures)
public static RWMol MolFromMol2Block(java.lang.String molBlock, boolean sanitize, boolean removeHs, Mol2Type variant)
public static RWMol MolFromMol2Block(java.lang.String molBlock, boolean sanitize, boolean removeHs)
public static RWMol MolFromMol2Block(java.lang.String molBlock, boolean sanitize)
public static RWMol MolFromMol2Block(java.lang.String molBlock)
public static RWMol MolFromPDBBlock(java.lang.String molB, boolean sanitize, boolean removeHs, long flavor, boolean proximityBonding)
public static RWMol MolFromPDBBlock(java.lang.String molB, boolean sanitize, boolean removeHs, long flavor)
public static RWMol MolFromPDBBlock(java.lang.String molB, boolean sanitize, boolean removeHs)
public static RWMol MolFromPDBBlock(java.lang.String molB, boolean sanitize)
public static RWMol MolFromPDBBlock(java.lang.String molB)
public static RWMol MolFromPDBFile(java.lang.String fName, boolean sanitize, boolean removeHs, long flavor, boolean proximityBonding)
public static RWMol MolFromPDBFile(java.lang.String fName, boolean sanitize, boolean removeHs, long flavor)
public static RWMol MolFromPDBFile(java.lang.String fName, boolean sanitize, boolean removeHs)
public static RWMol MolFromPDBFile(java.lang.String fName, boolean sanitize)
public static RWMol MolFromPDBFile(java.lang.String fName)
public static RWMol MolFromSequence(java.lang.String text, boolean sanitize, int flavor)
public static RWMol MolFromSequence(java.lang.String text, boolean sanitize)
public static RWMol MolFromSequence(java.lang.String text)
public static RWMol MolFromFASTA(java.lang.String text, boolean sanitize, int flavor)
public static RWMol MolFromFASTA(java.lang.String text, boolean sanitize)
public static RWMol MolFromFASTA(java.lang.String text)
public static RWMol MolFromHELM(java.lang.String text, boolean sanitize)
public static RWMol MolFromHELM(java.lang.String text)
public void DetectAtomStereoChemistry(Conformer conf)
public void Kekulize(boolean markAtomsBonds, long maxBackTracks)
public void Kekulize(boolean markAtomsBonds)
public void Kekulize()
public void sanitizeMol()