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The CHARMM molecular dynamics package [4] can read and write a number of standard chemical and biochemical file formats; however, the CARD (coordinate) and PSF (protein structure file) are largely unique to CHARMM. The CARD format is fixed-column-width, resembles the PDB format, and is used exclusively for storing atomic coordinates.
Unlike other chemical formula types, [a] which have a limited number of symbols and are capable of only limited descriptive power, structural formulas provide a more complete geometric representation of the molecular structure. For example, many chemical compounds exist in different isomeric forms, which have different enantiomeric structures ...
Retrieval of structures from a network database based on CAS number, formula, or name; Retrieval of information on a molecule based on a drawing; Symbols such as partial charge and radicals; Reading MDL Molfiles, CML (Chemical Markup Language), ChemDraw binary format, ChemDraw XML text format [2] Writing MDL Molfiles, CML, ChemDraw XML text format
This method works only if your molecule editor is able to export files in Windows Metafile format. For example, ChemDraw supports this, as does ChemSketch and BIOVIA Draw (.emf is preferable for the latter). Draw the structure in your molecule editor, and save it as a Windows Metafile (.wmf), Enhanced Metafile (.emf), or Encapsulated Postscript ...
SDF is one of a family of chemical-data file formats developed by MDL; it is intended especially for structural information. "SDF" stands for structure-data format, and SDF files actually wrap the molfile (MDL Molfile) format. Multiple records are delimited by lines consisting of four dollar signs ($$$$). A key feature of this format is its ...
The XYZ file format is a chemical file format. There is no formal standard and several variations exist, but a typical XYZ format specifies the molecule geometry by giving the number of atoms with Cartesian coordinates that will be read on the first line, a comment on the second, and the lines of atomic coordinates in the following lines. [ 1 ]
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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.