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// Copyright 2017 Global Phasing Ltd.
#include <cstdio> // for printf, fprintf
#include <exception> // for exception
#include <iostream> // for cout, cerr
#include <gemmi/polyheur.hpp> // for setup_entities
#include <gemmi/modify.hpp> // for remove_hydrogens
#include <gemmi/to_cif.hpp> // for write_cif_to_file
#include <gemmi/to_mmcif.hpp> // for make_mmcif_document
#include <gemmi/to_pdb.hpp> // for write_pdb
#include <gemmi/monlib.hpp> // for MonLib
#include <gemmi/topo.hpp> // for Topo, prepare_topology
#include <gemmi/fstream.hpp> // for Ofstream
#include <gemmi/mmread_gz.hpp> // for read_structure_gz
#include "monlib_opt.h"
#define GEMMI_PROG h
#include "options.h"
namespace cif = gemmi::cif;
namespace {
enum OptionIndex {
FormatIn=AfterMonLibOptions, Sort, Update, RemoveH, KeepH, Water, Unique, NoChange
};
const option::Descriptor Usage[] = {
{ NoOp, 0, "", "", Arg::None,
"Usage:"
"\n " EXE_NAME " [options] INPUT_FILE OUTPUT_FILE"
"\n\nAdd hydrogens in positions specified by the monomer library."
"\nBy default, it removes and re-adds all hydrogens."
"\nBy default, hydrogens are not added to water."
"\n\nOptions:" },
CommonUsage[Help],
CommonUsage[Version],
CommonUsage[Verbose],
MonLibUsage[0], // Monomers
MonLibUsage[1], // Libin
{ FormatIn, 0, "", "format", Arg::CoorFormat,
" --format=FORMAT \tInput format (default: from the file extension)." },
{ Sort, 0, "", "sort", Arg::None,
" --sort \tOrder atoms in residues according to _chem_comp_atom." },
{ Update, 0, "", "update", Arg::None,
" --update \tIf deprecated atom names (from _chem_comp_atom.alt_atom_id)"
" are used in the model, change them." },
{ NoOp, 0, "", "", Arg::None,
"Hydrogen options, mutually exclusive. Default: add hydrogens, but not to water." },
{ Water, 0, "", "water", Arg::None,
" --water \tAdd hydrogens also to water." },
{ Unique, 0, "", "unique", Arg::None,
" --unique \tAdd only hydrogens with uniquely determined positions." },
{ KeepH, 0, "", "keep", Arg::None,
" --keep \tDo not add/remove hydrogens, only change positions." },
{ NoChange, 0, "", "no-change", Arg::None,
" --no-change \tDo not change hydrogens, not even positions." },
{ RemoveH, 0, "", "remove", Arg::None,
" --remove \tOnly remove hydrogens." },
MonLibUsage[2], // details about Libin (--lib)
{ 0, 0, 0, 0, 0, 0 }
};
size_t count_hydrogens(const gemmi::Structure& st) {
size_t count = 0;
for (const gemmi::Model& model : st.models)
for (gemmi::const_CRA cra : model.all())
if (cra.atom->is_hydrogen())
++count;
return count;
}
} // anonymous namespace
int GEMMI_MAIN(int argc, char **argv) {
OptParser p(EXE_NAME);
p.simple_parse(argc, argv, Usage);
p.require_positional_args(2);
std::string input = p.coordinate_input_file(0);
std::string output = p.nonOption(1);
p.check_exclusive_group({KeepH, RemoveH, Water, Unique});
gemmi::HydrogenChange h_change = gemmi::HydrogenChange::ReAddButWater;
if (p.options[Water])
h_change = gemmi::HydrogenChange::ReAdd;
else if (p.options[Unique])
h_change = gemmi::HydrogenChange::ReAddKnown;
else if (p.options[KeepH])
h_change = gemmi::HydrogenChange::Shift;
else if (p.options[NoChange])
h_change = gemmi::HydrogenChange::NoChange;
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);
try {
gemmi::Structure st;
std::unique_ptr<cif::Document> doc;
if (preserve_doc)
doc.reset(new cif::Document);
st = gemmi::read_structure_gz(input, input_format, doc.get());
if (st.models.empty() || st.models[0].chains.empty()) {
std::fprintf(stderr, "No atoms in the input file. Wrong format?\n");
return 1;
}
gemmi::setup_entities(st);
size_t initial_h = 0;
if (p.options[Verbose])
initial_h = count_hydrogens(st);
if (h_change == gemmi::HydrogenChange::Remove)
gemmi::remove_hydrogens(st);
if (h_change != gemmi::HydrogenChange::Remove || p.options[Sort] || p.options[Update]) {
gemmi::MonLib monlib;
std::vector<std::string> wanted = st.models[0].get_all_residue_names();
read_monomer_lib_and_user_files(monlib, wanted, mon_args, doc.get());
if (!wanted.empty())
gemmi::fail("Please create definitions for missing monomers.");
if (p.options[Update]) {
std::string msg = monlib.update_old_atom_names(st);
std::printf("%s", msg.c_str());
}
for (size_t i = 0; i != st.models.size(); ++i) {
// preparing topology modifies hydrogens in the model
prepare_topology(st, monlib, i, h_change, p.options[Sort], &std::cerr);
}
}
if (p.options[Verbose])
std::printf("Hydrogen site count: %zu in input, %zu in output.\n",
initial_h, count_hydrogens(st));
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) {
shorten_ccd_codes(st);
gemmi::write_pdb(st, os.ref());
} else {
if (preserve_doc) {
gemmi::MmcifOutputGroups groups(false);
groups.atoms = true;
gemmi::update_mmcif_block(st, doc->blocks[0], groups);
} else {
doc.reset(new cif::Document(gemmi::make_mmcif_document(st)));
}
cif::WriteOptions cif_options;
cif_options.prefer_pairs = true;
cif::write_cif_to_stream(os.ref(), *doc, cif_options);
}
} catch (std::exception& e) {
std::fprintf(stderr, "ERROR: %s\n", e.what());
return 1;
}
return 0;
}
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