diff --git a/modules/mol/alg/src/molck.cc b/modules/mol/alg/src/molck.cc
index b3cfe016c342f9edbf87eca2a8b1d3524515c285..1eaf1988a9ac54947e639ad3615077eba5a959d0 100644
--- a/modules/mol/alg/src/molck.cc
+++ b/modules/mol/alg/src/molck.cc
@@ -5,12 +5,14 @@
#include <ost/conop/rule_based.hh>
#include <ost/mol/alg/molck.hh>
#include <ost/message.hh>
+#include <ost/log.hh>
using namespace ost::conop;
using namespace ost::mol;
+namespace ost{ namespace mol{ namespace alg{
-void ost::mol::alg::MapNonStandardResidues(EntityHandle& ent, CompoundLibPtr lib) {
+void MapNonStandardResidues(EntityHandle& ent, CompoundLibPtr lib, bool log_diags) {
// TODO: Maybe it is possible to make it in-place operation
if(!lib) {
@@ -45,18 +47,17 @@ void ost::mol::alg::MapNonStandardResidues(EntityHandle& ent, CompoundLibPtr lib
continue;
}
ResidueHandle dest_res = new_edi.AppendResidue(new_chain,OneLetterCodeToResidueName(compound->GetOneLetterCode()),r->GetNumber());
- ost::mol::alg::CopyResidue(*r,dest_res,new_edi,lib);
+ CopyResidue(*r,dest_res,new_edi,lib);
}
}
}
ent = new_ent;
// Since we didn't do it in-place: reprocess the new entity
RuleBasedProcessor pr(lib);
- pr.Process(ent);
+ pr.Process(ent, log_diags);
}
-void ost::mol::alg::RemoveAtoms(
- EntityHandle& ent,
+void RemoveAtoms(EntityHandle& ent,
CompoundLibPtr lib,
bool rm_unk_atoms,
bool rm_non_std,
@@ -73,29 +74,33 @@ void ost::mol::alg::RemoveAtoms(
Diagnostics diags;
Checker checker(lib, ent, diags);
if (rm_zero_occ_atoms) {
- std::cerr << "removing atoms with zero occupancy" << std::endl;
+ LOG_INFO("removing atoms with zero occupancy");
int zremoved=0;
AtomHandleList zero_atoms=checker.GetZeroOccupancy();
for (AtomHandleList::const_iterator i=zero_atoms.begin(), e=zero_atoms.end(); i!=e; ++i) {
edi.DeleteAtom(*i);
zremoved++;
}
- std::cerr << " --> removed " << zremoved << " atoms with zero occupancy" << std::endl;
+ std::stringstream ss;
+ ss << " --> removed " << zremoved << " atoms with zero occupancy";
+ LOG_INFO(ss.str());
}
if (rm_hyd_atoms) {
- std::cerr << "removing hydrogen atoms" << std::endl;
+ LOG_INFO("removing hydrogen atoms");
int hremoved=0;
AtomHandleList hyd_atoms=checker.GetHydrogens();
for (AtomHandleList::const_iterator i=hyd_atoms.begin(), e=hyd_atoms.end(); i!=e; ++i) {
edi.DeleteAtom(*i);
hremoved++;
}
- std::cerr << " --> removed " << hremoved << " hydrogen atoms" << std::endl;
+ std::stringstream ss;
+ ss << " --> removed " << hremoved << " hydrogen atoms";
+ LOG_INFO(ss.str());
}
if (rm_oxt_atoms) {
- std::cerr << "removing OXT atoms" << std::endl;
+ LOG_INFO("removing OXT atoms");
int oremoved=0;
AtomHandleList atoms=ent.GetAtomList();
for (AtomHandleList::const_iterator i=atoms.begin(), e=atoms.end(); i!=e; ++i) {
@@ -104,7 +109,9 @@ void ost::mol::alg::RemoveAtoms(
oremoved++;
}
}
- std::cerr << " --> removed " << oremoved << " OXT atoms" << std::endl;
+ std::stringstream ss;
+ ss << " --> removed " << oremoved << " OXT atoms";
+ LOG_INFO(ss.str());
}
checker.CheckForCompleteness();
@@ -113,28 +120,29 @@ void ost::mol::alg::RemoveAtoms(
for (Diagnostics::const_diag_iterator
j = diags.diags_begin(), e = diags.diags_end(); j != e; ++j) {
const Diag* diag=*j;
- std::cerr << diag->Format(colored);
+ std::stringstream ss;
+ ss << diag->Format(colored);
switch (diag->GetType()) {
case DIAG_UNK_ATOM:
if (rm_unk_atoms) {
edi.DeleteAtom(diag->GetAtom(0));
- std::cerr << " --> removed ";
+ ss << " --> removed ";
}
break;
case DIAG_NONSTD_RESIDUE:
if (rm_non_std) {
edi.DeleteResidue(diag->GetResidue(0));
- std::cerr << " --> removed ";
+ ss << " --> removed ";
}
break;
default:
break;
}
- std::cerr << std::endl;
+ LOG_INFO(ss.str());
}
}
-void ost::mol::alg::CleanUpElementColumn(EntityHandle& ent, CompoundLibPtr lib){
+void CleanUpElementColumn(EntityHandle& ent, CompoundLibPtr lib){
if(!lib) {
throw ost::Error("Require valid compound library!");
@@ -164,20 +172,19 @@ void ost::mol::alg::CleanUpElementColumn(EntityHandle& ent, CompoundLibPtr lib){
}
}
-void ost::mol::alg::Molck(
- ost::mol::EntityHandle& ent,
+void Molck(ost::mol::EntityHandle& ent,
ost::conop::CompoundLibPtr lib,
- const ost::mol::alg::MolckSettings& settings=ost::mol::alg::MolckSettings()){
+ const MolckSettings& settings = MolckSettings()){
if(!lib) {
throw ost::Error("Require valid compound library!");
}
if (settings.map_nonstd_res) {
- ost::mol::alg::MapNonStandardResidues(ent, lib);
+ MapNonStandardResidues(ent, lib, false);
}
- ost::mol::alg::RemoveAtoms(ent,
- lib,
+
+ RemoveAtoms(ent, lib,
settings.rm_unk_atoms,
settings.rm_non_std,
settings.rm_hyd_atoms,
@@ -185,7 +192,8 @@ void ost::mol::alg::Molck(
settings.rm_zero_occ_atoms,
settings.colored);
if (settings.assign_elem) {
- ost::mol::alg::CleanUpElementColumn(ent, lib);
+ CleanUpElementColumn(ent, lib);
}
}
+}}} // ns
\ No newline at end of file
diff --git a/modules/mol/alg/src/molck.hh b/modules/mol/alg/src/molck.hh
index d61e0218678bd07fba0e828fdf0f901dd69977e5..b25b1b81e3a428c132af56282a771f35e9303024 100644
--- a/modules/mol/alg/src/molck.hh
+++ b/modules/mol/alg/src/molck.hh
@@ -80,7 +80,8 @@ struct MolckSettings{
};
void MapNonStandardResidues(ost::mol::EntityHandle& ent,
- ost::conop::CompoundLibPtr lib);
+ ost::conop::CompoundLibPtr lib,
+ bool log_diags = true);
void RemoveAtoms(ost::mol::EntityHandle& ent,
ost::conop::CompoundLibPtr lib,
diff --git a/tools/molck/main.cc b/tools/molck/main.cc
index ef2d77c207213957a20d2d2d460da74fa0280b73..8507a1895b2d6f13d2aeecec94a826a392ce0dd0 100644
--- a/tools/molck/main.cc
+++ b/tools/molck/main.cc
@@ -11,6 +11,7 @@
#include <ost/io/mol/mmcif_reader.hh>
#include <ost/io/io_exception.hh>
#include <ost/mol/alg/molck.hh>
+#include <ost/log.hh>
#if defined(__APPLE__)
#include <mach-o/dyld.h>
#endif
@@ -47,7 +48,7 @@ const char* USAGE=
void usage()
{
- std::cerr << USAGE << std::endl;
+ LOG_INFO(USAGE);
exit(0);
}
@@ -69,12 +70,14 @@ EntityHandle load_x(const String& file, const IOProfile& profile)
reader.Import(ent);
return ent;
}
- std::cerr << "ERROR: '" << file << "' does not contain any ATOM records. "
- << "Are you sure this is a PDB file?" << std::endl;
+ std::stringstream ss;
+ ss << "ERROR: '" << file << "' does not contain any ATOM records. "
+ << "Are you sure this is a PDB file?";
+ LOG_INFO(ss.str());
return EntityHandle();
}
} catch (std::exception& e) {
- std::cerr << "ERROR: " << e.what() << std::endl;
+ LOG_ERROR("ERROR: " << e.what());
return EntityHandle();
}
}
@@ -86,7 +89,7 @@ ost::conop::CompoundLibPtr load_compound_lib(const String& custom_path)
if (fs::exists(custom_path)) {
return ost::conop::CompoundLib::Load(custom_path);
} else {
- std::cerr << "Could not find compounds.chemlib at the provided location, trying other options" << std::endl;
+ LOG_INFO("Could not find compounds.chemlib at the provided location, trying other options");
}
}
if (fs::exists("compounds.chemlib")) {
@@ -105,8 +108,8 @@ ost::conop::CompoundLibPtr load_compound_lib(const String& custom_path)
exe_path = std::string( result, (count > 0) ? count : 0 );
#endif
if (exe_path.empty()) {
- std::cerr << "Could not determine the path of the molck executable. Will only "
- "look for compounds.chemlib in the current working directory" << std::endl;
+ LOG_INFO("Could not determine the path of the molck executable. Will only "
+ "look for compounds.chemlib in the current working directory");
} else {
fs::path path_and_exe(exe_path);
fs::path path_only=path_and_exe.branch_path();
@@ -120,7 +123,7 @@ ost::conop::CompoundLibPtr load_compound_lib(const String& custom_path)
}
}
if (!lib) {
- std::cerr << "Could not load compounds.chemlib" << std::endl;
+ LOG_ERROR("Could not load compounds.chemlib");
exit(-1);
}
return ost::conop::CompoundLibPtr();
@@ -129,6 +132,9 @@ ost::conop::CompoundLibPtr load_compound_lib(const String& custom_path)
int main(int argc, char *argv[])
{
+ // setup logging
+ ost::Logger::Instance().PushVerbosityLevel(ost::Logger::INFO);
+
if (argc<2) {
usage();
}
@@ -166,7 +172,7 @@ int main(int argc, char *argv[])
options(desc).positional(p).run(),
vm);
} catch (std::exception& e) {
- std::cerr << e.what() << std::endl;
+ LOG_ERROR(e.what());
usage();
exit(-1);
}
@@ -206,7 +212,9 @@ int main(int argc, char *argv[])
} else if (rms[i] == StringRef("zeroocc", 7)) {
settings.rm_zero_occ_atoms = true;
} else {
- std::cerr << "unknown value to remove '" << rms[i] << "'" << std::endl;
+ std::stringstream ss;
+ ss << "unknown value to remove '" << rms[i] << "'";
+ LOG_ERROR(ss.str());
usage();
exit(-1);
}
@@ -246,8 +254,7 @@ int main(int argc, char *argv[])
try {
fs::path out_path(output_blueprint_string_copy);
if (out_path.has_parent_path() && !exists(out_path.parent_path())) {
- std::cerr << "Output path does not exist: "
- << output_blueprint_string_copy << std::endl;
+ LOG_ERROR("Output path does not exist: " + output_blueprint_string_copy);
exit(-1);
}
} catch (std::exception& e) {
@@ -255,15 +262,14 @@ int main(int argc, char *argv[])
size_t perden = String(e.what()).find("Permission denied");
if (perden != String::npos) {
- std::cerr << "Cannot write into output directory: "
- << output_blueprint_string_copy << std::endl;
+ LOG_ERROR("Cannot write into output directory: " + output_blueprint_string_copy);
exit(-1);
} else {
- std::cerr << e.what() << std::endl;
+ LOG_ERROR(e.what());
exit(-1);
}
}
- std::cerr << "Writing out file: " << output_blueprint_string_copy << std::endl;
+ LOG_INFO("Writing out file: " + output_blueprint_string_copy);
PDBWriter writer(output_blueprint_string_copy, prof);
writer.Write(ent);
}