bool OpNewS::Do(OBBase* pOb, const char* OptionText, OpMap* pmap, OBConversion* pConv)
{
OBMol* pmol = dynamic_cast<OBMol*>(pOb);
if(!pmol)
return false;
// The SMARTS and any other parameters are extracted on the first molecule
// and stored in the static variables vec, inv. The parameter is cleared so that:
// (a) the original -s option in transform.cpp is inactive, and
// (b) the parsing does not have to be done again for multi-molecule files
string txt(pmap->find(GetID())->second); // ID can be "s" or "v"
static vector<string> vec;
static bool inv;
static int nPatternAtoms; //non-zero for exact matches
static OBQuery* query;
static vector<OBQuery*> queries;
vector<OBQuery*>::iterator qiter;
if(!txt.empty())
{
//Set up on first call
tokenize(vec, txt);
inv = GetID()[0]=='v';
if(vec[0][0]=='~')
{
inv = true;
vec[0].erase(0,1);
}
//Interpret as a filename if possible
MakeQueriesFromMolInFile(queries, vec[0], &nPatternAtoms);
if(vec.size()>1 && vec[1]=="exact")
{
if(queries.empty())
{
//Convert SMARTS to SMILES to count number of atoms
OBConversion conv;
OBMol patmol;
if(!conv.SetInFormat("smi") || !conv.ReadString(&patmol, vec[0]))
{
obErrorLog.ThrowError(__FUNCTION__, "Cannot read the parameter of -s option, "
"which has to be valid SMILES when the exact option is used.", obError, onceOnly);
delete pmol;
pConv->SetOneObjectOnly(); //stop conversion
return false;
}
nPatternAtoms = patmol.NumHvyAtoms();
}
}
else
nPatternAtoms = 0;
//disable old versions
pConv->AddOption(GetID(), OBConversion::GENOPTIONS, "");
}
bool match;
//These are a vector of each mapping, each containing atom indxs.
vector<vector<int> > vecatomvec;
vector<vector<int> >* pMappedAtoms = NULL;
OBSmartsPattern sp;
if(nPatternAtoms)
if(pmol->NumHvyAtoms() != nPatternAtoms)
return false;
int imol=0; //index of mol in pattern file
if(!queries.empty()) //filename supplied
{
//match is set true if any of the structures match - OR behaviour
for(qiter=queries.begin();qiter!=queries.end();++qiter, ++imol)
{
OBIsomorphismMapper* mapper = OBIsomorphismMapper::GetInstance(*qiter);
OBIsomorphismMapper::Mappings mappings;
mapper->MapUnique(pmol, mappings);
if( (match = !mappings.empty()) ) // extra parens to indicate truth value
{
OBIsomorphismMapper::Mappings::iterator ita;
OBIsomorphismMapper::Mapping::iterator itb;
for(ita=mappings.begin(); ita!=mappings.end();++ita)//each mapping
{
vector<int> atomvec;
for(itb=ita->begin(); itb!=ita->end();++itb)//each atom index
atomvec.push_back(itb->second+1);
vecatomvec.push_back(atomvec);
atomvec.clear();
}
pMappedAtoms = &vecatomvec;
break;
}
}
}
else //SMARTS supplied
{
if(!sp.Init(vec[0]))
{
string msg = vec[0] + " cannot be interpreted as either valid SMARTS "
"or the name of a file with an extension known to OpenBabel "
"that contains one or more pattern molecules.";
obErrorLog.ThrowError(__FUNCTION__, msg, obError, onceOnly);
delete pmol;
pmol = NULL;
pConv->SetOneObjectOnly(); //stop conversion
return false;
}
if( (match = sp.Match(*pmol)) ) // extra parens to indicate truth value
pMappedAtoms = &sp.GetMapList();
}
if((!match && !inv) || (match && inv))
{
//delete a non-matching mol
delete pmol;
pmol = NULL;
return false;
}
if(!inv && vec.size()>=2 && !vec[1].empty() && !nPatternAtoms)
{
vector<vector<int> >::iterator iter;
if(vec[1]=="extract")
{
//Delete all unmatched atoms. Use only the first match
ExtractSubstruct(pmol, *pMappedAtoms->begin());
return true;
}
// color the substructure if there is a second parameter which is not "exact" or "extract"
// with multiple color parameters use the one corresponding to the query molecule, or the last
if(imol>vec.size()-2)
imol = vec.size()-2;
for(iter=pMappedAtoms->begin();iter!=pMappedAtoms->end();++iter)//each match
AddDataToSubstruct(pmol, *iter, "color", vec[imol+1]);
return true;
}
if(pConv && pConv->IsLast())
{
for(qiter=queries.begin();qiter!=queries.end();++qiter)
delete *qiter;
queries.clear();
}
return true;
}
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();
}
}
int main(int argc, char* argv[])
{
const array<string, 5> SmartsPatterns =
{
"[!#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
};
OBConversion obConversion;
obConversion.SetInFormat("pdbqt");
while (true)
{
vector<array<double, 3>> atoms;
atoms.reserve(80);
stringstream ss;
for (string line; getline(cin, line);)
{
ss << line << endl;
const auto record = line.substr(0, 6);
if (record == "TORSDO") break;
if (record != "ATOM " && record != "HETATM") continue;
atoms.push_back({ stod(line.substr(30, 8)), stod(line.substr(38, 8)), stod(line.substr(46, 8)) });
}
if (atoms.empty()) break;
OBMol obMol;
obConversion.Read(&obMol, &ss);
array<vector<int>, 5> subsets;
for (size_t k = 0; k < 5; ++k)
{
auto& subset = subsets[k];
subset.reserve(atoms.size());
OBSmartsPattern smarts;
smarts.Init(SmartsPatterns[k]);
smarts.Match(obMol);
for (const auto& map : smarts.GetMapList())
{
subset.push_back(map.front() - 1);
}
}
const auto& subset0 = subsets.front();
const auto n = subset0.size();
const auto v = 1.0 / n;
array<double, 3> ctd{};
array<double, 3> cst{};
array<double, 3> fct{};
array<double, 3> ftf{};
for (size_t k = 0; k < 3; ++k)
{
for (const auto i : subset0)
{
const auto& a = atoms[i];
ctd[k] += a[k];
}
ctd[k] *= 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 = atoms[i];
const auto this_dist = dist2(a, 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 = atoms[i];
const auto this_dist = dist2(a, fct);
if (this_dist > ftf_dist)
{
ftf = a;
ftf_dist = this_dist;
}
}
for (const auto& subset : subsets)
{
const auto n = subset.size();
const auto v = 1.0 / n;
for (const auto& rpt : { ctd, cst, fct, ftf })
{
vector<double> dists(n);
for (size_t i = 0; i < n; ++i)
{
dists[i] = sqrt(dist2(atoms[subset[i]], rpt));
}
array<double, 3> m{};
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);
cout.write(reinterpret_cast<char*>(m.data()), sizeof(m));
}
}
}
}