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//
// Copyright (C) 2018 Pat Lorton
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
#include <iostream>
#include <fstream>
#include <map>
#include <RDGeneral/BadFileException.h>
#include <RDGeneral/FileParseException.h>
#include <GraphMol/MolInterchange/details.h>
#include <GraphMol/MolOps.h>
#include <GraphMol/RWMol.h>
#include <GraphMol/FileParsers/MolSupplier.h>
#include <maeparser/Reader.hpp>
namespace RDKit {
using RDKit::MolInterchange::bolookup;
MaeMolSupplier::MaeMolSupplier(std::istream *inStream, bool takeOwnership,
bool sanitize, bool removeHs) {
PRECONDITION(inStream, "bad stream");
dp_inStream = inStream;
df_owner = takeOwnership;
df_sanitize = sanitize;
df_removeHs = removeHs;
d_reader.reset(new schrodinger::mae::Reader(*inStream));
d_next_struct = d_reader->next("f_m_ct");
}
MaeMolSupplier::MaeMolSupplier(const std::string &fileName, bool sanitize, bool removeHs) {
df_owner = true;
auto *ifs = new std::ifstream(fileName.c_str(), std::ios_base::binary);
if (!ifs || !(*ifs) || ifs->bad()) {
std::ostringstream errout;
errout << "Bad input file " << fileName;
throw BadFileException(errout.str());
}
dp_inStream = (std::istream *)ifs;
df_sanitize = sanitize;
df_removeHs = removeHs;
d_reader.reset(new schrodinger::mae::Reader(*ifs));
d_next_struct = d_reader->next("f_m_ct");
}
void MaeMolSupplier::init() {}
void MaeMolSupplier::reset() {}
ROMol *MaeMolSupplier::next() {
if (d_next_struct == nullptr) {
throw FileParseException("All structures read from Maestro file");
}
// Make sure even if later calls except, we're ready to read the next struct
auto current_struct = d_next_struct;
d_next_struct = d_reader->next("f_m_ct");
auto mol = new RWMol();
auto mol_title = current_struct->getStringProperty("s_m_title");
mol->setProp(common_properties::_Name, mol_title);
// Atom data is in the m_atom indexed block
{
const auto atom_data = current_struct->getIndexedBlock("m_atom");
// All atoms are gauranteed to have these three field names:
const auto atomic_numbers = atom_data->getIntProperty("i_m_atomic_number");
const auto xs = atom_data->getRealProperty("r_m_x_coord");
const auto ys = atom_data->getRealProperty("r_m_y_coord");
const auto zs = atom_data->getRealProperty("r_m_z_coord");
const auto size = atomic_numbers->size();
std::shared_ptr<schrodinger::mae::IndexedIntProperty> atomic_charges;
try {
atomic_charges = atom_data->getIntProperty("i_m_formal_charge");
} catch(std::out_of_range& e) { }
// atomic numbers, and x, y, and z coordinates
auto conf = new RDKit::Conformer(size);
conf->set3D(true);
conf->setId(0);
for (size_t i=0; i<size; ++i) {
Atom *atom = new Atom(atomic_numbers->at(i));
mol->addAtom(atom, true, true);
if(atomic_charges) {
atom->setFormalCharge(atomic_charges->at(i));
}
RDGeom::Point3D pos;
pos.x = xs->at(i);
pos.y = ys->at(i);
pos.z = zs->at(i);
conf->setAtomPos(i, pos);
}
mol->addConformer(conf, false);
}
// Bond data is in the m_bond indexed block
{
const auto bond_data = current_struct->getIndexedBlock("m_bond");
// All bonds are gauranteed to have these three field names:
auto from_atoms = bond_data->getIntProperty("i_m_from");
auto to_atoms = bond_data->getIntProperty("i_m_to");
auto orders = bond_data->getIntProperty("i_m_order");
const auto size = from_atoms->size();
for (size_t i=0; i<size; ++i) {
// Maestro atoms are 1 indexed!
const auto from_atom = from_atoms->at(i) - 1;
const auto to_atom = to_atoms->at(i) - 1;
const auto order = bolookup.find(orders->at(i))->second;
if(from_atom > to_atom) continue; // Maestro files double-list bonds
auto bond = new Bond(order);
bond->setOwningMol(mol);
bond->setBeginAtomIdx(from_atom);
bond->setEndAtomIdx(to_atom);
mol->addBond(bond, true);
}
}
if (df_sanitize) {
if (df_removeHs) {
MolOps::removeHs(*mol, false, false);
} else {
MolOps::sanitizeMol(*mol);
}
} else {
// we need some properties for the chiral setup
mol->updatePropertyCache(false);
}
/* Set tetrahedral chirality from 3D co-ordinates */
MolOps::assignChiralTypesFrom3D(*mol);
MolOps::detectBondStereochemistry(*mol);
return (ROMol *)mol;
}
bool MaeMolSupplier::atEnd() {
return d_next_struct == nullptr;
}
}
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