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// Copyright 2017-2022 Global Phasing Ltd.
#include <stdio.h> // for fprintf, stderr, putc
#include <iostream> // for cerr
#include <exception> // for exception
#include "gemmi/crd.hpp" // for prepare_refmac_crd
#include "gemmi/to_cif.hpp" // for write_cif_block_to_stream
#include "gemmi/fstream.hpp" // for Ofstream
#include "gemmi/monlib.hpp" // for MonLib, read_monomer_lib
#include "gemmi/mmread_gz.hpp" // for read_structure_gz
#include "monlib_opt.h"
#define GEMMI_PROG crd
#include "options.h"
using namespace gemmi;
namespace {
enum OptionIndex {
AutoCis=AfterMonLibOptions, AutoLink, AutoLigand,
NoAliases, NoZeroOccRestr, NoHydrogens, KeepHydrogens
};
const option::Descriptor Usage[] = {
{ NoOp, 0, "", "", Arg::None,
"Usage:"
"\n " EXE_NAME " [options] INPUT_FILE OUTPUT_FILE"
"\n\nPrepare intermediate Refmac files."
"\nINPUT_FILE can be in PDB, mmCIF or mmJSON format."
"\n\nOptions:" },
CommonUsage[Help],
CommonUsage[Version],
CommonUsage[Verbose],
MonLibUsage[0], // Monomers
MonLibUsage[1], // Libin
{ AutoCis, 0, "", "auto-cis", Arg::YesNo,
" --auto-cis=Y|N \tAssign cis/trans ignoring CISPEP record (default: Y)." },
{ AutoLink, 0, "", "auto-link", Arg::YesNo,
" --auto-link=Y|N \tFind links not included in LINK/SSBOND (default: N)." },
{ AutoLigand, 0, "", "auto-ligand", Arg::YesNo,
" --auto-ligand=Y|N \tIf ligand has no definition make ad-hoc restraints (N)." },
{ NoAliases, 0, "", "no-aliases", Arg::None,
" --no-aliases \tIgnore _chem_comp_alias." },
//{ NoZeroOccRestr, 0, "", "no-zero-occ", Arg::None,
// " --no-zero-occ \tNo restraints for zero-occupancy atoms." },
{ NoOp, 0, "", "", Arg::None,
"\nHydrogen options (default: remove and add on riding positions):" },
{ NoHydrogens, 0, "H", "no-hydrogens", Arg::None,
" -H, --no-hydrogens \tRemove (and do not add) hydrogens." },
{ KeepHydrogens, 0, "", "keep-hydrogens", Arg::None,
" --keep-hydrogens \tPreserve hydrogens from the input file." },
MonLibUsage[2], // details about Libin (--lib)
{ 0, 0, 0, 0, 0, 0 }
};
} // anonymous namespace
int GEMMI_MAIN(int argc, char **argv) {
OptParser p(EXE_NAME);
p.simple_parse(argc, argv, Usage);
p.require_positional_args(2);
p.check_exclusive_pair(KeepHydrogens, NoHydrogens);
// check if monomer dir is specified (--monomers or $CLIBD_MON)
MonArguments mon_args = get_monomer_args(p.options);
std::string input = p.coordinate_input_file(0);
std::string output = p.nonOption(1);
int verbose = p.options[Verbose].count();
try {
if (verbose)
fprintf(stderr, "Reading %s ...\n", input.c_str());
cif::Document st_doc;
Structure st = read_structure_gz(input, CoorFormat::Detect, &st_doc);
setup_for_crd(st);
if (st.models.empty()) {
fprintf(stderr, "No models found in the input file.\n");
return 1;
}
Model& model0 = st.models[0];
std::vector<std::string> wanted = model0.get_all_residue_names();
MonLib monlib;
read_monomer_lib_and_user_files(monlib, wanted, mon_args, &st_doc);
if (!wanted.empty()) {
for (const std::string& name : wanted)
fprintf(stderr, "WARNING: definition not found for %s.\n", name.c_str());
if (!p.is_yes(AutoLigand, false))
fail("Supply missing monomer definitions or use option --auto-ligand=Y");
fprintf(stderr, "Note: Using ad-hoc restraints for missing monomers.\n"
" Consider generating monomer CIFs with AceDRG or GRADE.\n");
}
if (p.options[NoAliases])
for (auto& name_monomer : monlib.monomers)
name_monomer.second.aliases.clear();
bool use_cispeps = !p.is_yes(AutoCis, true);
if (p.is_yes(AutoLink, false)) {
size_t before = st.connections.size();
add_automatic_links(model0, st, monlib);
if (verbose)
for (size_t i = before; i < st.connections.size(); ++i) {
const Connection& conn = st.connections[i];
fprintf(stderr, "Automatic link: %s - %s\n",
conn.partner1.str().c_str(), conn.partner2.str().c_str());
}
}
if (verbose)
fprintf(stderr, "Preparing topology, hydrogens, restraints...\n");
bool reorder = true;
bool ignore_unknown_links = false;
HydrogenChange h_change;
if (p.options[NoHydrogens])
h_change = HydrogenChange::Remove;
else if (p.options[KeepHydrogens])
h_change = HydrogenChange::NoChange;
else
h_change = HydrogenChange::ReAddButWater;
auto topo = prepare_topology(st, monlib, 0, h_change, reorder,
&std::cerr, ignore_unknown_links, use_cispeps);
if (!use_cispeps)
topo->set_cispeps_in_structure(st);
if (verbose)
fprintf(stderr, "Preparing data for Refmac...\n");
cif::Document crd = prepare_refmac_crd(st, *topo, monlib, h_change);
// expand the starting comment
cif::Item& first_item = crd.blocks.at(0).items.at(0);
if (first_item.type == cif::ItemType::Comment) {
std::string& comment = first_item.pair[1];
comment += "\n# Command line: " EXE_NAME;
for (int i = 1; i < argc; ++i)
comment.append(" ").append(argv[i]);
}
if (verbose)
fprintf(stderr, "Writing %s\n", output.c_str());
Ofstream os(output, &std::cout);
cif::WriteOptions cif_options;
cif_options.compact = true;
write_cif_to_stream(os.ref(), crd, cif_options);
} catch (std::exception& e) {
fprintf(stderr, "ERROR: %s\n", e.what());
return 1;
}
return 0;
}
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