1 / 78

Sketching and viewing with Marvin Features, tips and tricks

Sketching and viewing with Marvin Features, tips and tricks. Akos Papp. 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

Renfred
Download Presentation

Sketching and viewing with Marvin Features, tips and tricks

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  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

More Related