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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

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Sketching and viewing with Marvin Features, tips and tricks


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    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