/src/openbabel/src/stereo/cistrans.cpp

Source
#include <openbabel/stereo/cistrans.h>
#include <openbabel/mol.h>
#include <openbabel/atom.h>
#include <openbabel/oberror.h>

using namespace std;

namespace OpenBabel {

  //
  // OBCisTransStereo::Config struct
  //

  bool OBCisTransStereo::Config::operator==(const Config &other) const
  {
    if ((begin != other.begin) && (begin != other.end))
      return false;
    if ((end != other.begin) && (end != other.end))
      return false;
    if ((refs.size() != 4) || (other.refs.size() != 4))
      return false;

    Config u1, u2;
    if (!OBStereo::ContainsSameRefs(refs, other.refs)) {
      // find a ref that occurs in both
      for (OBStereo::ConstRefIter i = refs.begin(); i != refs.end(); ++i)
        if (OBStereo::ContainsRef(other.refs, *i)) {
          u1 = OBTetraPlanarStereo::ToConfig(*this, *i, OBStereo::ShapeU); // refs[0] = u1.refs[0]
          u2 = OBTetraPlanarStereo::ToConfig(other, *i, OBStereo::ShapeU); // refs[0] = u2.refs[0]
        }

      // check if they actualy share an id...
      if (u1.refs.empty())
        return false;
    } else {
      // normalize the other Config struct
      u1 = OBTetraPlanarStereo::ToConfig(*this, refs.at(0), OBStereo::ShapeU); // refs[0] = u1.refs[0]
      u2 = OBTetraPlanarStereo::ToConfig(other, refs.at(0), OBStereo::ShapeU); // refs[0] = u2.refs[0]
      // both now start with the same ref
      //
      // 2 possiblilities:
      //
      //   1 2 3 4      1 2 3 4
      //   |   |        |   |      <- in any case, refs[0] & refs[2] remain unchanged
      //   1 2 3 4      1 4 3 2
      //
      return (u1.refs[2] == u2.refs[2]);
    }

    // possibilities:
    //
    //   1 2 3 4
    //   |   |      <- refs[0] & refs[2] remain unchanged
    //   1 H 3 H
    //
    //   1 2 3 4
    //   |     |    <- refs[0] & refs[3] remain unchanged
    //   1 H H 4
    //
    //   1 2 3 4
    //   | |        <- refs[0] & refs[1] remain unchanged
    //   1 2 H H
    if ((u1.refs[2] == OBStereo::ImplicitRef) || (u2.refs[2] == OBStereo::ImplicitRef)) {
      // 1 2 H 4
      if ((u1.refs[3] == OBStereo::ImplicitRef) || (u2.refs[3] == OBStereo::ImplicitRef)) {
        return (u1.refs[1] == u2.refs[1]); // 1 2 H H
      } else {
        return (u1.refs[3] == u2.refs[3]); // 1 H H 4
      }
    } else
      return (u1.refs[2] == u2.refs[2]); // 1 2 3 4  &  1 H 3 4  &  1 2 3 H

    return false;
  }

  //
  // OBCisTransStereo class
  //

  OBCisTransStereo::OBCisTransStereo(OBMol *mol) : OBTetraPlanarStereo(mol)
  {
  }

  OBCisTransStereo::~OBCisTransStereo()
  {
  }

  bool OBCisTransStereo::IsValid() const
  {
    if ((m_cfg.begin == OBStereo::NoRef) || (m_cfg.end == OBStereo::NoRef))
      return false;
    if (m_cfg.refs.size() != 4)
      return false;
    return true;
  }

  void OBCisTransStereo::SetConfig(const Config &config)
  {
    if (config.begin == OBStereo::NoRef) {
      obErrorLog.ThrowError(__FUNCTION__,
          "OBCisTransStereo::SetConfig : double bond begin id is invalid.", obError);
      m_cfg = Config();
      return;
    }
    if (config.end == OBStereo::NoRef) {
      obErrorLog.ThrowError(__FUNCTION__,
          "OBCisTransStereo::SetConfig : double bond end id is invalid.", obError);
      m_cfg = Config();
      return;
    }
    if (config.refs.size() != 4) {
      std::stringstream ss;
      ss << "OBCisTransStereo::SetConfig : found " << config.refs.size();
      ss << " reference ids, should be 4.";
      obErrorLog.ThrowError(__FUNCTION__, ss.str(), obError);
      m_cfg = Config();
      return;
    }

    // store using U shape
    m_cfg = OBTetraPlanarStereo::ToConfig(config, config.refs.at(0), OBStereo::ShapeU);
  }

  OBCisTransStereo::Config OBCisTransStereo::GetConfig(OBStereo::Shape shape) const
  {
    if (!IsValid())
      return Config();

    return OBTetraPlanarStereo::ToConfig(m_cfg, m_cfg.refs.at(0), shape);
  }

  OBCisTransStereo::Config OBCisTransStereo::GetConfig(unsigned long start,
      OBStereo::Shape shape) const
  {
    if (!IsValid())
      return Config();

    return OBTetraPlanarStereo::ToConfig(m_cfg, start, shape);
  }

  bool OBCisTransStereo::IsTrans(unsigned long id1, unsigned long id2) const
  {
    return (GetTransRef(id1) == id2);
  }

  bool OBCisTransStereo::IsCis(unsigned long id1, unsigned long id2) const
  {
    return (GetCisRef(id1) == id2);
  }

  bool OBCisTransStereo::operator==(const OBCisTransStereo &other) const
  {
    if (!IsValid() || !other.IsValid())
      return false;

    Config u = OBTetraPlanarStereo::ToConfig(other.GetConfig(),
        m_cfg.refs.at(0), OBStereo::ShapeU);
    unsigned long a1 = u.refs.at(0);
    unsigned long b1 = u.refs.at(2);

    if ((a1 == OBStereo::ImplicitRef) && (b1 == OBStereo::ImplicitRef)) {
      a1 = u.refs.at(1);
      b1 = u.refs.at(3);
    }

    if (b1 != OBStereo::ImplicitRef)
      if (a1 == GetTransRef(b1))
        return true;
    if (a1 != OBStereo::ImplicitRef)
      if (b1 == GetTransRef(a1))
        return true;

    return false;
  }

  unsigned long OBCisTransStereo::GetCisOrTransRef(unsigned long id, bool getcisref) const
  {
    if (!IsValid())
      return OBStereo::NoRef;

    if (id == OBStereo::ImplicitRef)
      return OBStereo::NoRef;

    // find id
    for (int i = 0; i < 4; ++i) {
      if (m_cfg.refs.at(i) == id) {
        // Use its index to find the index of the cis (or trans) atom
        int j;
        if (getcisref) // GetCisRef
          j = 3 - i; // Convert 0 to 3, and 3 to 0
        else // GetTransRef
          j = (i > 1) ? i - 2 : i + 2;

        unsigned long refId = m_cfg.refs.at(j);
        return refId;
      }
    }

    // id not found
    return OBStereo::NoRef;
  }

  unsigned long OBCisTransStereo::GetTransRef(unsigned long id) const
  {
    return GetCisOrTransRef(id, false);
  }

  unsigned long OBCisTransStereo::GetCisRef(unsigned long id) const
  {
    return GetCisOrTransRef(id, true);
  }

  bool OBCisTransStereo::IsOnSameAtom(unsigned long id1, unsigned long id2) const
  {
    const OBMol *mol = GetMolecule();
    if (!mol) {
      obErrorLog.ThrowError(__FUNCTION__, "OBCisTransStereo::IsOnSameAtom : No valid molecule set", obError);
      return false;
    }

    OBAtom *begin = mol->GetAtomById(m_cfg.begin);
    if (!begin) {
      obErrorLog.ThrowError(__FUNCTION__, "OBCisTransStereo::IsOnSameAtom : Begin reference id is not valid.", obError);
      return false;
    }
    OBAtom *end = mol->GetAtomById(m_cfg.end);
    if (!end) {
      obErrorLog.ThrowError(__FUNCTION__, "OBCisTransStereo::IsOnSameAtom : End reference id is not valid.", obError);
      return false;
    }

    OBAtom *a = mol->GetAtomById(id1);
    OBAtom *b = mol->GetAtomById(id2);

    if (a && b) {
      // both on begin atom?
      if (a->IsConnected(begin) && b->IsConnected(begin))
          return true;
      // both on end atom?
      if (a->IsConnected(end) && b->IsConnected(end))
          return true;
      return false;
    } else {
      if (a) {
        // b atom not found, could be a deleted hydrogen...
        if (a->IsConnected(begin)) {
          // a is connected to begin. if this is the atom missing a hydrogen, return false
          if (begin->GetExplicitDegree() == 2)
            return true;
          // check if the end atom really is missing an atom
          if (end->GetExplicitDegree() != 2) {
            obErrorLog.ThrowError(__FUNCTION__,
                "OBCisTransStereo::IsOnSameAtom : id2 is not valid and is not a missing hydrogen.", obError);
            return false;
          }
          // inform user we are treating id2 as deleted hydrogen
          obErrorLog.ThrowError(__FUNCTION__,
              "OBCisTransStereo::IsOnSameAtom : Atom with id2 doesn't exist anymore, must be a (deleted) hydrogen.", obInfo);
        } else if (a->IsConnected(end)) {
          // a is connected to end. again, if this is the atom missing a hydrogen, return false
          if (end->GetExplicitDegree() == 2)
            return true;
          // check if the begin atom really is missing an atom
          if (begin->GetExplicitDegree() != 2) {
            obErrorLog.ThrowError(__FUNCTION__,
                "OBCisTransStereo::IsOnSameAtom : id2 is not valid and is not a missing hydrogen.", obError);
            return true;
          }
          // inform user we are treating id2 as deleted hydrogen
          obErrorLog.ThrowError(__FUNCTION__,
              "OBCisTransStereo::IsOnSameAtom : Atom with id2 doesn't exist, must be a (deleted) hydrogen.", obInfo);

        } else {
          obErrorLog.ThrowError(__FUNCTION__,
              "OBCisTransStereo::IsOnSameAtom : Atom with id1 isn't connected to the begin or end atom.", obError);
          return true;
        }
      } else if (b) {
        // a atom not found, could be a deleted hydrogen...
        if (b->IsConnected(begin)) {
          // b is connected to begin. if this is the atom missing a hydrogen, return false
          if (begin->GetExplicitDegree() == 2)
            return true;
          // check if the end atom really is missing an atom
          if (end->GetExplicitDegree() != 2) {
            obErrorLog.ThrowError(__FUNCTION__,
                "OBCisTransStereo::IsOnSameAtom : id1 is not valid and is not a missing hydrogen.", obError);
            return true;
          }
          // inform user we are treating id1 as deleted hydrogen
          obErrorLog.ThrowError(__FUNCTION__,
              "OBCisTransStereo::IsOnSameAtom : Atom with id1 doesn't exist, must be a (deleted) hydrogen.", obInfo);
        } else if (b->IsConnected(end)) {
          // a is connected to end. again, if this is the atom missing a hydrogen, return false
          if (end->GetExplicitDegree() == 2)
            return true;
          // check if the begin atom really is missing an atom
          if (begin->GetExplicitDegree() != 2) {
            obErrorLog.ThrowError(__FUNCTION__,
                "OBCisTransStereo::IsOnSameAtom : id1 is not valid and is not a missing hydrogen.", obError);
            return true;
          }
          // inform user we are treating id2 as deleted hydrogen
          obErrorLog.ThrowError(__FUNCTION__,
              "OBCisTransStereo::IsOnSameAtom : Atom with id1 doesn't exist, must be a (deleted) hydrogen.", obInfo);
        } else {
          obErrorLog.ThrowError(__FUNCTION__,
              "OBCisTransStereo::IsOnSameAtom : Atom with id1 isn't connected to the begin or end atom.", obError);
          return true;
        }
      } else {
        OBAtom *c = nullptr, *d = nullptr;
        // no a & b, check the remaining ids which will reveal same info
        for (int i = 0; i < 4; ++i) {
          if ((m_cfg.refs.at(i) == id1) || (m_cfg.refs.at(i) == id2))
            continue;
          if (!c) {
            c = mol->GetAtomById(m_cfg.refs.at(i));
          } else {
            d = mol->GetAtomById(m_cfg.refs.at(i));
          }
        }
        if (!c || !d) {
          obErrorLog.ThrowError(__FUNCTION__, "OBCisTransStereo::IsOnSameAtom : invalid stereochemistry!", obError);
          return true;
        }
        if ((begin->GetExplicitDegree() != 2) || (end->GetExplicitDegree() != 2)) {
          obErrorLog.ThrowError(__FUNCTION__, "OBCisTransStereo::IsOnSameAtom : invalid stereochemistry!", obError);
          return true;
        }
        obErrorLog.ThrowError(__FUNCTION__,
            "OBCisTransStereo::IsOnSameAtom : Atoms with id1 & id2 don't exist, must be a (deleted) hydrogens.", obInfo);
        return IsOnSameAtom(c->GetId(), d->GetId());
      }
    }

    return false;
  }

  OBGenericData* OBCisTransStereo::Clone(OBBase *mol) const
  {
    OBCisTransStereo *data = new OBCisTransStereo(static_cast<OBMol*>(mol));
    data->SetConfig(m_cfg);
    return data;
  }

} // namespace OpenBabel

namespace std {

  ostream& operator<<(ostream &out, const OpenBabel::OBCisTransStereo &ct)
  {
    OpenBabel::OBCisTransStereo::Config cfg = ct.GetConfig();
    out << "OBCisTransStereo(begin = " << cfg.begin;
    out << ", end = " << cfg.end;

    out << ", refs = ";
    for (OpenBabel::OBStereo::Refs::iterator i = cfg.refs.begin(); i != cfg.refs.end(); ++i)
      if (*i != OpenBabel::OBStereo::ImplicitRef)
        out << *i << " ";
      else
        out << "H ";

    switch (cfg.shape) {
      case OpenBabel::OBStereo::ShapeU:
        out << ", shape = U)";
        break;
      case OpenBabel::OBStereo::ShapeZ:
        out << ", shape = Z)";
        break;
      case OpenBabel::OBStereo::Shape4:
        out << ", shape = 4)";
        break;
    }

    return out;
  }

  ostream& operator<<(ostream &out, const OpenBabel::OBCisTransStereo::Config &cfg)
  {
    out << "OBCisTransStereo::Config(begin = " << cfg.begin;
    out << ", end = " << cfg.end;

    out << ", refs = ";
    for (OpenBabel::OBStereo::Refs::const_iterator i = cfg.refs.begin(); i != cfg.refs.end(); ++i)
      if (*i != OpenBabel::OBStereo::ImplicitRef)
        out << *i << " ";
      else
        out << "H ";

    switch (cfg.shape) {
      case OpenBabel::OBStereo::ShapeU:
        out << ", shape = U)";
        break;
      case OpenBabel::OBStereo::ShapeZ:
        out << ", shape = Z)";
        break;
      case OpenBabel::OBStereo::Shape4:
        out << ", shape = 4)";
        break;
    }

    return out;
  }

} // namespace std


Coverage Report

Created: 2026-02-26 07:06

Line	Count	Source
1		#include <openbabel/stereo/cistrans.h>
2		#include <openbabel/mol.h>
3		#include <openbabel/atom.h>
4		#include <openbabel/oberror.h>
5
6		using namespace std;
7
8		namespace OpenBabel {
9
10		//
11		// OBCisTransStereo::Config struct
12		//
13
14		bool OBCisTransStereo::Config::operator==(const Config &other) const
15	0	{
16	0	if ((begin != other.begin) && (begin != other.end))
17	0	return false;
18	0	if ((end != other.begin) && (end != other.end))
19	0	return false;
20	0	if ((refs.size() != 4) \|\| (other.refs.size() != 4))
21	0	return false;
22
23	0	Config u1, u2;
24	0	if (!OBStereo::ContainsSameRefs(refs, other.refs)) {
25		// find a ref that occurs in both
26	0	for (OBStereo::ConstRefIter i = refs.begin(); i != refs.end(); ++i)
27	0	if (OBStereo::ContainsRef(other.refs, *i)) {
28	0	u1 = OBTetraPlanarStereo::ToConfig(this, i, OBStereo::ShapeU); // refs[0] = u1.refs[0]
29	0	u2 = OBTetraPlanarStereo::ToConfig(other, *i, OBStereo::ShapeU); // refs[0] = u2.refs[0]
30	0	}
31
32		// check if they actualy share an id...
33	0	if (u1.refs.empty())
34	0	return false;
35	0	} else {
36		// normalize the other Config struct
37	0	u1 = OBTetraPlanarStereo::ToConfig(*this, refs.at(0), OBStereo::ShapeU); // refs[0] = u1.refs[0]
38	0	u2 = OBTetraPlanarStereo::ToConfig(other, refs.at(0), OBStereo::ShapeU); // refs[0] = u2.refs[0]
39		// both now start with the same ref
40		//
41		// 2 possiblilities:
42		//
43		// 1 2 3 4 1 2 3 4
44		// \| \| \| \| <- in any case, refs[0] & refs[2] remain unchanged
45		// 1 2 3 4 1 4 3 2
46		//
47	0	return (u1.refs[2] == u2.refs[2]);
48	0	}
49
50		// possibilities:
51		//
52		// 1 2 3 4
53		// \| \| <- refs[0] & refs[2] remain unchanged
54		// 1 H 3 H
55		//
56		// 1 2 3 4
57		// \| \| <- refs[0] & refs[3] remain unchanged
58		// 1 H H 4
59		//
60		// 1 2 3 4
61		// \| \| <- refs[0] & refs[1] remain unchanged
62		// 1 2 H H
63	0	if ((u1.refs[2] == OBStereo::ImplicitRef) \|\| (u2.refs[2] == OBStereo::ImplicitRef)) {
64		// 1 2 H 4
65	0	if ((u1.refs[3] == OBStereo::ImplicitRef) \|\| (u2.refs[3] == OBStereo::ImplicitRef)) {
66	0	return (u1.refs[1] == u2.refs[1]); // 1 2 H H
67	0	} else {
68	0	return (u1.refs[3] == u2.refs[3]); // 1 H H 4
69	0	}
70	0	} else
71	0	return (u1.refs[2] == u2.refs[2]); // 1 2 3 4 & 1 H 3 4 & 1 2 3 H
72
73	0	return false;
74	0	}
75
76		//
77		// OBCisTransStereo class
78		//
79
80	0	OBCisTransStereo::OBCisTransStereo(OBMol *mol) : OBTetraPlanarStereo(mol)
81	0	{
82	0	}
83
84		OBCisTransStereo::~OBCisTransStereo()
85	0	{
86	0	}
87
88		bool OBCisTransStereo::IsValid() const
89	0	{
90	0	if ((m_cfg.begin == OBStereo::NoRef) \|\| (m_cfg.end == OBStereo::NoRef))
91	0	return false;
92	0	if (m_cfg.refs.size() != 4)
93	0	return false;
94	0	return true;
95	0	}
96
97		void OBCisTransStereo::SetConfig(const Config &config)
98	0	{
99	0	if (config.begin == OBStereo::NoRef) {
100	0	obErrorLog.ThrowError(__FUNCTION__,
101	0	"OBCisTransStereo::SetConfig : double bond begin id is invalid.", obError);
102	0	m_cfg = Config();
103	0	return;
104	0	}
105	0	if (config.end == OBStereo::NoRef) {
106	0	obErrorLog.ThrowError(__FUNCTION__,
107	0	"OBCisTransStereo::SetConfig : double bond end id is invalid.", obError);
108	0	m_cfg = Config();
109	0	return;
110	0	}
111	0	if (config.refs.size() != 4) {
112	0	std::stringstream ss;
113	0	ss << "OBCisTransStereo::SetConfig : found " << config.refs.size();
114	0	ss << " reference ids, should be 4.";
115	0	obErrorLog.ThrowError(__FUNCTION__, ss.str(), obError);
116	0	m_cfg = Config();
117	0	return;
118	0	}
119
120		// store using U shape
121	0	m_cfg = OBTetraPlanarStereo::ToConfig(config, config.refs.at(0), OBStereo::ShapeU);
122	0	}
123
124		OBCisTransStereo::Config OBCisTransStereo::GetConfig(OBStereo::Shape shape) const
125	0	{
126	0	if (!IsValid())
127	0	return Config();
128
129	0	return OBTetraPlanarStereo::ToConfig(m_cfg, m_cfg.refs.at(0), shape);
130	0	}
131
132		OBCisTransStereo::Config OBCisTransStereo::GetConfig(unsigned long start,
133		OBStereo::Shape shape) const
134	0	{
135	0	if (!IsValid())
136	0	return Config();
137
138	0	return OBTetraPlanarStereo::ToConfig(m_cfg, start, shape);
139	0	}
140
141		bool OBCisTransStereo::IsTrans(unsigned long id1, unsigned long id2) const
142	0	{
143	0	return (GetTransRef(id1) == id2);
144	0	}
145
146		bool OBCisTransStereo::IsCis(unsigned long id1, unsigned long id2) const
147	0	{
148	0	return (GetCisRef(id1) == id2);
149	0	}
150
151		bool OBCisTransStereo::operator==(const OBCisTransStereo &other) const
152	0	{
153	0	if (!IsValid() \|\| !other.IsValid())
154	0	return false;
155
156	0	Config u = OBTetraPlanarStereo::ToConfig(other.GetConfig(),
157	0	m_cfg.refs.at(0), OBStereo::ShapeU);
158	0	unsigned long a1 = u.refs.at(0);
159	0	unsigned long b1 = u.refs.at(2);
160
161	0	if ((a1 == OBStereo::ImplicitRef) && (b1 == OBStereo::ImplicitRef)) {
162	0	a1 = u.refs.at(1);
163	0	b1 = u.refs.at(3);
164	0	}
165
166	0	if (b1 != OBStereo::ImplicitRef)
167	0	if (a1 == GetTransRef(b1))
168	0	return true;
169	0	if (a1 != OBStereo::ImplicitRef)
170	0	if (b1 == GetTransRef(a1))
171	0	return true;
172
173	0	return false;
174	0	}
175
176		unsigned long OBCisTransStereo::GetCisOrTransRef(unsigned long id, bool getcisref) const
177	0	{
178	0	if (!IsValid())
179	0	return OBStereo::NoRef;
180
181	0	if (id == OBStereo::ImplicitRef)
182	0	return OBStereo::NoRef;
183
184		// find id
185	0	for (int i = 0; i < 4; ++i) {
186	0	if (m_cfg.refs.at(i) == id) {
187		// Use its index to find the index of the cis (or trans) atom
188	0	int j;
189	0	if (getcisref) // GetCisRef
190	0	j = 3 - i; // Convert 0 to 3, and 3 to 0
191	0	else // GetTransRef
192	0	j = (i > 1) ? i - 2 : i + 2;
193
194	0	unsigned long refId = m_cfg.refs.at(j);
195	0	return refId;
196	0	}
197	0	}
198
199		// id not found
200	0	return OBStereo::NoRef;
201	0	}
202
203		unsigned long OBCisTransStereo::GetTransRef(unsigned long id) const
204	0	{
205	0	return GetCisOrTransRef(id, false);
206	0	}
207
208		unsigned long OBCisTransStereo::GetCisRef(unsigned long id) const
209	0	{
210	0	return GetCisOrTransRef(id, true);
211	0	}
212
213		bool OBCisTransStereo::IsOnSameAtom(unsigned long id1, unsigned long id2) const
214	0	{
215	0	const OBMol *mol = GetMolecule();
216	0	if (!mol) {
217	0	obErrorLog.ThrowError(__FUNCTION__, "OBCisTransStereo::IsOnSameAtom : No valid molecule set", obError);
218	0	return false;
219	0	}
220
221	0	OBAtom *begin = mol->GetAtomById(m_cfg.begin);
222	0	if (!begin) {
223	0	obErrorLog.ThrowError(__FUNCTION__, "OBCisTransStereo::IsOnSameAtom : Begin reference id is not valid.", obError);
224	0	return false;
225	0	}
226	0	OBAtom *end = mol->GetAtomById(m_cfg.end);
227	0	if (!end) {
228	0	obErrorLog.ThrowError(__FUNCTION__, "OBCisTransStereo::IsOnSameAtom : End reference id is not valid.", obError);
229	0	return false;
230	0	}
231
232	0	OBAtom *a = mol->GetAtomById(id1);
233	0	OBAtom *b = mol->GetAtomById(id2);
234
235	0	if (a && b) {
236		// both on begin atom?
237	0	if (a->IsConnected(begin) && b->IsConnected(begin))
238	0	return true;
239		// both on end atom?
240	0	if (a->IsConnected(end) && b->IsConnected(end))
241	0	return true;
242	0	return false;
243	0	} else {
244	0	if (a) {
245		// b atom not found, could be a deleted hydrogen...
246	0	if (a->IsConnected(begin)) {
247		// a is connected to begin. if this is the atom missing a hydrogen, return false
248	0	if (begin->GetExplicitDegree() == 2)
249	0	return true;
250		// check if the end atom really is missing an atom
251	0	if (end->GetExplicitDegree() != 2) {
252	0	obErrorLog.ThrowError(__FUNCTION__,
253	0	"OBCisTransStereo::IsOnSameAtom : id2 is not valid and is not a missing hydrogen.", obError);
254	0	return false;
255	0	}
256		// inform user we are treating id2 as deleted hydrogen
257	0	obErrorLog.ThrowError(__FUNCTION__,
258	0	"OBCisTransStereo::IsOnSameAtom : Atom with id2 doesn't exist anymore, must be a (deleted) hydrogen.", obInfo);
259	0	} else if (a->IsConnected(end)) {
260		// a is connected to end. again, if this is the atom missing a hydrogen, return false
261	0	if (end->GetExplicitDegree() == 2)
262	0	return true;
263		// check if the begin atom really is missing an atom
264	0	if (begin->GetExplicitDegree() != 2) {
265	0	obErrorLog.ThrowError(__FUNCTION__,
266	0	"OBCisTransStereo::IsOnSameAtom : id2 is not valid and is not a missing hydrogen.", obError);
267	0	return true;
268	0	}
269		// inform user we are treating id2 as deleted hydrogen
270	0	obErrorLog.ThrowError(__FUNCTION__,
271	0	"OBCisTransStereo::IsOnSameAtom : Atom with id2 doesn't exist, must be a (deleted) hydrogen.", obInfo);
272
273	0	} else {
274	0	obErrorLog.ThrowError(__FUNCTION__,
275	0	"OBCisTransStereo::IsOnSameAtom : Atom with id1 isn't connected to the begin or end atom.", obError);
276	0	return true;
277	0	}
278	0	} else if (b) {
279		// a atom not found, could be a deleted hydrogen...
280	0	if (b->IsConnected(begin)) {
281		// b is connected to begin. if this is the atom missing a hydrogen, return false
282	0	if (begin->GetExplicitDegree() == 2)
283	0	return true;
284		// check if the end atom really is missing an atom
285	0	if (end->GetExplicitDegree() != 2) {
286	0	obErrorLog.ThrowError(__FUNCTION__,
287	0	"OBCisTransStereo::IsOnSameAtom : id1 is not valid and is not a missing hydrogen.", obError);
288	0	return true;
289	0	}
290		// inform user we are treating id1 as deleted hydrogen
291	0	obErrorLog.ThrowError(__FUNCTION__,
292	0	"OBCisTransStereo::IsOnSameAtom : Atom with id1 doesn't exist, must be a (deleted) hydrogen.", obInfo);
293	0	} else if (b->IsConnected(end)) {
294		// a is connected to end. again, if this is the atom missing a hydrogen, return false
295	0	if (end->GetExplicitDegree() == 2)
296	0	return true;
297		// check if the begin atom really is missing an atom
298	0	if (begin->GetExplicitDegree() != 2) {
299	0	obErrorLog.ThrowError(__FUNCTION__,
300	0	"OBCisTransStereo::IsOnSameAtom : id1 is not valid and is not a missing hydrogen.", obError);
301	0	return true;
302	0	}
303		// inform user we are treating id2 as deleted hydrogen
304	0	obErrorLog.ThrowError(__FUNCTION__,
305	0	"OBCisTransStereo::IsOnSameAtom : Atom with id1 doesn't exist, must be a (deleted) hydrogen.", obInfo);
306	0	} else {
307	0	obErrorLog.ThrowError(__FUNCTION__,
308	0	"OBCisTransStereo::IsOnSameAtom : Atom with id1 isn't connected to the begin or end atom.", obError);
309	0	return true;
310	0	}
311	0	} else {
312	0	OBAtom c = nullptr, d = nullptr;
313		// no a & b, check the remaining ids which will reveal same info
314	0	for (int i = 0; i < 4; ++i) {
315	0	if ((m_cfg.refs.at(i) == id1) \|\| (m_cfg.refs.at(i) == id2))
316	0	continue;
317	0	if (!c) {
318	0	c = mol->GetAtomById(m_cfg.refs.at(i));
319	0	} else {
320	0	d = mol->GetAtomById(m_cfg.refs.at(i));
321	0	}
322	0	}
323	0	if (!c \|\| !d) {
324	0	obErrorLog.ThrowError(__FUNCTION__, "OBCisTransStereo::IsOnSameAtom : invalid stereochemistry!", obError);
325	0	return true;
326	0	}
327	0	if ((begin->GetExplicitDegree() != 2) \|\| (end->GetExplicitDegree() != 2)) {
328	0	obErrorLog.ThrowError(__FUNCTION__, "OBCisTransStereo::IsOnSameAtom : invalid stereochemistry!", obError);
329	0	return true;
330	0	}
331	0	obErrorLog.ThrowError(__FUNCTION__,
332	0	"OBCisTransStereo::IsOnSameAtom : Atoms with id1 & id2 don't exist, must be a (deleted) hydrogens.", obInfo);
333	0	return IsOnSameAtom(c->GetId(), d->GetId());
334	0	}
335	0	}
336
337	0	return false;
338	0	}
339
340		OBGenericData* OBCisTransStereo::Clone(OBBase *mol) const
341	0	{
342	0	OBCisTransStereo data = new OBCisTransStereo(static_cast<OBMol>(mol));
343	0	data->SetConfig(m_cfg);
344	0	return data;
345	0	}
346
347		} // namespace OpenBabel
348
349		namespace std {
350
351		ostream& operator<<(ostream &out, const OpenBabel::OBCisTransStereo &ct)
352	0	{
353	0	OpenBabel::OBCisTransStereo::Config cfg = ct.GetConfig();
354	0	out << "OBCisTransStereo(begin = " << cfg.begin;
355	0	out << ", end = " << cfg.end;
356
357	0	out << ", refs = ";
358	0	for (OpenBabel::OBStereo::Refs::iterator i = cfg.refs.begin(); i != cfg.refs.end(); ++i)
359	0	if (*i != OpenBabel::OBStereo::ImplicitRef)
360	0	out << *i << " ";
361	0	else
362	0	out << "H ";
363
364	0	switch (cfg.shape) {
365	0	case OpenBabel::OBStereo::ShapeU:
366	0	out << ", shape = U)";
367	0	break;
368	0	case OpenBabel::OBStereo::ShapeZ:
369	0	out << ", shape = Z)";
370	0	break;
371	0	case OpenBabel::OBStereo::Shape4:
372	0	out << ", shape = 4)";
373	0	break;
374	0	}
375
376	0	return out;
377	0	}
378
379		ostream& operator<<(ostream &out, const OpenBabel::OBCisTransStereo::Config &cfg)
380	0	{
381	0	out << "OBCisTransStereo::Config(begin = " << cfg.begin;
382	0	out << ", end = " << cfg.end;
383
384	0	out << ", refs = ";
385	0	for (OpenBabel::OBStereo::Refs::const_iterator i = cfg.refs.begin(); i != cfg.refs.end(); ++i)
386	0	if (*i != OpenBabel::OBStereo::ImplicitRef)
387	0	out << *i << " ";
388	0	else
389	0	out << "H ";
390
391	0	switch (cfg.shape) {
392	0	case OpenBabel::OBStereo::ShapeU:
393	0	out << ", shape = U)";
394	0	break;
395	0	case OpenBabel::OBStereo::ShapeZ:
396	0	out << ", shape = Z)";
397	0	break;
398	0	case OpenBabel::OBStereo::Shape4:
399	0	out << ", shape = 4)";
400	0	break;
401	0	}
402
403	0	return out;
404	0	}
405
406		} // namespace std
407