As 2011 draws to a close, Open Babel is over 10 years old! At this point, it's used by over 40 open source projects, downloaded over 200,000 times, and been used in over 400 academic papers. And of course, there have been 15 releases and dozens of contributors....Read the rest
"Unless something real and practical is done in the near future, it will become impossible to find or use scientific data with the resulting loss of time and money for those who need to repeat experiments."The future alluded to is the one in which we now live. A follow-up letter, "Computer readable analytical chemical data - comments on a critical need" in Trends in Anal. Chem. discusses this further.
Cinfony presents a common API to several cheminformatics toolkits. It uses the Python programming language, and builds on top of Open Babel, the RDKit, the CDK, Indigo, OPSIN and cheminformatics webservices.>>> from cinfony import opsin, webel
>>> mol = opsin.readstring("iupac",
"1-chloro-2-bromopropane")
>>> print webel.Molecule(mol).write("iupac")
2-Bromo-1-chloropropaneN.M. O'Boyle, G.R. Hutchison, Chem. Cent. J., 2008, 2, 24. [link]
With the ever-increasing number of publications, coupled with higher printing costs, there is great pressure brought on journal editors to keep manuscripts as short as possible. While this is quite understandable, it has, in my opinion, lead to a very serious problem. The vast majority of (hopefully) good analytical data, such as spectroscopic, kinetic and thermodynamic measurements, is never readily made available to the scientific community. Published data are often so "compressed" that one is unable to examine alternative interpretations, as the published data are not sufficient. Partial data are preferred to complete data...Note:
Why doesn't [______] make it a policy to require authors to submit full data on spectroscopic and other data for which there are existing data centres? Furthermore, I propose that the editors of this journal and other such journals establish criteria for collecting relevant data for which no data center exists today in order to prepare for the future. Perhaps it is time for a conference of journal editors to meet and propose a solution to this problem. Unless something real and practical is done in the near future, it will become impossible to find or use scientific data with the resulting loss of time and money for those who need to repeat experiments.
import os
latex="""\\documentclass[12pt,a4paper]{book}
\\usepackage{multido}
\\usepackage[hmargin=.8cm,vmargin=0.5cm,nohead,nofoot]{geometry}
\\usepackage[explicit]{titlesec}
\\newcommand*\\Hide{%%
\\titleformat{\\chapter}[display]
{}{}{0pt}{\\Huge\\thispagestyle{empty}}
\\titleformat{\\part}
{}{}{0pt}{}
}
\\begin{document}
\\pagestyle{empty}
\\title{Open Access Publications of\\\\Noel O'Boyle}
\\maketitle
\\tableofcontents
%s
\\end{document}
"""
data = {
"BO.pdf": [15,
"""Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk five years on
N. M. O'Boyle, R. Guha, E. L. Willighagen, S. E. Adams, J. Alvarsson, J.-C. Bradley, I. V. Filippov, R. M. Hanson, M. D. Hanwell, G. R. Hutchison, C. A. James, N. Jeliazkova, A. S. I. D. Lang, K. M. Langner, D. C. Lonie, D. M. Lowe, J. Pansanel, D. Pavlov, O. Spjuth, C. Steinbeck, A. L. Tenderholt, K. J. Theisen and P. Murray-Rust.
J. Cheminf. 2011, 3, 37."""],
"GM.pdf": [12,
"""Userscripts for the life sciences
E. L. Willighagen, N. M. O'Boyle, H. Gopalakrishnan, D. Jiao, R. Guha, C. Steinbeck and D. J. Wild.
BMC Bioinformatcs. 2007, 8, 487."""],
"Cinfony.pdf": [10, """Cinfony - combining Open Source cheminformatics toolkits behind a common interface
N. M. O'Boyle and G. R. Hutchison.
Chem. Cent. J. 2008, 2, 24."""],
"Confab.pdf": [9, """Confab - Systematic generation of diverse low-energy conformers
N. M. O'Boyle, T. Vandermeersch, C. J. Flynn, A. R. Maguire and G. R. Hutchison.
J. Cheminf. 2011, 3, 8."""],
"AntColony.pdf": [15, """Simultaneous feature selection and parameter optimisation using an artificial ant colony: case study of melting point prediction
N. M. O'Boyle, D. S. Palmer, F. Nigsch and J. B. O. Mitchell.
Chem. Cent. J. 2008, 2, 21."""],
"DataAnalysis.pdf": [2, """Review of ``Data Analysis with Open Source Tools"
N. M. O'Boyle.
J. Cheminf. 2011, 3, 10."""],
"MACIE2005.pdf": [2, """MACiE: a database of enzyme reaction mechanisms
G. L. Holliday, G. J. Bartlett, D. E. Almonacid, N. M. O'Boyle, P. Murray-Rust, J. M. Thornton and J. B. O. Mitchell.
Bioinformatics. 2005, 21, 4315-4316."""],
"MACIE2007.pdf": [6, """MACiE (Mechanism, Annotation and Classification in Enzymes): novel tools for searching catalytic mechanisms
G. L. Holliday, D. E. Almonacid, G. J. Bartlett, N. M. O'Boyle, J. W. Torrance, P. Murray-Rust, J. B. O. Mitchell and J. M. Thornton.
Nucleic Acid Res. 2007, 35, D515-D520."""],
"OB.pdf": [14, """Open Babel: An open chemical toolbox
N. M. O'Boyle, M. Banck, C. A. James, C. Morley, T. Vandermeersch and G. R. Hutchison.
J. Cheminf. 2011, 3, 33."""],
"PyChem.pdf": [2, """PYCHEM: a multivariate analysis package for python
R. M. Jarvis, D. Broadhurst, H. Johnson, N. M. O'Boyle and R. Goodacre.
Bioinformatics. 2006, 22, 2565-2566."""],
"Pybel.pdf": [7, """Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit
N. M. O'Boyle, C. Morley and G. R. Hutchison.
Chem. Cent. J. 2008, 2, 5."""]
}
order = [["Cheminformatics toolkits", ['Pybel', 'Cinfony', 'OB']],
["Enzyme reaction mechanisms", ['MACIE2005', 'MACIE2007']],
["QSAR", ['PyChem', 'AntColony']],
["The Rest", ["GM", "Confab", "DataAnalysis", "BO"]]
]
def formatjournal(text):
"""Format the journal metadata
>>> formatjournal("Chem. Cent. J. 2008, 2, 5.")
'\\\\textit{Chem. Cent. J.} \\\\textbf{2008}, \\\\textit{2}, 5.'
"""
broken = text.split(" ")
pages = broken[-1][:-1]
year = broken[-3][:-1]
volume = broken[-2][:-1]
journal = " ".join(broken[:-3])
return "\\textit{%s} \\textbf{%s}, \\textit{%s}, %s." % (journal, year, volume, pages)
def test():
import doctest
doctest.testmod()
if __name__ == "__main__":
# Sanity checks
N = 0
for x, y in data.iteritems():
assert os.path.isfile(x)
N += y[0]
assert len(data) == sum(len(y) for x, y in order)
# Write latex
output = []
for a, b, in order:
output.append("\\part{%s}{\\Hide" % a)
for paper in b:
pages, biblio = data["%s.pdf" % paper]
broken = biblio.split("\n")
title = broken[0]
output.append("\\chapter{%s}" % title)
authors = broken[2]
journaldata = formatjournal(broken[3])
output.append("""\\multido{}{%d}{\\null\\vfill
%s
\\newpage}""" % (pages, journaldata))
output.append("}")
with open("generated.tex", "w") as f:
f.write(latex % "\n".join(output))
# Join Papers together
pages = 1
paper_idx = 1
names = "A=generated.pdf"
cat = "A2 A2 A2 A2"
pages += 4
for a, b in order:
cat += " A2 A2"
pages += 2
for paper in b:
# New chapters always on odd-number pages
if pages % 2 == 0:
cat += " A2"
pages += 1
## print pages
paper_idx += 1
papername = chr(64+paper_idx)
names += " %s=%s.pdf" % (papername, paper)
cat += " %s" % papername
pages += data["%s.pdf" % paper][0]
print >> open("run.bat", "w"), "pdftk %s cat %s output combined.pdf" % (names, cat)
print """Now run...
pdflatex generated
pdflatex generated
run.bat
pdftk combined.pdf burst output tmp\\file_%03d.pdf
pdftk generated.pdf burst output tmp\\numbers_%03d.pdf
bash-3.2$ cd tmp && for i in `seq -w 1 109`; do pdftk file_$i.pdf background numbers_$i.pdf output new-$i.pdf; done
pdftk tmp\\new-???.pdf output new.pdf
"""
I am very happy to finally announce the release of Open Babel 2.3.1, a major update release of the open source chemistry toolbox.
Open Babel has been downloaded nearly 200,000 times and is used in over 45 projects and over 400 publications.
http://www.jcheminf.com/content/3/1/33
This release represents a major bug-fix-release and should be a stable upgrade, strongly recommended for all users of Open Babel. Many bugs and enhancements have been added in the last year since the 2.3.0 release.
What's new? See the full release notes
See the new user guide.
See the updated developer documentation.
To download, see:
http://sourceforge.net/projects/openbabel/files/
For more information, see the project website.
I'd particularly like to thank Chris Morley, Noel O'Boyle, and many others who put large amounts of time testing and improving this release.
This is a community project and we couldn't have made this release without you. Many thanks to all the contributors to Open Babel including those of you who submitted feedback, bug reports, and code.
Cheers,
-Geoff
---
Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
email: geoffh@pitt.edu
web: http://hutchison.chem.pitt.edu/
The Blue Obelisk group was established at the Spring ACS Meeting in 2005. Following on from the presentation/poster I gave at PMR's Symposium in January, I put together an overview of the activities of the group over the past 5 years with help from Rajarshi Guha, Egon Willighagen and Peter Murray-Rust, and further contributions on particular projects from many more.BackgroundCheck out the other papers in the themed series over at Journal of Cheminformatics.
The Blue Obelisk movement was established in 2005 as a response to the lack of Open Data, Open Standards and Open Source (ODOSOS) in chemistry. It aims to make it easier to carry out chemistry research by promoting interoperability between chemistry software, encouraging cooperation between Open Source developers, and developing community resources and Open Standards.
Results
This contribution looks back on the work carried out by the Blue Obelisk in thjavascript:void(0)e past 5 years and surveys progress and remaining challenges in the areas of Open Data, Open Standards, and Open Source in chemistry.
Conclusions
We show that the Blue Obelisk has been very successful in bringing together researchers and developers with common interests in ODOSOS, leading to development of many useful resources freely available to the chemistry community.
With the imminent release of Open Babel 2.3.1, I thought I'd come up with some examples of use for a new feature, PNG depiction.obabel -:CC(=O)Cl -O tmp.png
> obabel -:CC(=O)Cl -O tmp.png -xO smi > obabel tmp.png -osmi CC(=O)Cl
> for %a in (*.tif) do "C:\Program Files (x86)\osra\1.3.8\osra.bat" %a --format sdf | obabel -isdf -O %~na_osra.png -d > for %a in (*_chem.png) do "C:\Program Files\GGA Software\Imago Toolkit\alter_ego.exe" %a -o tmp.mol -q && obabel tmp.mol -O %~na_imago.png -d
Background
A frequent problem in computational modeling is the interconversion of chemical structures between different formats. While standard interchange formats exist (for example, Chemical Markup Language) and de facto standards have arisen (for example, SMILES format), the need to interconvert formats is a continuing problem due to the multitude of different application areas for chemistry data, differences in the data stored by different formats (0D versus 3D, for example), and competition between software along with a lack of vendor-neutral formats.
Results
We discuss, for the first time, Open Babel, an open-source chemical toolbox that speaks the many languages of chemical data. Open Babel version 2.3 interconverts over 110 formats. The need to represent such a wide variety of chemical and molecular data requires a library that implements a wide range of cheminformatics algorithms, from partial charge assignment and aromaticity detection, to bond order perception and canonicalization. We detail the implementation of Open Babel, describe key advances in the 2.3 release, and outline a variety of uses both in terms of software products and scientific research, including applications far beyond simple format interconversion.
Conclusions
Open Babel presents a solution to the proliferation of multiple chemical file formats. In addition, it provides a variety of useful utilities from conformer searching and 2D depiction, to filtering, batch conversion, and substructure and similarity searching. For developers, it can be used as a programming library to handle chemical data in areas such as organic chemistry, drug design, materials science, and computational chemistry. It is freely available under an open-source license from http://openbabel.org.
Andrew Dalke has just released V1.0 of his chemical fingerprint package, chemfp. The goal of the project is to produce a standardised file format called FPS for chemical fingerprints, as well as a set of tools around them. The project itself is a Python module with some superfast C code.
As previously discussed, I attended and presented at the 5th Meeting on U.S. Government Chemical Databases and Open Chemistry in Frederick, Maryland. Talks were 20 min plus 5 for questions and so quite a lot of ground was covered over the two days.
"""
In this example, we display the H2O molecule, and use volume rendering to
display the electron localization function.
The atoms and the bounds are displayed using mlab.points3d and
mlab.plot3d, with scalar information to control the color.
The electron localization function is displayed using volume rendering.
Good use of the `vmin` and `vmax` argument to
`mlab.pipeline.volume` is critical to achieve a good visualization: the
`vmin` threshold should placed high-enough for features to stand out.
The original is an electron localization function from Axel Kohlmeyer.
"""
# Author: Gael Varoquaux <gael.varoquaux@normalesup.org>
# Copyright (c) 2008, Enthought, Inc.
# License: BSD Style.
# Edited by: Noel O'Boyle <baoileach@gmail.com>
# Retrieve the electron localization data for H2O ##############################
import os
if not os.path.exists('h2o-elf.cube'):
# Download the data
import urllib
print 'Downloading data, please wait'
opener = urllib.urlopen(
'http://code.enthought.com/projects/mayavi/data/h2o-elf.cube'
)
open('h2o-elf.cube', 'wb').write(opener.read())
# Plot the atoms and the bonds #################################################
import numpy as np
from mayavi import mlab
mlab.options.offscreen = True
mlab.figure(1, bgcolor=(0, 0, 0), size=(350, 350))
mlab.clf()
# The position of the atoms
atoms_x = np.array([2.9, 2.9, 3.8])*40/5.5
atoms_y = np.array([3.0, 3.0, 3.0])*40/5.5
atoms_z = np.array([3.8, 2.9, 2.7])*40/5.5
O = mlab.points3d(atoms_x[1:-1], atoms_y[1:-1], atoms_z[1:-1],
scale_factor=3,
resolution=20,
color=(1, 0, 0),
scale_mode='none')
H1 = mlab.points3d(atoms_x[:1], atoms_y[:1], atoms_z[:1],
scale_factor=2,
resolution=20,
color=(1, 1, 1),
scale_mode='none')
H2 = mlab.points3d(atoms_x[-1:], atoms_y[-1:], atoms_z[-1:],
scale_factor=2,
resolution=20,
color=(1, 1, 1),
scale_mode='none')
# The bounds between the atoms, we use the scalar information to give
# color
mlab.plot3d(atoms_x, atoms_y, atoms_z, [1, 2, 1],
tube_radius=0.4, colormap='Reds')
# Display the electron localization function ###################################
## Load the data, we need to remove the first 8 lines and the '\n'
str = ' '.join(file('h2o-elf.cube').readlines()[9:])
data = np.fromstring(str, sep=' ')
data.shape = (40, 40, 40)
source = mlab.pipeline.scalar_field(data)
min = data.min()
max = data.max()
vol = mlab.pipeline.volume(source, vmin=min+0.65*(max-min),
vmax=min+0.9*(max-min))
mlab.view(132, 54, 45, [21, 20, 21.5])
##mlab.show()
f = mlab.gcf()
for i in range(36):
f.scene.camera.azimuth(10)
f.scene.render()
mlab.savefig('example_%02d.png' % i)C:\Tools\mayavi>..\MPlayer-p4-svn-33883\mencoder.exe "mf://example_%02d.png" -mf fps=10 -o anim.avi -ovc lavc -lavcopts vcodec=msmpeg4v2:vbitrate=500
C:\Tools\mayavi>convert -delay 10 -loop 0 example_*.png animation.gif
Avogadro has a plugin architecture that allows you to drop a Python script into a particular folder to add additional functionality, whether it be a new menu item, a new display method or whatever. I've previously used this to write an extension to read comp chem log files using cclib. This time I need to add a new display method (or Engine in the lingo of Avogadro) that will depict a pharmacophore.pharmer dbsearch -dbdir db_712_actives -in HSP90.txt -out results.sdf -reduceconfs 1 -sort-rmsd
import os
from PyQt4.Qt import *
import Avogadro as avo
from numpy import array
# Get JSON from my own Python installation
import sys
sys.path.append("C:\\Python26\\Lib\\site-packages")
sys.path.append("C:\\Python26\\lib")
import json
colorlookup = {
'Hydrophobic': [0, 139, 69],
'HydrogenAcceptor': [255, 165, 0],
'HydrogenDonor': [211, 211, 211],
'Aromatic': [205, 0, 205],
'PositiveIon': [0, 0, 238],
'NegativeIon': [255, 0, 0],
}
class Engine(QObject):
# declare the changed() signal
__pyqtSignals__ = ("changed()",)
# constructor
def __init__(self):
QObject.__init__(self)
self.widget = None
self.textbox = None
self.filename = ""
self.pharma = []
def name(self):
return "Pharmacophore"
def flags(self):
return avo.EngineFlags.NoFlags
def debug(self, text):
return
filename = os.path.join("C:\\", "Users", "Noel", "Desktop", "tmp.txt")
output = open(filename, "a")
print >> output, text
output.close()
@pyqtSignature("")
def browse(self):
self.filename = str(QFileDialog.getOpenFileName())
if not self.filename:
return
self.textbox.setText(self.filename)
with open(self.filename) as f:
query = json.load(f)
self.pharma = [x for x in query['points'] if x['enabled']]
if len(self.pharma) > 0:
for p in self.pharma:
x += p['x']
y += p['y']
z += p['z']
x /= len(self.pharma)
y /= len(self.pharma)
z /= len(self.pharma)
for p in self.pharma:
p['x'] -= x
p['y'] -= y
p['z'] -= z
self.debug("Pharma: %s" % self.pharma)
self.emit(SIGNAL("changed()"))
@pyqtSignature("")
def clear(self):
self.filename = ""
self.textbox.setText(self.filename)
self.pharma = []
self.emit(SIGNAL("changed()"))
def settingsWidget(self):
self.widget = QWidget()
layout = QVBoxLayout(self.widget)
self.textbox = QLineEdit(self.filename)
self.textbox.setReadOnly(True)
layout.addWidget(self.textbox)
buttons = QHBoxLayout(self.widget)
layout.addLayout(buttons)
self.browsebtn = QPushButton("Browse")
self.clearbtn = QPushButton("Clear")
buttons.addWidget(self.browsebtn)
buttons.addWidget(self.clearbtn)
QObject.connect(self.browsebtn, SIGNAL("clicked()"), self, SLOT("browse()"))
QObject.connect(self.clearbtn, SIGNAL("clicked()"), self, SLOT("clear()"))
return self.widget
def renderOpaque(self, pd):
self.debug("Len of pharma: %d" % len(self.pharma))
if len(self.pharma) == 0:
return
# Painter
painter = pd.painter
# Molecule
molecule = pd.molecule
# Color
color = pd.colorMap
for point in self.pharma:
if point['name'] in colorlookup:
colvals = [float(x) / 255. for x in colorlookup[point['name']]] + [1.0]
color.setFromRgba(*colvals)
else:
color.setFromRgba(0.3, 0.6, 1.0, 1.0)
painter.setColor(color)
r = point['radius']
self.debug("Radius: %.1f" % r)
x, y, z = point['x'], point['y'], point['z']
painter.drawSphere(array([x, y, z]), r)
In the previous post I described why it's useful to be able to generate SMILES strings starting and ending with particular atoms. This post describes how to do it.C[C@@H](Br)(Cl) + I gives C[C@@H](Br)(Cl)INote however that this may result in a SMILES string that does not accurately represent the original structure (but that's not the point of the exercise) e.g.
c1c[nH]cc1 -> c1c[n](cc1)What about the stereochemistry? Well, I toss that out too at the moment; an alternative would be to allow the user to specify the resulting stereochemistry at the start and end atoms.
I've just added a feature to the SMILES output in Open Babel that allows the user to specify a particular start and end atom for a SMILES string. No, no, come back! - don't go away! - it's really useful...>obabel -:"c1c(C(=O)O)c(OC(=O)C)ccc1" -osmi
c1c(C(=O)O)c(OC(=O)C)ccc1
1 molecule converted
>obabel -:"c1c(C(=O)O)c(OC(=O)C)ccc1" -osmi -xf 13
c1cc(C(=O)O)c(OC(=O)C)cc1
1 molecule converted
>obabel -:"c1c(C(=O)O)c(OC(=O)C)ccc1" -osmi -xl 10
c1c(C(=O)O)c(ccc1)OC(=O)C
1 molecule converted
>obabel -:"c1c(C(=O)O)c(OC(=O)C)ccc1" -osmi -xf 13 -xl 10
c1cc(C(=O)O)c(cc1)OC(=O)C
1 molecule converted
As part of a project led by Dr. Geoffrey Hutchison (University of Pittsburgh), I have been collaborating on the development of a method to design so-called "molecular wires" (conducting organic polymers) for use in organic solar cells. Using a combination of computational chemistry and cheminformatics, we have been able to find organic polymers with the required electronic structure predicted to perform well as the electron donor in solar cells.N.M. O'Boyle, C.M. Campbell, G.R. Hutchison.
Computational Design and Selection of Optimal Organic Photovoltaic Materials
J. Phys. Chem. C 2011. In press.
obabel PubChem3D.sdf -l100 -d -xC -O mols_100.svg
#include <stdio.h>
#include <string.h>
#include "inchi_api.h"
int InChI_to_Struct(char* inchi)
{
inchi_InputINCHI inp;
inchi_OutputStruct out;
int i, j, retval;
inp.szInChI = inchi;
memset(&out, 0, sizeof(out));
retval = GetStructFromINCHI(&inp, &out);
printf("number of atoms: %d\n" , out.num_atoms);
for(i=0;i<out.num_atoms;++i)
{
inchi_Atom* piat = &out.atom[i];
printf("Atom %d: %s\n", i, piat->elname);
for(j=0;j<piat->num_bonds;++j)
{
printf("Bond from %d to %d of type %d\n", i, piat->neighbor[j], piat->bond_type[j]);
}
}
FreeStructFromINCHI( &out );
return retval;
}
int test_InChI_to_Struct()
{
int retval;
char inchi [] = "InChI=1S/CHClO/c2-1-3/h1H";
retval = myInChI_to_Struct(inchi);
return retval;
}user@ubuntu:~/Tools/inchidemo$ ~/Tools/v8-repo/d8 inchi.js number of atoms: 3 Atom 0: C Bond from 0 to 1 of type 1 Bond from 0 to 2 of type 2 Atom 1: Cl Bond from 1 to 0 of type 1 Atom 2: O Bond from 2 to 0 of type 2
export EMMAKEN_COMPILER=/home/user/Tools/llvm-2.9/cbuild/Release/bin/clangThis creates libinchi.so.1.03.00.ll, composed of LLVM disassembled bytecode, which we now convert to JavaScript in the same way as with "Hello World" previously:
LINKER=/home/user/Tools/emscripten-git/tools/emmaken.py SHARED_LINK=/home/user/Tools/emscripten-git/tools/emmaken.py C_COMPILER=/home/user/Tools/emscripten-git/tools/emmaken.py make
cd result
export PATH=~/Tools/llvm-2.9/cbuild/Release/bin:$PATH
llvm-dis -show-annotations libinchi.so.1.03.00
# Run emscriptenRunning it, of course, does nothing - it's just a library. Well, I say "just", but it's about 400K lines of code weighing in at 15M. With minification (YUI Compressor) we can get that down to ~7.5M, which zips down to 2MB. The emscripten author recommends passing it through Google Closure (which optimises and minifies the code) but it crashes out with some complaint about hitting a recursion limit. I don't know if it's a problem with the JavaScript code, a bug in Closure or just a feature of InChI generation. It also causes Spidermonkey (and hence Firefox) to complain about maxing out on stack space. Again, I don't know whether there's a way around this.
$EMSCRIPTEN/emscripten.py libinchi.so.1.03.00.ll $V8/d8 > inchi.js
# Run the Javascript using v8
$V8/d8 inchi.js
>>> from cinfony import indy, opsinHere's the talk I gave:
>>> opsinmol = opsin.readstring("iupac",
"(1R,2R,3R,4S)-11-diazo-2,3,4,9-tetrahydroxy-2-"
"methyl-5,10-dioxo-2,3,4,5,10,11-hexahydro-1H-"
"benzo[b]fluoren-1-yl acetate")
>>> print indy.Molecule(opsinmol).molwt
412.349639893
#include <stdio.h>To start with, compile llvm, clang, spidermonkey and v8 as described in the install instructions.
int main()
{
printf("Hello World!\n");
return 0;
}
#!/bin/shAfter some trivial edits to the code, we can run hello.js in the browser.
LLVM_BINDIR=~/Tools/llvm-2.9/cbuild/Release/bin
EMSCRIPTEN=~/Tools/emscripten-git
V8=~/Tools/v8-repo
$LLVM_BINDIR/clang hello.c -o hello
$LLVM_BINDIR/clang hello.c -S -emit-llvm
$LLVM_BINDIR/llvm-as hello.s
$LLVM_BINDIR/llvm-dis hello.s.bc -show-annotations
# Run emscripten
$EMSCRIPTEN/emscripten.py hello.s.ll $V8/d8 > hello.js
# Run the Javascript using v8
$V8/d8 hello.js