Vida, Visualization and Visions

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Vida, Visualization and Visions
Jon Christopher Kevin Schmidt OpenEye Scientific
Software Sunday February 29, 2004
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Where we came fromThe original plan for VIDA

• Designed as a small molcule visualization
  application
• Focused on large numbers of molecules
• OpenEye's entry into visualization
• Lots of effort by Joe

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What happened Why VIDA has had problems

• VIDA began to be used more widely
• Feature creep - or how we blame the customers
• As VIDA grew, people wanted more
• VIDA began to do things outside of the original
  plan
• Relied heavily on OELib
• Upgrade was going to be long and difficult

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What happened cont.

• New stewardship of VIDA meant some new issues
• VIDA grew outside its goals and design
• As more features were shoe-horned in, problems
  grew
• VIDA became large and fragile.

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So now what?Why hasn't there been a new
release?!

• Needed a strong visualization and application
  framework
• Needed to be OEChemplete
• Make it easier to control development
• Easier to add (and remove) features
• Divide it up into workable parts

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So now what? cont.

• Needed to refocus VIDA back to small molecules
• Building other visualization applications
• Application front ends
• Protein visualization
• Modelling
• Make it STABLE

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No, really, what have you been doing?Enough
talk!

• The OpenEye visualization and application
  framework
• OEgg A new graphics library
• OEDepict A 2D depiction library
• OERepository A molecule database
• OEInterpreter An extensible python iterpreter
• OEMessageBoard A way for everyone to talk nicely
• Kernels Provides access to the above and to a GUI

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Put these together...So what?

• Combine the previous parts with visualization
  modules to make an application
• 3D, 2D viewers
• List browsers
• Modelling modules
• Python Interpreter
• More..

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Why this is goodWhy is this good?

• Easier to manage a few smaller parts than one
  massive piece
• Can easily extend any application
• Can share parts between applications
• Makes development easier
• Makes the application stable

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AFITT Advanced Fitting Tool

• Bring OE Expertise to bear on Crystallography
• 2-year partnership with 5 industry partners
• Project kickoff at CUP IV
• Features
• OEChemplete (handles small molecules well)
• Based on OEVidafitt kernel
• Python scriptable

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AFITT Modeling Featureswhat does it do?

• All the standard stuff
• Rotations, translations, rotamer library,
  append/prepend residue, mutate, etc.
• Stuff you wish was standard
• Structure Generation SMILES to 3D
• Refinement constraint generation
• Ligand fitting
• MMFF -based geometric refinement

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A little Python on the side
import oechem import oerepo import
oeomi _smilesMoloechem.OEMol() def
GenerateFromSmiles(str) global _smilesMol
genoeomi.OEFF3DGenerator()
oechem.OEParseSmiles(_smilesMol, str)
gen(_smilesMol) oerepo.OERepoAddCopy(_smilesMo
l.SCMol()) GenerateFromSmiles(PromptStrin
g())
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A little more Python
def LoadPDB(id) if (id "") return
import httplib print "Contacting www.rcsb.org"
connhttplib.HTTPConnection("www.rcsb.org")
conn.request("GET", "/pdb/cgi/export.cgi/" id
".pdb?formatPDBpdbId" id) r1
conn.getresponse() if r1.status 200
datar1.read() if len(data) gt 0
conn.close() fopen(id ".pdb", "w")
f.write(data) f.close() Open(id
".pdb") else raise IOError, "PDB id
not found" AddButtonToMenu(File", "Open from
PDB", 'LoadPDB(PromptString("Enter PDB id"))')
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Keeps on slithering
def GetCompound(registryNumber) dbcConnectToCor
porateDatabase(yourdatabase) sqlselect smiles
from compounds where regnums dbc.sth.execute(s
ql, registryNumber) comdbc.sth.fetchone() if
(com!None) GenerateFromSmiles(com) AddButtonTo
Menu(File", "Open from DB", 'GetCompound(PromptS
tring("Enter registry number"))')
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The not-so-distant future

• Loop construction
• More refinement options
• More QC
• Database integration
• Sequence/homology modeling?
• Residual density analysis