diff --git a/modules/conop/src/heuristic_builder.cc b/modules/conop/src/heuristic_builder.cc
index 3fbff0b9deed63803ab01f5bb049ebbb0010dbc8..eda01852e25d0437367738ac21bc77cc60b7311a 100644
--- a/modules/conop/src/heuristic_builder.cc
+++ b/modules/conop/src/heuristic_builder.cc
@@ -119,8 +119,8 @@ HeuristicBuilder::HeuristicBuilder():
heuristic_connect::CONN_DEF_ENTRY& def_entry = heuristic_connect::def_entry_table[ec];
detail::ConnResEntry entry(def_entry.abbrev, def_entry.single,
def_entry.chem_class);
- LOG_DEBUG("creating table entry for " << def_entry.abbrev);
- LOG_DEBUG("working on bond entries");
+ LOG_TRACE("creating table entry for " << def_entry.abbrev);
+ LOG_TRACE("working on bond entries");
for (int xx=0;xx<def_entry.name_count;++xx) {
String name=def_entry.name_list[xx];
if (name!="OXT")
@@ -152,9 +152,9 @@ HeuristicBuilder::HeuristicBuilder():
else if(conn_nam[1]==String("-")) { entry.SetPrev(conn_nam[0]);}
else if(conn_nam[0]==String("+")) { entry.SetNext(conn_nam[1]);}
else if(conn_nam[1]==String("+")) { entry.SetNext(conn_nam[0]);}
- LOG_DEBUG(" " << conn_nam[0] << " " << conn_nam[1]);
+ LOG_TRACE(" " << conn_nam[0] << " " << conn_nam[1]);
} else {
- LOG_DEBUG(" " << conn_nam[0] << " " << conn_nam[1]);
+ LOG_TRACE(" " << conn_nam[0] << " " << conn_nam[1]);
entry.AddConn(conn_nam[0],conn_nam[1]);
}
}
@@ -205,18 +205,18 @@ void HeuristicBuilder::ConnectivityFromAtomNames(const mol::ResidueHandle& res,
mol::AtomHandleList::iterator it2=it1;
++it2;
for (;it2!=atomlist.end();++it2) {
- LOG_DEBUG("checking for atom pair (" << it1->GetName() << ","
+ LOG_TRACE("checking for atom pair (" << it1->GetName() << ","
<< it2->GetName() << ") in connectivity table of "
<< res.GetKey() << "... ");
int conn=centry.Check(it1->GetName(),it2->GetName());
if (conn==1 && this->IsBondFeasible(*it1, *it2)) {
- LOG_DEBUG( "found");
+ LOG_TRACE( "found");
editor.Connect(*it1,*it2);
} else if(conn==2 && this->IsBondFeasible(*it2, *it1)) {
- LOG_DEBUG( "found (reversed)");
+ LOG_TRACE( "found (reversed)");
editor.Connect(*it2,*it1);
} else {
- LOG_DEBUG( "not found");
+ LOG_TRACE( "not found");
}
}
} else {
@@ -227,7 +227,7 @@ void HeuristicBuilder::ConnectivityFromAtomNames(const mol::ResidueHandle& res,
void HeuristicBuilder::ConnectAtomsOfResidue(mol::ResidueHandle res)
{
- LOG_DEBUG("HeuristicBuilder: ConnectAtomsOfResidue on " << res.GetKey() << " " << res.GetNumber());
+ LOG_TRACE("HeuristicBuilder: ConnectAtomsOfResidue on " << res.GetKey() << " " << res.GetNumber());
mol::AtomHandleList atomlist = res.GetAtomList();
mol::AtomHandleList unk_atomlist;
@@ -237,7 +237,7 @@ void HeuristicBuilder::ConnectAtomsOfResidue(mol::ResidueHandle res)
for(mol::AtomHandleList::iterator it=atomlist.begin();it!=atomlist.end();++it) {
ss << " " << it->GetName() << " @" << it->GetPos();
}
- LOG_DEBUG(ss.str());
+ LOG_TRACE(ss.str());
#endif
std::pair<detail::ConnResEntry,bool> ret = LookupResEntry(res.GetKey());
@@ -248,11 +248,11 @@ void HeuristicBuilder::ConnectAtomsOfResidue(mol::ResidueHandle res)
for(mol::AtomHandleList::iterator it1=unk_atomlist.begin();
it1!=unk_atomlist.end();
++it1) {
- LOG_DEBUG( "atom " << it1->GetName() << " not found, using distance based connect");
+ LOG_TRACE( "atom " << it1->GetName() << " not found, using distance based connect");
Builder::DistanceBasedConnect(*it1);
}
} else {
- LOG_DEBUG("no residue entry found, using distance based connect");
+ LOG_TRACE("no residue entry found, using distance based connect");
for(mol::AtomHandleList::iterator it1=atomlist.begin();
it1!=atomlist.end();
++it1) {
@@ -270,16 +270,16 @@ void ConnectPrevNext(HeuristicBuilder* builder,mol::ResidueHandle res0,
static String fname=flag ? "HeuristicBuilder: ConnectNextXCS" : "HeuristicBuilder: ConnectPrevXCS";
if(!res0) return; // return if invalid
mol::XCSEditor editor=res0.GetEntity().EditXCS(mol::BUFFERED_EDIT);
- LOG_DEBUG(fname << " on " << res0.GetKey() << " " << res0.GetNumber());
+ LOG_TRACE(fname << " on " << res0.GetKey() << " " << res0.GetNumber());
if(!res1) {
// auto-detect prev or next residue in chain
// and perform sequence check
if(flag) {
- LOG_DEBUG(fname << " autodecting next residue");
+ LOG_TRACE(fname << " autodecting next residue");
res1 = res0.GetChain().GetNext(res0);
} else {
- LOG_DEBUG(fname << " autodecting next residue");
+ LOG_TRACE(fname << " autodecting next residue");
res1 = res0.GetChain().GetPrev(res0);
}
} else {
@@ -292,7 +292,7 @@ void ConnectPrevNext(HeuristicBuilder* builder,mol::ResidueHandle res0,
}
if(!res1) return; // ignore if prev/next residue is invalid
- LOG_DEBUG(fname << " found second residue " << res1.GetKey()
+ LOG_TRACE(fname << " found second residue " << res1.GetKey()
<< " " << res1.GetNumber());
std::pair<detail::ConnResEntry,bool> res0_ret = builder->LookupResEntry(res0.GetKey());
@@ -300,7 +300,7 @@ void ConnectPrevNext(HeuristicBuilder* builder,mol::ResidueHandle res0,
if(!res0_ret.second) {
if(res0.FindAtom("N") && res0.FindAtom("CA") && res0.FindAtom("C")) {
- LOG_DEBUG("using default peptide for " << res0.GetKey());
+ LOG_TRACE("using default peptide for " << res0.GetKey());
res0_ret.first=builder->DefaultPeptide();
res0_ret.second=true;
}
@@ -308,7 +308,7 @@ void ConnectPrevNext(HeuristicBuilder* builder,mol::ResidueHandle res0,
if(!res1_ret.second) {
if(res1.FindAtom("N") && res1.FindAtom("CA") && res1.FindAtom("C")) {
- LOG_DEBUG("using default peptide for " << res1.GetKey());
+ LOG_TRACE("using default peptide for " << res1.GetKey());
res1_ret.first=builder->DefaultPeptide();
res1_ret.second=true;
}
@@ -321,13 +321,13 @@ void ConnectPrevNext(HeuristicBuilder* builder,mol::ResidueHandle res0,
String res1_atom_name = res1_centry.GetNext();
if(res0_atom_name.empty() || res1_atom_name.empty()) return;
- LOG_DEBUG(fname << ": looking up atom names " << res0_atom_name << " " << res1_atom_name);
+ LOG_TRACE(fname << ": looking up atom names " << res0_atom_name << " " << res1_atom_name);
// lookup both atoms in their respective residues
mol::AtomHandle res0_atom = res0.FindAtom(res0_atom_name);
mol::AtomHandle res1_atom = res1.FindAtom(res1_atom_name);
if(res0_atom && res1_atom) {
- LOG_DEBUG(fname << ": found atoms, connecting");
+ LOG_TRACE(fname << ": found atoms, connecting");
if(flag) {
if (builder->DoesPeptideBondExist(res0_atom, res1_atom)) {
editor.Connect(res0_atom,res1_atom);
@@ -405,11 +405,11 @@ void HeuristicBuilder::AssignTorsionsToResidue(mol::ResidueHandle res)
mol::TorsionHandle th = editor.AddTorsion(tel[ti].name, ah[0], ah[1],
ah[2], ah[3]);
if(th) {
- LOG_DEBUG("added torsion entry for " << tel[ti].a[0] << " "
+ LOG_TRACE("added torsion entry for " << tel[ti].a[0] << " "
<< tel[ti].a[1] << " " << tel[ti].a[2] << " "
<< tel[ti].a[3]);
} else {
- LOG_DEBUG("no torsion entry for " << tel[ti].a[0] << " "
+ LOG_TRACE("no torsion entry for " << tel[ti].a[0] << " "
<< tel[ti].a[1] << " " << tel[ti].a[2]
<< " " << tel[ti].a[3]);
}
@@ -469,10 +469,10 @@ std::pair<detail::ConnResEntry,bool> HeuristicBuilder::LookupResEntry(const mol:
detail::ConnResEntryMap::iterator pos = emap_.find(key);
if(pos!=emap_.end()) {
- LOG_DEBUG("reskey '" << key << "' found in connectivity map");
+ LOG_TRACE("reskey '" << key << "' found in connectivity map");
return std::make_pair(pos->second,true);
}
- LOG_DEBUG("reskey '" << key << "' not found connectivity map");
+ LOG_TRACE("reskey '" << key << "' not found connectivity map");
return std::make_pair(dummy,false);
}
diff --git a/modules/io/src/mol/entity_io_mae_handler.cc b/modules/io/src/mol/entity_io_mae_handler.cc
index 643630f8abcc567466777a8a2becac8e14ed6445..c1c477c3a3a6e1c159f8ec6b07c444d0a4717009 100644
--- a/modules/io/src/mol/entity_io_mae_handler.cc
+++ b/modules/io/src/mol/entity_io_mae_handler.cc
@@ -32,6 +32,7 @@
#include <boost/algorithm/string.hpp>
#include <boost/format.hpp>
#include <boost/regex.hpp>
+#include <boost/shared_array.hpp>
#include <ost/log.hh>
#include <ost/conop/conop.hh>
@@ -48,41 +49,6 @@ namespace ost { namespace io {
using boost::format;
- namespace {
-
- std::vector<std::string> tokenize(const std::string& line)
- {
- std::vector<std::string> nrvo;
- bool in_string=false;
- int p0=0;
- for(size_t p1=1;p1<line.size();++p1) {
- if(in_string) {
- if(line[p1]=='"') {
- in_string=false;
- nrvo.push_back(std::string(line.substr(p0,p1-p0)));
- ++p1;
- p0=p1;
- while(isspace(line[p1]) && p1<line.size()) {++p0;++p1;}
- --p0; --p1;
- }
- } else {
- if(isspace(line[p1])) {
- nrvo.push_back(std::string(line.substr(p0+1,p1-p0-1)));
- ++p1;
- p0=p1;
- while(isspace(line[p1]) && p1<line.size()) {++p0;++p1;}
- --p0; --p1;
- } else if(line[p1]=='"') {
- in_string=true;
- p0=p1+1;
- }
- }
- }
- return nrvo;
- }
-
- }
-
MAEReader::MAEReader(const boost::filesystem::path& loc):
curr_chain_(),
curr_residue_(),
@@ -106,6 +72,7 @@ void MAEReader::Import(mol::EntityHandle& ent)
static const boost::regex r_ct_block("f_m_ct +\\{");
static const boost::regex r_atom_block("m_atom\\[.*\\] +\\{");
static const boost::regex r_delim(":::");
+ static const boost::regex r_end(" *\\} *");
String line;
bool in_ct_block=false;
@@ -121,13 +88,15 @@ void MAEReader::Import(mol::EntityHandle& ent)
int i_chain_name=-1;
mol::XCSEditor editor=ent.EditXCS(mol::BUFFERED_EDIT);
+
+ boost::shared_array<char> xline(new char[512]);
while(std::getline(in_,line)) {
- line = boost::trim_copy(line);
+ //line = boost::trim_copy(line);
if(in_ct_block) {
if(in_atom_block) {
if(parsing_atoms) {
- if(boost::regex_match(line,r_delim)) {
+ if(boost::regex_search(line,r_delim)) {
LOG_TRACE( "stopping atom parsing" );
parsing_atoms=false;
prop_list.clear();
@@ -140,23 +109,14 @@ void MAEReader::Import(mol::EntityHandle& ent)
i_chain_name=-1;
} else {
// parsing atom line
- std::vector<std::string> tokens=tokenize(line);
- for(size_t i=0;i<tokens.size();++i) {
- LOG_TRACE( "[" << tokens[i] << "] ");
- }
- LOG_TRACE("");
-
- add_atom(ent,editor,
- i_atom_name>=0 && i_atom_name<(int)tokens.size() ? tokens[i_atom_name] : "X",
- i_atom_xpos>=0 && i_atom_xpos<(int)tokens.size() ? tokens[i_atom_xpos] : "0",
- i_atom_ypos>=0 && i_atom_ypos<(int)tokens.size() ? tokens[i_atom_ypos] : "0",
- i_atom_zpos>=0 && i_atom_zpos<(int)tokens.size() ? tokens[i_atom_zpos] : "0",
- i_res_name>=0 && i_res_name<(int)tokens.size() ? tokens[i_res_name] : "X",
- i_res_num>=0 && i_res_num<(int)tokens.size() ? tokens[i_res_num] : "0",
- i_chain_name>=0 && i_chain_name<(int)tokens.size() ? tokens[i_chain_name] : "X");
+ memset(xline.get(),0,512);
+ strncpy(xline.get(),line.c_str(),511);
+ parse_and_add_atom(ent,editor,xline.get(),line.size(),
+ i_atom_name, i_atom_xpos, i_atom_ypos, i_atom_zpos,
+ i_res_name, i_res_num, i_chain_name);
}
} else { // not parsing atoms
- if(boost::regex_match(line,r_delim)) {
+ if(boost::regex_search(line,r_delim)) {
if(i_atom_name==-1 ||
i_atom_xpos==-1 ||
i_atom_ypos==-1 ||
@@ -167,36 +127,37 @@ void MAEReader::Import(mol::EntityHandle& ent)
}
LOG_TRACE( "starting atom parsing" );
parsing_atoms=true;
- } else if(line[0]=='}') {
+ } else if(boost::regex_search(line,r_end)) {
LOG_TRACE( "exiting atom block" );
in_atom_block=false;
} else {
+ std::string line2=boost::trim_copy(line);
// parsing property line
- if(line[0]!='#') {
+ if(line2[0]!='#') {
int pid=prop_list.size()+1;
- prop_list.push_back(line);
+ prop_list.push_back(line2);
LOG_TRACE( "found property '" << prop_list.back() << "' id=" << pid );
- if(line=="s_m_pdb_atom_name") i_atom_name=pid;
- else if(line=="r_m_x_coord") i_atom_xpos=pid;
- else if(line=="r_m_y_coord") i_atom_ypos=pid;
- else if(line=="r_m_z_coord") i_atom_zpos=pid;
- else if(line=="s_m_pdb_residue_name") i_res_name=pid;
- else if(line=="i_m_residue_number") i_res_num=pid;
- else if(line=="s_m_pdb_segment_name") i_chain_name=pid;
+ if(line2=="s_m_pdb_atom_name") i_atom_name=pid;
+ else if(line2=="r_m_x_coord") i_atom_xpos=pid;
+ else if(line2=="r_m_y_coord") i_atom_ypos=pid;
+ else if(line2=="r_m_z_coord") i_atom_zpos=pid;
+ else if(line2=="s_m_pdb_residue_name") i_res_name=pid;
+ else if(line2=="i_m_residue_number") i_res_num=pid;
+ else if(line2=="s_m_pdb_segment_name") i_chain_name=pid;
}
}
}
} else { // not in atom block
- if(boost::regex_match(line,r_atom_block)) {
+ if(boost::regex_search(line,r_atom_block)) {
LOG_TRACE( "entering atom block" );
in_atom_block=true;
- } else if(line[0]=='}') {
+ } else if(boost::regex_search(line,r_end)) {
LOG_TRACE( "exiting ct block" );
in_ct_block=false;
}
}
} else { // not in ct block
- if(boost::regex_match(line,r_ct_block)) {
+ if(boost::regex_search(line,r_ct_block)) {
LOG_TRACE( "entering ct block" );
in_ct_block=true;
}
@@ -208,27 +169,95 @@ void MAEReader::Import(mol::EntityHandle& ent)
}
-void MAEReader::add_atom(mol::EntityHandle ent,
- mol::XCSEditor& editor,
- const std::string& aname2,
- const std::string& s_axpos,
- const std::string& s_aypos,
- const std::string& s_azpos,
- const std::string& rname2,
- const std::string& s_rnum,
- const std::string& cname2)
+void MAEReader::parse_and_add_atom(mol::EntityHandle ent,
+ mol::XCSEditor& editor,
+ char* line,
+ size_t line_len,
+ int i_atom_name,
+ int i_atom_xpos,
+ int i_atom_ypos,
+ int i_atom_zpos,
+ int i_res_name,
+ int i_res_num,
+ int i_chain_name)
{
- std::string aname=boost::trim_copy(aname2);
- std::string rname=boost::trim_copy(rname2);
- std::string cname=boost::trim_copy(cname2);
+ std::string aname("X");
+ std::string rname("UNK");
+ std::string cname("X");
+ geom::Vec3 apos;
+ int irnum;
+
+ LOG_TRACE("[" << std::string(line) << "]");
+
+ bool in_string=false;
+ char* p0=line;
+ char* p2=line+line_len;
+ while(isspace(*p0) && p0<=p2) ++p0;
+ int tcount=0;
+ for(char* p1=p0+1;p1<p2;++p1) {
+ if(in_string) {
+ if((*p1)=='"') {
+ in_string=false;
+ char* p3=p1;
+ (*p3)='\0';
+ while(isspace(*p0) && p0<=p3) ++p0;
+ while(isspace(*(p3-1)) && p3>p0) --p3;
+ (*p3)='\0';
+ if(tcount==i_atom_name) {
+ aname=std::string(p0);
+ } else if(tcount==i_atom_xpos) {
+ apos[0]=atof(p0);
+ } else if(tcount==i_atom_ypos) {
+ apos[1]=atof(p0);
+ } else if(tcount==i_atom_zpos) {
+ apos[2]=atof(p0);
+ } else if(tcount==i_res_name) {
+ rname=std::string(p0);
+ } else if(tcount==i_res_num) {
+ irnum=atoi(p0);
+ } else if(tcount==i_chain_name) {
+ cname=std::string(p0);
+ }
+ ++tcount;
+ ++p1;
+ p0=p1;
+ while(isspace((*p1)) && p1<p2) {++p0;++p1;}
+ --p0; --p1;
+ }
+ } else { // not instring
+ if(isspace((*p1))) {
+ (*p1)='\0';
+ ++p0;
+ if(tcount==i_atom_name) {
+ aname=std::string(p0);
+ } else if(tcount==i_atom_xpos) {
+ apos[0]=atof(p0);
+ } else if(tcount==i_atom_ypos) {
+ apos[1]=atof(p0);
+ } else if(tcount==i_atom_zpos) {
+ apos[2]=atof(p0);
+ } else if(tcount==i_res_name) {
+ rname=std::string(p0);
+ } else if(tcount==i_res_num) {
+ irnum=atoi(p0);
+ } else if(tcount==i_chain_name) {
+ cname=std::string(p0);
+ }
+ ++tcount;
+ ++p1;
+ p0=p1;
+ while(isspace((*p1)) && p1<p2) {++p0;++p1;}
+ --p0; --p1;
+ } else if((*p1)=='"') {
+ in_string=true;
+ p0=p1+1;
+ }
+ }
+ }
+
std::string ele=aname.empty() ? "X" : aname.substr(0,1);
if(isdigit(ele[0])) ele="H";
- int irnum = atoi(s_rnum.c_str());
- geom::Vec3 apos(atof(s_axpos.c_str()),
- atof(s_aypos.c_str()),
- atof(s_azpos.c_str()));
-
mol::ResidueKey rkey(rname);
mol::ResNum rnum(irnum);
@@ -335,14 +364,8 @@ mol::EntityHandle LoadMAE(const String& file_name)
MAEReader reader(file_name);
mol::EntityHandle ent=mol::CreateEntity();
mol::XCSEditor editor=ent.EditXCS(mol::BUFFERED_EDIT);
- {
- Profile profile("import MAE");
- reader.Import(ent);
- }
- {
- Profile profile("connect all");
- conop::Conopology::Instance().ConnectAll(builder,ent);
- }
+ reader.Import(ent);
+ conop::Conopology::Instance().ConnectAll(builder,ent);
return ent;
}
diff --git a/modules/io/src/mol/entity_io_mae_handler.hh b/modules/io/src/mol/entity_io_mae_handler.hh
index 9a50d6e3f8694329e0c6a02973f2f8c2bf5c6d5b..4921b9dafb0948dccc445f49d976c8db162378c9 100644
--- a/modules/io/src/mol/entity_io_mae_handler.hh
+++ b/modules/io/src/mol/entity_io_mae_handler.hh
@@ -34,14 +34,17 @@ public:
private:
- void add_atom(mol::EntityHandle ent,
- mol::XCSEditor& editor,const std::string& s_aname,
- const std::string& s_axpos,
- const std::string& s_aypos,
- const std::string& s_azpos,
- const std::string& s_rname,
- const std::string& s_rnum,
- const std::string& s_cname);
+ void parse_and_add_atom(mol::EntityHandle ent,
+ mol::XCSEditor& editor,
+ char* line,
+ size_t line_len,
+ int i_atom_name,
+ int i_atom_xpos,
+ int i_atom_ypos,
+ int i_atom_zpos,
+ int i_res_name,
+ int i_res_num,
+ int i_chain_name);
mol::ChainHandle curr_chain_;
mol::ResidueHandle curr_residue_;