diff --git a/modules/mol/alg/pymod/export_molck.cc b/modules/mol/alg/pymod/export_molck.cc
index a54c3678792119943f4a99f5ee9cc210af0a9b3c..643ffbd222e65a7b285d8e78c31417c1ff05b5f5 100644
--- a/modules/mol/alg/pymod/export_molck.cc
+++ b/modules/mol/alg/pymod/export_molck.cc
@@ -22,9 +22,8 @@ using namespace boost::python;
#include <ost/mol/alg/molck.hh>
-using namespace ost::mol::alg::molck;
-
void export_Molck()
{
- def("load_compound_lib", &load_compound_lib, (arg("custom_path")));
+ // def("load_compound_lib", &ost::mol::alg::load_compound_lib,
+ // (arg("custom_path")));
}
diff --git a/modules/mol/alg/src/molck.cc b/modules/mol/alg/src/molck.cc
index e2acc287768ce93bf5ba8e5fcdcb6d73e0144e0d..df931f8ed6474e4530711ba5bfb49ea13366d9e8 100644
--- a/modules/mol/alg/src/molck.cc
+++ b/modules/mol/alg/src/molck.cc
@@ -1,98 +1,14 @@
-#include <boost/filesystem/path.hpp>
-#include <boost/filesystem/convenience.hpp>
-#include <ost/base.hh>
-#include <ost/boost_filesystem_helper.hh>
+#include <ost/mol/xcs_editor.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/mmcif_reader.hh>
#include <ost/conop/nonstandard.hh>
#include <ost/mol/alg/molck.hh>
using namespace ost::conop;
using namespace ost::mol;
-using namespace ost::io;
-namespace fs=boost::filesystem;
-
-EntityHandle ost::mol::alg::molck::load_x(const String& file, const IOProfile& profile)
-{
- try {
- EntityHandle ent = CreateEntity();
- if(file.compare(file.length() - 6, 6, ".mmcif") == 0 ||
- file.compare(file.length() - 4, 4, ".cif") == 0){
- MMCifReader reader(file,ent,profile);
- reader.Parse();
- return ent;
- }
- //if its not mmcif, we assume the file to be in pdb format without even
- //looking at the filename
- else{
- PDBReader reader(file, profile);
- if (reader.HasNext()) {
- 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;
- return EntityHandle();
- }
- } catch (std::exception& e) {
- std::cerr << "ERROR: " << e.what() << std::endl;
- return EntityHandle();
- }
-}
-
-// load compound library, exiting if it could not be found...
-CompoundLibPtr ost::mol::alg::molck::load_compound_lib(const String& custom_path)
-{
- if (custom_path!="") {
- if (fs::exists(custom_path)) {
- return CompoundLib::Load(custom_path);
- } else {
- std::cerr << "Could not find compounds.chemlib at the provided location, trying other options" << std::endl;
- }
- }
- if (fs::exists("compounds.chemlib")) {
- return CompoundLib::Load("compounds.chemlib");
- }
- char result[ 1024 ];
- CompoundLibPtr lib;
- String exe_path;
- #if defined(__APPLE__)
- uint32_t size=1023;
- if (!_NSGetExecutablePath(result, &size)) {
- exe_path=String(result);
- }
- #else
- ssize_t count = readlink( "/proc/self/exe", result, 1024 );
- 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;
- } else {
- fs::path path_and_exe(exe_path);
- fs::path path_only=path_and_exe.branch_path();
- fs::path share_path = path_only.branch_path();
- share_path = share_path / "share" / "openstructure" / "compounds.chemlib";
-
- String share_path_string=BFPathToString(share_path);
-
- if (fs::exists(share_path_string)) {
- return CompoundLib::Load(share_path_string);
- }
- }
- if (!lib) {
- std::cerr << "Could not load compounds.chemlib" << std::endl;
- exit(-1);
- }
- return CompoundLibPtr();
-}
-
-EntityHandle ost::mol::alg::molck::MapNonStandardResidues(EntityHandle& ent, CompoundLibPtr lib) {
+EntityHandle ost::mol::alg::MapNonStandardResidues(EntityHandle& ent, CompoundLibPtr lib) {
EntityHandle new_ent=CreateEntity();
ChainHandleList chains=ent.GetChainList();
XCSEditor new_edi=new_ent.EditXCS();
@@ -127,7 +43,7 @@ EntityHandle ost::mol::alg::molck::MapNonStandardResidues(EntityHandle& ent, Com
return new_ent;
}
-void ost::mol::alg::molck::RemoveAtoms(
+void ost::mol::alg::RemoveAtoms(
EntityHandle& ent,
CompoundLibPtr lib,
bool rm_unk_atoms,
@@ -201,7 +117,7 @@ void ost::mol::alg::molck::RemoveAtoms(
}
}
-void ost::mol::alg::molck::CleanUpElementColumn(EntityHandle& ent, CompoundLibPtr lib){
+void ost::mol::alg::CleanUpElementColumn(EntityHandle& ent, CompoundLibPtr lib){
ChainHandleList chains=ent.GetChainList();
for (ChainHandleList::const_iterator c=chains.begin();c!=chains.end();++c) {
ResidueHandleList residues = c->GetResidueList();
@@ -226,14 +142,14 @@ void ost::mol::alg::molck::CleanUpElementColumn(EntityHandle& ent, CompoundLibPt
}
}
-void ost::mol::alg::molck::Molck(
+void ost::mol::alg::Molck(
ost::mol::EntityHandle& ent,
ost::conop::CompoundLibPtr lib,
- const ost::mol::alg::molck::MolckSettings& settings=ost::mol::alg::molck::MolckSettings()){
+ const ost::mol::alg::MolckSettings& settings=ost::mol::alg::MolckSettings()){
if (settings.map_nonstd_res) {
- ent = ost::mol::alg::molck::MapNonStandardResidues(ent, lib);
+ ent = ost::mol::alg::MapNonStandardResidues(ent, lib);
}
- ost::mol::alg::molck::RemoveAtoms(ent,
+ ost::mol::alg::RemoveAtoms(ent,
lib,
settings.rm_unk_atoms,
settings.rm_non_std,
@@ -242,35 +158,6 @@ void ost::mol::alg::molck::Molck(
settings.rm_zero_occ_atoms,
settings.colored);
if (settings.assign_elem) {
- ost::mol::alg::molck::CleanUpElementColumn(ent, lib);
+ ost::mol::alg::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
+}
\ No newline at end of file
diff --git a/modules/mol/alg/src/molck.hh b/modules/mol/alg/src/molck.hh
index 0664ea7960d2188d1263d63e892a3ce2b1e16efc..1034602e7986498c0306a2577ef892cd688cab8c 100644
--- a/modules/mol/alg/src/molck.hh
+++ b/modules/mol/alg/src/molck.hh
@@ -1,8 +1,7 @@
#include <ost/mol/entity_handle.hh>
-#include <ost/io/io_profile.hh>
#include <ost/conop/compound_lib.hh>
-namespace ost { namespace mol{ namespace alg{ namespace molck {
+namespace ost { namespace mol{ namespace alg {
struct MolckSettings;
@@ -28,10 +27,6 @@ struct MolckSettings{
};
-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,
@@ -46,9 +41,6 @@ void RemoveAtoms(ost::mol::EntityHandle& ent,
void CleanUpElementColumn(ost::mol::EntityHandle& ent, ost::conop::CompoundLibPtr lib);
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);
-}}}} // namespace
+}}} // namespace
diff --git a/tools/molck/main.cc b/tools/molck/main.cc
index db66fe9428c14070f567c7936a9ea43dc551cc03..610c074bfbd6a3e6578b9abd2989ff3fe24e355c 100644
--- a/tools/molck/main.cc
+++ b/tools/molck/main.cc
@@ -7,6 +7,8 @@
#include <ost/platform.hh>
#include <ost/conop/conop.hh>
#include <ost/io/mol/pdb_writer.hh>
+#include <ost/io/mol/pdb_reader.hh>
+#include <ost/io/mol/mmcif_reader.hh>
#include <ost/io/io_exception.hh>
#include <ost/mol/alg/molck.hh>
#if defined(__APPLE__)
@@ -16,7 +18,7 @@ using namespace ost;
using namespace ost::conop;
using namespace ost::mol;
using namespace ost::io;
-using namespace ost::mol::alg::molck;
+using namespace ost::mol::alg;
namespace po=boost::program_options;
namespace fs=boost::filesystem;
@@ -51,6 +53,82 @@ void usage()
exit(0);
}
+EntityHandle load_x(const String& file, const IOProfile& profile)
+{
+ try {
+ EntityHandle ent = CreateEntity();
+ if(file.compare(file.length() - 6, 6, ".mmcif") == 0 ||
+ file.compare(file.length() - 4, 4, ".cif") == 0){
+ MMCifReader reader(file,ent,profile);
+ reader.Parse();
+ return ent;
+ }
+ //if its not mmcif, we assume the file to be in pdb format without even
+ //looking at the filename
+ else{
+ PDBReader reader(file, profile);
+ if (reader.HasNext()) {
+ 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;
+ return EntityHandle();
+ }
+ } catch (std::exception& e) {
+ std::cerr << "ERROR: " << e.what() << std::endl;
+ return EntityHandle();
+ }
+}
+
+// load compound library, exiting if it could not be found...
+CompoundLibPtr load_compound_lib(const String& custom_path)
+{
+ if (custom_path!="") {
+ if (fs::exists(custom_path)) {
+ return CompoundLib::Load(custom_path);
+ } else {
+ std::cerr << "Could not find compounds.chemlib at the provided location, trying other options" << std::endl;
+ }
+ }
+ if (fs::exists("compounds.chemlib")) {
+ return CompoundLib::Load("compounds.chemlib");
+ }
+ char result[ 1024 ];
+ CompoundLibPtr lib;
+ String exe_path;
+ #if defined(__APPLE__)
+ uint32_t size=1023;
+ if (!_NSGetExecutablePath(result, &size)) {
+ exe_path=String(result);
+ }
+ #else
+ ssize_t count = readlink( "/proc/self/exe", result, 1024 );
+ 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;
+ } else {
+ fs::path path_and_exe(exe_path);
+ fs::path path_only=path_and_exe.branch_path();
+ fs::path share_path = path_only.branch_path();
+ share_path = share_path / "share" / "openstructure" / "compounds.chemlib";
+
+ String share_path_string=BFPathToString(share_path);
+
+ if (fs::exists(share_path_string)) {
+ return CompoundLib::Load(share_path_string);
+ }
+ }
+ if (!lib) {
+ std::cerr << "Could not load compounds.chemlib" << std::endl;
+ exit(-1);
+ }
+ return CompoundLibPtr();
+}
+
+
int main(int argc, char *argv[])
{
if (argc<2) {