socket.on("connect", function(){
reader = LineInputStream(socket);
reader.on("line", function(line){
var s = line.trim();
// Erste zwei vom Server gesendete Zeilen ignorieren
if(status < 0){
status++;
if(status == 0) checkQueue();
return;
}
// Antwort besteht aus ein bis zwei Zeilen: Zuletzt kommt immer error
var response = undefined;
if(s.indexOf("error") == 0){
response = parseResponse(s.substr("error ".length).trim());
executing.error = response;
if(executing.error.id == 0) delete executing.error;
if(executing.cb) executing.cb.call(executing, executing.result, executing.response);
executing = null;
checkQueue();
} else if(s.indexOf("notify") == 0){
s = s.substr("notify".length);
response = parseResponse(s);
self.emit(s.substr(0, s.indexOf(" ")), response);
} else {
response = parseResponse(s);
executing.response = response;
}
});
self.emit("connect");
});
User.prototype.initStream = function(code, str, optConsumer) {
//console.log('initStream: consumer=', optConsumer);
var user = this;
var ls = lins(str);
user.stdio[code] = new StreamLineHistory(str, ls);
ls.setEncoding('utf8');
ls.setDelimiter('\n');
ls.on('error', function(err) {
console.log(err + ', user ' + user.name);
});
ls.on('line', function(line) {
var ch = code == 0 ? '=>' : code == 1 ? '<=' : '):';
console.log('%s@equares %s %s', user.name, ch, line);
user.addStreamLine(code, line);
if(optConsumer !== undefined)
optConsumer.write(line+'\n');
});
}
function processFile(){
var timestamp = (new Date()).getTime();
if(dolineInputStream === true){
var LineInputStream = require('line-input-stream');
var stream = LineInputStream(fs.createReadStream(fileToRead, {flags:'r'}));
stream.setEncoding(encoding);
stream.setDelimiter('$$$$\n');
stream.on("error", function(err) {
fs.appendFileSync(errorFile, "\r\n"+JSON.stringify(err)+"\r\n");
});
stream.on('line', processLine);
stream.on("end", function() {processEnd();});
stream.on("close", function() {processEnd();});
}else{
var LineByLineReader = require('line-by-line');
var lr = new LineByLineReader(fileToRead, {encoding: encoding});
lr.on('error', function (err) {
fs.appendFileSync(errorFile, "\r\n"+JSON.stringify(err)+"\r\n");
});
lr.on('end', function () {processEnd();});
var data="";
lr.on('line', function (line) {
data = data + line +"\r\n";
if(line.indexOf("$$$$") !== -1){
processLine(data);
data = "";
}
});
}
var i=1;
var stepper=stepToShow;
var nbsuccess = 0;
var nberror = 0;
function processLine(line) {
if(i >= stepper){
monitor("#step "+i);
stepper+=stepToShow;
}
if(i >= start){//define point for start
// try {
/* var Lines = line.split('\n');
goodlines = Lines[0]+"\n";
cscart = false;
for (ij=1;ij<Lines.length;ij++)
{
if (Lines[ij].indexOf("CsCart") !==-1) cscart = true;
if (ij!=1 & cscart) goodlines+=Lines[ij]+"\n";
}
*/
var result = parse(line);
line = result.molecules[0].molfile.value;
console.log(line);
var mol= rdk.Molecule.MolBlockToMol(line);
var smile = mol.molToSmiles();
var binarymol = mol.pickleMol();
// this is the folded example (AllChem.GetHashedMorganFingerprint(mol, radius=self.radius, nBits = self.length))
// the unfolded (faster method is based on : AllChem.GetMorganFingerprint(mol, radius=self.radius)
// the bits are sorted using sorted(GetNonZeroElement().keys())
var mpf2 = mol.getMorganFingerprintsKeys(2); // unfolded keys storage using getMorganFingerprintsKeys // folded = mol.getMorganFingerprints_getOnBbits(2,2048);
var mpf = [];
var mpflen = mpf2.size();
for(var j=0;j < mpflen;j++){
mpf.push(mpf2.get(j));
}
moleculesCollection.insert(
{
'smiles': smile,
'chembl_id': i,
'rdmol': Binary(binarymol),
'mfp': {'bits': mpf, 'count': mpflen}
}
);
mol.delete();
nbsuccess++;
/* }catch (err) {
fs.appendFileSync(errorFile, "i="+i+"\r\n"+JSON.stringify(err)+"\r\n");
nberror++;
return;
}
*/
}
if (i >= end) {
processEnd();
}
i++;
}
function processEnd(){
var date1 = new Date(timestamp);
var date2 = new Date();
var timeDiff = Math.abs(date2.getTime() - date1.getTime());
var diffSec = parseInt(timeDiff / (1000 ));
var diffMin = parseInt(diffSec/60);
diffSec = diffSec - (diffMin*60);
var time = diffMin + "m" + diffSec + "s";
resumeTime("###i=" + i + " success: "+(nbsuccess-nberror)+" failed: "+nberror+" in "+time);
databaseMongo.close();
process.exit();
}
}
function create(params) {
var bridge = new events.EventEmitter();
// bake unique key to filter messages from stdout
var messageKey = crypto.createHash('md5')
.update('magic' + Date.now() + '|' + Math.random())
.digest('hex');
var messageScan = '["' + messageKey + '",';
var messageScanL = messageScan.length;
params.key = messageKey;
var spawnOpts = {
cwd: process.cwd(),
stdio: ['ignore', 'pipe', 'pipe']
};
var args = [];
args.push(path.resolve(__dirname, '..', 'slimer', 'main.js'));
args.push(JSON.stringify(params));
var cp;
if (params.xvfb) {
args.unshift(binPath);
cp = childProcess.spawn('xvfb-run', args, spawnOpts);
}
else {
cp = childProcess.spawn(binPath, args, spawnOpts);
}
var stream;
// parse console by lines
stream = lineInputStream(cp.stdout).on('line', function (line) {
if (line.substr(0, messageScanL) === messageScan) {
var data;
try {
data = JSON.parse(line);
}
catch (e) {
bridge.emit('error', e);
return;
}
if (data.length < 3 || data.length > 4) {
bridge.emit('error', new Error('bad message length ' + data.length));
}
data.shift();
var type = data[0];
switch (type) {
case 'mocha':
case 'error':
case 'exit':
bridge.emit(type, data[1]);
break;
default:
bridge.emit('log', data[1]);
}
}
else {
bridge.emit('log', line);
}
});
stream.setEncoding('utf8');
stream = lineInputStream(cp.stderr).on('line', function (line) {
bridge.emit('error', line);
});
stream.setEncoding('utf8');
// exit code is always null as slimer doesn't support it
cp.on('exit', function () {
bridge.emit('close');
});
return bridge;
}
function processFile(){
var timestamp = (new Date()).getTime();
var parser = require('sdf-parser')
//var result = parser('/Users/guilllaumegodin/Downloads/chembl_18.sdf');
var LineInputStream = require('line-input-stream')
var stream = LineInputStream(fs.createReadStream('/Users/guilllaumegodin/Downloads/chembl_18.sdf', {flags:'r'}));
stream.setEncoding('ascii');
stream.setDelimiter('$$$$\n');
stream.on("error", function(err) {
console.log(err);
});
stream.on('line', processLine);
stream.on("end", function() {
// No more data, all line events emitted before this event
});
stream.on("close", function() {
// Same as ReadableStream's close event
});
var smiles = [];
var i=0;
function processLine(line) {
++i;
//console.log(line);
try {
var mol= rdk.Molecule.MolBlockToMol(line);
var smile = mol.smilewrite();
var binarymol = mol.pickleMol();
var mpf2 = mol.getMorganFingerprints_getOnBbits(2,2048);
var mpf = [];
var mpflen = mpf2.size();
for(var j=0;j < mpflen;j++){
mpf.push(mpf2.get(j));
}
//console.log(mpf2.size());
moleculesCollection.insert({
'smiles': smile,
'chembl_id': i,
'rdmol': Binary(binarymol),
'mfp': {'bits': mpf, 'count': mpflen}
});
mol.delete();
}catch (err) {
console.log('err');
return;
}
smiles.push(smile)
if (smiles.length>100000) {
//console.log(smiles);
//console.log('done');
var date1 = new Date(timestamp);
var date2 = new Date();
var timeDiff = Math.abs(date2.getTime() - date1.getTime());
var diffSec = parseInt(timeDiff / (1000 ));
var diffMin = parseInt(diffSec/60);
diffSec = diffSec - (diffMin*60);
var time = diffMin + "m" + diffSec + "s";
console.log("success in: "+time);
monitor("end");
databaseMongo.close();
process.exit();
}
}
}