The Atom type exposes the following members.
Constructors
| Name | Description | |
|---|---|---|
 | Atom | Overloaded. |
Methods
| Name | Description | |
|---|---|---|
| AddBond |
Adds a bond to this atom.
|
| Bond | Overloaded. |
| BondedAtom |
Get bonded atom its position into bond list
|
| BondedTo |
Check if this atom is bonded to given atom
|
| BondSum |
Computes Bond Sum for this Atom (Aromatic bond provides 1.5 coef)
|
| BondSum2 |
Computes Bond Sum for this Atom (Aromatic bond provides 1 coef)
|
| Clear |
Clean up atom data
|
| Clone |
Clone return a new Atom object which is a copy of the current one
|
| CompareTo |
Compare two BaseObject object using Index value
(Inherited from BaseObject.) |
| Copy |
Copy values from atom
|
| CountAromaticBondedNitrogens |
Number of aromatic nitrogens with this atom
|
| CountDoubleBondedCarbons |
Number of double bonded carbons with this atom
|
| CountDoubleBondedNitrogens |
Number of double bonded nitrogens with this atom
|
| CountDoubleBondedOxygens |
Number of double bonded oxygens with this atom
|
| CountDoubleBondedSulfurs |
Number of double bonded sulfurs with this atom
|
| DeleteBond |
Delete the given Bond from this atom
|
| Equals | Overloaded. |
 | Finalize |
Allows an Object to attempt to free resources and perform other cleanup operations before the Object is reclaimed by garbage collection.
(Inherited from Object.) |
| GetAtomQueryList |
Returns Atom query list between brackets
|
| GetHashCode |
Override GetHashCode method of the base class
(Inherited from BaseObject.) |
| GetHybridation |
Computes Atom hybridation
|
| GetType |
Gets the Type of the current instance.
(Inherited from Object.) |
| HasFeature |
Get the AtomContextFeatures attribute of the atom object
|
| IsAlkyl |
Checks if atom is alkyl
|
| IsAryl |
Checks if atom is aryl
|
| isConnected |
Returns true if this atom is connected to the atom at
|
| IsCyano |
Check if atom is isocyano : *C(#N)
|
| IsExocyclicIminoC |
Check if atom is ExocyclicIminoC
|
| IsExocyclicMethyleneC |
Check if atom is ExocyclicMethyleneC
|
| IsHydroxyl |
Check if atom is Hydroxyl
|
| IsIminoC |
Check if atom is IminoC : C(=N)(*)
|
| IsInRingSize |
Check if this collection contains a Ring of given size
|
| IsIsoCyano |
Check if atom is isocyano : C(#N)(*)
|
| IsNitro |
Check if atom is Nitro -N(-O)(=0)
|
| IsNitroN |
Check if atom is NitroN
|
| IsNitroNneg |
Checks if atom is a NitroN negative
|
| IsO3 |
Check if atom is an Oxygen SP3
|
| IsOxoC |
Check if atom is OxoC
|
| IsS3 |
Check if atom is a Sulfur SP3
|
| IsThioxoC |
Check if atom is ThioxoC
|
| MaxBondOrder |
Computes greater bond Order : Aromatic bound are taken as 1.5
|
| MemberwiseClone |
Creates a shallow copy of the current Object.
(Inherited from Object.) |
| SetCoordinates | Overloaded. |
| SetFeature |
Sets the AtomContextFeatures attribute of the atom object
|
| SumBondType |
Summary of attached bond
|
| ToString |
Override ToString function
(Overrides Object..::.ToString()()().) |
Properties
| Name | Description | |
|---|---|---|
 | Anticlockwise |
Gets the antiClockwise attribute of the Atom object
|
| Aromatic |
Aromatic tag
(Inherited from ChemicalBase.) |
| AtomicElement |
Atomic Element property
|
| AtomicNumber |
Atomic Number property
|
| AtomicWeight |
Atomic mass :
If AtomicNumber is 0 returns 0
|
| AtomMappingNumber |
Reaction atom-atom mapping order property
|
| AtomNext |
Atom iterator throught bonded atoms to this
|
| AtomNextFlag |
Atom iterator : returns atoms with Flag sets as False
|
| AtomNextFlagBFS |
Atom iterator : returns atoms with Flag sets as False and CountBonds > 1
|
| AtomNoneChargedHydrogenNext |
Atom iterator throught bonded atoms to this no being a charged Hydrogen
|
| AtomNoneHydrogenNext |
Atom iterator throught bonded atoms to this no being an Hydrogen
|
| AtomSiblingSSSR |
Atom Sibling iterator throught bonded atoms (to this) having more than 1 bond
|
| BondNext |
Bond iterator
|
| Charge |
Atom charge property
|
| Chiral |
Gets chiral center flag for the Atom object
|
| Clockwise |
Gets the clockwise attribute of the Atom object
|
| Color |
Element color
(Inherited from ChemicalBase.) |
| Complement |
Returns complement value
|
| ConnectedAtoms |
Get list of connected atoms
|
| ConnectedAtomsFlag |
Get list of connected atoms where flag propery is False
|
| CountAttachedH |
Returns number of attached Hydrogen
|
| CountBonds |
Returns number of Bonds attached to this atom
|
| CountBondsWithoutH |
Returns number of Bonds attached to this atom that do not implied an Hydrogen
|
| CountTotalH |
Returns total number of hygrogens: [Attached + missing] hygrogens
|
| CustomCode |
Custom atom code property for N, O, S, P
|
| CustomType |
Custom atom type (Patty like)
|
| Flag |
Byte Flag property
(Inherited from BaseObject.) |
| Hybridation |
Hybridation
|
| Index |
Index property
(Inherited from BaseObject.) |
| InSuperatom |
Atom is part of a super atom group
|
| InversionRetentionFlag |
Reaction Inversion-Retention flag property:
0 = property not applied
1 = configuration is inverted,
2 = configuration is retained,
|
| IsBoron |
Is a boron atom
|
| IsBromine |
Is a bromine atom
|
| IsCarbon |
Is a carbon atom
|
| IsChlorine |
Is a chlorine atom
|
| IsHeteroAtom |
Is a heteroatom (not H, not C)
|
| IsHydrogen |
Is a hygrogen atom
|
| IsInRing |
Is in ring
(Inherited from ChemicalBase.) |
| IsIodine |
Is a iodine atom
|
| IsMetal |
Is a Metalic atom
|
| IsNitrogen |
Is a nitrogen atom
|
| IsOrganic |
Atom is Organic (B, C, N, O, F, P, S, Cl, Br, I)
|
| Isotope |
Absolute mass of the atom isotope as a positive integer.
When present, this property supersedes all isotope values in the atom block.
|
| IsOxygen |
Is an oxygen atom
|
| IsPhosphor |
Is a phosphor atom
|
| IsPolar |
Atom is Polar (N, O, P, S)
|
| IsQuery |
Is this atom has query features
|
| IsQueryFeature |
Is a query feature
(Inherited from ChemicalBase.) |
| IsSP1 |
Atom is SP1
|
| IsSP2 |
Atom is SP2
|
| IsSP3 |
Atom is SP3
|
| IsSulfur |
Is a sulfur atom
|
| IsTerminal |
Is a terminal atom
|
| Item |
BondDictionary list is defined as the Indexer. Indexer allow Get/Set procedure but do not control BondDictionary.Count ! |
| MissingHydrogens |
Computes missing number of Hydrogen
|
| Parent |
Reference of the parent Molecule object
(Inherited from ChemicalBase.) |
| QueryAtomList |
Defined atom list for atom query feature
|
| Radical |
Radical value :
Default of 0 = no radical, 1 = singlet (:), 2 = doublet ( . or ^), 3 = triplet (^^)
|
| ReactionCenter |
Set Reaction center
|
| ReactionIndex |
Set Reaction Index
|
| Ring |
Iterator for linked Ring object
|
| Stereo |
Stereo : 0 = not stereo, 1 = odd, 2 = even, 3 = either or unmarked stereo center
|
| Valence |
Valence property
|
| X |
X _coordinates
|
| Y |
Y _coordinates
|
| Z |
Z _coordinates
|
