Sketching and viewing with Marvin Features, tips and tricks

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Sketching and viewing with Marvin Features,
tips and tricks

• Akos Papp

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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

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Main original features 1

• 2D and 3D sketching and viewing
• Isotopes, charges, radicals, maps

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Isotopes, charges, radicals
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Main original features 1

• 2D and 3D sketching and viewing
• Isotopes, charges, radicals, maps
• Stereo features (tetrahedral, double bond,
  diastereo)

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Stereo features
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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

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Valence check, lone pairs
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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

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Alias, pseudo, attached data
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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)

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Rich formatting
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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

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Any atom, atom list, link nodes
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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.)

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Atom properties
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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)

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Bond and reaction topology
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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

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Recursive SMARTS
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Main original features 2

• Markush structure drawing features

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Markush structure drawing
Play feature animation http//www.chemaxon.com/co
nf/Marvin08/MarkushDrawingBenzodiazepine.swf
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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.)

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Abbreviated groups
Play feature animation http//www.chemaxon.com/co
nf/Marvin08/AbbrevTosGroupCreate.swf
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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

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Component autorecognition
Play feature animation http//www.chemaxon.com/co
nf/Marvin08/ComponentAutoRecognition.swf
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Manual and automapping
Play feature animation http//www.chemaxon.com/co
nf/Marvin08/Automapping.swf
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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

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Electron flow arrows
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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

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2D and 3D clean

• CC(C)NCC(O)COC1C2CC(C)NC2CCC1

topology
2D
3D
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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

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Aromatization/dearomatization
Play feature animation http//www.chemaxon.com/co
nf/Marvin08/Aromatization.swf
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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

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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

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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

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Multipage documents
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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

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Molecule matrix view
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Main original technical features

• Import/export of all important molecular file
  formats
• Inter-conversion, automatic recognition

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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

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Main original technical features

• Import/export of all important molecular file
  formats
• Inter-conversion, automatic recognition
• Image export to the major image file formats

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Image export

• JPG, JPEG
• PNG
• PPM
• PDF
• SVG, SVGZ
• BMP
• EMF

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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

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MarvinView and MarvinSpace
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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

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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

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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

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System compatibility

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

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Browser compatibility

• Internet Explorer
• Firefox
• Mozilla
• Netscape
• Safari
• Opera

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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
• Features are available from API
• Additional, applet specific features

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Developing with Marvin Beans
Use Marvin Beans to add MarvinSketch or
MarvinView as a graphical component to your
standalone application

• Additional API is accessible for
• Import / Export
• Performing calculations with plugins
• 2D and 3D cleaning of structures
• All operations accessible in the GUIs are also
  available in the API.

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Applet specific features

• The appropriate version for the browser / JRE is
  automatically selected
• Signed (trusted) applets enable access to local
  files, system clipboard and allow printing.
• Applet API accessible from JavaScript to
• fetch the current structure from the applet and
  send it to the server for further processing.
• change the structure or display options of the
  applet without reloading the page.

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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
• Features are available from API
• Additional, applet specific features
• Free for
• Open access, non commercial websites
• Academic research and teaching
• Evaluation

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Major new features 5.0

• New GUI design
• Customizable menu
• Customizable toolbar

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Customizable menu
Play feature animation http//www.chemaxon.com/co
nf/Marvin08/menucustom.swf
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Customizable toolbar
Play feature animation http//www.chemaxon.com/co
nf/Marvin08/toolbarcustom.swf
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Major new features 5.0

• New GUI design
• Customizable menu
• Customizable toolbar
• ISIS/Draw-like and ChemDraw-like configurations

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Configurations
ISIS/Draw like
ChemDraw like
Play feature animation http//www.chemaxon.com/co
nf/Marvin08/configurations.swf
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Major new features 5.0

• New GUI design
• Customizable menu
• Customizable toolbar
• ISIS/Draw-like and ChemDraw-like configurations
• OLE component for Office documents

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OLE component
Play feature animation http//www.chemaxon.com/co
nf/Marvin08/OLE.swf
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Major new features 5.0

• New GUI design
• Customizable menu
• Customizable toolbar
• ISIS/Draw-like and ChemDraw-like configurations
• OLE component for Office documents
• Periodic system Query tab containing
• Generic query features and periodic table groups

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Periodic table Query tab
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Major new features 5.0

• New GUI design
• Customizable menu
• Customizable toolbar
• ISIS/Draw-like and ChemDraw-like configurations
• OLE component for Office documents
• Periodic system Query tab containing
• Generic query features and periodic table groups
• Dynamic IUPAC name text box

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Dynamic IUPAC name
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Major new features 5.0

• New GUI design
• Customizable menu
• Customizable toolbar
• ISIS/Draw-like and ChemDraw-like configurations
• OLE component for Office documents
• Periodic system Query tab containing
• Generic query features and periodic table groups
• Dynamic IUPAC name text box
• Creating templates by drag-drawing to toolbar

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Dragdrop to MyTemplates
Play feature animation http//www.chemaxon.com/co
nf/Marvin08/template_rovid.swf
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Major new features 5.0

• New GUI design
• Customizable menu
• Customizable toolbar
• ISIS/Draw-like and ChemDraw-like configurations
• OLE component for Office documents
• Periodic system Query tab containing
• Generic query features and periodic table groups
• Dynamic IUPAC name text box
• Creating templates by drag-drawing to toolbar
• Spreadsheet-like view in MarvinView for SD and
  RDfiles

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Spreadsheet view
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Minor new features 5.0

• Multicenter atom
• Position variation bond
• Coordinate bond

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Multicenter, coordinate bond
Play feature animation http//www.chemaxon.com/co
nf/Marvin08/Ferrocene.swf
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Minor new features 5.0

• Multicenter atom
• Position variation bond
• Coordinate bond
• Generalized placement of groups and templates
• Shift button changes between expanded and
  contracted form of groups when placing to the
  canvas (since 5.0.3)
• Chain drawing displays the last carbon number
• New group types
• Repeating unit, monomer, polymer, generic, etc.
• Improved quality both in 2D and 3D clean
• Recent file list
• Markush structure specific
• Zoom to scaffold and r-group lists

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Zoom to scaffold or Rgroup
Play feature animation http//www.chemaxon.com/co
nf/Marvin08/MarkushZoomTo.swf
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Features coming 5.1

• Accelerated initialization of Marvin at startup
• Name to structure conversion
• Importing IUPAC names through the source
• On the fly conversion of names pasted to the
  canvas
• Opening .name files
• Printing redesign
• Print preview
• Print to PDF
• Structure preview (optional) on the file open
  dialog window
• Browsing capability in multistructure files

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Structure preview
Play feature animation http//www.chemaxon.com/co
nf/Marvin08/StructurePreview.swf
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Future features 5.2

• Transparent structure drawing
• Multistep reaction support
• Real arrows with automatic assignment of
  reactants
• MarvinView GUI redesign
• Structure checker component
• Copy/Cut/Paste/(Ctrl)Drag(Drop) redesign
• CDX (ChemDraw) file import/export
• Load templates from specified directories
• New Markush related features
• Enhanced handling of group attachment points
• Dynamic font size change

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• Questions?

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• Thank you for your attention!
• For more information please visit www.chemaxon.com