diff --git a/tools/molck/main.cc b/tools/molck/main.cc
index 0e6c3a41d2c18ee4696de5e92592347fa02a45df..3ae8c9a9497c90b70ea792aa8a05ad5ff8113f9c 100644
--- a/tools/molck/main.cc
+++ b/tools/molck/main.cc
@@ -40,8 +40,15 @@ EntityHandle load_x(const String& file, const IOProfile& profile)
}
// load compound library, exiting if it could not be found...
-CompoundLibPtr load_compound_lib()
+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");
}
@@ -71,9 +78,11 @@ CompoundLibPtr load_compound_lib()
String share_path_string=share_path.string();
#else
String share_path_string=share_path.file_string();
- #endif
-
- return CompoundLib::Load(share_path_string);
+ #endif
+
+ if (fs::exists(share_path_string)) {
+ return CompoundLib::Load(share_path_string);
+ }
}
if (!lib) {
std::cerr << "Could not load compounds.chemlib" << std::endl;
@@ -86,6 +95,13 @@ void usage()
{
std::cerr << "usage: molck [options] file1.pdb [file2.pdb [...]]" << std::endl;
std::cerr << "options" << std::endl;
+ std::cerr << " --complib location of the compound library file" << std::endl;
+ std::cerr << " If not provided, the following locations are searched" << std::endl;
+ std::cerr << " in this order:" << std::endl;
+ std::cerr << " 1. Working directory" << std::endl;
+ std::cerr << " 2. OpenStructure standard library location" << std::endl;
+ std::cerr << " (if the executable is part of a standard" << std::endl;
+ std::cerr << " OpenStructure installation)" << std::endl;
std::cerr << " --rm=<a>,<b> remove atoms and residues matching some criteria" << std::endl;
std::cerr << " zeroocc - Remove atoms with zero occupancy" << std::endl;
std::cerr << " hyd - Remove hydrogen atoms" << std::endl;
@@ -95,13 +111,17 @@ void usage()
std::cerr << " unk - Remove unknown atoms and atoms that " << std::endl
<< " are not supposed to be part of a residue" << std::endl;
std::cerr << " --fix-ele clean up element column" << std::endl;
- std::cerr << " --stdout write cleaned files to stdout" << std::endl;
+ std::cerr << " --stdout write cleaned file(s) to stdout" << std::endl;
+ std::cerr << " --fileout=blueprint write cleaned file(s) to disk." << std::endl;
+ std::cerr << " The blueprint is used to generate the output path and" << std::endl;
+ std::cerr << " filemane, substituting % with the original file name" << std::endl;
+ std::cerr << " minus the extension" << std::endl;
std::cerr << " --color=auto|on|off " << std::endl
<< " whether output should be colored" << std::endl;
std::cerr << " --map-nonstd maps modified residues back to the parent amino " << std::endl
<< " acid, e.g. MSE -> MET, SEP -> SER." << std::endl;
exit(0);
-}
+}
int main(int argc, char *argv[])
{
@@ -114,24 +134,29 @@ int main(int argc, char *argv[])
String color;
bool colored = false;
- CompoundLibPtr lib=load_compound_lib();
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="";
+
po::options_description desc("Options");
desc.add_options()
("rm", po::value<String>(&rm)->default_value("hyd"), "atoms to be removed")
("color", po::value<String>(&color)->default_value("auto"),
"whether the output should be colored.")
("files", po::value< std::vector<String> >(), "input file(s)")
- ("stdout", "write cleaned structure to stdout")
+ ("stdout", "write cleaned file(s) to stdout")
+ ("fileout", po::value<String>(&output_blueprint_string), "write cleaned file to output using blueprint to determine path")
("map-nonstd", "map non standard residues back to standard ones (e.g.: MSE->MET,SEP->SER,etc.)")
- ("fix-ele", "insert element")
+ ("fix-ele", "insert element")
+ ("complib", po::value<String>(&custom_path)->default_value(""),"location of the compound library file")
;
po::positional_options_description p;
p.add("files", -1);
@@ -154,9 +179,16 @@ int main(int argc, char *argv[])
usage();
exit(-1);
}
+ if (vm.count("complib")) {
+ custom_path = vm["complib"].as<String>();
+ }
if (vm.count("stdout")) {
write_to_stdout = true;
}
+ if (vm.count("fileout")) {
+ write_to_file = true;
+ output_blueprint_string = vm["fileout"].as<String>();
+ }
if (vm.count("map-nonstd")) {
map_nonstd_res = true;
}
@@ -192,6 +224,7 @@ int main(int argc, char *argv[])
usage();
exit(-1);
}
+ CompoundLibPtr lib=load_compound_lib(custom_path);
for (unsigned int i = 0; i < files.size(); ++i) {
EntityHandle ent=load_x(files[i], prof);
if (!ent.IsValid()) {
@@ -330,10 +363,55 @@ int main(int argc, char *argv[])
}
}
}
+
if (write_to_stdout) {
PDBWriter writer(std::cout, prof);
writer.Write(ent);
}
+ if (write_to_file) {
+ fs::path input_file_path(files[i]);
+ fs::path input_filename = input_file_path.stem();
+
+
+ #if BOOST_FILESYSTEM_VERSION==3 || BOOST_VERSION<103400
+ String input_filename_string=input_filename.string();
+ #else
+ String input_filename_string=input_filename.file_string();
+ #endif
+
+ size_t replstart =output_blueprint_string.find('%');
+
+ if (replstart == String::npos) {
+ std::cerr << "The output blueprint string does not contain a % character" << std::endl;
+ exit(-1);
+ }
+ String output_blueprint_string_copy = output_blueprint_string;
+ output_blueprint_string_copy.replace(replstart,1,input_filename_string);
+ output_blueprint_string_copy+=".pdb";
+
+ try {
+ fs::path out_path(output_blueprint_string_copy);
+ if (!exists(out_path)) {
+ std::cerr << "Output path does not exist: " << output_blueprint_string_copy << std::endl;
+ exit(-1);
+ }
+ } catch (std::exception& e) {
+
+ 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;
+ exit(-1);
+ } else {
+ std::cerr << e.what() << std::endl;
+ exit(-1);
+ }
+ }
+ std::cerr << "Writing out file: " << output_blueprint_string_copy << std::endl;
+ PDBWriter writer(output_blueprint_string_copy, prof);
+ writer.Write(ent);
+ }
}
+
return 0;
}