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/* pyrogen/restraints-boost.hh
*
* Copyright 2011 by the University of Oxford
* Copyright 2014 by Medical Research Council
* Author: Paul Emsley
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 3 of the License, or (at
* your option) any later version.
*
* This program is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
* General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA
* 02110-1301, USA
*/
#ifndef RESTRAINTS_HH
#define RESTRAINTS_HH
#include <Python.h>
#include <cstddef>
#include <string>
#include <vector>
#include "compat/coot-sysdep.h"
#include <GraphMol/GraphMol.h>
#include <GraphMol/MolOps.h>
#include <GraphMol/Bond.h>
#include <geometry/protein-geometry.hh>
#include <analysis/mogul-interface.hh>
#include "restraints-private.hh"
namespace coot {
class quartet_set {
public:
quartet_set() {
idx.resize(4,0);
}
explicit quartet_set(const std::vector<unsigned int> &q_in) {
unsigned int n_max = 4;
idx.resize(4,0);
if (q_in.size() < n_max)
n_max = q_in.size();
for (unsigned int i=0; i<n_max; i++)
idx[i] = q_in[i];
}
std::vector<unsigned int> idx;
const unsigned int & operator[](unsigned int i) const { return idx[i]; }
};
class indexed_name_and_rank_t {
public:
unsigned int atom_index;
unsigned int cip_rank;
std::string atom_name;
indexed_name_and_rank_t(unsigned int i, unsigned int r, const std::string &n) : atom_name(n) {
atom_index = i;
cip_rank = r;
}
bool operator<(const indexed_name_and_rank_t &o) const {
return (o.cip_rank < cip_rank);
}
};
int get_volume_sign_from_coordinates(const RDKit::ROMol &mol,
unsigned int idx_chiral_centre_atom,
const std::vector<indexed_name_and_rank_t> &neighb_names_and_ranks);
void mogul_out_to_mmcif_dict(const std::string &mogul_file_name,
const std::string &comp_id,
const std::string &compound_name,
const std::vector<std::string> &atom_names,
int n_atoms_all,
int n_atoms_non_hydrogen,
PyObject *bond_order_restraints_py,
const std::string &mmcif_out_file_name,
bool quartet_planes, bool quartet_hydrogen_planes);
// return restraints
PyObject *mogul_out_to_mmcif_dict_by_mol(const std::string &mogul_file_name,
const std::string &comp_id,
const std::string &compound_name,
PyObject *rdkit_mol,
PyObject *bond_order_restraints_py,
const std::string &mmcif_out_file_name,
bool quartet_planes, bool quartet_hydrogen_planes,
bool replace_with_mmff_b_a_restraints=true);
PyObject *
mmcif_dict_from_mol(const std::string &comp_id,
const std::string &compound_name,
PyObject *rdkit_mol,
bool do_minimization,
const std::string &mmcif_out_file_name,
bool quartet_planes, bool quartet_hydrogen_planes,
bool replace_with_mmff_b_a_restraints=true);
// which is a wrapper for:
std::pair<bool, coot::dictionary_residue_restraints_t>
mmcif_dict_from_mol_using_energy_lib(const std::string &comp_id,
const std::string &compound_name,
PyObject *rdkit_mol,
bool quartet_planes, bool quartet_hydrogen_planes);
void write_restraints(PyObject *restraints_py,
const std::string &monomer_type,
const std::string &file_name);
void regularize(PyObject *rdkit_mol, PyObject *restraints_py,
const std::string &res_name);
//
void regularize_and_write_pdb(PyObject *rdkit_mol, PyObject *restraints_py,
const std::string &res_name,
const std::string &pdb_file_name);
void write_pdb_from_mol(PyObject *rdkit_mol_py,
const std::string &res_name,
const std::string &file_name);
PyObject *types_from_mmcif_dictionary(const std::string &file_name);
PyObject *test_tuple();
PyObject *match_restraints_to_dictionaries(PyObject *restraints_in,
PyObject *template_comp_id_list,
PyObject *template_cif_dict_file_names);
void write_restraints(PyObject *restraints_py, const std::string &file_name);
}
#endif // RESTRAINTS_HH
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