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// Copyright Global Phasing Ltd.
//
// Options for reading a monomer library + user-provided CIF files.
#include "monlib_opt.h"
#include <cstdlib> // for getenv, exit
#include <gemmi/read_cif.hpp> // for read_cif_gz
#define GEMMI_PROG n/a
#include "options.h"
const option::Descriptor MonLibUsage[] = {
{ Monomers, 0, "", "monomers", Arg::Required,
" --monomers=DIR \tMonomer library directory (default: $CLIBD_MON)." },
{ Libin, 0, "L", "lib", Arg::Required,
" -L CIF, --lib=CIF \tUser's restraint file(s). See more info below." },
{ NoOp, 0, "", "", Arg::None,
"\nOption -L/--lib can be used multiple times, in order of priority."
"\nIts argument is either a file path or one of the two special values:"
"\n '+' = monomer blocks in mmCIF INPUT_FILE (ignored by default)"
"\n '@' = the priority of the monomer library (ML, default: lowest)"
"\nExample 1: -L file.cif -L+ order: file.cif, input file, ML"
"\nExample 2: -L@ -L file.cif order: ML, file.cif" }
};
MonArguments get_monomer_args(const std::vector<option::Option>& options) {
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);
}
args.libin = options[Libin];
args.verbose = options[Verbose].count();
return args;
}
void read_monomer_lib_and_user_files(gemmi::MonLib& monlib,
std::vector<std::string>& wanted,
const MonArguments& args,
const gemmi::cif::Document* st_doc) {
auto read_user_file = [&](const char* path) {
if (path[0] == '+' && path[1] == '\0') {
if (args.verbose)
fprintf(stderr, "Checking coordinate file for restraint library...\n");
if (st_doc && !st_doc->blocks.empty())
monlib.read_monomer_doc(*st_doc);
else
fprintf(stderr, "Input file is not mmCIF, ignoring option --lib=+\n");
} else {
if (args.verbose)
fprintf(stderr, "Reading user's library %s ...\n", path);
monlib.read_monomer_cif(path, gemmi::read_cif_gz);
}
};
auto libin = args.libin;
for (; libin; libin = libin->next()) {
if (libin->arg[0] == '@' && libin->arg[1] == '\0')
break;
read_user_file(libin->arg);
}
if (!monlib.monomers.empty()) {
if (args.verbose >= 2) {
fprintf(stderr, "Monomers read first:");
for (auto& mpair : monlib.monomers)
fprintf(stderr, " %s", mpair.first.c_str());
putc('\n', stderr);
}
}
if (args.verbose)
fprintf(stderr, "Reading monomer library...\n");
std::string error;
monlib.read_monomer_lib(args.monomer_dir, wanted, gemmi::read_cif_gz, &error);
auto is_found = [&](const std::string& s) { return monlib.monomers.count(s); };
gemmi::vector_remove_if(wanted, is_found);
if (!error.empty())
fprintf(stderr, "%s", error.c_str());
if (libin) {
for (libin = libin->next(); libin; libin = libin->next()) {
if (libin->arg[0] == '@' && libin->arg[1] == '\0')
gemmi::fail("option --lib=/ can be given only once");
read_user_file(libin->arg);
}
gemmi::vector_remove_if(wanted, is_found);
}
}
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