Ligand Sketcher Review · Ketcher 1 (beta) – javascript, AGPL Would be part of a bespoke...
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Transcript of Ligand Sketcher Review · Ketcher 1 (beta) – javascript, AGPL Would be part of a bespoke...
Ligand Sketcher Review (Open Source)
Conclusions:
• Therearegoodproprietaryones
Ligand Sketcher Review (Open Source)
Conclusions:
• Therearegoodproprietaryones• Thereappearstobenoperfectsolu7on
PeterMurray-Rust:
OpenSourceMolecularEditors:• BKchemh?p://bkchem.zirael.orgGPL,C3–pythonTkGUI.• Chemtoolh?p://ruby.chemie.uni-freiburg.de/~mar7n/chemtoolGPL,B3-linuxonly(poten7alwindows
supportinfuture),usesGTK.• JChemPainth?p://jchempaint.github.ioLGPL,B1[51]–Java,usesCDK.• LeViewh?p://www.pegase-biosciences.com/leview-ligand-environment-viewerGPL,B3[52]-forligand-
proteininterac7onvisulisa7on.RequiresJava.• SketchElh?p://sketchel.sourceforge.netGPL,A1–Java,mul7-moleculesupport.• Molsketchh?p://sourceforge.net/projects/molsketchGPL,A1–C++Qt,supportforandroid.• JSMEh?p://peter-ertl.com/jsmeBSD,A1[66]–purejavascript2Deditor.• CWCh?ps://web.chemdoodle.comGPL,A1[65]–suiteofweb-basedtoolsfor2D/3D.
Notinthereview:• Ketcherh?p://lifescience.opensource.epam.com/ketcherAGPL-2Deditor,javascript(SVG).• MolViewh?p://molview.org/Usesavarietyoflibraries(Ketcher,CWC,JSmol,GSmol)foranonlinesolu7on.
JSME–javascriptMolSketch–standaloneC++/Qt,requiresOpenBabel
CWC(ChemDoodleWebComponents)–HTML5Ketcher–javascript
MolSketch–standaloneC++/Qt,requiresOpenBabel Standalonesolu7on.Rela7velylightweight,withacceptabledependencies–Qt4&OpenBabel(notpackaged).Chemistryfunc7onalitycomesfromOpenBabel.Ihadissuescompiling/installing:• Ihadtofixafewminorissuesinthesource
filesinordertogetittocompileusingmodernOSX/compiler(includecmathinminimise.h,includeQtCore/qmath.hinmolscene.cpp).
• Issueswithlibrarylinkingusingdefaultbuildsystem,butthatshouldn’tbeanissueforaCCP4distributedversion.
• Encountered“OpenBabelSupportMissing”issue,whichisacknowledgedonline(despitebeingmarkedasfixedin2015…).
• Ul7matelycouldn’tgetitworkingproperlyonMacOSX…abitmore7meandeffortmayseeitworkingproperly.
• Couldn’tgettheprecompiledbinaryworking(quickly)onWindows,againdueissueswiththeOpenBabeldependency.
JSME–javascriptcomponentsWouldbepartofabespokeintegratedsolu7on–it’snot(quite)apre-madestandalonesolu7on.Shouldbelightweight.Looksrela7velydated,anddoesitdomuchmorethanlidia?Features:• Canimport/outputto/fromsmiles,molfile.Op7onto
outputcanonicalSMILES.• Canaddfunc7onalgroups,switchbetweenallowed
chargedstates,andperformqueries(e.g.usingSMARTS).• Cantogglebetweenedit&visualiza7onmodes,which
couldbeusefulinsomeapplica7ons:h?p://peter-ertl.com/jsme/JSME_2016-07-31/JSME_depict_edit_toggle.html
• CanhighlightatomsandseethecorrespondingatomsinthedisplayedSMILESstring:h?p://peter-ertl.com/jsme/JSME_2016-07-31/JSME_smiles_atom_highlight.html
• Poten7allyextensible,allowinginterac7onwithotherHTMLcomponents,e.g.onmouseoverevents:h?p://peter-ertl.com/jsme/JSME_2016-07-31/JSME_depict_ac7on_callback.html
CWC(ChemDoodleWebComponents)–HTML5components
Suiteofweb-basedtoolsfor2D/3D.Again,it’snotapre-madesolu7on–workwouldberequiredtointegratethisintoabespokesolu7on.MoreheavyweightthanJSME–bigcompany,notindependentdevelopers.2Dsketcherlooksgreat-modern&customizable,loadsoffeatures,variousdisplaypreferences.• Fullstandalonepackageisproprietary,individual
HTML5/javascriptwebcomponentsareGPL.• DependencieshaveMITlicense.
CanimportfromMOL,PDB,CIF,andothers.Nona7vesupportforimpor7ngSMILES…butitcandoviaiChemLabsCloudServices(freetoacademicsonly),whichalsoallowstextsearchusingdatabases(e.g.pubmed).Onlineaccessforcloudservices(notfree)mayberequiredtoaccessfullfunc7onality,althoughsomeworkaroundsmaybepossible(e.g.incorporateaseparateMOLtoSMILES).Canexporttomanydifferentformats.Alsodoes2D->3Dconversion,3Dedi7ng,extendingtomacromoleculeribbonrepresenta7on,etc.
Ketcher1(beta)–javascript,AGPL
Wouldbepartofabespokeintegratedsolu7on–it’snot(quite)apre-madestandalonesolu7on.Shouldbelightweight…maybe.Verymuchin-development:Ketcher1didn’tworkout-of-the-boxKetcher2downloaddidn’tevenincludeallsource…Sourceishuman-readable(unlikeCWC)Theirsolu7oninvolvesembeddingKetcherbeingembeddedinaniframe…yuck.Features:• Canimport/outputto/fromsmiles,molfile.• ServerrequiredforSMILES.
Ketcher2(alpha)–javascript,AGPL
MolView–notsuitable,butgoodexampleofimplementa7on • 2DEngine:Ketcher
• 3DEnginechoice:GLmol,JSmol,ChemDoodleWC• DatabaseAPIs(incPDB&COD)
Howsuitablearethesesolu7onsforourpurpose?Keyques7ons:• Canwekeeptrackofatomnames?• Canwecolourlinks?• Canwemodifycode?Ifyes,thenitmaybeaworkablesolu7on…
Doweevenneedsomethingnew?• Jligand
• AlreadypartofCCP4• Notreallydeveloped• 3Dnot2D• Java
• Lidia–seemstohavemorefunc7onalitythanavailableopen-source2Deditors
• AlreadypartofCCP4• CanbeseparatedfromCoot• Notweb-based
