chemaxon.marvin.alignment

Class RotatableBondDetector

java.lang.Object

chemaxon.marvin.alignment.RotatableBondDetector

public final class RotatableBondDetector
extends Object

Author:

Adrian Kalaszi

Constructor Summary

Constructors

Constructor and Description
RotatableBondDetector(Molecule m, boolean forcedFlexible)

Method Summary

Methods

Modifier and Type

Method and Description

boolean

isRotatableBond(int bond) Not flexible if: double, aromatic, triple bond single bond neighboring a triple like at cyanide chain end bonds amide thioamide: -C(=S)-NR2 sulphonamide R-S(=O)2-NR2 aniline N : C(aromatic)-N(sp3) aromatic amidine : C(aromatic)-C(=NH)-NH2 aromatic nitroso : C(aromatic)-N=O aromatic nitro : C(aromatic)-NO2 (although at some substituent position it may be rotatable) C(aromatic)-N(amide) flexible Warning there are three intentional but unexpected feature: Ring bonds may be rotatable also.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

RotatableBondDetector

public RotatableBondDetector(Molecule m,
                     boolean forcedFlexible)

Method Detail

isRotatableBond

public boolean isRotatableBond(int bond)

Not flexible if:

• double, aromatic, triple bond
• single bond neighboring a triple like at cyanide
• chain end bonds
• amide
• thioamide: -C(=S)-NR2
• sulphonamide R-S(=O)2-NR2
• aniline N : C(aromatic)-N(sp3)
• aromatic amidine : C(aromatic)-C(=NH)-NH2
• aromatic nitroso : C(aromatic)-N=O
• aromatic nitro : C(aromatic)-NO2 (although at some substituent position it may be rotatable)

C(aromatic)-N(amide) flexible Warning there are three intentional but unexpected feature:

• Ring bonds may be rotatable also.
• The single bond in biphenyl is also rotatable.
• Single bond in acetylene, which should be rotatable, kept rigid.

Parameters:

bond - bondSeq in molecule

Returns:

if rotatable or not