Sketch Class |
Sketch Class representing a generic sketch, which could be one Molecule, Reaction, or many structure
with annotation text and shapes.
Call AsReaction() to test if it is a Reaction; AsMolecule() to test if it is a Molecule.
Sketch contains Atom, Bond, Arrow, Text, Plus objects.
Inheritance HierarchyNamespace: Scilligence.MolEngine
Assembly: Scilligence.MolEngine (in Scilligence.MolEngine.dll) Version: 1.3.0.0 (7.0.0.39951)
SyntaxC#
public class Sketch : Molecule
The Sketch type exposes the following members.
Constructors| Name | Description | |
|---|---|---|
 | Sketch |
Construct a blank sketch object
|
| Sketch(ABSet) |
Construct a sketch object from atom-bond collection
|
| Sketch(MolBase) |
Construct a sktech object from a Molecule, Reaction or another Sketch
|
Properties| Name | Description | |
|---|---|---|
 | Atoms |
The collection contains all atoms.
(Inherited from Molecule.) |
| Bonds |
The collection contains all bonds.
(Inherited from Molecule.) |
| CanonicalCode |
Canonical Code of the structure
(Inherited from MolBase.) |
| Chiralities | (Inherited from Molecule.) |
| Composition |
Returns element composition
(Inherited from Molecule.) |
| ExactMass |
Returns the molecular exact mass
(Inherited from Molecule.) |
| ExSMILES |
Extended SMILES string
(Inherited from MolBase.) |
| Fingerprints |
The fingerprints of the structure. (documents)
(Inherited from MolBase.) |
| FingerprintsAsString |
The string version of the fingerprints of the structure. (link)
(Inherited from MolBase.) |
| Formula |
Formula in plain-text
(Inherited from MolBase.) |
| FormulaHtml |
Formula in HTML
(Inherited from MolBase.) |
| FormulaSearchable |
Normalized searchable formula
(Inherited from MolBase.) |
| HashCode |
Compute the topological hash code of molecule. Each identical chemical structure has its own hash code.
(Inherited from Molecule.) |
| HashCodeRelax |
Compute the topological hash code of molecule, but ignore stereochemistry.
(Inherited from Molecule.) |
| InChI |
Returns the InChI (The IUPAC International Chemical Identifier).
InChI extension has to be installed to call this function. If not installed, it always return null.
(Inherited from Molecule.) |
| InChIKey |
InChIKey is hashed InChI, which is more efficient to be used as structure key.
(Inherited from Molecule.) |
| IsEmpty | (Overrides MoleculeIsEmpty.) |
| IUPACName | (Inherited from Molecule.) |
| IUPACNameHtml | (Inherited from Molecule.) |
| MolWeight |
Returns the molecular weight
(Inherited from Molecule.) |
| MolWeightKnown | (Inherited from Molecule.) |
| Objects |
All objects except Atom and Bond, includiing Arrow, Text and Plus
|
| OrderedAtoms |
Get ordered atom list.
(Inherited from Molecule.) |
| PSA |
Returns the molecule t-PSA (Topological Polar Surface Area), which is invented by Peter Ertl etc.
(Inherited from Molecule.) |
| Set |
The object contains of the sketch, which can be Atom, Bond, Arrow, Text and Plus
|
| SMILES |
SMILES string
(Inherited from MolBase.) |
| SSSR |
Returns Smallest Set of Smallest Rings (SSSR) from the molecule topological graph.
(Inherited from Molecule.) |
| StructureKeys |
A higher level of structure characterization (link)
(Inherited from MolBase.) |
| StructureKeysAsString |
The string version of StructureKeys
(Inherited from MolBase.) |
Methods| Name | Description | |
|---|---|---|
| AddMixtureBracket | (Inherited from Molecule.) |
| AllTexts | |
| Aromatize | (Inherited from MolBase.) |
| AsReaction |
Create a Reaction object based on the sketch.
To be a Reaction, the sketch has to have one Arrow, and some structure in either or both side
|
| BackupEnhanceStereoChemistry | |
| BondedAtoms |
Find all connected bonds of a given atom
(Inherited from Molecule.) |
| BreakMetalBonds |
Break metal bonds
(Inherited from Molecule.) |
| CheckHELMMonomer | (Inherited from Molecule.) |
| Cleanup |
Change atoms' position to make the structure looks nicer.
If no coordinates, new 2D coordinates will be assigned.
If it is a reaction, it also re-layout the reaction components.
(Inherited from MolBase.) |
| Cleanup(SetAtom) |
Change atoms's position to make the structure looks nicers
(Inherited from MolBase.) |
| CleanupIfNoCoordinates | (Inherited from MolBase.) |
| Clear |
Clear all contained objects, including atoms and bonds.
(Inherited from Molecule.) |
| ClearColor |
Clear Atom/Bond colors
(Inherited from Molecule.) |
| ClearRxnMapping | (Inherited from MolBase.) |
| CLogP | (Inherited from Molecule.) |
| Clone | (Overrides MoleculeClone.) |
| Clone2 | (Overrides MoleculeClone2(DictionaryBaseObj, BaseObj).) |
| ComputeHashCode | (Inherited from Molecule.) |
| ConnectFragments | (Inherited from Molecule.) |
| ConnectMulticenter | (Inherited from Molecule.) |
| ConvertAttachPoints2Rs | (Inherited from Molecule.) |
| ConvertRs2AttachPoints | (Inherited from Molecule.) |
| ConvertTo3D |
Generate 3D coordinates.
ForceField extension has to be installed.
(Inherited from Molecule.) |
| CopyTo(Molecule) |
Copy all objects, including atoms and bonds, to another molecule.
(Inherited from Molecule.) |
| CopyTo(Molecule, DictionaryBaseObj, BaseObj) | (Inherited from Molecule.) |
 | CopyToImp | (Overrides MoleculeCopyToImp(Molecule, DictionaryBaseObj, BaseObj).) |
| CorrectMolChiral | (Inherited from Molecule.) |
| CorrectNitroGroup | (Inherited from Molecule.) |
| CountAtoms(Int32) |
Count atoms
(Inherited from Molecule.) |
| CountAtoms(String) |
Count atoms
(Inherited from Molecule.) |
| CountRings |
Count atoms
(Inherited from Molecule.) |
| CountTextFields(String) | |
| CountTextFields(Regex) | |
| Dekekulize |
Convert rings to aromatic
(Inherited from MolBase.) |
| DetectChirality | (Overrides MoleculeDetectChirality.) |
| DetectMoleculeType | |
| Dump |
Dump all contents to console for debugging purpose
(Inherited from Molecule.) |
| ElementalAnalysis | (Inherited from Molecule.) |
| Equals | (Inherited from Object.) |
| EqualsTo |
Test if this molecule is topologically identical to the query molecule
(Inherited from Molecule.) |
| ExpandAllBios | (Inherited from MolBase.) |
| ExpandSuperAtoms(Boolean) | (Inherited from Molecule.) |
| ExpandSuperAtoms(DictionaryAtom, ABSet) | (Inherited from Molecule.) |
| ExpandSuperAtoms(DictionaryAtom, ABSet, Boolean) | (Inherited from Molecule.) |
| ExpandSuperAtoms(DictionaryAtom, ABSet, DictionaryBaseObj, BaseObj) | (Inherited from Molecule.) |
| ExpandSuperAtoms(DictionaryAtom, ABSet, DictionaryBaseObj, BaseObj, Boolean) | (Inherited from Molecule.) |
| ExpandSuperAtomsAndCleanup | (Inherited from Molecule.) |
| Finalize | Allows an object to try to free resources and perform other cleanup operations before it is reclaimed by garbage collection. (Inherited from Object.) |
| FindBond | (Inherited from MolBase.) |
| FindBonds | (Inherited from MolBase.) |
| FindFirstBond | (Inherited from MolBase.) |
| FlattenMol | (Inherited from Molecule.) |
| FormalCharge |
Compute the neat formal charges of the molecule, which actually add all atom formal charges together.
(Inherited from Molecule.) |
| GetAllChiralCenters | (Inherited from Molecule.) |
| GetAllMarkedChiralCenters | (Inherited from Molecule.) |
| GetAllObjectsT | |
| GetAllUnmarkedChiralCenters | (Inherited from Molecule.) |
| GetAtomByAtomMap | (Inherited from Molecule.) |
| GetAtomByAtomType | (Inherited from Molecule.) |
| GetAtomCIP |
Returns Atom stereochemistry CIP
(Inherited from Molecule.) |
| GetBound | (Overrides MoleculeGetBound.) |
| GetBracketDataFields | |
| GetBrackets | |
| GetCanonicalCode |
Create the canonical code
(Inherited from MolBase.) |
| GetChiralAtom | |
| GetDataFields | |
| GetEnhanceStereo | |
| GetExtinctionCoefficient | (Inherited from Molecule.) |
| GetFingerprints | (Inherited from Molecule.) |
| GetFormula | (Inherited from Molecule.) |
| GetHashCode | Serves as a hash function for a particular type. (Inherited from Object.) |
| GetHelm | (Inherited from Molecule.) |
| GetInChI | (Inherited from MolBase.) |
| GetIsotopicAtoms | (Inherited from Molecule.) |
| GetJSDraw | (Inherited from MolBase.) |
| GetMFwithSalt | (Inherited from Molecule.) |
| GetMoleculeBrackets | |
| GetMolfile | (Inherited from MolBase.) |
| GetMolWeight | (Overrides MoleculeGetMolWeight(Boolean).) |
| GetMWwithSalt | (Inherited from Molecule.) |
| GetRadar(Int32, Single) |
Draw a radar chart to visualize druglikeness of the molecular using MW, CLogP, NoHA, NoHD, NoRB, tPSA
(Inherited from Molecule.) |
| GetRadar(Int32, Int32, Single) | (Inherited from Molecule.) |
| GetRadar(Int32, Int32, Single, MolDrawingFormat) |
Return the image bytes of the radar chart
(Inherited from Molecule.) |
| GetRGroups |
Find all R groups.
(Inherited from Molecule.) |
| GetSequence | (Inherited from Molecule.) |
| GetSequenceComments | (Inherited from Molecule.) |
| GetSequences | (Inherited from Molecule.) |
| GetSequences(Boolean) | (Inherited from Molecule.) |
| GetSgroupText | |
| GetSMILES | (Inherited from MolBase.) |
| GetStructureKeys | (Inherited from Molecule.) |
| GetText | |
| GetTexts | (Overrides MoleculeGetTexts.) |
| GetType | Gets the Type of the current instance. (Inherited from Object.) |
| GetUnknownBonds | (Inherited from Molecule.) |
| GetVariableAtoms | (Inherited from Molecule.) |
| GuessBond | (Inherited from Molecule.) |
| GuessSuperAtoms | (Inherited from Molecule.) |
| HasAromaticBonds | (Inherited from Molecule.) |
| HasBio | (Inherited from Molecule.) |
| HasCoordinates | (Inherited from Molecule.) |
| HasEnhancedStereochemistry | (Inherited from Molecule.) |
| HasEnhancedStereochemistry(String, Boolean) | (Overrides MoleculeHasEnhancedStereochemistry(String, Boolean).) |
| HasHelmNodes | (Inherited from Molecule.) |
| HasQueryAtoms | (Inherited from Molecule.) |
| HasRGroups |
Test if the molecule contains any R group. R group defines a structure variable.
(Inherited from Molecule.) |
| HasStereoCenter | (Inherited from Molecule.) |
| HasSuperAtom | (Inherited from Molecule.) |
| HasUnmarkedChiralCenter | (Inherited from Molecule.) |
| HasUnmarkedChiralCenter(Boolean) | (Inherited from Molecule.) |
| HasZCoordinates |
Test if the atoms have Z coordaintes
(Inherited from Molecule.) |
| Highlight |
Highlight scaffold with a given color
(Inherited from Molecule.) |
| IsGenericStructure | (Overrides MoleculeIsGenericStructure.) |
| IsMacroMolecule | (Inherited from Molecule.) |
| Kekulize |
Convert aromatic rings into kekule form
(Inherited from MolBase.) |
| LayoutScaffold | (Inherited from Molecule.) |
| MarkAtomChirality | |
| MarkEnhanceStereoChemistry | |
| MarkLockedAtomExcluded | (Inherited from Molecule.) |
| MemberwiseClone | Creates a shallow copy of the current Object. (Inherited from Object.) |
| Merge(Molecule) |
Merge from all contents of a molecule
(Inherited from Molecule.) |
| Merge(DictionaryAtom, Atom, ABSet) | (Inherited from Molecule.) |
| Merge(Atom, Atom, ABSet) | (Inherited from Molecule.) |
| mZ | (Inherited from Molecule.) |
| NeedV3000 | (Inherited from Molecule.) |
| Neutralize |
Neutrialize atom charges
(Inherited from Molecule.) |
| NeutralizeIonBonds |
Neutralize ionic bonds
(Inherited from Molecule.) |
| NeutralizeIonBonds(SetAtom) | (Inherited from Molecule.) |
| NumberOfHydrogenAcceptors |
Compute the total number of hydrogen bond acceptors.
(Inherited from Molecule.) |
| NumberOfHydrogenDonors |
Compute the total number of hydrogen bond donors.
(Inherited from Molecule.) |
| NumberOfRotableBonds | (Inherited from Molecule.) |
| NumberOfRotatableBonds |
Compute the total number of rotable bonds.
Rotatable bond is defined as any single non-ring bond, bounded to nonterminal heavy (i.e., non-hydrogen) atom
(Inherited from Molecule.) |
| ParseADC | |
| RelayoutMols | (Inherited from Molecule.) |
| RemoveAtomIsotopes | (Inherited from Molecule.) |
| RemoveAtomMaps | (Inherited from Molecule.) |
| RemoveDummyBonds | (Inherited from Molecule.) |
| RemoveHydrogens | (Inherited from MolBase.) |
| RemoveHydrogens(Boolean) |
Remove all explicit hydrogen atoms
(Inherited from Molecule.) |
| RemoveTexts | |
| ResetAtomID |
Reset atom ID, starting from 1
(Inherited from Molecule.) |
| ResetAtomID(Int32) |
Reset atom ID, starting from a given number
(Inherited from Molecule.) |
| RestoreEnhanceStereoChemistry | |
| SaltStripping |
Strip salts and solvates
(Inherited from Molecule.) |
| SaveImage(String) |
Generate an image for the structure
(Inherited from MolBase.) |
| SaveImage(Stream, String, Double) | (Inherited from MolBase.) |
| SaveImage(Stream, String, Boolean, Boolean) |
Generate an image for the structure
(Inherited from MolBase.) |
| SaveImage(String, Int32, Int32, Int32) | (Inherited from MolBase.) |
| SaveImage(String, Int32, Int32, Int32, Boolean) | (Inherited from MolBase.) |
| SaveImage(Stream, String, Int32, Int32, Int32, Int32, Int32) |
Generate structure image
(Inherited from MolBase.) |
| SaveImage(Stream, String, Int32, Int32, Int32, Int32, Int32, Single) | (Inherited from MolBase.) |
| SaveImage(Stream, String, Int32, Int32, Int32, Int32, Int32, Boolean, Boolean) |
Generate structure image
(Inherited from MolBase.) |
| SaveImage(Stream, String, Int32, Int32, Int32, Int32, Int32, Single, Boolean, Boolean) | (Inherited from MolBase.) |
| SaveImage(Stream, String, Double, Int32, Int32, Int32, Int32, Int32, Single, Boolean, Boolean) | (Inherited from MolBase.) |
| SetColor | (Inherited from Molecule.) |
| SetModified |
Mark this molecule modified, so cached topological data, such as SSSR, will be invalidated.
(Inherited from Molecule.) |
| SetSgroup | |
| SplitAsMol |
Split fragments to different Molecule
(Inherited from Molecule.) |
| SplitAsSet |
Split fragments to different atom-bond set
(Inherited from Molecule.) |
| StripSalts | (Inherited from Molecule.) |
| SubstructureOf |
Test if the molecule is a substructure of the input query
(Inherited from Molecule.) |
| SuperstructureOf |
Test if the molecule is a super structure of the input query
(Inherited from Molecule.) |
| ToHtmlImgData | (Inherited from MolBase.) |
| ToHtmlImgTag | (Inherited from MolBase.) |
| ToImage |
Generate an image of the structure
(Inherited from MolBase.) |
| ToImage(Int32, Int32, Int32) |
Generate an image of the structure
(Inherited from MolBase.) |
| ToImage(Int32, Int32, Int32, Boolean) |
Generate an image of the structure
(Inherited from MolBase.) |
| ToMetafile |
Generate a vector image, which is resizable
(Inherited from MolBase.) |
| ToMetafile(Boolean) |
Generate a vector image, which is resizable
(Inherited from MolBase.) |
| ToMetafile(Single, Boolean) | (Inherited from MolBase.) |
| ToString | (Inherited from MolBase.) |
| ToString(String) |
Serialize the object to a string
(Inherited from MolBase.) |
| Translate | (Overrides MolBaseTranslate(Point3D).) |
| Write(String) |
Write object into a file
(Inherited from MolBase.) |
| Write(Stream, String) |
Store the object into a stream
(Inherited from MolBase.) |
| Write(Stream, String, Boolean) |
Store the object into a stream
(Inherited from MolBase.) |
| XLogP |
Compute XLogP of the molcule.
ForceField extension has to be installed. It returns NaN if not installed.
(Inherited from Molecule.) |
Fields| Name | Description | |
|---|---|---|
 | Attributes | (Inherited from MolBase.) |
 | cano | (Inherited from MolBase.) |
| chiral | (Inherited from Molecule.) |
| MolName | (Inherited from MolBase.) |
| NotSearchable | (Inherited from MolBase.) |
| set | (Inherited from Molecule.) |
| Source | (Inherited from MolBase.) |
| Tag | (Inherited from MolBase.) |
See Also