gemmi h: don't require option --monomers when reading chemcomp file

docs/program.rst

@@ -925,6 +925,11 @@ that atom is assigned one of possible positions and its occupancy is zeroed.
 .. literalinclude:: h-help.txt
    :language: console
 
+To test the addition of hydrogen to a single chemical component
+from a monomer library, run::
+
+    gemmi h --format=chemcomp -L+ XYZ.cif output.pdb
+
 mondiff
 =======
 

prog/h.cpp

@@ -92,22 +92,25 @@ int GEMMI_MAIN(int argc, char **argv) {
   else if (p.options[RemoveH])
     h_change = gemmi::HydrogenChange::Remove;
 
-  MonArguments mon_args;
-  if (h_change != gemmi::HydrogenChange::Remove)
-    mon_args = get_monomer_args(p.options);
-
-  if (p.options[Verbose])
-    std::printf("Reading coordinates from %s\n", input.c_str());
   gemmi::CoorFormat input_format = coor_format_as_enum(p.options[FormatIn]);
   if (input_format == gemmi::CoorFormat::Unknown)
     input_format = gemmi::coor_format_from_ext_gz(input);
   gemmi::CoorFormat output_format = gemmi::coor_format_from_ext_gz(output);
   bool preserve_doc = (input_format == gemmi::CoorFormat::Mmcif &&
                        output_format == gemmi::CoorFormat::Mmcif);
+
+  MonArguments mon_args;
+  if (h_change != gemmi::HydrogenChange::Remove) {
+    bool needs_monlib = input_format != gemmi::CoorFormat::ChemComp;
+    mon_args = get_monomer_args(p.options, needs_monlib);
+  }
+
+  if (p.options[Verbose])
+    std::printf("Reading coordinates from %s\n", input.c_str());
   try {
     gemmi::Structure st;
     std::unique_ptr<cif::Document> doc;
-    if (preserve_doc)
+    if (preserve_doc || mon_args.has_plus())
       doc.reset(new cif::Document);
     st = gemmi::read_structure_gz(input, input_format, doc.get());
     if (st.models.empty() || st.models[0].chains.empty()) {
@@ -139,7 +142,7 @@ int GEMMI_MAIN(int argc, char **argv) {
     if (p.options[Verbose])
       std::printf("Writing coordinates to %s\n", output.c_str());
     gemmi::Ofstream os(output, &std::cout);
-    if (gemmi::coor_format_from_ext_gz(output) == gemmi::CoorFormat::Pdb) {
+    if (output_format == gemmi::CoorFormat::Pdb) {
       shorten_ccd_codes(st);
       gemmi::write_pdb(st, os.ref());
     } else {

prog/monlib_opt.cpp

@@ -22,13 +22,16 @@ const option::Descriptor MonLibUsage[] = {
     "\nExample 2:   -L@ -L file.cif    order: ML, file.cif" }
 };
 
-MonArguments get_monomer_args(const std::vector<option::Option>& options) {
+MonArguments get_monomer_args(const std::vector<option::Option>& options, bool needs_monlib) {
   MonArguments args;
   const option::Option* mon = options[Monomers];
   args.monomer_dir = mon ? mon->arg : std::getenv("CLIBD_MON");
   if (args.monomer_dir == nullptr || args.monomer_dir[0] == '\0') {
-    fprintf(stderr, "Set $CLIBD_MON or use option --monomers.\n");
-    std::exit(1);
+    if (needs_monlib) {
+      fprintf(stderr, "Set $CLIBD_MON or use option --monomers.\n");
+      std::exit(1);
+    }
+    args.monomer_dir = nullptr;
   }
   args.libin = options[Libin];
   args.verbose = options[Verbose].count();
@@ -68,9 +71,11 @@ void read_monomer_lib_and_user_files(gemmi::MonLib& monlib,
       putc('\n', stderr);
     }
   }
-  if (args.verbose)
-    fprintf(stderr, "Reading monomer library...\n");
-  monlib.read_monomer_lib(args.monomer_dir, wanted, {&gemmi::Logger::to_stderr});
+  if (args.monomer_dir) {
+    if (args.verbose)
+      fprintf(stderr, "Reading monomer library...\n");
+    monlib.read_monomer_lib(args.monomer_dir, wanted, {&gemmi::Logger::to_stderr});
+  }
   auto is_found = [&](const std::string& s) { return monlib.monomers.count(s); };
   gemmi::vector_remove_if(wanted, is_found);
   if (libin) {

prog/monlib_opt.h

@@ -13,10 +13,18 @@ struct MonArguments {
   const char* monomer_dir;
   const option::Option* libin;
   int verbose;
+
+  bool has_plus() const {
+    for (auto it = libin; it; it = it->next())
+      if (it->arg[0] == '+' && it->arg[1] == '\0')
+        return true;
+    return false;
+  }
 };
 
+
 // Exits w/ error if monomer dir is not specified (--monomers or $CLIBD_MON)
-MonArguments get_monomer_args(const std::vector<option::Option>& options);
+MonArguments get_monomer_args(const std::vector<option::Option>& options, bool needs_monlib=true);
 
 // Read monomer library and user-provided cif files according to args.
 // st_doc is used if we read monomer blocks from coordinate mmCIF.