wrapping open babel with ruby

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Rubabel: Wrapping OpenBab

Journal of Cheminformatics 2013, 5:35 do

Rob Smith (2robsmith@gmRyan Williamson (rwilliamson88Dan Ventura ([email protected]

John T Prince (jtprince@chem

Journal of Cheminformatics
mailto:[email protected]:[email protected]:[email protected]:[email protected]:[email protected]:[email protected]:[email protected]:[email protected]


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Rubabel: wrapping open Babel

Rob Smith1

Corresponding author

Email: [email protected]

Ryan Williamson1


Dan Ventura

1


J h T P i 2


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Keywords

Chemoinformatics, Open Babel, Ruby

Background

Despite the fact that chemoinformatics tools have been de

field has yet to rally in support of a single library. The intri

the low-level programming prowess required for these lang

to adoption by less programming-oriented practitioners. W

dont share complete coverage of implemented tasks, meabe struggling with the language barrier, has to shoulder

versed in the differences between the libraries, including d


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Ruby has penetrated the applied sciences where the need

meets appreciation for an easy learning curve [15,16]. A m

ing, and powerful language paradigm have made Ruby an

matics tools, such as BioRuby [17].

For those who are not comfortable enough with programm

who prefer the Ruby way, and for those who want to do

present Rubabel. Rubabel offers a convenient, intuitive m

intra-molecular navigation with minimal lines of code per

developed project with a substantial amount of implemen

accessible extension mechanism for customization.

Implementation


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Listing 1 Creating a molecule from a SMILES string with

bindings

obmol = OpenBabel::OBMol.new

obconv = OpenBabel::OBConversion.new

obconv.set_in_format("smi")

obconv.read_string(obmol, "CN2C(=O)N(C)C(=O)C1=

Rubyists will notice that this code seems strikingly more l

that despite the uncharacteristic simplicity of this exampl

explicit details of the Open Babel architecture including th

jects and modification methods for OBConversion. For msuch as highlighting a substructure within a molecule in a

parable to C++. Adding Ruby-style objects and idioms to


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Figure 2 Novel functionality in Rubabel. Besides pro

functions, Rubabel provides a host of novel functionality.

Rubabel: Ruby idioms for concise and convenient code

Ruby is a language designed to be easy to use, intuitive

embody as many of these admittedly subjective qualitie

object behavior in ways consistent with established Ruby i

Object orientation

Rubabels object-oriented paradigm defines behaviors for

For example, Open Babels Tanimoto coefficient logic w


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Listing 3 Report how many SD file records are within a

weight range

require rubabel

puts Rubabel.foreach("benzodiazepine.sdf.gz").

String idiom

To assist in convenience and minimize syntax lookup time

neered for frequent exposure in Rubabel. For example, the

treated as a string, allowing splitting and matching operatioexample, the user can collect all atoms with two bonds (e

and append a carbon to the first atom in the filtered collect


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Access methods

Rubabel is designed to simplify common IO tasks to prov

matics functionality. Rubabel allows creation of MolecuBabel accepts, including SMILES strings (see Listing 7).

line where the SWIG code requires 4 (compare with Listin

Listing 7 Creating a molecule from a SMILES string with

mol = Rubabel["CN2C(=O)N(C)C(=O)C1=C2N=CN1C"]

Efficiency in accessing objects is very important to redu

Listing 8 gives some examples of object traversal in Ruba

cessing that can be done with very few lines of code in R


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Listing 9 Finding a certain molecule in an SDF file in Rub

require "rubabel"

mol = Rubabel.foreach("benzodiazepine.sdf.gz")

Listing 10 Finding a certain molecule in an SDF file in RD

from rdkit import Chem

suppl = Chem.SDMolSupplier(benzodiazepine.sdf

tgt=None

for mol in suppl:

if not mol: continueif mol.GetProp(_Name)==3016:

tgt=mol

break


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Custom behavior

We have provided explicit Molecule methods for commo

calculation, substructure highlighting, and graph diameter musers need custom extended behavior in Rubabel, they can

as Ruby open classes. Objects in Ruby are more accessib

some other languages. Writing custom behavior into Rub

Although Open Babel has a plugin mechanism which allow

the toolkit, usage is not trivial. In contrast, Rubabel can

using Rubys open classes. A class is open when it allows

functionality in the local scope. For example, the authors a

Rubabel that defines fragmentation behavior for lipid mo

behavior defined by Rubabel and also need to add descript

to accomplish their task With Rubabel this is as simple


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Table 2 Ruby extensions accessible to Rubabel

Extension Possible a

Sinatra [20], a web application framework Quick and

bel, allow

chemoinfo

Sciruby [16], a scientific library Plotting, s

ming lang

Rubyvis graphical library [22] Open end

representa

IRB, the interactive Ruby shell Quick acc

a terminalRspec, an automated code testing library [21] Automate

Rubabel (


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The simplicity of this example readily extends to virtually

The interactive Ruby shell (IRB)

Though space will not permit an exhaustive consideratio

used in conjunction with Rubabel, the interactive Ruby s

with languages like Python, Rubys interactive shell allow

experiments, test syntax, or debug their scripts. IRB can

Rubygems) by typing gem install irb. Simply ent

terminal) and type require rubabel and all of Ru

an interactive terminal. This is particularly useful given th

accomplish in just one line. Rubabel in IRB provides an i

realtime with instant feedbacka refreshing alternative to

d li t A ti d b f thi i l


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Figure 4 Average lines of code per CTR task. On aver

code than any other toolkit.

Figure 5 Number of CTR tasks listed. Rubabel has mor

Figure 6 Lines of code per CTR task. Rubabel has m

toolkit, and also requires fewer lines of code than any oth

9, where Pybel uses one fewer line of code, and task 10,

concise.

Rubabel has some features which users may find useful th

include an explicit Bond object and the associated functi


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Operating System(s): Platform independent

Programming language: Ruby

Other requirements: Open Babels Install Requirements

License: MIT

Any restrictions to use by non-academics: None

Competing interests

The authors declare that they have no competing interest.


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9. OBoyle N, Banck M, James C, Morley C, Vanderme

an open chemical toolbox. J Cheminformatics 2011,

1758-2946-3-33] [10.1186/1758-2946-3-33]

10. Rubygems. [http://www.rubygems.org]

11. Pavlov D, Rybalkin M, Karulin B, Kozhevnikov M

universal cheminformatics API. J Cheminformatics

doi.org/10.1186/1758-2946-3- S1-P4] [10.1186/1758-

12. RDKit. [http://www.rdkit.org]

13. OEChem: OpenEye Scientific Software: Sante Fe,

14. Ihlenfeldt WD, Takahashi Y, Abe H, Sasaki S: Comp


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Figure 6

wrapping open babel with ruby

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