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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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Presentation Transcript
outline
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
main original features 1
Main original features – 1
  • 2D and 3D sketching and viewing
    • Isotopes, charges, radicals, maps
main original features 15
Main original features – 1
  • 2D and 3D sketching and viewing
    • Isotopes, charges, radicals, maps
    • Stereo features (tetrahedral, double bond, diastereo)
main original features 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
main original features 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
main original features 111
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)
main original features 113
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
main original features 115
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.)
main original features 117
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)
main original features 119
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
main original features 2
Main original features – 2
  • Markush structure drawing features
markush structure drawing
Markush structure drawing

Play feature animation:

http://www.chemaxon.com/conf/Marvin08/MarkushDrawingBenzodiazepine.swf

main original features 223
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.)
abbreviated groups
Abbreviated groups

Play feature animation:

http://www.chemaxon.com/conf/Marvin08/AbbrevTosGroupCreate.swf

main original features 225
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
component autorecognition
Component autorecognition

Play feature animation:

http://www.chemaxon.com/conf/Marvin08/ComponentAutoRecognition.swf

manual and automapping
Manual– and automapping

Play feature animation:

http://www.chemaxon.com/conf/Marvin08/Automapping.swf

main original features 228
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
main original features 230
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
2d and 3d clean
2D and 3D clean

CC(C)NCC(O)COC1=C2C=C(C)NC2=CC=C1

topology

2D

3D

main original features 232
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
aromatization dearomatization
Aromatization/dearomatization

Play feature animation:

http://www.chemaxon.com/conf/Marvin08/Aromatization.swf

main original features 234
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
calculator plugins
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
main original features 236
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
main original features 238
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
main original technical features
Main original technical features
  • Import/export of all important molecular file formats
    • Inter-conversion, automatic recognition
file formats
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
main original technical features42
Main original technical features
  • Import/export of all important molecular file formats
    • Inter-conversion, automatic recognition
  • Image export to the major image file formats
image export
Image export
  • JPG, JPEG
  • PNG
  • PPM
  • PDF
  • SVG, SVGZ
  • BMP
  • EMF
main original technical features44
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
main original technical features46
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
beans vs applets
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
main original technical features48
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
system compatibility
System compatibility
  • Windows
    • 95, 98, Me, NT, 2000, XP
  • Mac OS X
  • Unix/Linux
  • Linux, Solaris, etc.
browser compatibility
Browser compatibility
  • Internet Explorer
  • Firefox
  • Mozilla
  • Netscape
  • Safari
  • Opera
main original technical features51
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
developing with marvin beans
Developing with Marvin Beans

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.

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

applet specific features
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.
main original technical features54
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
major new features 5 0
Major new features – 5.0
  • New GUI design
  • Customizable menu
  • Customizable toolbar
customizable menu
Customizable menu

Play feature animation:

http://www.chemaxon.com/conf/Marvin08/menucustom.swf

customizable toolbar
Customizable toolbar

Play feature animation:

http://www.chemaxon.com/conf/Marvin08/toolbarcustom.swf

major new features 5 058
Major new features – 5.0
  • New GUI design
  • Customizable menu
  • Customizable toolbar
  • ISIS/Draw-like and ChemDraw-like configurations
configurations
Configurations

ISIS/Draw like

ChemDraw like

Play feature animation:

http://www.chemaxon.com/conf/Marvin08/configurations.swf

major new features 5 060
Major new features – 5.0
  • New GUI design
  • Customizable menu
  • Customizable toolbar
  • ISIS/Draw-like and ChemDraw-like configurations
  • OLE component for Office documents
ole component
OLE component

Play feature animation:

http://www.chemaxon.com/conf/Marvin08/OLE.swf

major new features 5 062
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
major new features 5 064
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
major new features 5 066
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
drag drop to mytemplates
Drag&drop to MyTemplates

Play feature animation:

http://www.chemaxon.com/conf/Marvin08/template_rovid.swf

major new features 5 068
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
minor new features 5 0
Minor new features – 5.0
  • Multicenter atom
  • Position variation bond
  • Coordinate bond
multicenter coordinate bond
Multicenter, coordinate bond

Play feature animation:

http://www.chemaxon.com/conf/Marvin08/Ferrocene.swf

minor new features 5 072
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
zoom to scaffold or r group
Zoom to scaffold or R–group

Play feature animation:

http://www.chemaxon.com/conf/Marvin08/MarkushZoomTo.swf

features coming 5 1
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
structure preview
Structure preview

Play feature animation:

http://www.chemaxon.com/conf/Marvin08/StructurePreview.swf

future features 5 2
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
slide78
Thank you for your attention!

For more information please visit www.chemaxon.com