diff --git a/modules/mol/alg/src/molck.cc b/modules/mol/alg/src/molck.cc
index 8ce012cf783faa396c8efecfd713ba7355db05f3..e2acc287768ce93bf5ba8e5fcdcb6d73e0144e0d 100644
--- a/modules/mol/alg/src/molck.cc
+++ b/modules/mol/alg/src/molck.cc
@@ -1,30 +1,22 @@
-// #include <unistd.h>
-// #include <boost/program_options.hpp>
#include <boost/filesystem/path.hpp>
#include <boost/filesystem/convenience.hpp>
#include <ost/base.hh>
#include <ost/boost_filesystem_helper.hh>
-// #include <ost/platform.hh>
#include <ost/conop/model_check.hh>
#include <ost/conop/conop.hh>
#include <ost/conop/amino_acids.hh>
#include <ost/io/mol/pdb_reader.hh>
-// #include <ost/io/mol/pdb_writer.hh>
#include <ost/io/mol/mmcif_reader.hh>
-// #include <ost/io/io_exception.hh>
#include <ost/conop/nonstandard.hh>
#include <ost/mol/alg/molck.hh>
-// #if defined(__APPLE__)
-// #include <mach-o/dyld.h>
-// #endif
-// using namespace ost;
+
using namespace ost::conop;
using namespace ost::mol;
using namespace ost::io;
-// namespace po=boost::program_options;
namespace fs=boost::filesystem;
+
EntityHandle ost::mol::alg::molck::load_x(const String& file, const IOProfile& profile)
{
try {
@@ -135,7 +127,8 @@ EntityHandle ost::mol::alg::molck::MapNonStandardResidues(EntityHandle& ent, Com
return new_ent;
}
-void ost::mol::alg::molck::RemoveAtoms(EntityHandle& ent,
+void ost::mol::alg::molck::RemoveAtoms(
+ EntityHandle& ent,
CompoundLibPtr lib,
bool rm_unk_atoms,
bool rm_non_std,
@@ -231,4 +224,53 @@ void ost::mol::alg::molck::CleanUpElementColumn(EntityHandle& ent, CompoundLibPt
}
}
}
-}
\ No newline at end of file
+}
+
+void ost::mol::alg::molck::Molck(
+ ost::mol::EntityHandle& ent,
+ ost::conop::CompoundLibPtr lib,
+ const ost::mol::alg::molck::MolckSettings& settings=ost::mol::alg::molck::MolckSettings()){
+ if (settings.map_nonstd_res) {
+ ent = ost::mol::alg::molck::MapNonStandardResidues(ent, lib);
+ }
+ ost::mol::alg::molck::RemoveAtoms(ent,
+ lib,
+ settings.rm_unk_atoms,
+ settings.rm_non_std,
+ settings.rm_hyd_atoms,
+ settings.rm_oxt_atoms,
+ settings.rm_zero_occ_atoms,
+ settings.colored);
+ if (settings.assign_elem) {
+ ost::mol::alg::molck::CleanUpElementColumn(ent, lib);
+ }
+}
+
+// ost::mol::EntityHandle ost::mol::alg::molck::Molck(
+// String& file,
+// ost::conop::CompoundLibPtr lib,
+// const ost::mol::alg::molck::MolckSettings& settings=ost::mol::alg::molck::MolckSettings()){
+// IOProfile prof;
+// prof.fault_tolerant=true;
+// EntityHandle ent = ost::mol::alg::molck::load_x(file, prof);
+// if (!ent.IsValid()) {
+// throw std::runtime_error("Entity is invalid!");
+// }
+
+// if (settings.map_nonstd_res) {
+// ent = ost::mol::alg::molck::MapNonStandardResidues(ent, lib);
+// }
+// ost::mol::alg::molck::RemoveAtoms(ent,
+// lib,
+// settings.rm_unk_atoms,
+// settings.rm_non_std,
+// settings.rm_hyd_atoms,
+// settings.rm_oxt_atoms,
+// settings.rm_zero_occ_atoms,
+// settings.colored);
+// if (settings.assign_elem) {
+// ost::mol::alg::molck::CleanUpElementColumn(ent, lib);
+// }
+
+// return ent;
+// }
\ No newline at end of file
diff --git a/modules/mol/alg/src/molck.hh b/modules/mol/alg/src/molck.hh
index 4f7f75fccf93824515fe6c75f71e172d4f24632f..0664ea7960d2188d1263d63e892a3ce2b1e16efc 100644
--- a/modules/mol/alg/src/molck.hh
+++ b/modules/mol/alg/src/molck.hh
@@ -5,9 +5,35 @@
namespace ost { namespace mol{ namespace alg{ namespace molck {
struct MolckSettings;
+
+struct MolckSettings{
+
+ bool rm_unk_atoms;
+ bool rm_non_std;
+ bool rm_hyd_atoms;
+ bool rm_oxt_atoms;
+ bool rm_zero_occ_atoms;
+ bool colored;
+ bool map_nonstd_res;
+ bool assign_elem;
+
+ MolckSettings(): rm_unk_atoms(false), // Remove unknown and atoms not following the nomenclature
+ rm_non_std(false), // Remove all residues not one of the 20 standard amino acids
+ rm_hyd_atoms(true), // Remove hydrogen atoms
+ rm_oxt_atoms(false), // Remove terminal oxygens
+ rm_zero_occ_atoms(false), // Remove atoms with zero occupancy
+ colored(false), // Whether the output should be colored
+ map_nonstd_res(true), // Map non standard residues back to standard ones (e.g.: MSE->MET,SEP->SER,etc.)
+ assign_elem(true){} // Clean up element column
+
+};
+
ost::mol::EntityHandle load_x(const String& file, const ost::io::IOProfile& profile);
+
ost::conop::CompoundLibPtr load_compound_lib(const String& custom_path);
+
ost::mol::EntityHandle MapNonStandardResidues(ost::mol::EntityHandle& ent, ost::conop::CompoundLibPtr lib);
+
void RemoveAtoms(ost::mol::EntityHandle& ent,
ost::conop::CompoundLibPtr lib,
bool rm_unk_atoms,
@@ -16,19 +42,13 @@ void RemoveAtoms(ost::mol::EntityHandle& ent,
bool rm_oxt_atoms,
bool rm_zero_occ_atoms,
bool colored=true);
+
void CleanUpElementColumn(ost::mol::EntityHandle& ent, ost::conop::CompoundLibPtr lib);
-struct MolckSettings{
-
- String rm;
- String color;
- bool map_nonstd_res;
- bool assign_elem;
+void Molck(ost::mol::EntityHandle& ent, ost::conop::CompoundLibPtr lib, const MolckSettings& settings);
+// void Molck(ost::mol::EntityHandle& ent, String& custom_path, const MolckSettings& settings);
+// ost::mol::EntityHandle Molck(String& file, ost::conop::CompoundLibPtr lib, const MolckSettings& settings);
+// ost::mol::EntityHandle Molck(String& file, String& custom_path, const MolckSettings& settings);
- MolckSettings(): rm("hyd"), // atoms to be removed
- color("auto"), // whether the output should be colored
- map_nonstd_res(true), // map non standard residues back to standard ones (e.g.: MSE->MET,SEP->SER,etc.)
- assign_elem(true){} // clean up element column
-};
}}}} // namespace
diff --git a/tools/molck/main.cc b/tools/molck/main.cc
index 882c3e36ab108cf7790392cc0ed37eeb85c9d31b..db66fe9428c14070f567c7936a9ea43dc551cc03 100644
--- a/tools/molck/main.cc
+++ b/tools/molck/main.cc
@@ -5,14 +5,9 @@
#include <ost/base.hh>
#include <ost/boost_filesystem_helper.hh>
#include <ost/platform.hh>
-#include <ost/conop/model_check.hh>
#include <ost/conop/conop.hh>
-#include <ost/conop/amino_acids.hh>
-#include <ost/io/mol/pdb_reader.hh>
#include <ost/io/mol/pdb_writer.hh>
-#include <ost/io/mol/mmcif_reader.hh>
#include <ost/io/io_exception.hh>
-#include <ost/conop/nonstandard.hh>
#include <ost/mol/alg/molck.hh>
#if defined(__APPLE__)
#include <mach-o/dyld.h>
@@ -63,19 +58,12 @@ int main(int argc, char *argv[])
}
IOProfile prof;
prof.fault_tolerant=true;
+ MolckSettings settings;
String rm;
String color;
- bool colored = false;
- bool rm_unk_atoms=false;
- bool rm_hyd_atoms=false;
- bool rm_non_std=false;
- bool rm_oxt_atoms=false;
- bool rm_zero_occ_atoms=false;
bool write_to_stdout = false;
bool write_to_file = false;
- bool map_nonstd_res = false;
- bool assign_elem = false;
String output_blueprint_string;
String custom_path="";
@@ -123,24 +111,24 @@ int main(int argc, char *argv[])
output_blueprint_string = vm["out"].as<String>();
}
if (vm.count("map-nonstd")) {
- map_nonstd_res = true;
+ settings.map_nonstd_res = true;
}
if (vm.count("fix-ele")) {
- assign_elem = true;
+ settings.assign_elem = true;
}
std::vector<StringRef> rms=StringRef(rm.c_str(), rm.size()).split(',');
for (size_t i=0; i<rms.size(); ++i) {
if (rms[i] == StringRef("unk", 3)) {
- rm_unk_atoms = true;
+ settings.rm_unk_atoms = true;
} else if (rms[i] == StringRef("nonstd", 6)) {
- rm_non_std = true;
+ settings.rm_non_std = true;
} else if (rms[i] == StringRef("hyd", 3)) {
- rm_hyd_atoms = true;
+ settings.rm_hyd_atoms = true;
} else if (rms[i] == StringRef("oxt", 3)) {
- rm_oxt_atoms = true;
+ settings.rm_oxt_atoms = true;
} else if (rms[i] == StringRef("zeroocc", 7)) {
- rm_zero_occ_atoms = true;
+ settings.rm_zero_occ_atoms = true;
} else {
std::cerr << "unknown value to remove '" << rms[i] << "'" << std::endl;
usage();
@@ -148,11 +136,11 @@ int main(int argc, char *argv[])
}
}
if (color=="auto") {
- colored = isatty(STDERR_FILENO);
+ settings.colored = isatty(STDERR_FILENO);
} else if (color == "on" || color == "1" || color == "yes") {
- colored = true;
+ settings.colored = true;
} else if (color == "off" || color == "0" || color == "no") {
- colored = false;
+ settings.colored = false;
} else {
usage();
exit(-1);
@@ -163,22 +151,8 @@ int main(int argc, char *argv[])
if (!ent.IsValid()) {
continue;
}
- if (map_nonstd_res) {
- ent = MapNonStandardResidues(ent, lib);
- }
-
- RemoveAtoms(ent,
- lib,
- rm_unk_atoms,
- rm_non_std,
- rm_hyd_atoms,
- rm_oxt_atoms,
- rm_zero_occ_atoms,
- colored);
- if (assign_elem) {
- CleanUpElementColumn(ent, lib);
- }
+ Molck(ent, lib, settings);
if (write_to_stdout) {
PDBWriter writer(std::cout, prof);