"Unfolding" a fixed-length ECFP

Hi guys,

I'm using a fixed-length ECFP in binary format created with generatemd. Is it possible from this binary fingerprint representation to understand which bit is set up by which atom type?

Regards

Hi, 

I'm afraid that this is not possible. To get this information you will need to use the unfolded variable length decimal representation. Those are not the atom types directly that set particular bits, the situation is more complex: the local neighbourhood (with a given radius) of each atom is taken into acount. This includes (may include) the atom type as well.

You may wish to follow this link to read more about the structure of ECFP.

Regards,

Miklos

Hi Miklos,

Thank you for you answer. I red the description that you gave me. According to this information this should be possible by using this class. Is this correct or I haven't understood the document?

I have some other questions. Is it possible in the config files to set up poperties like this:

<Property Name="Test prop" Value="1"><![CDATA[ valence()*charge()]]></Property>
<Property Name="Test prop" Value="1">valence()*hCount()</Property>

Is the above lines correct and if not what is the correct form for such properties?

And what is the difference between these two properties:

<Property Name="Mass" Value="1"/>
<Property Name="MassNumber" Value="0"/>

Regards

Hi,

According to this information this should be possible by using this class. Is this correct or I haven't understood the document?

That's correct. Here's a sample code of its typical usage:

   ECFPFeatureLookup lookup = new ECFPFeatureLookup();


   lookup.processMolecule(mol);
   for ( ECFPFeature f: lookup.getFeaturesFromIdentifier(key) ) {
       System.out.println(f.getSubstructure().toFormat("SMARTS"));
   }

Is the above lines correct and if not what is the correct form for such properties?

<Property Name="Mass" Value="1"/>
<Property Name="MassNumber" Value="0"/>

The first refers to the atomic weight (the second is as its name says the mass number).

Does this help?

Miklos

According to this information this should be possible by using this class. Is this correct or I haven't understood the document?

   ECFPFeatureLookup lookup = new ECFPFeatureLookup();


   lookup.processMolecule(mol);
   for ( ECFPFeature f: lookup.getFeaturesFromIdentifier(key) ) {
       System.out.println(f.getSubstructure().toFormat("SMARTS"));
   }

Is the above lines correct and if not what is the correct form for such properties?

<Property Name="Mass" Value="1"/>
<Property Name="MassNumber" Value="0"/>

Thank you for your answer. It was useful.

I have some other questions about ECFP.

What about H-atoms? If I'm using molecules with implicit H-atoms and "HCount" is set up in config file how this property is calculated? By free valence of atoms in molecules or...? And what is the situation wih molecules with explicit hydrogens?

Do I have to use CDATA form when I'm using -/+ operations in property definitions?

Regards

Hi,

hcount() considers both explicit and implicit hydrogens, and yes, the implicit ones are aclculated form valence.

Use CDATA always with complex expresion just to be on the safe side.

Regards,

Miklos