Reaction Class |
Reaction Class representing a single-step chemical reaction, which is composed of reactants, products and an arrow
Inheritance HierarchyNamespace: Scilligence.MolEngine
Assembly: Scilligence.MolEngine (in Scilligence.MolEngine.dll) Version: 1.3.0.0 (7.0.0.39951)
SyntaxC#
public class Reaction : MolBase
The Reaction type exposes the following members.
Constructors| Name | Description | |
|---|---|---|
 | Reaction |
Construct a blank reaction
|
| Reaction(Molecule, Molecule) |
Construct a single reactant and single product reaction
|
| Reaction(Molecule, Molecule) |
Construct a reaction from reactants and products
|
| Reaction(Molecule, Molecule, Molecule) | Initializes a new instance of the Reaction class |
Properties| Name | Description | |
|---|---|---|
 | Atoms |
All atoms of reactants and products
(Overrides MolBaseAtoms.) |
| Bonds |
All bonds of reactants and products
(Overrides MolBaseBonds.) |
| CanonicalCode |
Canonical Code of the structure
(Inherited from MolBase.) |
| 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.) |
| IsEmpty |
Test if the reaction contatins any reactant or product
(Overrides MolBaseIsEmpty.) |
| Products |
An array of products
|
| Reactants |
An array of reactants
|
| Reagents | |
| SMILES |
SMILES string
(Inherited from MolBase.) |
| StructureKeys |
A higher level of structure characterization (link)
(Inherited from MolBase.) |
| StructureKeysAsString |
The string version of StructureKeys
(Inherited from MolBase.) |
Methods| Name | Description | |
|---|---|---|
| AddDefaultArrow | |
| AddProduct | |
| AddReactant | |
| AddReagent | |
| Aromatize | (Inherited from MolBase.) |
| 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.) |
| ClearRxnMapping | |
| ClearRxnMapping(Int32) | (Overrides MolBaseClearRxnMapping(Int32).) |
| Clone |
Clone the whole reaction
|
| Dekekulize |
Convert rings to aromatic
(Inherited from MolBase.) |
| EqualizeBondLength |
Make all bonds have the same bond length
|
| Equals | (Inherited from Object.) |
| ExpandAllBios | (Inherited from MolBase.) |
| ExpandSuperAtoms | |
 | 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.) |
| GetBound |
Get the 3D bounds of the reaction
(Overrides MolBaseGetBound.) |
| GetCanonicalCode |
Create the canonical code
(Inherited from MolBase.) |
| GetFingerprints | (Overrides MolBaseGetFingerprints.) |
| GetHashCode | Serves as a hash function for a particular type. (Inherited from Object.) |
| GetInChI | (Inherited from MolBase.) |
| GetJSDraw | (Inherited from MolBase.) |
| GetMolfile | (Inherited from MolBase.) |
| GetRxnFile | |
| GetSMILES | (Inherited from MolBase.) |
| GetStructureKeys | (Overrides MolBaseGetStructureKeys.) |
| GetTexts | (Overrides MolBaseGetTexts.) |
| GetType | Gets the Type of the current instance. (Inherited from Object.) |
| HasCoordinates |
Test if any molecule has coordinates
(Overrides MolBaseHasCoordinates.) |
| HasZCoordinates |
Test if any atom has Z coordinates
(Overrides MolBaseHasZCoordinates.) |
| Kekulize |
Convert aromatic rings into kekule form
(Inherited from MolBase.) |
| MemberwiseClone | Creates a shallow copy of the current Object. (Inherited from Object.) |
| NeedV3000 | (Overrides MolBaseNeedV3000.) |
| ProductContains | |
| ReactantContains | |
 | Read(Byte) |
Read a binary data
|
| Read(Stream) |
Read a string
|
| Read(String) |
Parse a generic reaction string
|
| Read(Byte, String) |
Read a binary data
|
| Read(Byte, String) |
Read a binary data, and output the data's file format
|
| Read(Stream, String) |
Read a stream
|
| Read(Stream, String) |
Read a stream
|
| Read(String, String) |
Read a reaction string which file format is known
|
| Read(String, String) |
Parse a reaction string, and output the string's file format
|
| ReadFile |
Read a file
|
| ReadSMILES |
Parse a SMILES string. e.g. c1ccccc1Cl>>c1ccccc1O
|
| Relayout(Boolean) | |
| Relayout(Boolean, Sketch) |
Re-layout the reaction to make it looks nicer
|
| RemoveAtomMaps | (Overrides MolBaseRemoveAtomMaps.) |
| RemoveHydrogens | (Inherited from MolBase.) |
| RemoveHydrogens(Boolean) |
Remove all hydrogen atoms
(Overrides MolBaseRemoveHydrogens(Boolean).) |
| 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.) |
| SortByXCoordinates | |
| 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.) |
| ToSketch |
Convert the Reaction object into a Sketch object
|
| ToString | (Inherited from MolBase.) |
| ToString(String) |
Serialize the object to a string
(Inherited from MolBase.) |
| Translate |
Translate the whole structure
(Inherited from MolBase.) |
| TreatReagentAsReactant | |
| 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.) |
Fields| Name | Description | |
|---|---|---|
 | Arrow | |
| Attributes | (Inherited from MolBase.) |
 | cano | (Inherited from MolBase.) |
| MolName | (Inherited from MolBase.) |
| NotSearchable | (Inherited from MolBase.) |
| Source | (Inherited from MolBase.) |
| Tag | (Inherited from MolBase.) |
| textsabove | |
| textsbelow |
ExamplesMolecule reactant = Molecule.ReadSMILES("c1ccccc1Cl"); Molecule product = Molecule.ReadSMILES("c1ccccc1O"); Reaction r = new Reaction(reactant, product);
See Also