Sketching and viewing with marvin features tips and tricks
Download
1 / 78

Sketching and viewing with Marvin - PowerPoint PPT Presentation


  • 666 Views
  • Uploaded on

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

loader
I am the owner, or an agent authorized to act on behalf of the owner, of the copyrighted work described.
capcha
Download Presentation

PowerPoint Slideshow about 'Sketching and viewing with Marvin' - Renfred


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.While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server.


- - - - - - - - - - - - - - - - - - - - - - - - - - E N D - - - - - - - - - - - - - - - - - - - - - - - - - -
Presentation Transcript
Sketching and viewing with marvin features tips and tricks l.jpg

Sketching and viewing with MarvinFeatures, tips and tricks

Akos Papp


Outline l.jpg
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 l.jpg
Main original features – 1

  • 2D and 3D sketching and viewing

    • Isotopes, charges, radicals, maps



Main original features 15 l.jpg
Main original features – 1

  • 2D and 3D sketching and viewing

    • Isotopes, charges, radicals, maps

    • Stereo features (tetrahedral, double bond, diastereo)



Main original features 17 l.jpg
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 l.jpg
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 l.jpg
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 l.jpg
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 l.jpg
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 l.jpg
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 l.jpg
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 l.jpg
Main original features – 2

  • Markush structure drawing features


Markush structure drawing l.jpg
Markush structure drawing

Play feature animation:

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


Main original features 223 l.jpg
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 l.jpg
Abbreviated groups

Play feature animation:

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


Main original features 225 l.jpg
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 l.jpg
Component autorecognition

Play feature animation:

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


Manual and automapping l.jpg
Manual– and automapping

Play feature animation:

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


Main original features 228 l.jpg
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 l.jpg
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 l.jpg
2D and 3D clean

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

topology

2D

3D


Main original features 232 l.jpg
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 l.jpg
Aromatization/dearomatization

Play feature animation:

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


Main original features 234 l.jpg
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 l.jpg
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 l.jpg
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 l.jpg
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 l.jpg
Main original technical features

  • Import/export of all important molecular file formats

    • Inter-conversion, automatic recognition


File formats l.jpg
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 l.jpg
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 l.jpg
Image export

  • JPG, JPEG

  • PNG

  • PPM

  • PDF

  • SVG, SVGZ

  • BMP

  • EMF


Main original technical features44 l.jpg
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 l.jpg
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 l.jpg
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 l.jpg
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 l.jpg
System compatibility

  • Windows

    • 95, 98, Me, NT, 2000, XP

  • Mac OS X

  • Unix/Linux

  • Linux, Solaris, etc.


Browser compatibility l.jpg
Browser compatibility

  • Internet Explorer

  • Firefox

  • Mozilla

  • Netscape

  • Safari

  • Opera


Main original technical features51 l.jpg
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 l.jpg
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 l.jpg
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 l.jpg
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 l.jpg
Major new features – 5.0

  • New GUI design

  • Customizable menu

  • Customizable toolbar


Customizable menu l.jpg
Customizable menu

Play feature animation:

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


Customizable toolbar l.jpg
Customizable toolbar

Play feature animation:

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


Major new features 5 058 l.jpg
Major new features – 5.0

  • New GUI design

  • Customizable menu

  • Customizable toolbar

  • ISIS/Draw-like and ChemDraw-like configurations


Configurations l.jpg
Configurations

ISIS/Draw like

ChemDraw like

Play feature animation:

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


Major new features 5 060 l.jpg
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 l.jpg
OLE component

Play feature animation:

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


Major new features 5 062 l.jpg
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 l.jpg
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 l.jpg
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 l.jpg
Drag&drop to MyTemplates

Play feature animation:

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


Major new features 5 068 l.jpg
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 l.jpg
Minor new features – 5.0

  • Multicenter atom

  • Position variation bond

  • Coordinate bond


Multicenter coordinate bond l.jpg
Multicenter, coordinate bond

Play feature animation:

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


Minor new features 5 072 l.jpg
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 l.jpg
Zoom to scaffold or R–group

Play feature animation:

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


Features coming 5 1 l.jpg
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 l.jpg
Structure preview

Play feature animation:

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


Future features 5 2 l.jpg
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 l.jpg

Thank you for your attention!

For more information please visit www.chemaxon.com


ad