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Sketching and viewing with Marvin Features, tips and tricks

Sketching and viewing with Marvin Features, tips and tricks

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Sketching and viewing with Marvin Features, tips and tricks

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  1. Sketching and viewing with MarvinFeatures, tips and tricks Akos Papp

  2. Outline • Main original features • Main original technical features • New features – 5.0 • Features coming – 5.1 • Future features – 5.2 • Feature videos (throughout the presentation) • Configurations • Customization • Some drawing tips and tricks • Where to use keyboard for quick drawing • Right click options • Useful shortcuts

  3. Main original features – 1 • 2D and 3D sketching and viewing • Isotopes, charges, radicals, maps

  4. Isotopes, charges, radicals

  5. Main original features – 1 • 2D and 3D sketching and viewing • Isotopes, charges, radicals, maps • Stereo features (tetrahedral, double bond, diastereo)

  6. Stereo features

  7. Main original features – 1 • 2D and 3D sketching and viewing • Isotopes, charges, radicals, maps • Stereo features (tetrahedral, double bond, diastereo) • Valence check, lone pairs, implicit hydrogens

  8. Valence check, lone pairs

  9. Main original features – 1 • 2D and 3D sketching and viewing • Isotopes, charges, radicals, maps • Stereo features (tetrahedral, double bond, diastereo) • Valence check, lone pairs, implicit hydrogens • Aliases, pseudo-atoms • Attached data

  10. Alias, pseudo, attached data

  11. Main original features – 1 • 2D and 3D sketching and viewing • Isotopes, charges, radicals, maps • Stereo features (tetrahedral, double bond, diastereo) • Valence check, lone pairs, implicit hydrogens • Aliases, pseudo-atoms • Attached data • Nice structures (antialiasing) • Rich formatting (fonts, colors, bond thickness)

  12. Rich formatting

  13. Main original features – 1 • 2D and 3D sketching and viewing • Isotopes, charges, radicals, maps • Stereo features (tetrahedral, double bond, diastereo) • Valence check, lone pairs, implicit hydrogens • Aliases, pseudo-atoms • Attached data • Nice structures (antialiasing) • Rich formatting (fonts, colors, bond thickness) • Query drawing features • Any atom, atom list/not-list, link nodes

  14. Any atom, atom list, link nodes

  15. Main original features – 1 • 2D and 3D sketching and viewing • Isotopes, charges, radicals, maps • Stereo features (tetrahedral, double bond, diastereo) • Valence check, lone pairs, implicit hydrogens • Aliases, pseudo-atoms • Attached data • Nice structures (antialiasing) • Rich formatting (fonts, colors, bond thickness) • Query drawing features • Any atom, atom list/not-list, link nodes • Atom properties (substitution count, aromatic, etc.)

  16. Atom properties

  17. Main original features – 1 • 2D and 3D sketching and viewing • Isotopes, charges, radicals, maps • Stereo features (tetrahedral, double bond, diastereo) • Valence check, lone pairs, implicit hydrogens • Aliases, pseudo-atoms • Attached data • Nice structures (antialiasing) • Rich formatting (fonts, colors, bond thickness) • Query drawing features • Any atom, atom list/not-list, link nodes • Atom properties (substitution count, aromatic, etc.) • Bond topology (ring, chain) • Reaction topology (reacting center, inversion/retention)

  18. Bond and reaction topology

  19. Main original features – 1 • 2D and 3D sketching and viewing • Isotopes, charges, radicals, maps • Stereo features (tetrahedral, double bond, diastereo) • Valence check, lone pairs, implicit hydrogens • Aliases, pseudo-atoms • Attached data • Nice structures (antialiasing) • Rich formatting (fonts, colors, bond thickness) • Query drawing features • Any atom, atom list/not-list, link nodes • Atom properties (substitution count, aromatic, etc.) • Bond topology (ring, chain) • Reaction topology (reacting center, inversion/retention) • Recursive SMARTS

  20. Recursive SMARTS

  21. Main original features – 2 • Markush structure drawing features

  22. Markush structure drawing Play feature animation: http://www.chemaxon.com/conf/Marvin08/MarkushDrawingBenzodiazepine.swf

  23. Main original features – 2 • Markush structure drawing features • Groups • Large collection of abbreviated groups • Quick drawing using the keyboard • Custom group creation (R-group, S-group, etc.)

  24. Abbreviated groups Play feature animation: http://www.chemaxon.com/conf/Marvin08/AbbrevTosGroupCreate.swf

  25. Main original features – 2 • Markush structure drawing features • Groups • Large collection of abbreviated groups • Quick drawing using the keyboard • Custom group creation (R-group, S-group, etc.) • Single step reaction drawing • Automatic component recognition • Manual- and automapping

  26. Component autorecognition Play feature animation: http://www.chemaxon.com/conf/Marvin08/ComponentAutoRecognition.swf

  27. Manual– and automapping Play feature animation: http://www.chemaxon.com/conf/Marvin08/Automapping.swf

  28. Main original features – 2 • Markush structure drawing features • Groups • Large collection of abbreviated groups • Quick drawing using the keyboard • Custom group creation (R-group, S-group, etc.) • Single step reaction drawing • Automatic component recognition • Manual- and automapping • Graphics, text boxes, electron flow arrows

  29. Electron flow arrows

  30. Main original features – 2 • Markush structure drawing features • Groups • Large collection of abbreviated groups • Quick drawing using the keyboard • Custom group creation (R-group, S-group, etc.) • Single step reaction drawing • Automatic component recognition • Manual- and automapping • Graphics, text boxes, electron flow arrows • 2D and 3D structure clean

  31. 2D and 3D clean CC(C)NCC(O)COC1=C2C=C(C)NC2=CC=C1 topology 2D 3D

  32. Main original features – 2 • Markush structure drawing features • Groups • Large collection of abbreviated groups • Quick drawing using the keyboard • Custom group creation (R-group, S-group, etc.) • Single step reaction drawing • Automatic component recognition • Manual- and automapping • Graphics, text boxes, electron flow arrows • 2D and 3D structure clean • Aromatization /dearomatization

  33. Aromatization/dearomatization Play feature animation: http://www.chemaxon.com/conf/Marvin08/Aromatization.swf

  34. Main original features – 2 • Markush structure drawing features • Groups • Large collection of abbreviated groups • Quick drawing using the keyboard • Custom group creation (R-group, S-group, etc.) • Single step reaction drawing • Automatic component recognition • Manual- and automapping • Graphics, text boxes, electron flow arrows • 2D and 3D structure clean • Aromatization /dearomatization • Calculator plugins

  35. Calculator plugins • Elemental analysis • Protonation (pKa, major microsp., isoelectric point) • Partitioning (logP, logD) • Charge (charge, polarizability, orbital electronegativity) • Isomers (tautomers, resonance, stereoisomers) • Conformation (conformers, molecular dynamics) • Geometry (topology analysis, geometry, polar surface area (2D), molecular surface area (3D)) • H-bond donors/acc., Huckel analysis, refractivity • IUPAC name generation • Markush enumeration

  36. Main original features – 2 • Markush structure drawing features • Groups • Large collection of abbreviated groups • Quick drawing using the keyboard • Custom group creation (R-group, S-group, etc.) • Single step reaction drawing • Automatic component recognition • Automapping • Graphics, text boxes, electron flow arrows • 2D and 3D structure clean • Aromatization /dearomatization • Calculator plugins • Multipage sketches

  37. Multipage documents

  38. Main original features – 2 • Markush structure drawing features • Groups • Large collection of abbreviated groups • Quick drawing using the keyboard • Custom group creation (R-group, S-group, etc.) • Single step reaction drawing • Automatic component recognition • Automapping • Graphics, text boxes, electron flow arrows • 2D and 3D structure clean • Aromatization /dearomatization • Calculator plugins • Multipage sketches • Molecule matrix view in MarvinView

  39. Molecule matrix view

  40. Main original technical features • Import/export of all important molecular file formats • Inter-conversion, automatic recognition

  41. File Formats • Marvin • CML • IUPAC InChI • IUPAC Name • MDL Molfile • Extended Molfile • Rxnfile • Extended Rxnfile • RDfile • SDfile • Peptide sequence • SMILES • SMARTS • Tripos SYBYL Mol • Mol2 • Gaussian Cube • Gaussian Input • PDB • XYZ

  42. Main original technical features • Import/export of all important molecular file formats • Inter-conversion, automatic recognition • Image export to the major image file formats

  43. Image export • JPG, JPEG • PNG • PPM • PDF • SVG, SVGZ • BMP • EMF

  44. Main original technical features • Import/export of all important molecular file formats • Inter-conversion, automatic recognition • Image export to the major image file formats • Visualization with MarvinView and MarvinSpace

  45. MarvinView and MarvinSpace

  46. Main original technical features • Import/export of all important molecular file formats • Inter-conversion, automatic recognition • Image export to the major image file formats • Visualization with MarvinView and MarvinSpace • Distributions: Standalone, JWS, Beans, Applets

  47. Beans vs. Applets • Desktop applications (deployment with Installer, Java Web Start) • Recommended for end-users • Easy installation • Recommended for developers • Quick GUI building • Easy customization • Marvin integration into web pages • Wide range of layout customization • Recommended for web developers • Simple web base deployment • Modular architecture ensures short download time

  48. Main original technical features • Import/export of all important molecular file formats • Inter-conversion, automatic recognition • Image export to the major image file formats • Visualization with MarvinView and MarvinSpace • Distributions: Standalone, JWS, Beans, Applets • Pure JAVA based • Platform and browser independent

  49. System compatibility • Windows • 95, 98, Me, NT, 2000, XP • Mac OS X • Unix/Linux • Linux, Solaris, etc.

  50. Browser compatibility • Internet Explorer • Firefox • Mozilla • Netscape • Safari • Opera