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Chemical graph generator. A chemical graph generator is a software package to generate computer representations of chemical structures adhering to certain boundary conditions. The development of such software packages is a research topic of cheminformatics.
The Simplified Molecular Input Line Entry System ( SMILES) is a specification in the form of a line notation for describing the structure of chemical species using short ASCII strings. SMILES strings can be imported by most molecule editors for conversion back into two-dimensional drawings or three-dimensional models of the molecules.
ChemMantis, [14] the Chemistry Markup And Nomenclature Transformation Integrated System uses algorithms to identify and extract chemical names from documents and web pages and converts the chemical names to chemical structures using name-to-structure conversion algorithms and dictionary look-ups in the ChemSpider database. The result is an ...
A chemical structure of a molecule is a spatial arrangement of its atoms and their chemical bonds. Its determination includes a chemist 's specifying the molecular geometry and, when feasible and necessary, the electronic structure of the target molecule or other solid. Molecular geometry refers to the spatial arrangement of atoms in a molecule ...
Fluency in both the construction and interpretation of molecular structures is a critical learning objective in the second-year organic chemistry curriculum. With the introduction of PerkinElmer's ChemDraw structure drawing tool into undergraduate laboratory courses, students are challenged to develop fundamental molecular drawing skills using authentic, industry-standard software and to ...
Name Description Knots [Note 1]Links References trRosettaRNA: trRosettaRNA is an algorithm for automated prediction of RNA 3D structure. It builds the RNA structure by Rosetta energy minimization, with deep learning restraints from a transformer network (RNAformer). trRosettaRNA has been validated in blind tests, including CASP15 and RNA-Puzzles, which suggests that that the automated ...
Skeletal structural formula of Vitamin B 12.Many organic molecules are too complicated to be specified by a molecular formula.. The structural formula of a chemical compound is a graphic representation of the molecular structure (determined by structural chemistry methods), showing how the atoms are possibly arranged in the real three-dimensional space.
students were able to visualize atomic structures, molecules and crystals better when taught chemical bonding using three-dimensional virtual models. As a result, various visualization tools have been developed to create virtual molecular structures. A survey by Craig et al. (2013) of 32 visualization tools found Pymol and Jmol were the most ...