chemaxon european ugm visegrad 2008 sketching and viewing with marvin features, tips and tricks akos...

ChemAxon European UGM Visegrad 2008

Sketching and viewing with Marvin Features, tips and tricksAkos Papp

ChemAxon European UGM Visegrad 2008 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


Main original features – 1

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


Isotopes, charges, radicals



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

diastereo)


Stereo features




diastereo) Valence check, lone pairs, implicit hydrogens


Valence check, lone pairs




diastereo) Valence check, lone pairs, implicit hydrogens Aliases, pseudo-atoms Attached data


Alias, pseudo, attached data




diastereo) Valence check, lone pairs, implicit hydrogens Aliases, pseudo-atoms Attached data Nice structures (antialiasing) Rich formatting (fonts, colors, bond thickness)


Rich formatting





Query drawing features Any atom, atom list/not-list, link nodes


Any atom, atom list, link nodes





Query drawing features Any atom, atom list/not-list, link nodes Atom properties (substitution count, aromatic,

etc.)


Atom properties





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)


Bond and reaction topology



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


Recursive SMARTS



Markush structure drawing features

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Markush structure drawing

Play feature animation:http://www.chemaxon.com/conf/Marvin08/MarkushDrawingBenzodiazepine.swf

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





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/conf/Marvin08/AbbrevTosGroupCreate.swf

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







Single step reaction drawing Automatic component recognition Manual- and automapping

Play feature animation:http://www.chemaxon.com/conf/Marvin08/ComponentAutoRecognition.swf

26

Component autorecognition

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



Play feature animation:http://www.chemaxon.com/conf/Marvin08/Automapping.swf

27

Manual– and automapping

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








Graphics, text boxes, electron flow arrows


Electron flow arrows






Graphics, text boxes, electron flow arrows 2D and 3D structure clean


2D and 3D clean

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

topology

2D 3D






Graphics, text boxes, electron flow arrows 2D and 3D structure clean Aromatization /dearomatization

Play feature animation:http://www.chemaxon.com/conf/Marvin08/Aromatization.swf

33

Aromatization/dearomatization

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








Graphics, text boxes, electron flow arrows 2D and 3D structure clean Aromatization /dearomatization 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





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


Multipage documents





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


Molecule matrix view


Main original technical features

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


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




Image export to the major image file formats


Image export

JPG, JPEG PNG PPM PDF SVG, SVGZ BMP EMF





Visualization with MarvinView and MarvinSpace


MarvinView and MarvinSpace






Distributions: Standalone, JWS, Beans, 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







Pure JAVA based Platform and browser independent


System compatibility

Windows 95, 98, Me, NT, 2000,

XP Mac OS X Unix/Linux Linux, Solaris, etc.


Browser compatibility

Internet Explorer Firefox Mozilla Netscape Safari Opera







Pure JAVA based Platform and browser independent

Features are available from API Additional, applet specific features


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

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.




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

New GUI design Customizable menu Customizable toolbar

Play feature animation:http://www.chemaxon.com/conf/Marvin08/menucustom.swf

56

Customizable menu

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



Play feature animation:http://www.chemaxon.com/conf/Marvin08/toolbarcustom.swf

57

Customizable toolbar

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





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

configurations

Play feature animation:http://www.chemaxon.com/conf/Marvin08/configurations.swf

59

ConfigurationsISIS/Draw like

ChemDraw like

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




configurations OLE component for Office documents

Play feature animation:http://www.chemaxon.com/conf/Marvin08/OLE.swf

61

OLE component




configurations OLE component for Office documents Periodic system ‘Query’ tab containing

Generic query features and periodic table groups


Periodic table Query tab






Dynamic IUPAC name text box


Dynamic IUPAC name






Dynamic IUPAC name text box Creating templates by drag-drawing to

toolbar

Play feature animation:http://www.chemaxon.com/conf/Marvin08/template_rovid.swf

67

Drag&drop to MyTemplates





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


Spreadsheet view


Minor new features – 5.0

Multicenter atom Position variation bond Coordinate bond

Play feature animation:http://www.chemaxon.com/conf/Marvin08/Ferrocene.swf

71

Multicenter, coordinate bond


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

Play feature animation:http://www.chemaxon.com/conf/Marvin08/MarkushZoomTo.swf

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Zoom to scaffold or R–group


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

Play feature animation:http://www.chemaxon.com/conf/Marvin08/StructurePreview.swf

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Structure preview


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


Questions?


Thank you for your attention!For more information please

visit www.chemaxon.com

chemaxon european ugm visegrad 2008 sketching and viewing with marvin features, tips and tricks akos...

Documents

chemaxon european ugm

marvin features

future features

radicals slide

stereo features tetrahedral

diastereo slide

data slide

bond thickness slide