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molfile_saver.cpp
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/****************************************************************************
* Copyright (C) from 2009 to Present EPAM Systems.
*
* This file is part of Indigo toolkit.
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
***************************************************************************/
#include "molecule/molfile_saver.h"
#include <ctime>
#include <map>
#include <sstream>
#include "base_cpp/locale_guard.h"
#include "base_cpp/output.h"
#include "layout/sequence_layout.h"
#include "math/algebra.h"
#include "molecule/base_molecule.h"
#include "molecule/elements.h"
#include "molecule/molecule.h"
#include "molecule/molecule_automorphism_search.h"
#include "molecule/molecule_cip_calculator.h"
#include "molecule/molecule_savers.h"
#include "molecule/molecule_stereocenter_options.h"
#include "molecule/molecule_stereocenters.h"
#include "molecule/monomer_commons.h"
#include "molecule/query_molecule.h"
using namespace indigo;
IMPL_ERROR(MolfileSaver, "molfile saver");
CP_DEF(MolfileSaver);
MolfileSaver::MolfileSaver(Output& output) : _output(output), CP_INIT, TL_CP_GET(_atom_mapping), TL_CP_GET(_bond_mapping), add_mrv_sma(true)
{
mode = MODE_AUTO;
no_chiral = false;
chiral_flag = -1;
skip_date = false;
add_stereo_desc = false;
add_implicit_h = true;
}
/*
* Utility functions
*/
const float XYZ_EPSILON = 0.0001f;
void write_c(float c, std::stringstream& coords)
{
int strip = (int)c;
if (fabs(c - strip) < XYZ_EPSILON)
{
coords << strip << ".0";
}
else
{
coords << c;
}
}
/*
* Converts float to string
*/
void convert_xyz_to_string(Vec3f& xyz, std::stringstream& coords)
{
coords.str("");
write_c(xyz.x, coords);
coords << " ";
write_c(xyz.y, coords);
coords << " ";
write_c(xyz.z, coords);
}
/*
* Remove added implicit sgroups
*/
void _removeImplicitSGroups(BaseMolecule& mol, std::list<int>& implicit_sgroups_indexes)
{
for (int idx : implicit_sgroups_indexes)
{
SGroup& sg = mol.sgroups.getSGroup(idx);
if (sg.sgroup_type == SGroup::SG_TYPE_DAT)
{
DataSGroup& dsg = static_cast<DataSGroup&>(sg);
if (dsg.isMrv_implicit())
{
mol.sgroups.remove(idx);
}
else
{
throw MolfileSaver::Error("internal: wanted mrv_implicit sgroup but got other");
}
}
else
{
throw MolfileSaver::Error("internal: wanted data sgroup but got other");
}
}
}
void MolfileSaver::saveBaseMolecule(BaseMolecule& mol)
{
_saveMolecule(mol, mol.isQueryMolecule());
}
void MolfileSaver::saveMolecule(Molecule& mol)
{
_saveMolecule(mol, false);
}
void MolfileSaver::saveQueryMolecule(QueryMolecule& mol)
{
_saveMolecule(mol, true);
}
void MolfileSaver::_handleMonomers(BaseMolecule& mol)
{
SequenceLayout sl(mol);
std::vector<std::deque<int>> sequences;
sl.sequenceExtract(sequences);
const auto& directions_map = sl.directionsMap();
_calculateSEQIDs(mol, directions_map, sequences);
// MonomersToSgroupFilter mon_filter(mol, directions_map);
// mol.transformTemplatesToSuperatoms(mon_filter);
}
void MolfileSaver::_calculateSEQIDs(BaseMolecule& mol, const std::vector<std::map<int, int>>& directions_map, std::vector<std::deque<int>>& sequences)
{
for (auto& sequence : sequences)
{
int seq_id = 1;
for (auto atom_idx : sequence)
{
if (mol.isTemplateAtom(atom_idx))
{
std::string mon_class = mol.getTemplateAtomClass(atom_idx);
if (isBackboneClass(mon_class) && mon_class != kMonomerClassCHEM) // No SEQID for chem
{
mol.asMolecule().setTemplateAtomSeqid(atom_idx, seq_id);
if (mon_class == kMonomerClassSUGAR)
{
// set seq_id for base
std::string seq_name;
auto& dirs = directions_map[atom_idx];
if (dirs.size())
{
auto br_it = dirs.find(kBranchAttachmentPointIdx);
if (br_it != dirs.end() && mol.isTemplateAtom(br_it->second))
{
std::string br_class = mol.getTemplateAtomClass(br_it->second);
seq_name = mol.getTemplateAtom(br_it->second);
if (br_class == kMonomerClassBASE)
{
mol.asMolecule().setTemplateAtomSeqid(br_it->second, seq_id);
mol.asMolecule().setTemplateAtomSeqName(br_it->second, seq_name.c_str());
mol.asMolecule().setTemplateAtomSeqName(atom_idx, seq_name.c_str());
}
}
if (seq_name.size())
{
br_it = dirs.find(kRightAttachmentPointIdx);
if (br_it != dirs.end() && mol.isTemplateAtom(br_it->second))
{
std::string br_class = mol.getTemplateAtomClass(br_it->second);
if (br_class == kMonomerClassPHOSPHATE)
mol.asMolecule().setTemplateAtomSeqName(br_it->second, seq_name.c_str());
}
}
}
}
else if (isAminoAcidClass(mon_class) || isNucleotideClass(mon_class) || mon_class == kMonomerClassPHOSPHATE)
seq_id++;
}
}
}
}
}
void MolfileSaver::_handleCIP(BaseMolecule& mol)
{
MoleculeCIPCalculator mcc;
mcc.removeCIPSgroups(mol); // remove old CIP-Sroups
if (add_stereo_desc && mcc.addCIPStereoDescriptors(mol))
{
mcc.addCIPSgroups(mol);
}
}
void MolfileSaver::_saveMolecule(BaseMolecule& bmol, bool query)
{
LocaleGuard locale_guard;
_validate(bmol);
BaseMolecule* pmol = &bmol;
std::unique_ptr<BaseMolecule> mol(bmol.neu());
if (mode == MODE_2000)
{
_v2000 = true;
if (bmol.tgroups.getTGroupCount())
{
mol->clone(bmol);
mol->transformTemplatesToSuperatoms();
pmol = mol.get();
}
}
else if (mode == MODE_3000)
_v2000 = false;
else
{
// auto-detect the format: save to v3000 molfile only
// if v2000 is not enough
_v2000 = !(pmol->hasHighlighting() || pmol->stereocenters.haveEnhancedStereocenter() ||
(pmol->vertexCount() > 999 || pmol->edgeCount() > 999 || pmol->tgroups.getTGroupCount()));
}
bool rg2000 = (_v2000 && pmol->rgroups.getRGroupCount() > 0);
if (rg2000)
{
struct tm lt;
if (skip_date)
memset(<, 0, sizeof(lt));
else
{
time_t tm = time(NULL);
lt = *localtime(&tm);
}
_output.printfCR("$MDL REV 1 %02d%02d%02d%02d%02d", lt.tm_mon + 1, lt.tm_mday, lt.tm_year % 100, lt.tm_hour, lt.tm_min);
_output.writeStringCR("$MOL");
_output.writeStringCR("$HDR");
}
_writeHeader(*pmol, _output, BaseMolecule::hasZCoord(*pmol));
if (rg2000)
{
_output.writeStringCR("$END HDR");
_output.writeStringCR("$CTAB");
}
if (_v2000)
{
_writeCtabHeader2000(_output, *pmol);
_writeCtab2000(_output, *pmol, query);
}
else
{
_writeCtabHeader(_output);
_writeCtab(_output, *pmol, query);
}
if (_v2000)
{
_writeRGroupIndices2000(_output, *pmol);
_writeAttachmentValues2000(_output, *pmol);
}
if (rg2000)
{
int i, j;
MoleculeRGroups& rgroups = pmol->rgroups;
int n_rgroups = rgroups.getRGroupCount();
for (i = 1; i <= n_rgroups; i++)
{
RGroup& rgroup = rgroups.getRGroup(i);
if (rgroup.fragments.size() == 0)
continue;
_output.printf("M LOG 1 %3d %3d %3d ", i, rgroup.if_then, rgroup.rest_h);
QS_DEF(Array<char>, occ);
ArrayOutput occ_out(occ);
rgroup.writeOccurrence(occ_out);
for (j = 0; j < 3 - occ.size(); j++)
_output.writeChar(' ');
_output.write(occ.ptr(), occ.size());
_output.writeCR();
}
_output.writeStringCR("M END");
_output.writeStringCR("$END CTAB");
for (i = 1; i <= n_rgroups; i++)
{
PtrPool<BaseMolecule>& frags = rgroups.getRGroup(i).fragments;
if (frags.size() == 0)
continue;
_output.writeStringCR("$RGP");
_output.printfCR("%4d", i);
for (j = frags.begin(); j != frags.end(); j = frags.next(j))
{
BaseMolecule* fragment = frags[j];
_output.writeStringCR("$CTAB");
_writeCtabHeader2000(_output, *fragment);
_writeCtab2000(_output, *fragment, query);
_writeRGroupIndices2000(_output, *fragment);
_writeAttachmentValues2000(_output, *fragment);
_output.writeStringCR("M END");
_output.writeStringCR("$END CTAB");
}
_output.writeStringCR("$END RGP");
}
_output.writeStringCR("$END MOL");
}
else
_output.writeStringCR("M END");
}
void MolfileSaver::_validate(BaseMolecule& bmol)
{
std::string unresolved;
if (bmol.getUnresolvedTemplatesList(bmol, unresolved))
throw Error("%s cannot be written in MDL Molfile format.", unresolved.c_str());
}
void MolfileSaver::saveCtab3000(Molecule& mol)
{
_writeCtab(_output, mol, false);
}
void MolfileSaver::saveQueryCtab3000(QueryMolecule& mol)
{
_writeCtab(_output, mol, true);
}
int MolfileSaver::parseFormatMode(const char* mode)
{
if (strcasecmp(mode, "2000") == 0)
return MolfileSaver::MODE_2000;
else if (strcasecmp(mode, "3000") == 0)
return MolfileSaver::MODE_3000;
else if (strcasecmp(mode, "auto") == 0)
return MolfileSaver::MODE_AUTO;
else
throw Error("unknown format mode: %s, supported values: 2000, 3000, auto", mode);
}
void MolfileSaver::saveFormatMode(int mode, Array<char>& output)
{
switch (mode)
{
case MolfileSaver::MODE_2000:
output.readString("2000", true);
break;
case MolfileSaver::MODE_3000:
output.readString("3000", true);
break;
case MolfileSaver::MODE_AUTO:
output.readString("auto", true);
break;
default:
throw Error("unknown format mode: %d", mode);
}
}
void MolfileSaver::_writeHeader(BaseMolecule& mol, Output& output, bool zcoord)
{
struct tm lt;
if (skip_date)
memset(<, 0, sizeof(lt));
else
{
time_t tm = time(NULL);
lt = *localtime(&tm);
}
const char* dim;
if (zcoord)
dim = "3D";
else
dim = "2D";
if (mol.name.ptr() != 0)
output.printfCR("%s", mol.name.ptr());
else
output.writeCR();
output.printfCR(" -INDIGO-%02d%02d%02d%02d%02d%s", lt.tm_mon + 1, lt.tm_mday, lt.tm_year % 100, lt.tm_hour, lt.tm_min, dim);
output.writeCR();
}
void MolfileSaver::_writeCtabHeader(Output& output)
{
output.printfCR("%3d%3d%3d%3d%3d%3d%3d%3d%3d%3d%3d V3000", 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0);
}
void MolfileSaver::_writeCtabHeader2000(Output& output, BaseMolecule& mol)
{
int chiral = 0;
if (!no_chiral && mol.isChiral())
chiral = 1;
if (chiral_flag != -1)
chiral = chiral_flag;
output.printfCR("%3d%3d%3d%3d%3d%3d%3d%3d%3d%3d%3d V2000", mol.vertexCount(), mol.edgeCount(), 0, 0, chiral, 0, 0, 0, 0, 0, 999);
}
void MolfileSaver::_writeAtomLabel(Output& output, int label)
{
output.writeString(Element::toString(label));
}
void MolfileSaver::_writeMultiString(Output& output, const char* string, int len)
{
int limit = 70;
while (len > 0)
{
output.writeString("M V30 ");
if (len <= limit)
limit = len;
output.write(string, limit);
if (len != limit)
output.writeString("-");
output.writeCR();
len -= limit;
string += limit;
}
}
void MolfileSaver::_writeCtab(Output& output, BaseMolecule& mol, bool query)
{
_validate(mol);
_handleCIP(mol);
if (mol.tgroups.getTGroupCount())
_handleMonomers(mol);
QueryMolecule* qmol = 0;
if (query)
qmol = (QueryMolecule*)(&mol);
int i;
int iw = 1;
QS_DEF(Array<char>, buf);
std::list<int> implicit_sgroups_indexes;
_atom_mapping.clear_resize(mol.vertexEnd());
_bond_mapping.clear_resize(mol.edgeEnd());
for (i = mol.vertexBegin(); i < mol.vertexEnd(); i = mol.vertexNext(i), iw++)
_atom_mapping[i] = iw;
if (add_implicit_h && qmol == 0)
{
for (i = mol.vertexBegin(); i < mol.vertexEnd(); i = mol.vertexNext(i))
{
int atom_number = mol.getAtomNumber(i);
int charge = mol.getAtomCharge(i);
int hcount = MoleculeSavers::getHCount(mol, i, atom_number, charge);
if (Molecule::shouldWriteHCount(mol.asMolecule(), i) && hcount > 0)
{
int sg_idx = mol.sgroups.addSGroup(SGroup::SG_TYPE_DAT);
implicit_sgroups_indexes.push_front(sg_idx);
DataSGroup& sgroup = static_cast<DataSGroup&>(mol.sgroups.getSGroup(sg_idx));
sgroup.setMrv_implicit(i, hcount);
}
}
}
output.writeStringCR("M V30 BEGIN CTAB");
output.printfCR("M V30 COUNTS %d %d %d 0 0", mol.vertexCount(), mol.edgeCount(), mol.countSGroups());
output.writeStringCR("M V30 BEGIN ATOM");
std::stringstream coords;
for (i = mol.vertexBegin(); i < mol.vertexEnd(); i = mol.vertexNext(i))
{
int atom_number = mol.getAtomNumber(i);
int isotope = mol.getAtomIsotope(i);
ArrayOutput out(buf);
out.printf("%d ", _atom_mapping[i]);
std::vector<std::unique_ptr<QueryMolecule::Atom>> list;
std::map<int, std::unique_ptr<QueryMolecule::Atom>> properties;
int query_atom_type;
if (atom_number == ELEM_H && isotope == DEUTERIUM)
{
out.writeChar('D');
isotope = 0;
}
else if (atom_number == ELEM_H && isotope == TRITIUM)
{
out.writeChar('T');
isotope = 0;
}
else if (mol.isPseudoAtom(i))
out.writeString(mol.getPseudoAtom(i));
else if (mol.isTemplateAtom(i))
out.writeString(mol.getTemplateAtom(i));
else if (mol.isRSite(i))
out.writeString("R#");
else if (atom_number > 0)
{
_writeAtomLabel(out, atom_number);
}
else if (qmol != 0 && (query_atom_type = QueryMolecule::parseQueryAtomSmarts(*qmol, i, list, properties)) != -1)
{
if (query_atom_type == QueryMolecule::QUERY_ATOM_A)
out.writeChar('A');
else if (query_atom_type == QueryMolecule::QUERY_ATOM_Q)
out.writeChar('Q');
else if (query_atom_type == QueryMolecule::QUERY_ATOM_X)
out.writeChar('X');
else if (query_atom_type == QueryMolecule::QUERY_ATOM_M)
out.writeChar('M');
else if (query_atom_type == QueryMolecule::QUERY_ATOM_AH)
out.writeString("AH");
else if (query_atom_type == QueryMolecule::QUERY_ATOM_QH)
out.writeString("QH");
else if (query_atom_type == QueryMolecule::QUERY_ATOM_XH)
out.writeString("XH");
else if (query_atom_type == QueryMolecule::QUERY_ATOM_MH)
out.writeString("MH");
else if (query_atom_type == QueryMolecule::QUERY_ATOM_LIST || query_atom_type == QueryMolecule::QUERY_ATOM_NOTLIST)
{
if (query_atom_type == QueryMolecule::QUERY_ATOM_NOTLIST)
out.writeString("NOT");
out.writeChar('[');
bool not_first = false;
for (auto& qatom : list)
{
if (not_first)
out.writeChar(',');
else
not_first = true;
if (qatom->type == QueryMolecule::ATOM_NUMBER)
_writeAtomLabel(out, qatom->value_max);
else if (qatom->type == QueryMolecule::ATOM_PSEUDO)
out.writeString(qatom->alias.ptr());
}
out.writeChar(']');
}
}
else if (atom_number == -1)
out.writeChar('A');
else
throw Error("molfile 3000: can not save atom %d because of unsupported "
"query feature",
i);
int aam = 0, ecflag = 0, irflag = 0;
aam = mol.reaction_atom_mapping[i];
irflag = mol.reaction_atom_inversion[i];
ecflag = mol.reaction_atom_exact_change[i];
Vec3f& xyz = mol.getAtomXyz(i);
int charge = mol.getAtomCharge(i);
int radical = 0;
int valence = mol.getExplicitValence(i);
int stereo_parity = _getStereocenterParity(mol, i);
if (!mol.isRSite(i) && !mol.isPseudoAtom(i) && !mol.isTemplateAtom(i))
radical = mol.getAtomRadical_NoThrow(i, 0);
/*
* Trailing zeros workaround
*/
convert_xyz_to_string(xyz, coords);
out.printf(" %s %d", coords.str().c_str(), aam);
if ((mol.isQueryMolecule() && charge != CHARGE_UNKNOWN) || (!mol.isQueryMolecule() && charge != 0))
out.printf(" CHG=%d", charge);
if (qmol != 0)
{
int hcount = MoleculeSavers::getHCount(mol, i, atom_number, charge);
if (hcount > 0)
out.printf(" HCOUNT=%d", hcount);
else if (hcount == 0)
out.printf(" HCOUNT=-1");
}
if (radical > 0)
out.printf(" RAD=%d", radical);
if (stereo_parity > 0)
out.printf(" CFG=%d", stereo_parity);
if (isotope > 0)
out.printf(" MASS=%d", isotope);
if (valence > 0)
out.printf(" VAL=%d", valence);
if (valence == 0)
out.printf(" VAL=-1");
if (irflag > 0)
out.printf(" INVRET=%d", irflag);
if (ecflag > 0)
out.printf(" EXACHG=%d", ecflag);
if (mol.isRSite(i))
{
int k;
QS_DEF(Array<int>, rg_list);
mol.getAllowedRGroups(i, rg_list);
if (rg_list.size() > 0)
{
out.printf(" RGROUPS=(%d", rg_list.size());
for (k = 0; k < rg_list.size(); k++)
out.printf(" %d", rg_list[k]);
out.writeChar(')');
if (!_checkAttPointOrder(mol, i))
{
const Vertex& vertex = mol.getVertex(i);
out.printf(" ATTCHORD=(%d", vertex.degree() * 2);
for (k = 0; k < vertex.degree(); k++)
out.printf(" %d %d", _atom_mapping[mol.getRSiteAttachmentPointByOrder(i, k)], k + 1);
out.writeChar(')');
}
}
}
if (mol.isTemplateAtom(i))
{
std::string tclass;
if (mol.getTemplateAtomClass(i) != 0 && strlen(mol.getTemplateAtomClass(i)) > 0)
{
tclass = mol.getTemplateAtomClass(i);
// convert CHEM to LINKER for BIOVIA
out.printf(" CLASS=%s", tclass == kMonomerClassCHEM ? kMonomerClassLINKER : tclass.c_str());
}
if (mol.getTemplateAtomSeqid(i) != -1 && tclass != kMonomerClassCHEM) // No SEQID for chem
out.printf(" SEQID=%d", mol.getTemplateAtomSeqid(i));
// if (mol.getTemplateAtomSeqName(i) && strlen(mol.getTemplateAtomSeqName(i)))
// out.printf(" SEQNAME=%s", mol.getTemplateAtomSeqName(i));
if (mol.template_attachment_points.size() > 0)
{
int ap_count = mol.getTemplateAtomAttachmentPointsCount(i);
if (ap_count)
{
out.printf(" ATTCHORD=(%d", ap_count * 2);
for (int j = mol.template_attachment_points.begin(); j != mol.template_attachment_points.end(); j = mol.template_attachment_points.next(j))
{
BaseMolecule::TemplateAttPoint& ap = mol.template_attachment_points.at(j);
if (ap.ap_occur_idx == i)
{
out.printf(" %d %s", _atom_mapping[ap.ap_aidx], ap.ap_id.ptr());
}
}
out.printf(")");
}
}
}
if (mol.attachmentPointCount() > 0)
{
int val = 0;
for (int idx = 1; idx <= mol.attachmentPointCount(); idx++)
{
for (int j = 0; mol.getAttachmentPoint(idx, j) != -1; j++)
if (mol.getAttachmentPoint(idx, j) == i)
{
val |= 1 << (idx - 1);
break;
}
}
if (val > 0)
out.printf(" ATTCHPT=%d", val == 3 ? -1 : val);
}
if (qmol != 0)
{
int unsat;
if (qmol->getAtom(i).sureValue(QueryMolecule::ATOM_UNSATURATION, unsat))
out.printf(" UNSAT=1");
int subst;
if (MoleculeSavers::getSubstitutionCountFlagValue(*qmol, i, subst))
out.printf(" SUBST=%d", subst);
int rbc;
if (MoleculeSavers::getRingBondCountFlagValue(*qmol, i, rbc))
out.printf(" RBCNT=%d", rbc > MAX_RING_BOND_COUNT ? MAX_RING_BOND_COUNT : rbc);
}
_writeMultiString(output, buf.ptr(), buf.size());
}
output.writeStringCR("M V30 END ATOM");
output.writeStringCR("M V30 BEGIN BOND");
iw = 1;
for (i = mol.edgeBegin(); i < mol.edgeEnd(); i = mol.edgeNext(i), iw++)
{
const Edge& edge = mol.getEdge(i);
int bond_order = mol.getBondOrder(i);
ArrayOutput out(buf);
_bond_mapping[i] = iw;
if (bond_order < 0 && qmol != 0)
{
int qb = QueryMolecule::getQueryBondType(qmol->getBond(i));
if (qb == _BOND_SINGLE_OR_DOUBLE || qb == _BOND_SINGLE_OR_AROMATIC || qb == _BOND_DOUBLE_OR_AROMATIC || qb == _BOND_ANY)
bond_order = qb;
}
if (bond_order < 0)
throw Error("unrepresentable query bond");
if (bond_order == BOND_ZERO)
{
bond_order = _BOND_COORDINATION;
if ((mol.getAtomNumber(edge.beg) == ELEM_H) || (mol.getAtomNumber(edge.end) == ELEM_H))
bond_order = _BOND_HYDROGEN;
}
out.printf("%d %d %d %d", iw, bond_order, _atom_mapping[edge.beg], _atom_mapping[edge.end]);
int direction = mol.getBondDirection(i);
switch (direction)
{
case BOND_UP:
out.printf(" CFG=1");
break;
case BOND_EITHER:
out.printf(" CFG=2");
break;
case BOND_DOWN:
out.printf(" CFG=3");
break;
case 0:
if (mol.cis_trans.isIgnored(i))
if (!_hasNeighborEitherBond(mol, i))
out.printf(" CFG=2");
break;
}
int reacting_center = 0;
reacting_center = mol.reaction_bond_reacting_center[i];
if (reacting_center != 0)
out.printf(" RXCTR=%d", reacting_center);
int indigo_topology = -1;
if (qmol != 0)
qmol->getBond(i).sureValue(QueryMolecule::BOND_TOPOLOGY, indigo_topology);
int topology = 0;
if (indigo_topology == TOPOLOGY_RING)
topology = 1;
else if (indigo_topology == TOPOLOGY_CHAIN)
topology = 2;
if (topology != 0)
out.printf(" TOPO=%d", topology);
_writeMultiString(output, buf.ptr(), buf.size());
}
output.writeStringCR("M V30 END BOND");
MoleculeStereocenters& stereocenters = mol.stereocenters;
if (stereocenters.begin() != stereocenters.end() || mol.hasHighlighting())
{
output.writeStringCR("M V30 BEGIN COLLECTION");
QS_DEF(Array<int>, processed);
processed.clear_resize(mol.vertexEnd());
processed.zerofill();
for (i = mol.vertexBegin(); i != mol.vertexEnd(); i = mol.vertexNext(i))
{
if (processed[i])
continue;
ArrayOutput out(buf);
int j, type = stereocenters.getType(i);
if (type == MoleculeStereocenters::ATOM_ABS)
out.writeString("MDLV30/STEABS ATOMS=(");
else if (type == MoleculeStereocenters::ATOM_OR)
out.printf("MDLV30/STEREL%d ATOMS=(", stereocenters.getGroup(i));
else if (type == MoleculeStereocenters::ATOM_AND)
out.printf("MDLV30/STERAC%d ATOMS=(", stereocenters.getGroup(i));
else
continue;
QS_DEF(Array<int>, list);
list.clear();
list.push(i);
for (j = mol.vertexNext(i); j < mol.vertexEnd(); j = mol.vertexNext(j))
if (stereocenters.sameGroup(i, j))
{
list.push(j);
processed[j] = 1;
}
out.printf("%d", list.size());
for (j = 0; j < list.size(); j++)
out.printf(" %d", _atom_mapping[list[j]]);
out.writeChar(')');
_writeMultiString(output, buf.ptr(), buf.size());
}
if (mol.hasHighlighting())
{
if (mol.countHighlightedBonds() > 0)
{
ArrayOutput out(buf);
out.printf("MDLV30/HILITE BONDS=(%d", mol.countHighlightedBonds());
for (i = mol.edgeBegin(); i != mol.edgeEnd(); i = mol.edgeNext(i))
if (mol.isBondHighlighted(i))
out.printf(" %d", _bond_mapping[i]);
out.writeChar(')');
_writeMultiString(output, buf.ptr(), buf.size());
}
if (mol.countHighlightedAtoms() > 0)
{
ArrayOutput out(buf);
out.printf("MDLV30/HILITE ATOMS=(%d", mol.countHighlightedAtoms());
for (i = mol.vertexBegin(); i != mol.vertexEnd(); i = mol.vertexNext(i))
if (mol.isAtomHighlighted(i))
out.printf(" %d", _atom_mapping[i]);
out.writeChar(')');
_writeMultiString(output, buf.ptr(), buf.size());
}
}
if (mol.custom_collections.size() > 0)
{
for (i = mol.custom_collections.begin(); i != mol.custom_collections.end(); i = mol.custom_collections.next(i))
{
ArrayOutput out(buf);
out.printf("%s", mol.custom_collections.at(i));
_writeMultiString(output, buf.ptr(), buf.size());
}
}
output.writeStringCR("M V30 END COLLECTION");
}
QS_DEF(Array<int>, sgs_sorted);
_checkSGroupIndices(mol, sgs_sorted);
if (mol.countSGroups() > 0)
{
MoleculeSGroups* sgroups = &mol.sgroups;
int idx = 1;
output.writeStringCR("M V30 BEGIN SGROUP");
for (i = 0; i < sgs_sorted.size(); i++)
{
ArrayOutput out(buf);
int sg_idx = sgs_sorted[i];
SGroup& sgroup = sgroups->getSGroup(sg_idx);
_writeGenericSGroup3000(sgroup, idx++, out);
if (sgroup.sgroup_type == SGroup::SG_TYPE_GEN)
{
_writeMultiString(output, buf.ptr(), buf.size());
}
else if (sgroup.sgroup_type == SGroup::SG_TYPE_SUP)
{
Superatom& sup = static_cast<Superatom&>(sgroup);
if (sup.bond_connections.size() > 0)
{
for (int j = 0; j < sup.bond_connections.size(); j++)
{
out.printf(" CSTATE=(4 %d %f %f %f)", _bond_mapping[sup.bond_connections[j].bond_idx], sup.bond_connections[j].bond_dir.x,
sup.bond_connections[j].bond_dir.y, 0.f);
}
}
if (sup.subscript.size() > 1)
{
if (sup.subscript.find(' ') > -1)
out.printf(" LABEL=\"%s\"", sup.subscript.ptr());
else
out.printf(" LABEL=%s", sup.subscript.ptr());
}
// convert CHEM to LINKER for BIOVIA
if (sup.sa_class.size() > 1)
out.printf(" CLASS=%s", sup.sa_class.ptr() == std::string(kMonomerClassCHEM) ? kMonomerClassLINKER : sup.sa_class.ptr());
if (sup.contracted == DisplayOption::Expanded)
out.printf(" ESTATE=E");
if (sup.attachment_points.size() > 0)
{
for (int j = sup.attachment_points.begin(); j < sup.attachment_points.end(); j = sup.attachment_points.next(j))
{
int leave_idx = 0;
if (sup.attachment_points[j].lvidx > -1)
leave_idx = _atom_mapping[sup.attachment_points[j].lvidx];
out.printf(" SAP=(3 %d %d %s)", _atom_mapping[sup.attachment_points[j].aidx], leave_idx, sup.attachment_points[j].apid.ptr());
}
}
if (sup.seqid > 0)
out.printf(" SEQID=%d", sup.seqid);
if (sup.sa_natreplace.size() > 1)
out.printf(" NATREPLACE=%s", sup.sa_natreplace.ptr());
_writeMultiString(output, buf.ptr(), buf.size());
}
else if (sgroup.sgroup_type == SGroup::SG_TYPE_DAT)
{
DataSGroup& dsg = static_cast<DataSGroup&>(sgroup);
const char* name = dsg.name.ptr();
if (name != 0 && strlen(name) > 0)
{
out.writeString(" FIELDNAME=");
bool space_found = (strchr(name, ' ') != NULL);
if (space_found)
out.writeString("\"");
out.writeString(name);
if (space_found)
out.writeString("\"");
}
const char* desc = dsg.description.ptr();
if (desc != 0 && strlen(desc) > 0)
{
out.writeString(" FIELDINFO=");
bool space_found = (strchr(desc, ' ') != NULL);
if (space_found)
out.writeString("\"");
out.writeString(desc);
if (space_found)
out.writeString("\"");
}
const char* querycode = dsg.querycode.ptr();
if (querycode != 0 && strlen(querycode) > 0)
{
out.writeString(" QUERYTYPE=");
bool space_found = (strchr(querycode, ' ') != NULL);
if (space_found)
out.writeString("\"");
out.writeString(querycode);
if (space_found)
out.writeString("\"");
}
const char* queryoper = dsg.queryoper.ptr();
if (queryoper != 0 && strlen(queryoper) > 0)
{
out.writeString(" QUERYOP=");
bool space_found = (strchr(queryoper, ' ') != NULL);
if (space_found)
out.writeString("\"");
out.writeString(queryoper);
if (space_found)
out.writeString("\"");
}
out.printf(" FIELDDISP=\"");
_writeDataSGroupDisplay(dsg, out);
out.printf("\"");
if (dsg.data.size() > 0 && dsg.data[0] != 0)
{
// Split field data by new lines
int len = dsg.data.size();
char* data = dsg.data.ptr();
while (len > 0)
{
int j;