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// Copyright 2019 Global Phasing Ltd.
//
// Compare two CIF files with monomer restraints.
#include <stdio.h>
#include <cstdlib>
#include <set>
#include <gemmi/chemcomp.hpp> // for make_chemcomp_from_block
#include <gemmi/read_cif.hpp> // for read_cif_gz
#define GEMMI_PROG mondiff
#include "options.h"
using namespace gemmi;
namespace {
enum OptionIndex { Bond=4, BondEsd, Angle, AngleEsd, Relative };
const option::Descriptor Usage[] = {
{ NoOp, 0, "", "", Arg::None,
"Usage:"
"\n " EXE_NAME " [options] FILE1 FILE2"
"\nOptions:"},
CommonUsage[Help],
CommonUsage[Version],
CommonUsage[Verbose],
{ NoOp, 0, "", "", Arg::None, "\nMinimal reported differences:" },
{ Bond, 0, "", "bond", Arg::Float,
" --bond=DELTA \tdifference in distance value (default: 0.01)." },
{ BondEsd, 0, "", "bond-esd", Arg::Float,
" --bond-esd=DELTA \tdifference in distance esd (default: 0.1)." },
{ Angle, 0, "", "angle", Arg::Float,
" --angle=DELTA \tdifference in angle value (default: 0.1)." },
{ AngleEsd, 0, "", "angle-esd", Arg::Float,
" --angle-esd=DELTA \tdifference in angle esd (default: 1.0)." },
{ Relative, 0, "", "rel", Arg::Float,
" --rel=SIGMA \t abs(value difference) / esd > SIGMA (default: 0.0)." },
{ 0, 0, 0, 0, 0, 0 }
};
struct MinDelta {
double bond = 0.01;
double bond_esd = 0.1;
double angle = 0.1;
double angle_esd = 1.0;
double rel = 0.0;
};
std::string str(const ChemComp& cc, const Restraints::Bond& b) {
return gemmi::cat("bond ", b.id1.atom, '-', b.id2.atom,
" (", cc.get_atom(b.id1.atom).chem_type,
'-', cc.get_atom(b.id2.atom).chem_type, ')');
}
std::string str(const ChemComp& cc, const Restraints::Angle& a) {
return gemmi::cat("angle ", a.id1.atom, '-', a.id2.atom, '-', a.id3.atom,
" (", cc.get_atom(a.id1.atom).chem_type,
'-', cc.get_atom(a.id2.atom).chem_type,
'-', cc.get_atom(a.id3.atom).chem_type, ')');
}
std::string str(const ChemComp&, const Restraints::Torsion& a) {
return "torsion " + a.str();
}
std::string str(const ChemComp&, const Restraints::Chirality& a) {
return "chirality " + a.str();
}
const char* mark(double delta, double eps) {
if (delta < eps) return "";
if (delta < 2*eps) return "*";
if (delta < 4*eps) return "**";
if (delta < 8*eps) return "***";
return "****";
}
void compare_chemcomps(const ChemComp& cc1, const ChemComp& cc2,
const MinDelta& delta) {
// atoms
for (const ChemComp::Atom& a : cc1.atoms) {
auto b = cc2.find_atom(a.id);
if (b == cc2.atoms.end())
printf("- atom %s (%s)\n", a.id.c_str(), a.chem_type.c_str());
else if (a.chem_type != b->chem_type)
printf("! atom %s (%s : %s)\n",
a.id.c_str(), a.chem_type.c_str(), b->chem_type.c_str());
}
for (const ChemComp::Atom& a : cc2.atoms)
if (cc1.find_atom(a.id) == cc1.atoms.end())
printf("+ atom %s (%s)\n", a.id.c_str(), a.chem_type.c_str());
// bonds
for (const Restraints::Bond& a : cc1.rt.bonds) {
auto b = cc2.rt.find_bond(a.id1, a.id2);
if (b == cc2.rt.bonds.end()) {
printf("- %s\n", str(cc1, a).c_str());
} else {
if (a.type != b->type)
printf("! %-30s %s : %s\n", str(cc1, a).c_str(),
bond_type_to_string(a.type),
bond_type_to_string(b->type));
double d = std::fabs(a.value - b->value);
if ((d > delta.bond || std::fabs(a.esd - b->esd) > delta.bond_esd) &&
d > delta.rel * std::min(a.esd, b->esd))
printf("! %-30s %4s %.3f : %.3f esd %.3f : %.3f\n",
str(cc1, a).c_str(), mark(d, a.esd),
a.value, b->value, a.esd, b->esd);
}
}
for (const Restraints::Bond& a : cc2.rt.bonds)
if (cc1.rt.find_bond(a.id1, a.id2) == cc1.rt.bonds.end())
printf("+ %s\n", str(cc2, a).c_str());
// angles
for (const Restraints::Angle& a : cc1.rt.angles) {
auto b = cc2.rt.find_angle(a.id1, a.id2, a.id3);
if (b == cc2.rt.angles.end()) {
printf("- %s\n", str(cc1, a).c_str());
} else {
double d = std::fabs(a.value - b->value);
if ((d > delta.angle || std::fabs(a.esd - b->esd) > delta.angle_esd) &&
d > delta.rel * std::min(a.esd, b->esd))
printf("! %-30s %4s %6.2f : %6.2f esd %.2f : %.2f\n",
str(cc1, a).c_str(), mark(d, a.esd),
a.value, b->value, a.esd, b->esd);
}
}
for (const Restraints::Angle& a : cc2.rt.angles)
if (cc1.rt.find_angle(a.id1, a.id2, a.id3) == cc1.rt.angles.end())
printf("+ %s\n", str(cc2, a).c_str());
// torsion angles
for (const Restraints::Torsion& a : cc1.rt.torsions) {
auto b = cc2.rt.find_torsion(a.id1, a.id2, a.id3, a.id4);
if (b == cc2.rt.torsions.end()) {
printf("- %s\n", str(cc1, a).c_str());
} else {
double d = std::fabs(a.value - b->value);
if ((d > delta.angle || std::fabs(a.esd - b->esd) > delta.angle_esd) &&
d > delta.rel * std::min(a.esd, b->esd))
printf("! %-30s %4s %6.2f : %6.2f esd %.2f : %.2f\n",
str(cc1, a).c_str(), mark(d, a.esd),
a.value, b->value, a.esd, b->esd);
}
}
for (const Restraints::Torsion& a : cc2.rt.torsions)
if (cc1.rt.find_torsion(a.id1, a.id2, a.id3,a.id4) == cc1.rt.torsions.end())
printf("+ %s\n", str(cc2, a).c_str());
// chiralities
std::vector<bool> matched_chir(cc2.rt.chirs.size(), false);
for (const Restraints::Chirality& a : cc1.rt.chirs) {
if (a.sign == ChiralityType::Both) // not interesting
continue;
auto b = cc2.rt.find_chir(a.id_ctr, a.id1, a.id2, a.id3);
if (b != cc2.rt.chirs.end()) {
if (a.sign != b->sign)
printf("! %-30s %s : %s\n", str(cc1, a).c_str(),
chirality_to_string(a.sign), chirality_to_string(b->sign));
matched_chir[b - cc2.rt.chirs.begin()] = true;
continue;
}
b = cc2.rt.find_chir(a.id_ctr, a.id1, a.id3, a.id2);
if (b == cc2.rt.chirs.end()) {
printf("- %s %s\n", str(cc1, a).c_str(), chirality_to_string(a.sign));
} else {
matched_chir[b - cc2.rt.chirs.begin()] = true;
if (b->sign == ChiralityType::Both || b->sign == a.sign)
printf("! %-30s %s : -%s\n", str(cc1, a).c_str(),
chirality_to_string(a.sign), chirality_to_string(b->sign));
}
}
for (size_t i = 0; i != cc2.rt.chirs.size(); ++i)
if (!matched_chir[i]) {
const Restraints::Chirality& a = cc2.rt.chirs[i];
printf("+ %s %s\n", str(cc2, a).c_str(), chirality_to_string(a.sign));
}
// planes
std::vector<bool> matched_planes(cc2.rt.planes.size(), false);
std::vector<std::set<Restraints::AtomId>> planes2;
planes2.reserve(cc2.rt.planes.size());
for (const Restraints::Plane& b : cc2.rt.planes)
planes2.emplace_back(b.ids.begin(), b.ids.end());
for (const Restraints::Plane& a : cc1.rt.planes) {
std::set<Restraints::AtomId> plane1(a.ids.begin(), a.ids.end());
auto b = std::find(planes2.begin(), planes2.end(), plane1);
if (b == planes2.end()) {
printf("- plane %s\n", a.str().c_str());
continue;
}
double b_esd = cc2.rt.planes[b - planes2.begin()].esd;
if (std::fabs(a.esd - b_esd) > 0.02)
printf("! plane %-53s esd %.2f : %.2f\n", a.str().c_str(), a.esd, b_esd);
b->clear();
}
for (size_t i = 0; i != planes2.size(); ++i)
if (!planes2[i].empty())
printf("+ plane %s\n", cc2.rt.planes[i].str().c_str());
}
} // anonymous namespace
int GEMMI_MAIN(int argc, char **argv) {
OptParser p(EXE_NAME);
p.simple_parse(argc, argv, Usage);
p.require_positional_args(2);
bool verbose = p.options[Verbose];
const char* path1 = p.nonOption(0);
const char* path2 = p.nonOption(1);
MinDelta delta;
if (p.options[Bond])
delta.bond = std::atof(p.options[Bond].arg);
if (p.options[BondEsd])
delta.bond_esd = std::atof(p.options[BondEsd].arg);
if (p.options[Angle])
delta.angle = std::atof(p.options[Angle].arg);
if (p.options[AngleEsd])
delta.angle_esd = std::atof(p.options[AngleEsd].arg);
if (p.options[Relative])
delta.rel = std::atof(p.options[Relative].arg);
try {
if (verbose)
fprintf(stderr, "Reading %s ...\n", path1);
cif::Document doc1 = read_cif_gz(path1);
const cif::Block* block1 = &doc1.blocks.at(0);
if (block1->name == "comp_list")
block1 = &doc1.blocks.at(1);
if (verbose)
fprintf(stderr, "Reading %s ...\n", path2);
cif::Document doc2 = read_cif_gz(path2);
const cif::Block* block2 = doc2.find_block(block1->name);
if (!block2)
fail("Block ", block1->name, " not found in ", path2);
ChemComp cc1 = make_chemcomp_from_block(*block1);
ChemComp cc2 = make_chemcomp_from_block(*block2);
compare_chemcomps(cc1, cc2, delta);
} catch (std::runtime_error& e) {
fprintf(stderr, "ERROR: %s\n", e.what());
return 1;
} catch (std::out_of_range& e) {
fprintf(stderr, "ERROR: %s\n", e.what());
return 2;
}
return 0;
}
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