Generic atom properties are used to describe unknown residuals attached
to a functional group. These residuals are represented by a generic atom.
Its properties describe the chemical environment around a functional group
by a number of parameters as described in the following:
Values set to 0 are ignored!
If any value in the generic atom properties dialog is set to 0, the
parameter will be ignored.
Connections
Connections
Gives the total number of neighbouring atoms or groups with respect
to the generic atom.
Example:
Number
of connections: 4
3
Imagine, the R group attached to the carboxylic acid functional group is
replaced by a Methyl-group or an Ethenyl-group. The double bond in the
Ethenyl-group decreases the number of connections by one.
Explicit Connections
Sets the number of neighbouring atoms around the generic atom without
consideration of implicit hydrogen atoms.
Example:
No. of
explicit connections: 3
2
In case,
hydrogen atoms will be explicitly drawn, this will have an effect on the
number of explicit connections. Otherwise they are neglected.
Valence
The valence specifies the total bond order of the very next atom attached
to the functional group. It is meant to be the highest available bonding.
Single bond = 1
Double bond = 2
Tripple bond = 3
General
This section offers the following settings:
Aliphatic
This flag indicates, whether the residual is aliphatic or not. If the
flag is set false, this setting is ignored.
Aromatic
This flag indicates, whether the residual is aromatic or not. If the
flag is set false, this setting is ignored.
Atom Pattern
This is meant to be the most important setting
in this dialog. Atom patterns or whole residuals can be described here
following the SMILES and SMARTS nomenclature. Please refer to the chapter
"SMILES
and SMARTS Nomenclature" for details. A logical expression describing
the chemical environment can be entered here. Expressions for whole molecular
fragments can be included here, if required. This Atom pattern description
overrides any of the other settings in this dialog.
Example:
Atom
Pattern: *&A; C; !N; !S; !O; !$(C(=O))
*&A means:the residue can be anything aliphatic.
The separator ";" means a logical
AND operator.
C means: the very next atom must be an aliphatic
Carbon.
!N means: the very next atom must not be
an aliphatic Nitrogen.
!O means: the very next atom must not be
an aliphatic Oxygen.
!S means: the very next atom must not be
an aliphatic Sulfur.
!$(C(=O)) means: the neighbouring group is
not a carbonyl group, which means, the following substance types are excluded:
Charge
Indicates the total positive or negative charge of the generic atom.
This is a useful feature to define ions or salts.
Displayed Name
For convenience, chemists prefer particular abbreviations for some residual
types as described in the following. This is not a mandatory setting,
but it helps to visualize certain functional groups:
R, R', R'', R''', ... = any kind of Alkyl-group
Ph = any kind of aromatic system e.g. a Phenyl-group
Ar = aromatic residual
G = anything aliphatic or aromatic with no restrictions.
Hydrogens
This section offers the following settings:
Attached Hydrogens
Sets the number of attached explicit hydrogens of the generic atoms.
This number must not be greater than the valence.
Implicit Hydrogens
Sets the number of implicit hydrogens.
Example:
If a Methylene-group (CH2) needs to be defined
as neighbouring generic atom, the implicit hydrogen count is set to 2.
Ring
This section offers the following settings:
Ring Membership
This option is useful for defining bridging atoms of e.g. bicycles.
It sets the number of rings the generic atom is a member of.
Example:
The bridge atoms in Norbornan are members
of two 5-membered rings.
Smallest Ring Size
This option sets the smallest allowed ring size, if the generic atom
is member of a ring. The ring size represents the number of atoms forming
a ring. If the generic atom is member
of a greater ring than specified here, it will be considered. Otherwise
it will be ignored.
