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Align the depiction using a fixed substructure
This task comes from working with researchers who have a desktop tool which displays a large number (a few hundred) structures on a scrolling page. The structures are the database hits from searching with a -
Highlight a substructure in the depiction
The benzodiazepine data set was generated by doing a PubChem search for the SMARTS query "C2(CN=C(C1=CC(=CC=C1N2[*])[*])C3=CC=CC=C3[*])=[*]" where the [*] are for the R-groups. The query -
Working with SD tag data
An SD file contains a set of records. Each record has a connection table and set of fields which together describe the molecule. This is call the'molfile'. A record also contains a set of -
Depict a compound as an image
I don't know about you, but I have a hard time looking at anything other than trivial SMILES strings and SD files and understanding the contained molecular structure. Images help, a lot. Noel O -
Heavy atom counts from an SD file
For each record from the benzodiazepine file, print the total number of heavy atoms in each record (that is, exclude hydrogens). You must get the data from the connection table and not from the tag -
Report the similarity between two structures
Use the toolkit's preferred comparison method to compare two different molecules for similarity. The result must be 0.0 if the molecules are not at all similar and 1.0 if they are completely -
Find the 10 nearest neighbors in a data set
This task uses the toolkit appropriate way of computing molecular similarities to find the 10 most similar structures in a data set. A common task in cheminformatics is to find target structures in a data -
Break rotatable bonds and report the fragments
This task is meant to give examples of how to add and delete atoms and bonds from the molecular graph, using the graph API. One of the researchers I worked with asked me for a -
Ring counts in a SMILES file
The goals of this task are to show how to read molecules from a SMILES file and how to get the number of cycles in a molecule. As is usual in chemistry software, the data -
Calculate TPSA
Ertl, Rohde, and Selzer (J. Med. Chem., 43:3714-3717, 2000) published an algorithm for fast molecular polar surface area (PSA). Part of it involves summing up partial surface values based on fragment contributions. Each -
Perform a substructure search on SDF file and report the number of false positives
Take a SMILES query and an SDF file; compute fingerprints for the given query and molecules from the SDF file; perform a substructure search (using the fingerprints for screening); report the total amount of molecules -
Convert a SMILES string to canonical SMILES
A SMILES string is a way to represent a 2D molecular graph as a 1D string. In most cases there are many possible SMILES strings for the same structure. Canonicalization is a way to determine -
Change stereochemistry of certain atoms in SMILES file
Run a SMILES file containing multiple structures. Perform a substructure match of a query SMILES structure against each input structure. In every found substructure, invert the stereo configuration of selected stereocenters of the query, then -
Find the graph diameter
Almost every cheminformatics toolkit uses a graph model based on the valance bond model of chemistry. The node and edges are labeled with properties like atomic number, bond type, and chirality to make them represent -
Unique SMARTS matches against a SMILES string
A number of molecular descriptors are based on how many times a given SMARTS pattern is uniquely found in a structure. For example, the CACTVS substructure key 122 is set if there are "= 2 any -
Convert SMILES file to SD file
Convert a SMILES file (yet to be determined) into an SD file. The conversion must do its best to use the MDL conventions for the SD file, including aromaticity perception. Note that the use of -
Chemistry Toolkit Rosetta Wiki
The Chemistry Toolkit Rosetta is a wiki for sharing how to use different chemistry toolkits for the same set of common tasks. The main focus is on chemical informatics, with toolkits that handle molecular structures -
Benzodiazepine
The gzip compressed "benzodiazepine" SD file is used in many of the code examples. It is the result of a SMARTS substructure search of PubChem on 19 December 2009. The query SMARTS was "C2(CN -
Report how many SD file records are within a certain molecular weight range
Read the benzodiazepine file and report the number of records which contain a molecular weight between 300 and 400. This should include the end ranges, so 300 ≤ weight ≤ 400 but as none of the compounds -
Detect and report SMILES and SDF parsing errors
Parse the strings "Q" and "C1C1" as if they were SMILES and store any error or warning messages to a file. These should not be accepted as valid SMILES strings. There needs to be a -
Iteration through an SD file
copied from http://www.redbrick.dcu.ie/~noel/CDKJython.html The original author is Noel O'Boyle. from org.openscience.cdk import* from org.openscience.cdk.qsar.descriptors.molecular import BCUTDescriptor from org.openscience.cdk -
Calculate 0, 1st, 2nd order Molecular Connectivity Indices (MCIs) using openbabel/pybel
Molecular Connectivity Indices (MCIs), also known as Kier-Hall connectivity indices were useful molecular descriptors for predicting properties for chemicals. To calculate these MCIs, the connectivity count for each atom needs to be obtained. This
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