fix in sorting atoms in prepper

git-svn-id: svn+ssh://gitlab/srv/svn-repos/pdb-redo/trunk@436 a1961a4f-ab94-4bcc-80e8-33b5a54de466

README.md

 libcif++ and pdb-redo tools
 ===========================
 
-This is the README file for libcif++ and the suite of PDB-REDO tools using this library.
+This is the README file for libcif++ and the suite of PDB-REDO tools
+using this library.
 
-### Requirements
+Requirements
+------------
 
-The code for this library was written in C++14. You therefore need a recent compiler to be able to build it.
+The code for this library was written in C++14. You therefore need a
+recent compiler to be able to build it. For the development gcc 7.4
+and clang 6.0 have been used.
 
 Other requirements are:
 
 - GNU make version 4.1 or higher.
 - Boost libraries, the current version was developed using version 1.65
-- [mrc](https://github.com/mhekkel/mrc), a resource compiler that allows including data files into the executable making them easier to install. Strictly this is optional, but at the expense of a lot of functionality.
-- [newuoa-cpp](https://github.com/elsid/newuoa-cpp), required to calculate atom radii.
-- [libzeep](https://github.com/mhekkel/libzeep), a library that contains a full validating XML parser as well as a complete HTTP and SOAP server implementation.
-- [nlohmann/json](https://github.com/nlohmann/json), a header only library to parse and write JSON. This requirement will be removed in a future release (once libzeep 4 is out of beta).
-
-Make sure you install the libraries and tools in this list first before building. You don't have to install them in system locations, paths can be set as described in the next section.
-
-### Building
-
-There are two makefiles, one located in the directory libcif++ and one in tools.
-
-Both makefiles will include a *make.config* file (which will be generated if it doesn't exist). This configuration file can be used to override local settings, e.g. the location of certain libraries.
\ No newline at end of file
+- [mrc](https://github.com/mhekkel/mrc), a resource compiler that
+  allows including data files into the executable making them easier to
+  install. Strictly this is optional, but at the expense of a lot of
+  functionality.
+- [newuoa-cpp](https://github.com/elsid/newuoa-cpp), required to
+  calculate atom radii.
+- [libzeep](https://github.com/mhekkel/libzeep), a library that
+  contains a full validating XML parser as well as a complete HTTP,
+  SOAP and REST server implementation.
+- [nlohmann/json](https://github.com/nlohmann/json), a header only
+  library to parse and write JSON. This is only a requirement if you
+  have a libzeep version older than version 4.
+
+As stated, the nlohmann library is only needed if you use libzeep 3.0.x
+which is bundled with Debian and derivatives. If you clone the version
+of libzeep on github the nlohmann json library will not be used.
+
+Building
+--------
+
+Make sure you install the libraries and tools in list above first
+before building. You don't have to install them in system locations,
+paths can be set as described in the next section.
+
+There are two makefiles, one located in the directory libcif++ and one
+in tools.
+
+Both makefiles will include a *make.config* file (which will be
+generated if it doesn't exist). This configuration file can be used to
+override local settings, e.g. the location of certain libraries.
+
+Before running make, first `source` the ccp4 environment. This will
+take care of setting up the make.config file correctly. You then only
+have to edit the `ZEEP_DIR` variable to point to the correct
+directory in case you did not install libzeep, and if you use
+libzeep version 4, you will have to change `ZEEP_INCL` and `ZEEP_LIB`
+to be `$(ZEEP_DIR)/include` and `$(ZEEP_DIR)/lib` respectively.

src/Cif2PDB.cpp

@@ -1458,8 +1458,7 @@ void WriteRemark3Shelxl(ostream& pdbFile, Datablock& db)
 	
 	auto c = [](const char* t) -> cif::Condition { return cif::Key("type") == t; };
 	
-	pdbFile	<< RM3("  AUTHORS     : G.M.SHELDRICK") << endl
-			<< RM3("") << endl
+	pdbFile	<< RM3("") << endl
 			<< RM3(" DATA USED IN REFINEMENT.") << endl
 			<< RM3("  RESOLUTION RANGE HIGH (ANGSTROMS) : ", 5, 2)	<< Ff(refine, "ls_d_res_high") << endl
 			<< RM3("  RESOLUTION RANGE LOW  (ANGSTROMS) : ", 5, 2)	<< Ff(refine, "ls_d_res_low") << endl
@@ -3563,7 +3562,7 @@ tuple<int,int> WriteCoordinatesForModel(ostream& pdbFile, Datablock& db,
 		
 		cif::tie(id, group, name, altLoc, resName, chainID, resSeq, iCode, x, y, z, occupancy, tempFactor, element, charge) =
 			r.get("id", "group_PDB", "label_atom_id", "label_alt_id", "auth_comp_id", "auth_asym_id", "auth_seq_id",
-				"pdbx_PDB_ins_code", "Cartn_x", "Cartn_y", "Cartn_z", "occupancy", "B_iso_or_equiv", "type_symbol", "pdbx_format_charge");
+				"pdbx_PDB_ins_code", "Cartn_x", "Cartn_y", "Cartn_z", "occupancy", "B_iso_or_equiv", "type_symbol", "pdbx_formal_charge");
 		
 		if (name.length() < 4 and (element.length() == 1 or not cif::iequals(name, element)))
 			name.insert(name.begin(), ' ');

src/PDB2Cif.cpp

@@ -5120,7 +5120,8 @@ void PDBFileParser::ParseCoordinate(int modelNr)
 		
 		charge = pdb2cifCharge(charge);
 
-		if (CompoundFactory::instance().isKnownPeptide(resName) or CompoundFactory::instance().isKnownBase(resName))
+		// if (CompoundFactory::instance().isKnownPeptide(resName) or CompoundFactory::instance().isKnownBase(resName))
+		if (mmcif::kAAMap.count(resName) or mmcif::kBaseMap.count(resName))
 		{
 			if (groupPDB == "HETATM")
 			{