1 ×

CIR

CIR-Node extension for KNIME Workbench version 1.0.5 by Alvascience Srl

This node uses the network service CIR (Chemical Identifier Resolver) by the CADD Group at the NCI/NIH as a resolver for different chemical structure identifiers and allows to convert a given structure identifier into another representation or structure identifier.

Options

Select chemical structure identifier column
The column in the input data table that contains the molecule representation.

The input structure identifier type can be one of the following:
- stdinchi - Standard InChI (input must be 'InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H');
- stdinchikey - Standard InChIKey;
- smiles - SMILES of the Structure;
- ficts - NCI/CADD FICTS Identifier;
- ficus - NCI/CADD FICuS Identifier;
- uuuuu - NCI/CADD uuuuu Identifier;
- hashisy - CACTVS HASHISY Hashcode;
- name - Chemical Name for the Structure;
- iupac_name - IUPAC Name;
- cas - CAS Registry Number.
Output format
New structure representation.

The output structure identifier type can be one of the following:
- stdinchi - Standard InChI;
- stdinchikey - Standard InChIKey;
- smiles - SMILES of the Structure;
- ficts - NCI/CADD FICTS Identifier;
- ficus - NCI/CADD FICuS Identifier;
- uuuuu - NCI/CADD uuuuu Identifier;
- hashisy - CACTVS HASHISY Hashcode;
- sdf - SD File of the Structure;
- names - List of Chemical Names for the Structure;
- iupac_name - IUPAC Name;
- cas - CAS Registry Number;
- mw - Molecular Weight;
- formula - Chemical Formula;
- h_bond_donor_count - Number of Hydrogen Bond Donors;
- h_bond_acceptor_count - Number of Hydrogen Bond Acceptors;
- h_bond_center_count - Number of Hydrogen Bond Acceptors and Donors;
- rule_of_5_violation_count - Number of Rule of 5 Violations;
- rotor_count - Number of Freely Rotatable Bonds;
- effective_rotor_count - Number of Effectively Rotatable Bonds;
- ring_count - Number of Rings;
- ringsys_count - Number of Ring Systems.

Sometimes an input structure identifier can return multiple results (e.g. output as structure names or CAS). The query function will return every result.

Input Ports

Icon
Table containing the molecule identifier

Output Ports

Icon
Table containing the requested structure identifier

Best Friends (Incoming)

Best Friends (Outgoing)

Workflows

Installation

To use this node in KNIME, install CIR KNIME integration from the following update site:

KNIME 4.3

A zipped version of the software site can be downloaded here.

You don't know what to do with this link? Read our NodePit Product and Node Installation Guide that explains you in detail how to install nodes to your KNIME Analytics Platform.

Wait a sec! You want to explore and install nodes even faster? We highly recommend our NodePit for KNIME extension for your KNIME Analytics Platform. Browse NodePit from within KNIME, install nodes with just one click and share your workflows with NodePit Space.

Developers

You want to see the source code for this node? Click the following button and we’ll use our super-powers to find it for you.