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#include <BALL/MOLMEC/AMBER/GAFFTypeProcessor.h>
#include <BALL/QSAR/ringPerceptionProcessor.h>
#include <BALL/QSAR/aromaticityProcessor.h>
#include <BALL/KERNEL/PTE.h>
#include <BALL/KERNEL/selector.h>
#include <BALL/KERNEL/forEach.h>
#include <BALL/SYSTEM/path.h>
#include <BALL/STRUCTURE/assignBondOrderProcessor.h>
#include <queue>
//#define DEBUG
#undef DEBUG
namespace BALL
{
const String GAFFTypeProcessor::Option::ATOMTYPE_FILENAME = "atomtype_filename";
const String GAFFTypeProcessor::Default::ATOMTYPE_FILENAME = "Amber/GAFFTypes.dat";
// const String GAFFTypeProcessor::Default::ATOMTYPE_FILENAME = "Amber/AMBERTypes.dat";
const String GAFFTypeProcessor::Option::GAFF_ATOMTYPE_POSTPROCESSING = "gaff_atomtype_postprocessing";
const bool GAFFTypeProcessor::Default::GAFF_ATOMTYPE_POSTPROCESSING = true;
GAFFTypeProcessor::GAFFTypeProcessor()
: UnaryProcessor<Composite>()
{
options.setDefault(Option::ATOMTYPE_FILENAME, Default::ATOMTYPE_FILENAME);
options.setDefault(Option::GAFF_ATOMTYPE_POSTPROCESSING, Default::GAFF_ATOMTYPE_POSTPROCESSING);
parseAtomtypeTableFile_();
}
GAFFTypeProcessor::GAFFTypeProcessor(const Options& new_options)
: UnaryProcessor<Composite>(),
options(new_options)
{
options.setDefault(Option::ATOMTYPE_FILENAME, Default::ATOMTYPE_FILENAME);
options.setDefault(Option::GAFF_ATOMTYPE_POSTPROCESSING, Default::GAFF_ATOMTYPE_POSTPROCESSING);
parseAtomtypeTableFile_();
}
GAFFTypeProcessor::~GAFFTypeProcessor()
{
StringHashMap<GAFFCESParser*>::Iterator parser_it = ces_parsers_.begin();
for (; parser_it != ces_parsers_.end(); ++parser_it)
delete(parser_it->second);
}
Processor::Result GAFFTypeProcessor::operator() (Composite &composite)
{
// TODO: think whether application to other things than molecules would make sense...
if (RTTI::isKindOf<Molecule>(&composite))
{
Molecule *mol = RTTI::castTo<Molecule>(composite);
precomputeBondProperties_(mol);
precomputeAtomProperties_(mol);
AtomIterator atom_it = mol->beginAtom();
for ( ;+atom_it; ++atom_it)
{
try
{
assignAtomtype_(*atom_it);
}
catch(...)
{
Log.error()<< "GAFFTypeProcessor: Atom type could not be assigned!" << std::endl;
}
}
// decide whether we want post-processing of atom types
if (options.getBool(Option::GAFF_ATOMTYPE_POSTPROCESSING))
{
postProcessAtomTypes_(mol);
}
}
return Processor::CONTINUE;
}
std::set<String> GAFFTypeProcessor::getTypeNames() const
{
std::set<String> result;
for (std::map<Position, std::vector<TypeDefinition> >::const_iterator type_it = atom_types_.begin();
type_it != atom_types_.end();
++type_it)
{
std::vector<TypeDefinition> const& types = type_it->second;
for (Position i=0; i<types.size(); ++i)
{
result.insert(types[i].atom_type);
}
}
return result;
}
//read File with table of atomtypes and push atomtypes
//and their TypeDefinition in corresponding vector
//and store a GAFFCESParser for every CESstring
void GAFFTypeProcessor::parseAtomtypeTableFile_()
{
StringHashMap<GAFFCESParser*>::Iterator parser_it = ces_parsers_.begin();
for (; parser_it != ces_parsers_.end(); ++parser_it)
delete(parser_it->second);
ces_parsers_.clear();
std::ifstream atomfile;
Path path;
String filename = path.find(options.get(Option::ATOMTYPE_FILENAME));
atomfile.open(filename.c_str());
if (!atomfile)
{
Log.error() << "atomtype table could not be read!" << std::endl;
throw(Exception::FileNotFound(__FILE__, __LINE__, filename));
}
String table_line;
while (getline(atomfile,table_line))
{
TypeDefinition typeDefinition;
typeDefinition.atom_type = table_line.getField(0);
typeDefinition.atomic_number = table_line.getField(1).toInt();
typeDefinition.connectivity = table_line.getField(2).toInt();
typeDefinition.attached_hydrogens = table_line.getField(3);
typeDefinition.electron_withdrawal_atoms = table_line.getField(4);
typeDefinition.atomic_property = table_line.getField(5);
typeDefinition.chemical_environment = table_line.getField(6);
// create new parser to parse the given CESstring and store it
String to_parse = "";
if (typeDefinition.atomic_property != "*")
to_parse = typeDefinition.atomic_property;
else
// for our parser to work, we need to convert the GAFF
// wildcard * to a grammatically correct APS
to_parse = "[*]";
to_parse += typeDefinition.chemical_environment;
parser_it = ces_parsers_.find(to_parse);
if(parser_it == ces_parsers_.end()) {
ces_parsers_.insert(to_parse, new GAFFCESParser(to_parse));
}
// insert the type definition at the corresponding position
if (atom_types_.find(typeDefinition.atomic_number) == atom_types_.end())
{
std::vector<TypeDefinition> v;
atom_types_[typeDefinition.atomic_number] = v;
}
atom_types_[typeDefinition.atomic_number].push_back(typeDefinition);
}
}
// compute aromaticity, ring memberships, GAFF bond typization, ...
void GAFFTypeProcessor::precomputeBondProperties_(Molecule* molecule)
{
current_molecule_ = molecule;
RingPerceptionProcessor rpp;
rpp.calculateSSSR(sssr_, *molecule);
AromaticityProcessor arp;
arp.options.setBool(AromaticityProcessor::Option::OVERWRITE_BOND_ORDERS, false);
arp.aromatize(sssr_, *molecule);
annotateBondTypes_();
}
// store connectivity, number of attached H-atoms and
// number of attached N,O,F,Cl and Br-atoms for every atom in molecule
// NOTE: this function requires that precomputeBondProperties_ has been
// called previously
void GAFFTypeProcessor::precomputeAtomProperties_(Molecule* molecule)
{
annotateRingSizes_();
annotateAliphaticAndAromaticRingAtoms_();
annotatePlanarRingAtoms_();
AtomIterator atom_it = molecule->beginAtom();
for ( ; +atom_it; ++atom_it)
{
int connectivity = (atom_it->countBonds());
atom_it->setProperty("connectivity", connectivity);
int attached_hydrogens_int = 0;
int electron_withdrawal_atoms_int = 0;
String attached_hydrogens;
String electron_withdrawal_atoms;
Atom::BondIterator bond_it = atom_it->beginBond();
for ( ; +bond_it; ++bond_it)
{
const Atom& partner_atom = *(bond_it->getBoundAtom(*atom_it));
if (partner_atom.getElement() == PTE[Element::H])
{
++attached_hydrogens_int;
}
else
{
for (Atom::BondConstIterator constBond_it = partner_atom.beginBond(); +constBond_it; ++constBond_it)
{
//not to consider the atom we started at
if (constBond_it->getBoundAtom(partner_atom) == &(*atom_it))
continue;
const Atom& partner_partner_atom = *(constBond_it->getBoundAtom(partner_atom));
if ( (partner_partner_atom.getElement()== PTE[Element::N])
||(partner_partner_atom.getElement()== PTE[Element::O])
||(partner_partner_atom.getElement()== PTE[Element::F])
||(partner_partner_atom.getElement()== PTE[Element::Cl])
||(partner_partner_atom.getElement()== PTE[Element::Br])
||(partner_partner_atom.getElement()== PTE[Element::S]))
{
++electron_withdrawal_atoms_int;
}
}
}
}
String attached(attached_hydrogens_int);
String electron(electron_withdrawal_atoms_int);
attached_hydrogens = attached;
electron_withdrawal_atoms = electron;
atom_it->setProperty("attached hydrogens", (String) attached_hydrogens);
atom_it->setProperty("electron withdrawal atoms", (String) electron_withdrawal_atoms);
}
}
void GAFFTypeProcessor::annotateBondTypes_()
{
// store the old selection
std::list<Atom*> old_atom_selection;
std::list<Bond*> old_bond_selection;
// NOTE: we store each bond twice, but this does not really matter...
for (AtomIterator a_it = current_molecule_->beginAtom(); +a_it; ++a_it)
{
if (a_it->isSelected())
{
old_atom_selection.push_back(&*a_it);
}
for (Atom::BondIterator b_it = a_it->beginBond(); +b_it; ++b_it)
{
if (b_it->isSelected())
{
old_bond_selection.push_back(&*b_it);
}
}
}
current_molecule_->deselect();
// find conjugated atoms:
// select all carboxyl anions and nitro groups for delocalized bond types
Selector select("SMARTS([#16D1,#8D1]) AND SMARTS([#16D1,#8D1]~[*D3]~[#16D1,#8D1])");
// Selector select("SMARTS([#16D1,#8D1]) AND SMARTS([#16D1,#8D1]~*~[#16D1,#8D1]) AND (SMARTS(a) OR SMARTS(*=,#*-,=*=,#*) OR SMARTS([N,P,O,S]=,#*-[*;!H0]) OR SMARTS(*=,#*-[F,Cl,Br,I]) OR SMARTS(*=,#*-[N,P,O,S;!H0]))");
current_molecule_->apply(select);
// we know that the selected atoms only have one bond each. so we only need to make sure it really is a double bond
list<Atom*> selected_atoms = select.getSelectedAtoms();
list<Atom*>::iterator it = selected_atoms.begin();
for ( ; it != selected_atoms.end(); ++it)
{
Atom::BondIterator bond_it = (*it)->beginBond();
for( ; +bond_it; ++bond_it)
{
if (bond_it->getOrder() == Bond::ORDER__DOUBLE)
bond_it->setProperty("GAFFBondType", DL);
}
}
// restore the old selection
current_molecule_->deselect();
for (list<Atom*>::iterator al_it = old_atom_selection.begin(); al_it != old_atom_selection.end(); ++al_it)
(*al_it)->select();
for (list<Bond*>::iterator bl_it = old_bond_selection.begin(); bl_it != old_bond_selection.end(); ++bl_it)
(*bl_it)->select();
AtomIterator a_it = current_molecule_->beginAtom();
Atom::BondIterator b_it;
BALL_FOREACH_BOND(*current_molecule_, a_it, b_it)
{
// b_it is no delocalized bond
if ( !b_it->hasProperty("GAFFBondType")
|| (b_it->getProperty("GAFFBondType").getInt() != DL))
{
switch(b_it->getOrder())
{
case Bond::ORDER__SINGLE:
if (b_it->isAromatic())
{
b_it->setProperty("GAFFBondType", sb);
}
else
{
b_it->setProperty("GAFFBondType", SB);
}
break;
case Bond::ORDER__DOUBLE:
if (b_it->isAromatic())
{
b_it->setProperty("GAFFBondType", db);
}
else
{
b_it->setProperty("GAFFBondType", DB);
}
break;
case Bond::ORDER__TRIPLE:
b_it->setProperty("GAFFBondType", TB);
break;
case Bond::ORDER__AROMATIC:
b_it->setProperty("GAFFBondType", AB);
break;
}
}
}
}
void GAFFTypeProcessor::annotateRingSizes_()
{
std::vector<std::vector<Atom* > >::iterator ring_it = sssr_.begin();
for ( ; ring_it != sssr_.end(); ++ring_it)
{
String in_ring_property;
String num_rings_property;
// mark the number of occurence for the given feature
int occurence = 0;
bool in_ring = false;
switch (ring_it->size())
{
case 3: in_ring_property = "In3Ring";
num_rings_property = "NumberOf3Rings";
occurence = 1;
in_ring = true;
break;
case 4: in_ring_property = "In4Ring";
num_rings_property = "NumberOf4Rings";
occurence = 1;
in_ring = true;
break;
case 5: in_ring_property = "In5Ring";
num_rings_property = "NumberOf5Rings";
occurence = 1;
in_ring = true;
break;
case 6: in_ring_property = "In6Ring";
num_rings_property = "NumberOf6Rings";
occurence = 1;
in_ring = true;
break;
case 7: in_ring_property = "In7Ring";
num_rings_property = "NumberOf7Rings";
occurence = 1;
in_ring = true;
break;
case 8: in_ring_property = "In8Ring";
num_rings_property = "NumberOf8Rings";
occurence = 1;
in_ring = true;
break;
case 9: in_ring_property = "In9Ring";
num_rings_property = "NumberOf9Rings";
occurence = 1;
in_ring = true;
break;
default: in_ring = false;
}
// set property to current in ring for every atom
// note: we count the occurence of the property within an atom
std::vector<Atom*>::iterator atom_it = ring_it->begin();
for ( ; atom_it != ring_it->end(); ++atom_it)
{
occurence = ((*atom_it)->getProperty(num_rings_property).getInt()) + occurence;
(*atom_it)->setProperty(in_ring_property, (bool) in_ring);
(*atom_it)->setProperty(num_rings_property, (int) occurence);
}
}
}
// checks if current atom is in an aliphatic ringsystem,
// which is made of sp3 Carbon or a purely aromatic six-membered ring
void GAFFTypeProcessor::annotateAliphaticAndAromaticRingAtoms_()
{
std::vector<std::vector<Atom* > >::iterator ring_it = sssr_.begin();
for ( ; ring_it != sssr_.end(); ++ring_it)
{
bool purely_aliphatic = true;
bool purely_aromatic = true;
// bool has_sp3_carbon = false;
vector<Atom*>::iterator atom_it = ring_it->begin();
for ( ; atom_it != ring_it->end(); ++atom_it)
{
//TODO why needed? has_sp3_carbon is just local and used nowhere else...
// if( ((*atom_it)->getElement() == PTE[Element::C]) && ((*atom_it)->countBonds() == 4))
// has_sp3_carbon = true;
// if one ring member is not sp3 carbon, the whole thing isn't
if( ((*atom_it)->getElement() != PTE[Element::C]) || ((*atom_it)->countBonds() != 4))
{
purely_aliphatic = false;
}
// NOTE: antechamber defines purely aromatic only for 6-membered rings!
if ( !(*atom_it)->getProperty("IsAromatic").getBool() || (ring_it->size() != 6))
{
purely_aromatic = false;
}
}
for (atom_it = ring_it->begin(); atom_it != ring_it->end(); ++atom_it)
{
// do not overwrite the property if we have already detected a suitable ring!
if ( !(*atom_it)->hasProperty("IsPureAliphatic")
||!(*atom_it)->getProperty("IsPureAliphatic").getBool())
(*atom_it)->setProperty("IsPureAliphatic",(bool) purely_aliphatic);
if ( !(*atom_it)->hasProperty("IsPureAromatic")
||!(*atom_it)->getProperty("IsPureAromatic").getBool())
(*atom_it)->setProperty("IsPureAromatic",(bool) purely_aromatic);
}
}
}
// checks if current atom is in a planar ringsystem
void GAFFTypeProcessor::annotatePlanarRingAtoms_()
{
std::vector<std::vector<Atom* > >::iterator ring_it = sssr_.begin();
for( ; ring_it != sssr_.end(); ++ring_it)
{
bool is_planar = true;
bool has_db_to_non_ring = false;
vector<Atom*>::iterator atom_it = ring_it->begin();
for ( ; atom_it != ring_it->end(); ++atom_it)
{
// if one atom isn't planar, the whole ring isn't.
if ( !planarAtom_(**atom_it) )
{
is_planar = false;
break;
}
// is there one atom with a double bond to a non-ring?
if (!has_db_to_non_ring) // otherwise, we don't need to look for another one!
{
Atom::BondConstIterator constBond_it = (*atom_it)->beginBond();
for ( ; +constBond_it; ++constBond_it)
{
if ( (constBond_it->hasProperty("GAFFBondType"))
&& ( (constBond_it->getProperty("GAFFBondType").getInt() == DB)
|| (constBond_it->getProperty("GAFFBondType").getInt() == db))
)
{
const Atom* partner_atom = constBond_it->getBoundAtom(**atom_it);
if (!partner_atom->getProperty("InRing").getBool())
has_db_to_non_ring = true;
}
}
}
}
// if the ring is planar
if (is_planar)
{
for (atom_it = ring_it->begin(); atom_it != ring_it->end(); ++atom_it)
{
(*atom_it)->setProperty("IsPlanarRingAtom", true);
if (has_db_to_non_ring)
(*atom_it)->setProperty("IsPlanarWithDBtoNR", true);
else
(*atom_it)->setProperty("IsPlanarWithDBtoNR", false);
}
}
}
}
// check if current atom could be in a planar ring
// s.t. atom is a C(X3),N(X2),N(X3),O(X2),S(X2),P(X2),P(X3)
bool GAFFTypeProcessor::planarAtom_(const Atom& atom)
{
Element element = atom.getElement();
int num_bonds = atom.countBonds();
// C(X2) or C(X3)
if ( (element == PTE[Element::C])
&& ((num_bonds == 2) || (num_bonds == 3)))
return true;
// N(X2) or N(X3)
if ( (element == PTE[Element::N])
&& ((num_bonds == 2) || (num_bonds == 3)))
return true;
// P(X2) or P(X3)
if ( (element == PTE[Element::P])
&& ((num_bonds == 2) || (num_bonds == 3)))
return true;
// O(X2)
if ( (element == PTE[Element::O])
&& (num_bonds == 2))
return true;
// S(X2)
if ( (element == PTE[Element::S])
&& (num_bonds == 2))
return true;
return false;
}
bool GAFFTypeProcessor::assignAtomtype_(Atom& atom)
{
// can we match this atom at all?
if (atom_types_.find(atom.getElement().getAtomicNumber()) == atom_types_.end())
{
Log.error() << "GAFFTypeProcessor: could not assign atom type for " << atom.getFullName() << std::endl;
Log.error() << " Reason: no type definition for atomic number " << atom.getElement().getAtomicNumber() << " available!" << std::endl;
return false;
}
std::vector<TypeDefinition>& type_defs = atom_types_[atom.getElement().getAtomicNumber()];
for (Position i=0; i<type_defs.size(); i++)
{
TypeDefinition& typeDefinition = type_defs[i];
#ifdef DEBUG
Log.info() << "GAFFTypeProcessor: match atom " << atom.getFullName() << " against type " << typeDefinition.atom_type << std::endl;
Log.info() << "GAFFTypeProcessor: connectivity is " << atom.getProperty("connectivity").getInt() << " but should be " << typeDefinition.connectivity
<< std::endl;
#endif
// all fields with "*" are invalid and therefore considered as True
if ( (typeDefinition.connectivity < 0)
||(atom.getProperty("connectivity").getInt() == typeDefinition.connectivity))
{
#ifdef DEBUG
Log.info() << "GAFFTypeProcessor: number of attached hydrogens is " << atom.getProperty("attached hydrogens").getString()
<< " but should be " << typeDefinition.attached_hydrogens
<< std::endl;
#endif
if ( (atom.getProperty("attached hydrogens").getString() == typeDefinition.attached_hydrogens)
||(typeDefinition.attached_hydrogens == "*"))
{
#ifdef DEBUG
Log.info() << "GAFFTypeProcessor: number of electron withdrawal atoms is " << atom.getProperty("electron withdrawal atoms").getString()
<< " should be " << typeDefinition.electron_withdrawal_atoms
<< std::endl;
#endif
if ( (atom.getProperty("electron withdrawal atoms").getString() == typeDefinition.electron_withdrawal_atoms)
||(typeDefinition.electron_withdrawal_atoms == "*"))
{
String atomic_property = typeDefinition.atomic_property;
// add aps string to ces string for parsing
String to_match = "";
if (typeDefinition.atomic_property != "*")
{
to_match = typeDefinition.atomic_property;
}
else
{
// for our parser to work, we need to convert the GAFF
// wildcard * to a grammatically correct APS
to_match = "[*]";
}
to_match += typeDefinition.chemical_environment;
#ifdef DEBUG
Log.info() << "GAFFTypeProcessor: combined APS/CES to match is " << to_match << std::endl;
#endif
if ( (ces_parsers_.find(to_match) != ces_parsers_.end())
&& (ces_parsers_[to_match]->match(atom)))
{
#ifdef DEBUG
Log.info() << "atom name: " << atom.getName() << " atomtype:" << typeDefinition.atom_type << endl;
#endif
atom.setProperty("atomtype", typeDefinition.atom_type);
return true;
}
}
}
}
}
// if no type could be assigned return false
Log.error() << "GAFFTypeProcessor: could not assing a type for atom " << atom.getFullName()
<< "! Setting type to DU" << std::endl;
atom.setProperty("atomtype", String("DU")); //ANNE
return false;
}
void GAFFTypeProcessor::postProcessAtomTypes_(Molecule* molecule)
{
// first the code that corresponds to atadjust() in antechamber/atomtype.c
// what we try to do is the following: for each pair of conjugated atoms of particular atom types,
// try to achieve that the types differ along double bonds and are identical along single bonds.
//
// To this end, we will do a breadth-first search
std::queue<Atom*> search_queue;
std::map<Atom*, Index> new_type;
for (AtomIterator at_it = molecule->beginAtom(); +at_it; ++at_it)
{
for (Atom::BondIterator bond_it = at_it->beginBond(); +bond_it; ++bond_it)
{
const String& atomtype_first = at_it->getProperty("atomtype").getString();
const String& atomtype_second = bond_it->getPartner(*at_it)->getProperty("atomtype").getString();
if ( ( (atomtype_first == "cc") || (atomtype_first == "ce") || (atomtype_first == "cg")
|| (atomtype_first == "pc") || (atomtype_first == "pe") || (atomtype_first == "nc")
|| (atomtype_first == "ne") )
&&( (atomtype_second == "cc") || (atomtype_second == "ce") || (atomtype_second == "cg")
|| (atomtype_second == "pc") || (atomtype_second == "pe") || (atomtype_second == "nc")
|| (atomtype_second == "ne") ) )
{
new_type[&*at_it] = 0;
new_type[bond_it->getPartner(*at_it)] = 0;
}
}
}
Size number_to_cleanup = new_type.size();
// do we still have atom types to fix?
while (number_to_cleanup > 0)
{
// start the search at the first non-fixed atom
std::map<Atom*, Index>::iterator map_it = new_type.begin();
while ((map_it != new_type.end() && (map_it->second != 0)))
++map_it;
search_queue.push(map_it->first);
// and set its value fixed to 1
map_it->second = 1;
// one atom has now been fixed
--number_to_cleanup;
while (!search_queue.empty())
{
Atom* current_atom = search_queue.front();
search_queue.pop();
// iterate over current_atom's children
for (Atom::BondIterator bond_it = current_atom->beginBond(); +bond_it; ++bond_it)
{
// is this one of the interesting atoms?
Atom* child = bond_it->getPartner(*current_atom);
if (new_type.find(child) != new_type.end())
{
// have we seen it before?
if (new_type[child] == 0)
{
// nope => set its type and insert it into the queue
if (!bond_it->hasProperty("GAFFBondType"))
{
Log.error() << "GAFFTypeProcessor::postProcessAtomTypes_: missing bond type information! aborting!" << std::endl;
return;
}
Index bond_type = bond_it->getProperty("GAFFBondType").getInt();
if ( (bond_type == SB) || (bond_type == sb) )
{
// this is a single or aromatic single bond => propagate the same type as the parent atom
new_type[child] = new_type[current_atom];
--number_to_cleanup;
}
else if ( (bond_type == DB)
|| (bond_type == db)
|| (bond_type == TB) )
{
// this is a double, aromatic double, or triple bond => invert the type
new_type[child] = -new_type[current_atom];
--number_to_cleanup;
}
else
{
Log.error() << "GAFFTypeProcessor::postProcessAtomTypes_: delocalized or conjugated bond not allowed for this atom type! aborting!" << std::endl;
return;
}
search_queue.push(child);
}
}
}
}
}
// now compute the new types for our atoms
std::map<Atom*, Index>::iterator map_it = new_type.begin();
for (; map_it != new_type.end(); ++map_it)
{
if (map_it->second == -1)
{
// we compute the name of the new type by increasing the second letter by one position in the alphabet (e.g. cc => cd)
String new_atom_type = map_it->first->getProperty("atomtype").getString();
new_atom_type[1]+=1;
map_it->first->setProperty("atomtype", new_atom_type);
}
}
// now the code that corresponds to cpadjust() in antechamber/atomtype.c
// This is nearly equivalent to atadjust, just for cp only and with slightly different propagation rules
new_type.clear();
for (AtomIterator at_it = molecule->beginAtom(); +at_it; ++at_it)
{
for (Atom::BondIterator bond_it = at_it->beginBond(); +bond_it; ++bond_it)
{
const String& atomtype_first = at_it->getProperty("atomtype").getString();
const String& atomtype_second = bond_it->getPartner(*at_it)->getProperty("atomtype").getString();
if ( (atomtype_first == "cp")
&& (atomtype_second == "cp") )
{
new_type[&*at_it] = 0;
new_type[bond_it->getPartner(*at_it)] = 0;
}
}
}
number_to_cleanup = new_type.size();
// do we still have atom types to fix?
while (number_to_cleanup > 0)
{
// start the search at the first non-fixed atom
std::map<Atom*, Index>::iterator map_it = new_type.begin();
while ((map_it != new_type.end() && (map_it->second != 0)))
++map_it;
search_queue.push(map_it->first);
// and set its value fixed to 1
map_it->second = 1;
// one atom has now been fixed
--number_to_cleanup;
while (!search_queue.empty())
{
Atom* current_atom = search_queue.front();
search_queue.pop();
// iterate over current_atom's children
for (Atom::BondIterator bond_it = current_atom->beginBond(); +bond_it; ++bond_it)
{
// is this one of the interesting atoms?
Atom* child = bond_it->getPartner(*current_atom);
if (new_type.find(child) != new_type.end())
{
// have we seen it before?
if (new_type[child] == 0)
{
// nope => set its type and insert it into the queue
if (!bond_it->hasProperty("GAFFBondType"))
{
Log.error() << "GAFFTypeProcessor::postProcessAtomTypes_: missing bond type information! aborting!" << std::endl;
return;
}
Index bond_type = bond_it->getProperty("GAFFBondType").getInt();
if (bond_type == SB)
{
// this is a single bond => propagate the same type as the parent atom
new_type[child] = new_type[current_atom];
--number_to_cleanup;
}
else
{
// this is anything but a single bond => invert the type
new_type[child] = -new_type[current_atom];
--number_to_cleanup;
}
search_queue.push(child);
}
}
}
}
}
// now compute the new types for our atoms
map_it = new_type.begin();
for (; map_it != new_type.end(); ++map_it)
{
if (map_it->second == -1)
{
// we compute the name of the new type by increasing the second letter by one position in the alphabet (e.g. cc => cd)
String new_atom_type = map_it->first->getProperty("atomtype").getString();
new_atom_type[1]+=1;
map_it->first->setProperty("atomtype", new_atom_type);
}
}
}
}
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