chemaxon.core.calculations.valencecheck

Class ValenceCheckOptions

java.lang.Object

chemaxon.core.calculations.valencecheck.ValenceCheckOptions

All Implemented Interfaces:

java.io.Serializable

@PublicAPI
public class ValenceCheckOptions
extends java.lang.Object
implements java.io.Serializable

Class created to make valence calculation configurable. There are two options at the moment:

• Use local or global aromatic calculation:
  • Local aromatic calculation does not check the Huckel rule in aromatic rings, it checks only if the atom has a correct aromatic valence. E.g.: c1cccn1 and c1cccc[nH]1 is accepted
  • Global aromatic calculation checks the Huckel rule and reports if the aromatic system is incorrect. Because it needs to find all the rings of the aromatic system, it's slower that the local method.
• Allow or deny traditional forms of 5 valence Nitrogen
  • If allowed the following 5 valence Nitrogen atoms are not marked as valence errors:
    • CN(=O)=O
    • CN(=O)=C
    • CN(C)=O
    • CN(C)(C)=O
    • c1ccccn1=O
  • If denied, only the following forms are allowed (they allowed with both setting)
    • C[N+](=O)[O-]
    • C[N+]([O-])=C
    • C[N+](C)(C)[O-]
    • c1cccc[n1+][O-]

Since:

version 6.0

Author:

Peter Cseh

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	ValenceCheckOptions.Builder Builder for ValenceCheckOptions.

Field Summary

Fields

Modifier and Type	Field and Description
static ValenceCheckOptions	DEFAULT

Constructor Summary

Constructors

Constructor and Description
ValenceCheckOptions(boolean localAromatic, boolean traditionalNallowed) Deprecated. since Marvin 6.2, Use ValenceCheckOptions.Builder for building ValenceCheckOptions.

Method Summary

Modifier and Type	Method and Description
boolean	equals(java.lang.Object other)
int	hashCode()
boolean	isLocalAromatic() Do not calculate valence for ambiguous aromatic atoms behaving like aromatic Nitrogens (e.g.
boolean	isTraditionalNitrogensAllowed() Returns if the traditional way of the ylidene and nitro groups if true the N in CN(=O)=O, CN(C)(C)=O, CN(=C)=O and c1ccccn1=O is accepted if false they are marked as valence error.
java.lang.String	toString()

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Field Detail

DEFAULT

public static final ValenceCheckOptions DEFAULT

Constructor Detail

ValenceCheckOptions

@Deprecated
public ValenceCheckOptions(boolean localAromatic,
                                       boolean traditionalNallowed)

Deprecated. since Marvin 6.2, Use ValenceCheckOptions.Builder for building ValenceCheckOptions.

Parameters:

localAromatic - Do not calculate valence for ambiguous aromatic atoms behaving like aromatic Nitrogens (e.g. N, O+ or C-) or Borons (e.g. B, C+). Ambiguous aromatic atoms are ignored in valence calculations if set to true and no global aromatic rules are checked

traditionalNallowed - traditionalNitrogenAllowed the traditional way of the ylidene and nitro groups if true the N in CN(=O)=O, CN(C)(C)=O, CN(=C)=O and c1ccccn1=O is accepted if false they are marked as valence error.

Method Detail

isLocalAromatic

public boolean isLocalAromatic()

Do not calculate valence for ambiguous aromatic atoms behaving like aromatic Nitrogens (e.g. N, O+ or C-) or Borons (e.g. B, C+). Ambiguous aromatic atoms are ignored in valence calculations if set to true and no global aromatic rules are checked

Returns:

the local aromatic setting

isTraditionalNitrogensAllowed

public boolean isTraditionalNitrogensAllowed()

Returns if the traditional way of the ylidene and nitro groups if true the N in CN(=O)=O, CN(C)(C)=O, CN(=C)=O and c1ccccn1=O is accepted if false they are marked as valence error.

Returns:

if the traditional Nitrogen representation is allowed

equals

public boolean equals(java.lang.Object other)

Overrides:

equals in class java.lang.Object

hashCode

public int hashCode()

Overrides:

hashCode in class java.lang.Object

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object