Enhancements to Chemical Explorer

Chemical Explorer, developed by Minesoft to take advantage of Chemical NER (Named Entity Recognition) technology to add chemical structure search capability throughout the entire text of millions of patent documents, can interrogate patent data in several ways. Similarity, substructure and exact structure searching are available, with structure input possible from chemical name, trade name, SMILES, Mol file, or by drawing the structure.

Chemical Explorer has recently been further developed, with the following improvements:

  • Query atoms
    • Any element, heteroatom, halogen
    • List of user selected elements
    • NOT list of user selected elements
    • Ring bond count, H count, substitution count and unsaturation
  • Query bonds
    • Any bond type, aromatic bond, and combinations of bond types
    • Ring bond or chain bond
  • Crossed bond, to match both cis and trans configurations
  • Hydrogens placed by the user i.e. explicit hydrogens, are not substitutable
  • And more…

New feature usable in any search type – crossed bond added

The cross bond allows a user to search cis and trans isomers around a double bond with the same query structure. (Whether the bond is cis or trans will be ignored for the bond where a cross bond is used)

For example, a query on the structure below will find both the cis and trans isomers for hexene:

This will find any references to cis hexene, trans hexene or hexene where cis-trans configuration was not specified.

New Query features (usable in substructure searches)

Query bond feature: when searching using the substructure search it is possible to use a query bond to broaden your search.

The feature comes with 3 available options:

 Option 1: Any bond

The system will retrieve any structures that can have any bond type at the reference location.

Option 2: Aromatic bond

The system will retrieve any structures that have an aromatic bond type at the reference location.

Option 3: Single/double bond, Single/aromatic bond, Aromatic/double bond

These options will return molecules that have either of the two stated bond types at the selected location as a hit.

Ability to select which elements an atom can or cannot be

It is now possible to define a list of elements that are allowed at a given position. To do this, open the periodic table within the sketch tool and check the List box shown in the box at the bottom of the screen below.

In the example, an atom at the specified location can be any of H, Li, F or Cl for the structure to flag as a hit.

The Not List functions in the same way as the previously mentioned List, except that in this case you are instructing the system that the atom at the given location should NOT be any of the selected atoms.

In the example, if a Fluorine or Chlorine are present at the given location, the structure would not flag as a hit even if it met all other criteria for the structure.

New Extended tab added to the periodic table with generic atoms

There is also a new Extended tab within the periodic table. Here you can specify more general criteria for the atom at a given location, with 3 options to choose from…

  1. Any atom: there are no restrictions placed on the given location and any atom can be present there
  2. Except hydrogen or carbon: any heteroatom (not carbon or hydrogen) can be present at the given location
  3. Any halogen: the atom at the given location must be a halogen

Atom and bond properties

Set atom properties node by node

Double clicking on an atom will open the atom properties window. This window contains multiple options that can be used to constrain the atom at the given node as shown in the screenshot below, including atom ring bond count/H count/Substitution count and whether the atom is saturated or unsaturated.

Set bond topology quickly and easily

Double clicking on a bond will open the bond properties window for that bond, allowing you to set the bond type and the topology can be constrained to ring or chain. 

Hydrogens will now be treated as explicit when placed by the user

When drawing a query, hydrogens are automatically added to organic elements to provide standard valences. These hydrogens can be substituted by other elements when doing a substructure search. This change means that if the user adds a hydrogen atom to the query, it is treated like any other element and hence is not substitutable.

Other improvements…

  • History now shows depiction of search query
  • Mol file import method has been simplified, allowing you to upload a mol file directly from your computer, or to copy-paste mole file text directly into the tool and load to the sketcher

If you have any comments or feedback on the new look and tools, please let us know at support@minesoft.com, where we’d love to hear your thoughts on the new and improved Chemical Explorer!