JOELib Tutorial: A Java based cheminformatics/computational chemistry package | ||
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Here all examples are presented, which does not fit in another category.
Here is an example for the brute force symmetry analyzer identifying primitive rotations, planes and inversion centres.
Example 9-30. Calculate point group symmetries
if (symmetry.readCoordinates(mol) < 0) { System.err.println("Error reading in atomic coordinates"); System.exit(1); } // start symmetry estimation try { symmetry.findSymmetryElements(true); } catch (SymmetryException e) { e.printStackTrace(); System.exit(1); } if (symmetry.getBadOptimization()) System.out.println("Refinement of some symmetry elements was"+ " terminated before convergence was reached.\n" + "Some symmetry elements may remain unidentified.\n"); symmetry.reportSymmetryElementsVerbose(); System.out.println("Molecule has the following symmetry elements:\n"+ symmetry.getSymmetryCode()); PointGroup pointGroup = symmetry.identifyPointGroup(); if (pointGroup != null) { System.out.println("It seems to be the "+ pointGroup.getGroupName()+ " point group"); } else { System.out.println("These symmetry elements match more than one group I know of."); }
Sloppy Hashcode which uses only topological informations without E/Z isomerism and S/R chirality. This hascode is really helpfull to identify duplicate topological molecule entries.
Parse JCAMP-DX data.
Fragemted molecules can be generated by splitting contiguous fragments or using SMARTS splice definitions.
The standard procedure to generate molecules is using s scaffold and R-groups. New coordinates will be generated if the scaffold contains already 2D or 3D coordinates.