bool DBClientReplicaSet::auth(const string &dbname, const string &username, const string &pwd, string& errmsg, bool digestPassword ) {
DBClientConnection * m = checkMaster();
// first make sure it actually works
if( ! m->auth(dbname, username, pwd, errmsg, digestPassword ) )
return false;
// now that it does, we should save so that for a new node we can auth
_auths.push_back( AuthInfo( dbname , username , pwd , digestPassword ) );
return true;
}
inline void kill_wrapper( pid_t pid, int sig, int port, const BSONObj& opt ) {
#ifdef _WIN32
if (sig == SIGKILL || port == 0) {
verify( registry._handles.count(pid) );
TerminateProcess(registry._handles[pid], 1); // returns failure for "zombie" processes.
}
else {
DBClientConnection conn;
try {
conn.connect("127.0.0.1:" + BSONObjBuilder::numStr(port));
BSONElement authObj = opt["auth"];
if ( !authObj.eoo() ){
string errMsg;
conn.auth( "admin", authObj["user"].String(),
authObj["pwd"].String(), errMsg );
if ( !errMsg.empty() ) {
cout << "Failed to authenticate before shutdown: "
<< errMsg << endl;
}
}
BSONObj info;
BSONObjBuilder b;
b.append( "shutdown", 1 );
b.append( "force", 1 );
conn.runCommand( "admin", b.done(), info );
}
catch (...) {
//Do nothing. This command never returns data to the client and the driver doesn't like that.
}
}
#else
int x = kill( pid, sig );
if ( x ) {
if ( errno == ESRCH ) {
}
else {
log() << "killFailed: " << errnoWithDescription() << endl;
verify( x == 0 );
}
}
#endif
}
/* TODO: unit tests should run this? */
void testDbEval() {
DBClientConnection c;
string err;
if ( !c.connect("localhost", err) ) {
out() << "can't connect to server " << err << endl;
return;
}
if( !c.auth("dwight", "u", "p", err) ) {
out() << "can't authenticate " << err << endl;
return;
}
BSONObj info;
BSONElement retValue;
BSONObjBuilder b;
b.append("0", 99);
BSONObj args = b.done();
bool ok = c.eval("dwight", "function() { return args[0]; }", info, retValue, &args);
out() << "eval ok=" << ok << endl;
out() << "retvalue=" << retValue.toString() << endl;
out() << "info=" << info.toString() << endl;
out() << endl;
int x = 3;
assert( c.eval("dwight", "function() { return 3; }", x) );
out() << "***\n";
BSONObj foo = fromjson("{\"x\":7}");
out() << foo.toString() << endl;
int res=0;
ok = c.eval("dwight", "function(parm1) { return parm1.x; }", foo, res);
out() << ok << " retval:" << res << endl;
}
bool HostAndPort::isSelf() const {
if( dyn() ) {
MONGO_LOG(2) << "isSelf " << _dynName << ' ' << dynHostMyName() << endl;
return dynHostMyName() == _dynName;
}
int _p = port();
int p = _p == -1 ? CmdLine::DefaultDBPort : _p;
if( p != cmdLine.port ) {
// shortcut - ports have to match at the very least
return false;
}
string host = str::stream() << this->host() << ":" << p;
{
// check cache for this host
// debatably something _could_ change, but I'm not sure right now (erh 10/14/2010)
scoped_lock lk( isSelfCommand._cacheLock );
map<string,bool>::const_iterator i = isSelfCommand._cache.find( host );
if ( i != isSelfCommand._cache.end() )
return i->second;
}
#if !defined(_WIN32) && !defined(__sunos__)
// on linux and os x we can do a quick check for an ip match
const vector<string> myaddrs = getMyAddrs();
const vector<string> addrs = getAllIPs(_host);
for (vector<string>::const_iterator i=myaddrs.begin(), iend=myaddrs.end(); i!=iend; ++i) {
for (vector<string>::const_iterator j=addrs.begin(), jend=addrs.end(); j!=jend; ++j) {
string a = *i;
string b = *j;
if ( a == b ||
( str::startsWith( a , "127." ) && str::startsWith( b , "127." ) ) // 127. is all loopback
) {
// add to cache
scoped_lock lk( isSelfCommand._cacheLock );
isSelfCommand._cache[host] = true;
return true;
}
}
}
#endif
if ( ! Listener::getTimeTracker() ) {
// this ensures we are actually running a server
// this may return true later, so may want to retry
return false;
}
try {
isSelfCommand.init();
DBClientConnection conn;
string errmsg;
if ( ! conn.connect( host , errmsg ) ) {
// should this go in the cache?
return false;
}
if (!noauth && cmdLine.keyFile &&
!conn.auth("local", internalSecurity.user, internalSecurity.pwd, errmsg, false)) {
return false;
}
BSONObj out;
bool ok = conn.simpleCommand( "admin" , &out , "_isSelf" );
bool me = ok && out["id"].type() == jstOID && isSelfCommand._id == out["id"].OID();
// add to cache
scoped_lock lk( isSelfCommand._cacheLock );
isSelfCommand._cache[host] = me;
return me;
}
catch ( std::exception& e ) {
warning() << "could't check isSelf (" << host << ") " << e.what() << endl;
}
return false;
}
int main(int argc, char* argv[])
{
// Check the required number of command line arguments.
if (argc != 5)
{
cout << "usr host user pwd jobs_path" << endl;
return 0;
}
// Fetch command line arguments.
const auto host = argv[1];
const auto user = argv[2];
const auto pwd = argv[3];
const path jobs_path = argv[4];
// Connect to host and authenticate user.
DBClientConnection conn;
{
cout << local_time() << "Connecting to " << host << " and authenticating " << user << endl;
string errmsg;
if ((!conn.connect(host, errmsg)) || (!conn.auth("istar", user, pwd, errmsg)))
{
cerr << local_time() << errmsg << endl;
return 1;
}
}
// Initialize constants.
cout << local_time() << "Initializing" << endl;
const auto collection = "istar.usr";
const auto epoch = date(1970, 1, 1);
const size_t num_usrs = 2;
constexpr array<size_t, num_usrs> qn{{ 12, 60 }};
constexpr array<double, num_usrs> qv{{ 1.0 / qn[0], 1.0 / qn[1] }};
const size_t num_references = 4;
const size_t num_subsets = 5;
const array<string, num_subsets> SubsetSMARTS
{{
"[!#1]", // heavy
"[#6+0!$(*~[#7,#8,F]),SH0+0v2,s+0,S^3,Cl+0,Br+0,I+0]", // hydrophobic
"[a]", // aromatic
"[$([O,S;H1;v2]-[!$(*=[O,N,P,S])]),$([O,S;H0;v2]),$([O,S;-]),$([N&v3;H1,H2]-[!$(*=[O,N,P,S])]),$([N;v3;H0]),$([n,o,s;+0]),F]", // acceptor
"[N!H0v3,N!H0+v4,OH+0,SH+0,nH+0]", // donor
}};
// Initialize variables.
array<array<double, qn.back()>, 1> qw;
array<array<double, qn.back()>, 1> lw;
auto q = qw[0];
auto l = lw[0];
// Read ZINC ID file.
const string_array<size_t> zincids("16_zincid.txt");
const auto num_ligands = zincids.size();
// Read SMILES file.
const string_array<size_t> smileses("16_smiles.txt");
assert(smileses.size() == num_ligands);
// Read supplier file.
const string_array<size_t> suppliers("16_supplier.txt");
assert(suppliers.size() == num_ligands);
// Read property files of floating point types and integer types.
const auto zfproperties = read<array<float, 4>>("16_zfprop.f32");
assert(zfproperties.size() == num_ligands);
const auto ziproperties = read<array<int16_t, 5>>("16_ziprop.i16");
assert(ziproperties.size() == num_ligands);
// Open files for subsequent reading.
std::ifstream usrcat_bin("16_usrcat.f64");
stream_array<size_t> ligands("16_ligand.pdbqt");
assert(ligands.size() == num_ligands);
array<vector<double>, 2> scores
{{
vector<double>(num_ligands, 0),
vector<double>(num_ligands, 0)
}};
const auto& u0scores = scores[0];
const auto& u1scores = scores[1];
vector<size_t> scase(num_ligands);
// Enter event loop.
cout << local_time() << "Entering event loop" << endl;
bool sleeping = false;
while (true)
{
// Fetch an incompleted job in a first-come-first-served manner.
if (!sleeping) cout << local_time() << "Fetching an incompleted job" << endl;
BSONObj info;
conn.runCommand("istar", BSON("findandmodify" << "usr" << "query" << BSON("done" << BSON("$exists" << false) << "started" << BSON("$exists" << false)) << "sort" << BSON("submitted" << 1) << "update" << BSON("$set" << BSON("started" << Date_t(duration_cast<std::chrono::milliseconds>(system_clock::now().time_since_epoch()).count())))), info); // conn.findAndModify() is available since MongoDB C++ Driver legacy-1.0.0
const auto value = info["value"];
if (value.isNull())
{
// No incompleted jobs. Sleep for a while.
if (!sleeping) cout << local_time() << "Sleeping" << endl;
sleeping = true;
this_thread::sleep_for(chrono::seconds(10));
continue;
}
sleeping = false;
const auto job = value.Obj();
// Obtain job properties.
const auto _id = job["_id"].OID();
cout << local_time() << "Executing job " << _id.str() << endl;
const auto job_path = jobs_path / _id.str();
const auto format = job["format"].String();
const auto email = job["email"].String();
// Parse the user-supplied ligand.
OBMol obMol;
OBConversion obConversion;
obConversion.SetInFormat(format.c_str());
obConversion.ReadFile(&obMol, (job_path / ("ligand." + format)).string());
const auto num_atoms = obMol.NumAtoms();
// obMol.AddHydrogens(); // Adding hydrogens does not seem to affect SMARTS matching.
// Classify subset atoms.
array<vector<int>, num_subsets> subsets;
for (size_t k = 0; k < num_subsets; ++k)
{
auto& subset = subsets[k];
subset.reserve(num_atoms);
OBSmartsPattern smarts;
smarts.Init(SubsetSMARTS[k]);
smarts.Match(obMol);
for (const auto& map : smarts.GetMapList())
{
subset.push_back(map.front());
}
}
const auto& subset0 = subsets.front();
// Check user-provided ligand validity.
if (subset0.empty())
{
// Record job completion time stamp.
const auto millis_since_epoch = duration_cast<std::chrono::milliseconds>(system_clock::now().time_since_epoch()).count();
conn.update(collection, BSON("_id" << _id), BSON("$set" << BSON("done" << Date_t(millis_since_epoch))));
// Send error notification email.
cout << local_time() << "Sending an error notification email to " << email << endl;
MailMessage message;
message.setSender("usr <*****@*****.**>");
message.setSubject("Your usr job has failed");
message.setContent("Description: " + job["description"].String() + "\nSubmitted: " + to_simple_string(ptime(epoch, boost::posix_time::milliseconds(job["submitted"].Date().millis))) + " UTC\nFailed: " + to_simple_string(ptime(epoch, boost::posix_time::milliseconds(millis_since_epoch))) + " UTC\nReason: failed to parse the provided ligand.");
message.addRecipient(MailRecipient(MailRecipient::PRIMARY_RECIPIENT, email));
SMTPClientSession session("137.189.91.190");
session.login();
session.sendMessage(message);
session.close();
continue;
}
// Calculate the four reference points.
const auto n = subset0.size();
const auto v = 1.0 / n;
array<vector3, num_references> references{};
auto& ctd = references[0];
auto& cst = references[1];
auto& fct = references[2];
auto& ftf = references[3];
for (const auto i : subset0)
{
ctd += obMol.GetAtom(i)->GetVector();
}
ctd *= v;
double cst_dist = numeric_limits<double>::max();
double fct_dist = numeric_limits<double>::lowest();
double ftf_dist = numeric_limits<double>::lowest();
for (const auto i : subset0)
{
const auto& a = obMol.GetAtom(i)->GetVector();
const auto this_dist = a.distSq(ctd);
if (this_dist < cst_dist)
{
cst = a;
cst_dist = this_dist;
}
if (this_dist > fct_dist)
{
fct = a;
fct_dist = this_dist;
}
}
for (const auto i : subset0)
{
const auto& a = obMol.GetAtom(i)->GetVector();
const auto this_dist = a.distSq(fct);
if (this_dist > ftf_dist)
{
ftf = a;
ftf_dist = this_dist;
}
}
// Precalculate the distances between each atom and each reference point.
array<vector<double>, num_references> dista;
for (size_t k = 0; k < num_references; ++k)
{
const auto& reference = references[k];
auto& dists = dista[k];
dists.resize(1 + num_atoms); // OpenBabel atom index starts from 1. dists[0] is dummy.
for (size_t i = 0; i < n; ++i)
{
dists[subset0[i]] = sqrt(obMol.GetAtom(subset0[i])->GetVector().distSq(reference));
}
}
// Calculate USR and USRCAT features of the input ligand.
size_t qo = 0;
for (const auto& subset : subsets)
{
const auto n = subset.size();
for (size_t k = 0; k < num_references; ++k)
{
const auto& distp = dista[k];
vector<double> dists(n);
for (size_t i = 0; i < n; ++i)
{
dists[i] = distp[subset[i]];
}
array<double, 3> m{};
if (n > 2)
{
const auto v = 1.0 / n;
for (size_t i = 0; i < n; ++i)
{
const auto d = dists[i];
m[0] += d;
}
m[0] *= v;
for (size_t i = 0; i < n; ++i)
{
const auto d = dists[i] - m[0];
m[1] += d * d;
}
m[1] = sqrt(m[1] * v);
for (size_t i = 0; i < n; ++i)
{
const auto d = dists[i] - m[0];
m[2] += d * d * d;
}
m[2] = cbrt(m[2] * v);
}
else if (n == 2)
{
m[0] = 0.5 * (dists[0] + dists[1]);
m[1] = 0.5 * fabs(dists[0] - dists[1]);
}
else if (n == 1)
{
m[0] = dists[0];
}
#pragma unroll
for (const auto e : m)
{
q[qo++] = e;
}
}
}
assert(qo == qn.back());
// Compute USR and USRCAT scores.
usrcat_bin.seekg(0);
for (size_t k = 0; k < num_ligands; ++k)
{
usrcat_bin.read(reinterpret_cast<char*>(l.data()), sizeof(l));
double s = 0;
#pragma unroll
for (size_t i = 0, u = 0; u < num_usrs; ++u)
{
#pragma unroll
for (const auto qnu = qn[u]; i < qnu; ++i)
{
s += fabs(q[i] - l[i]);
}
scores[u][k] = s;
}
}
assert(usrcat_bin.tellg() == sizeof(l) * num_ligands);
// Sort ligands by USRCAT score and then by USR score and then by ZINC ID.
iota(scase.begin(), scase.end(), 0);
sort(scase.begin(), scase.end(), [&](const size_t val0, const size_t val1)
{
const auto u1score0 = u1scores[val0];
const auto u1score1 = u1scores[val1];
if (u1score0 == u1score1)
{
const auto u0score0 = u0scores[val0];
const auto u0score1 = u0scores[val1];
if (u0score0 == u0score1)
{
return zincids[val0] < zincids[val1];
}
return u0score0 < u0score1;
}
return u1score0 < u1score1;
});
// Write results.
filtering_ostream log_csv_gz;
log_csv_gz.push(gzip_compressor());
log_csv_gz.push(file_sink((job_path / "log.csv.gz").string()));
log_csv_gz.setf(ios::fixed, ios::floatfield);
log_csv_gz << "ZINC ID,USR score,USRCAT score\n" << setprecision(8);
filtering_ostream ligands_pdbqt_gz;
ligands_pdbqt_gz.push(gzip_compressor());
ligands_pdbqt_gz.push(file_sink((job_path / "ligands.pdbqt.gz").string()));
ligands_pdbqt_gz.setf(ios::fixed, ios::floatfield);
for (size_t t = 0; t < 10000; ++t)
{
const size_t k = scase[t];
const auto zincid = zincids[k].substr(0, 8); // Take another substr() to get rid of the trailing newline.
const auto u0score = 1 / (1 + scores[0][k] * qv[0]);
const auto u1score = 1 / (1 + scores[1][k] * qv[1]);
log_csv_gz << zincid << ',' << u0score << ',' << u1score << '\n';
// Only write conformations of the top ligands to ligands.pdbqt.gz.
if (t >= 1000) continue;
const auto zfp = zfproperties[k];
const auto zip = ziproperties[k];
ligands_pdbqt_gz
<< "MODEL " << '\n'
<< "REMARK 911 " << zincid
<< setprecision(3)
<< ' ' << setw(8) << zfp[0]
<< ' ' << setw(8) << zfp[1]
<< ' ' << setw(8) << zfp[2]
<< ' ' << setw(8) << zfp[3]
<< ' ' << setw(3) << zip[0]
<< ' ' << setw(3) << zip[1]
<< ' ' << setw(3) << zip[2]
<< ' ' << setw(3) << zip[3]
<< ' ' << setw(3) << zip[4]
<< '\n'
<< "REMARK 912 " << smileses[k] // A newline is already included in smileses[k].
<< "REMARK 913 " << suppliers[k] // A newline is already included in suppliers[k].
<< setprecision(8)
<< "REMARK 951 USR SCORE: " << setw(10) << u0score << '\n'
<< "REMARK 952 USRCAT SCORE: " << setw(10) << u1score << '\n'
;
const auto lig = ligands[k];
ligands_pdbqt_gz.write(lig.data(), lig.size());
ligands_pdbqt_gz << "ENDMDL\n";
}
// Update progress.
cout << local_time() << "Setting done time" << endl;
const auto millis_since_epoch = duration_cast<std::chrono::milliseconds>(system_clock::now().time_since_epoch()).count();
conn.update(collection, BSON("_id" << _id), BSON("$set" << BSON("done" << Date_t(millis_since_epoch))));
// Send completion notification email.
cout << local_time() << "Sending a completion notification email to " << email << endl;
MailMessage message;
message.setSender("istar <*****@*****.**>");
message.setSubject("Your usr job has completed");
message.setContent("Description: " + job["description"].String() + "\nSubmitted: " + to_simple_string(ptime(epoch, boost::posix_time::milliseconds(job["submitted"].Date().millis))) + " UTC\nCompleted: " + to_simple_string(ptime(epoch, boost::posix_time::milliseconds(millis_since_epoch))) + " UTC\nResult: http://istar.cse.cuhk.edu.hk/usr/iview/?" + _id.str());
message.addRecipient(MailRecipient(MailRecipient::PRIMARY_RECIPIENT, email));
SMTPClientSession session("137.189.91.190");
session.login();
session.sendMessage(message);
session.close();
}
}
inline void kill_wrapper( ProcessId pid, int sig, int port, const BSONObj& opt ) {
#ifdef _WIN32
if (sig == SIGKILL || port == 0) {
verify( registry._handles.count(pid) );
TerminateProcess(registry._handles[pid], 1); // returns failure for "zombie" processes.
return;
}
std::string eventName = getShutdownSignalName(pid.asUInt32());
HANDLE event = OpenEventA(EVENT_MODIFY_STATE, FALSE, eventName.c_str());
if (event == NULL) {
int gle = GetLastError();
if (gle != ERROR_FILE_NOT_FOUND) {
warning() << "kill_wrapper OpenEvent failed: " << errnoWithDescription();
}
else {
log() << "kill_wrapper OpenEvent failed to open event to the process "
<< pid.asUInt32()
<< ". It has likely died already or server is running an older version."
<< " Attempting to shutdown through admin command.";
// Back-off to the old way of shutting down the server on Windows, in case we
// are managing a pre-2.6.0rc0 service, which did not have the event.
//
try {
DBClientConnection conn;
conn.connect("127.0.0.1:" + BSONObjBuilder::numStr(port));
BSONElement authObj = opt["auth"];
if (!authObj.eoo()){
string errMsg;
conn.auth("admin", authObj["user"].String(),
authObj["pwd"].String(), errMsg);
if (!errMsg.empty()) {
cout << "Failed to authenticate before shutdown: "
<< errMsg << endl;
}
}
BSONObj info;
BSONObjBuilder b;
b.append("shutdown", 1);
b.append("force", 1);
conn.runCommand("admin", b.done(), info);
}
catch (...) {
// Do nothing. This command never returns data to the client and the driver
// doesn't like that.
//
}
}
return;
}
ON_BLOCK_EXIT(CloseHandle, event);
bool result = SetEvent(event);
if (!result) {
error() << "kill_wrapper SetEvent failed: " << errnoWithDescription();
return;
}
#else
int x = kill( pid.toNative(), sig );
if ( x ) {
if ( errno == ESRCH ) {
}
else {
log() << "killFailed: " << errnoWithDescription() << endl;
verify( x == 0 );
}
}
#endif
}
int main(int argc, char* argv[])
{
// Check the required number of command line arguments.
if (argc != 5)
{
cout << "usr host user pwd jobs_path" << endl;
return 0;
}
// Fetch command line arguments.
const auto host = argv[1];
const auto user = argv[2];
const auto pwd = argv[3];
const path jobs_path = argv[4];
DBClientConnection conn;
{
// Connect to host and authenticate user.
cout << local_time() << "Connecting to " << host << " and authenticating " << user << endl;
string errmsg;
if ((!conn.connect(host, errmsg)) || (!conn.auth("istar", user, pwd, errmsg)))
{
cerr << local_time() << errmsg << endl;
return 1;
}
}
// Initialize constants.
cout << local_time() << "Initializing" << endl;
const auto collection = "istar.usr2";
const size_t num_usrs = 2;
const array<string, 2> usr_names{{ "USR", "USRCAT" }};
constexpr array<size_t, num_usrs> qn{{ 12, 60 }};
constexpr array<double, num_usrs> qv{{ 1.0 / qn[0], 1.0 / qn[1] }};
const size_t num_refPoints = 4;
const size_t num_subsets = 5;
const array<string, num_subsets> SubsetSMARTS
{{
"[!#1]", // heavy
"[#6+0!$(*~[#7,#8,F]),SH0+0v2,s+0,S^3,Cl+0,Br+0,I+0]", // hydrophobic
"[a]", // aromatic
"[$([O,S;H1;v2]-[!$(*=[O,N,P,S])]),$([O,S;H0;v2]),$([O,S;-]),$([N&v3;H1,H2]-[!$(*=[O,N,P,S])]),$([N;v3;H0]),$([n,o,s;+0]),F]", // acceptor
"[N!H0v3,N!H0+v4,OH+0,SH+0,nH+0]", // donor
}};
const size_t num_hits = 100;
// Wrap SMARTS strings to RWMol objects.
array<unique_ptr<ROMol>, num_subsets> SubsetMols;
for (size_t k = 0; k < num_subsets; ++k)
{
SubsetMols[k].reset(reinterpret_cast<ROMol*>(SmartsToMol(SubsetSMARTS[k])));
}
// Read ZINC ID file.
const string_array<size_t> zincids("16/zincid.txt");
const auto num_ligands = zincids.size();
cout << local_time() << "Found " << num_ligands << " database molecules" << endl;
// Read SMILES file.
const string_array<size_t> smileses("16/smiles.txt");
assert(smileses.size() == num_ligands);
// Read supplier file.
const string_array<size_t> suppliers("16/supplier.txt");
assert(suppliers.size() == num_ligands);
// Read property files of floating point types and integer types.
const auto zfproperties = read<array<float, 4>>("16/zfprop.f32");
assert(zfproperties.size() == num_ligands);
const auto ziproperties = read<array<int16_t, 5>>("16/ziprop.i16");
assert(ziproperties.size() == num_ligands);
// Read cumulative number of conformers file.
const auto mconfss = read<size_t>("16/mconfs.u64");
const auto num_conformers = mconfss.back();
assert(mconfss.size() == num_ligands);
assert(num_conformers >= num_ligands);
cout << local_time() << "Found " << num_conformers << " database conformers" << endl;
// Read feature file.
const auto features = read<array<double, qn.back()>>("16/usrcat.f64");
assert(features.size() == num_conformers);
// Read ligand footer file and open ligand SDF file for seeking and reading.
stream_array<size_t> ligands("16/ligand.sdf");
assert(ligands.size() == num_conformers);
// Initialize variables.
array<vector<int>, num_subsets> subsets;
array<vector<double>, num_refPoints> dista;
alignas(32) array<double, qn.back()> q;
// Initialize vectors to store compounds' primary score and their corresponding conformer.
vector<double> scores(num_ligands); // Primary score of molecules.
vector<size_t> cnfids(num_ligands); // ID of conformer with the best primary score.
const auto compare = [&](const size_t val0, const size_t val1) // Sort by the primary score.
{
return scores[val0] < scores[val1];
};
// Initialize an io service pool and create worker threads for later use.
const size_t num_threads = thread::hardware_concurrency();
cout << local_time() << "Creating an io service pool of " << num_threads << " worker threads" << endl;
io_service_pool io(num_threads);
safe_counter<size_t> cnt;
// Initialize the number of chunks and the number of molecules per chunk.
const auto num_chunks = num_threads << 4;
const auto chunk_size = 1 + (num_ligands - 1) / num_chunks;
assert(chunk_size * num_chunks >= num_ligands);
assert(chunk_size >= num_hits);
cout << local_time() << "Using " << num_chunks << " chunks and a chunk size of " << chunk_size << endl;
vector<size_t> scase(num_ligands);
vector<size_t> zcase(num_hits * (num_chunks - 1) + min(num_hits, num_ligands - chunk_size * (num_chunks - 1))); // The last chunk might have fewer than num_hits records.
// Enter event loop.
cout << local_time() << "Entering event loop" << endl;
cout.setf(ios::fixed, ios::floatfield);
bool sleeping = false;
while (true)
{
// Fetch an incompleted job in a first-come-first-served manner.
if (!sleeping) cout << local_time() << "Fetching an incompleted job" << endl;
BSONObj info;
const auto started = milliseconds_since_epoch();
conn.runCommand("istar", BSON("findandmodify" << "usr2" << "query" << BSON("started" << BSON("$exists" << false)) << "sort" << BSON("submitted" << 1) << "update" << BSON("$set" << BSON("started" << started))), info); // conn.findAndModify() is available since MongoDB C++ Driver legacy-1.0.0
const auto value = info["value"];
if (value.isNull())
{
// No incompleted jobs. Sleep for a while.
if (!sleeping) cout << local_time() << "Sleeping" << endl;
sleeping = true;
this_thread::sleep_for(chrono::seconds(2));
continue;
}
sleeping = false;
const auto job = value.Obj();
// Obtain job properties.
const auto _id = job["_id"].OID();
cout << local_time() << "Executing job " << _id.str() << endl;
const auto job_path = jobs_path / _id.str();
const size_t usr0 = job["usr"].Int(); // Specify the primary sorting score. 0: USR; 1: USRCAT.
assert(usr0 == 0 || usr0 == 1);
const auto usr1 = usr0 ^ 1;
const auto qnu0 = qn[usr0];
const auto qnu1 = qn[usr1];
// Read and validate the user-supplied SDF file.
cout << local_time() << "Reading and validating the query file" << endl;
SDMolSupplier sup((job_path / "query.sdf").string(), true, false, true); // sanitize, removeHs, strictParsing
if (!sup.length() || !sup.atEnd())
{
const auto error = 1;
cout << local_time() << "Failed to parse the query file, error code = " << error << endl;
conn.update(collection, BSON("_id" << _id), BSON("$set" << BSON("completed" << milliseconds_since_epoch() << "error" << error)));
continue;
}
// Process each of the query molecules sequentially.
const auto num_queries = 1; // Restrict the number of query molecules to 1. Setting num_queries = sup.length() to execute any number of query molecules.
for (unsigned int query_number = 0; query_number < num_queries; ++query_number)
{
cout << local_time() << "Parsing query molecule " << query_number << endl;
const unique_ptr<ROMol> qry_ptr(sup.next()); // Calling next() may print "ERROR: Could not sanitize molecule on line XXXX" to stderr.
auto& qryMol = *qry_ptr;
// Get the number of atoms, including and excluding hydrogens.
const auto num_atoms = qryMol.getNumAtoms();
const auto num_heavy_atoms = qryMol.getNumHeavyAtoms();
assert(num_heavy_atoms);
cout << local_time() << "Found " << num_atoms << " atoms and " << num_heavy_atoms << " heavy atoms" << endl;
// Create an output directory.
cout << local_time() << "Creating output directory" << endl;
const auto output_dir = job_path / to_string(query_number);
create_directory(output_dir);
// Draw a SVG.
cout << local_time() << "Drawing a SVG" << endl;
{
const unique_ptr<ROMol> qrz_ptr(removeHs(qryMol));
auto& qrzMol = *qrz_ptr;
compute2DCoords(qrzMol);
boost::filesystem::ofstream ofs(output_dir / "query.svg");
ofs << DrawingToSVG(MolToDrawing(qrzMol));
}
// Calculate Morgan fingerprint.
cout << local_time() << "Calculating Morgan fingerprint" << endl;
const unique_ptr<SparseIntVect<uint32_t>> qryFp(getFingerprint(qryMol, 2));
// Classify atoms to pharmacophoric subsets.
cout << local_time() << "Classifying atoms into subsets" << endl;
for (size_t k = 0; k < num_subsets; ++k)
{
vector<vector<pair<int, int>>> matchVect;
SubstructMatch(qryMol, *SubsetMols[k], matchVect);
const auto num_matches = matchVect.size();
auto& subset = subsets[k];
subset.resize(num_matches);
for (size_t i = 0; i < num_matches; ++i)
{
subset[i] = matchVect[i].front().second;
}
cout << local_time() << "Found " << num_matches << " atoms for subset " << k << endl;
}
const auto& subset0 = subsets.front();
assert(subset0.size() == num_heavy_atoms);
// Calculate the four reference points.
cout << local_time() << "Calculating " << num_refPoints << " reference points" << endl;
const auto qryRefPoints = calcRefPoints(qryMol, subset0);
const Point3DConstPtrVect qryRefPointv
{{
&qryRefPoints[0],
&qryRefPoints[1],
&qryRefPoints[2],
&qryRefPoints[3],
}};
// Precalculate the distances of heavy atoms to the reference points, given that subsets[1 to 4] are subsets of subsets[0].
cout << local_time() << "Calculating " << num_heavy_atoms * num_refPoints << " pairwise distances" << endl;
const auto& qryCnf = qryMol.getConformer();
for (size_t k = 0; k < num_refPoints; ++k)
{
const auto& refPoint = qryRefPoints[k];
auto& distp = dista[k];
distp.resize(num_atoms);
for (size_t i = 0; i < num_heavy_atoms; ++i)
{
distp[subset0[i]] = sqrt(dist2(qryCnf.getAtomPos(subset0[i]), refPoint));
}
}
// Loop over pharmacophoric subsets and reference points.
cout << local_time() << "Calculating " << 3 * num_refPoints * num_subsets << " moments of USRCAT feature" << endl;
size_t qo = 0;
for (const auto& subset : subsets)
{
const auto n = subset.size();
for (size_t k = 0; k < num_refPoints; ++k)
{
// Load distances from precalculated ones.
const auto& distp = dista[k];
vector<double> dists(n);
for (size_t i = 0; i < n; ++i)
{
dists[i] = distp[subset[i]];
}
// Compute moments.
array<double, 3> m{};
if (n > 2)
{
const auto v = 1.0 / n;
for (size_t i = 0; i < n; ++i)
{
const auto d = dists[i];
m[0] += d;
}
m[0] *= v;
for (size_t i = 0; i < n; ++i)
{
const auto d = dists[i] - m[0];
m[1] += d * d;
}
m[1] = sqrt(m[1] * v);
for (size_t i = 0; i < n; ++i)
{
const auto d = dists[i] - m[0];
m[2] += d * d * d;
}
m[2] = cbrt(m[2] * v);
}
else if (n == 2)
{
m[0] = 0.5 * (dists[0] + dists[1]);
m[1] = 0.5 * fabs(dists[0] - dists[1]);
}
else if (n == 1)
{
m[0] = dists[0];
}
for (const auto e : m)
{
q[qo++] = e;
}
}
}
assert(qo == qn.back());
// Compute USR and USRCAT scores.
cout << local_time() << "Calculating " << num_ligands << " " << usr_names[usr0] << " scores" << endl;
scores.assign(scores.size(), numeric_limits<double>::max());
iota(scase.begin(), scase.end(), 0);
cnt.init(num_chunks);
for (size_t l = 0; l < num_chunks; ++l)
{
io.post([&,l]()
{
// Loop over molecules of the current chunk.
const auto chunk_beg = chunk_size * l;
const auto chunk_end = min(chunk_beg + chunk_size, num_ligands);
for (size_t k = chunk_beg; k < chunk_end; ++k)
{
// Loop over conformers of the current molecule and calculate their primary score.
auto& scorek = scores[k];
size_t j = k ? mconfss[k - 1] : 0;
for (const auto mconfs = mconfss[k]; j < mconfs; ++j)
{
const auto& d = features[j];
double s = 0;
for (size_t i = 0; i < qnu0; ++i)
{
s += abs(q[i] - d[i]);
if (s >= scorek) break;
}
if (s < scorek)
{
scorek = s;
cnfids[k] = j;
}
}
}
// Sort the scores of molecules of the current chunk.
sort(scase.begin() + chunk_beg, scase.begin() + chunk_end, compare);
// Copy the indexes of top hits of the current chunk to a global vector for final sorting.
copy_n(scase.begin() + chunk_beg, min(num_hits, chunk_end - chunk_beg), zcase.begin() + num_hits * l);
cnt.increment();
});
}
cnt.wait();
// Sort the top hits from chunks.
cout << local_time() << "Sorting " << zcase.size() << " hits by " << usr_names[usr0] << " score" << endl;
sort(zcase.begin(), zcase.end(), compare);
// Create output directory and write output files.
cout << local_time() << "Writing output files" << endl;
SDWriter hits_sdf((output_dir / "hits.sdf").string());
boost::filesystem::ofstream hits_csv(output_dir / "hits.csv");
hits_csv.setf(ios::fixed, ios::floatfield);
hits_csv << "ZINC ID,USR score,USRCAT score,2D Tanimoto score,Molecular weight (g/mol),Partition coefficient xlogP,Apolar desolvation (kcal/mol),Polar desolvation (kcal/mol),Hydrogen bond donors,Hydrogen bond acceptors,Polar surface area tPSA (Å^2),Net charge,Rotatable bonds,SMILES,Vendors and annotations\n";
for (size_t l = 0; l < num_hits; ++l)
{
// Obtain indexes to the hit molecule and the hit conformer.
const auto k = zcase[l];
const auto j = cnfids[k];
// Read SDF content of the hit conformer.
const auto lig = ligands[j];
// Construct a RDKit ROMol object.
istringstream iss(lig);
SDMolSupplier sup(&iss, false, true, false, true);
assert(sup.length() == 1);
assert(sup.atEnd());
const unique_ptr<ROMol> hit_ptr(sup.next());
auto& hitMol = *hit_ptr;
// Calculate Morgan fingerprint.
const unique_ptr<SparseIntVect<uint32_t>> hitFp(getFingerprint(hitMol, 2));
// Calculate Tanimoto similarity.
const auto ts = TanimotoSimilarity(*qryFp, *hitFp);
// Find heavy atoms.
vector<vector<pair<int, int>>> matchVect;
SubstructMatch(hitMol, *SubsetMols[0], matchVect);
const auto num_matches = matchVect.size();
assert(num_matches == hitMol.getNumHeavyAtoms());
vector<int> hitHeavyAtoms(num_matches);
for (size_t i = 0; i < num_matches; ++i)
{
hitHeavyAtoms[i] = matchVect[i].front().second;
assert(hitHeavyAtoms[i] == i); // hitHeavyAtoms can be constructed using iota(hitHeavyAtoms.begin(), hitHeavyAtoms.end(), 0); because for RDKit-generated SDF molecules, heavy atom are always the first few atoms.
}
// Calculate the four reference points.
const auto hitRefPoints = calcRefPoints(hitMol, hitHeavyAtoms);
const Point3DConstPtrVect hitRefPointv
{{
&hitRefPoints[0],
&hitRefPoints[1],
&hitRefPoints[2],
&hitRefPoints[3],
}};
// Calculate a 3D transform from the four reference points of the hit conformer to those of the query molecule.
Transform3D trans;
AlignPoints(qryRefPointv, hitRefPointv, trans);
// Apply the 3D transform to all atoms of the hit conformer.
auto& hitCnf = hitMol.getConformer();
transformConformer(hitCnf, trans);
// Write the aligned hit conformer.
hits_sdf.write(hitMol);
// Calculate the secondary score of the saved conformer, which has the best primary score.
const auto& d = features[j];
double s = 0;
for (size_t i = 0; i < qnu1; ++i)
{
s += abs(q[i] - d[i]);
}
const auto u0score = 1 / (1 + scores[k] * qv[usr0]); // Primary score of the current molecule.
const auto u1score = 1 / (1 + s * qv[usr1]); // Secondary score of the current molecule.
const auto zincid = zincids[k].substr(0, 8); // Take another substr() to get rid of the trailing newline.
const auto zfp = zfproperties[k];
const auto zip = ziproperties[k];
const auto smiles = smileses[k]; // A newline is already included in smileses[k].
const auto supplier = suppliers[k]; // A newline is already included in suppliers[k].
hits_csv
<< zincid
<< setprecision(8)
<< ',' << (usr1 ? u0score : u1score)
<< ',' << (usr1 ? u1score : u0score)
<< ',' << ts
<< setprecision(3)
<< ',' << zfp[0]
<< ',' << zfp[1]
<< ',' << zfp[2]
<< ',' << zfp[3]
<< ',' << zip[0]
<< ',' << zip[1]
<< ',' << zip[2]
<< ',' << zip[3]
<< ',' << zip[4]
<< ',' << smiles.substr(0, smiles.length() - 1) // Get rid of the trailing newline.
<< ',' << supplier.substr(0, supplier.length() - 1) // Get rid of the trailing newline.
<< '\n'
;
}
}
// Update job status.
cout << local_time() << "Setting completed time" << endl;
const auto completed = milliseconds_since_epoch();
conn.update(collection, BSON("_id" << _id), BSON("$set" << BSON("completed" << completed << "nqueries" << num_queries)));
// Calculate runtime in seconds and screening speed in million conformers per second.
const auto runtime = (completed - started) * 0.001;
const auto speed = num_conformers * 0.000001 * num_queries / runtime;
cout
<< local_time() << "Completed " << num_queries << " " << (num_queries == 1 ? "query" : "queries") << " in " << setprecision(3) << runtime << " seconds" << endl
<< local_time() << "Screening speed was " << setprecision(0) << speed << " M conformers per second" << endl
;
}
}
void DBClientReplicaSet::_auth( const BSONObj& params ) {
// We prefer to authenticate against a primary, but otherwise a secondary is ok too
// Empty tag matches every secondary
shared_ptr<ReadPreferenceSetting> readPref(
new ReadPreferenceSetting( ReadPreference_PrimaryPreferred, TagSet() ) );
LOG(3) << "dbclient_rs authentication of " << _getMonitor()->getName() << endl;
// NOTE that we retry MAX_RETRY + 1 times, since we're always primary preferred we don't
// fallback to the primary.
Status lastNodeStatus = Status::OK();
for ( size_t retry = 0; retry < MAX_RETRY + 1; retry++ ) {
try {
DBClientConnection* conn = selectNodeUsingTags( readPref );
if ( conn == NULL ) {
break;
}
conn->auth( params );
// Cache the new auth information since we now validated it's good
_auths[params[saslCommandUserDBFieldName].str()] = params.getOwned();
// Ensure the only child connection open is the one we authenticated against - other
// child connections may not have full authentication information.
// NOTE: _lastSlaveOkConn may or may not be the same as _master
dassert(_lastSlaveOkConn.get() == conn || _master.get() == conn);
if ( conn != _lastSlaveOkConn.get() ) {
_lastSlaveOkHost = HostAndPort();
_lastSlaveOkConn.reset();
}
if ( conn != _master.get() ) {
_masterHost = HostAndPort();
_master.reset();
}
return;
}
catch ( const DBException &ex ) {
// We care if we can't authenticate (i.e. bad password) in credential params.
if ( isAuthenticationException( ex ) ) {
throw;
}
StringBuilder errMsgB;
errMsgB << "can't authenticate against replica set node "
<< _lastSlaveOkHost.toString();
lastNodeStatus = ex.toStatus( errMsgB.str() );
LOG(1) << lastNodeStatus.reason() << endl;
invalidateLastSlaveOkCache();
}
}
if ( lastNodeStatus.isOK() ) {
StringBuilder assertMsgB;
assertMsgB << "Failed to authenticate, no good nodes in " << _getMonitor()->getName();
uasserted( ErrorCodes::NodeNotFound, assertMsgB.str() );
}
else {
uasserted( lastNodeStatus.code(), lastNodeStatus.reason() );
}
}