void IndigoInchi::generateInchiInput (Molecule &mol, inchi_Input &input,
Array<inchi_Atom> &atoms, Array<inchi_Stereo0D> &stereo)
{
QS_DEF(Array<int>, mapping);
mapping.clear_resize(mol.vertexEnd());
mapping.fffill();
int index = 0;
for (int v = mol.vertexBegin(); v != mol.vertexEnd(); v = mol.vertexNext(v))
mapping[v] = index++;
atoms.clear_resize(index);
atoms.zerofill();
stereo.clear();
for (int v = mol.vertexBegin(); v != mol.vertexEnd(); v = mol.vertexNext(v))
{
inchi_Atom &atom = atoms[mapping[v]];
int atom_number = mol.getAtomNumber(v);
if (atom_number == ELEM_PSEUDO)
throw IndigoError("Molecule with pseudoatom (%s) cannot be converted into InChI", mol.getPseudoAtom(v));
if (atom_number == ELEM_RSITE)
throw IndigoError("Molecule with RGroups cannot be converted into InChI");
strncpy(atom.elname, Element::toString(atom_number), ATOM_EL_LEN);
Vec3f &c = mol.getAtomXyz(v);
atom.x = c.x;
atom.y = c.y;
atom.z = c.z;
// connectivity
const Vertex &vtx = mol.getVertex(v);
int nei_idx = 0;
for (int nei = vtx.neiBegin(); nei != vtx.neiEnd(); nei = vtx.neiNext(nei))
{
int v_nei = vtx.neiVertex(nei);
atom.neighbor[nei_idx] = mapping[v_nei];
int edge_idx = vtx.neiEdge(nei);
atom.bond_type[nei_idx] = getInchiBondType(mol.getBondOrder(edge_idx));
int bond_stereo = INCHI_BOND_STEREO_NONE;
if (mol.cis_trans.isIgnored(edge_idx))
bond_stereo = INCHI_BOND_STEREO_DOUBLE_EITHER;
else
{
int dir = mol.getBondDirection2(v, v_nei);
if (mol.getBondDirection2(v, v_nei) == BOND_EITHER)
bond_stereo = INCHI_BOND_STEREO_SINGLE_1EITHER;
else if (mol.getBondDirection2(v_nei, v) == BOND_EITHER)
bond_stereo = INCHI_BOND_STEREO_SINGLE_2EITHER;
}
atom.bond_stereo[nei_idx] = bond_stereo;
nei_idx++;
}
atom.num_bonds = vtx.degree();
// Other properties
atom.isotopic_mass = mol.getAtomIsotope(v);
atom.radical = mol.getAtomRadical(v);
atom.charge = mol.getAtomCharge(v);
// Hydrogens
int hcount = -1;
if (Molecule::shouldWriteHCount(mol, v) || mol.isExplicitValenceSet(v) || mol.isImplicitHSet(v))
{
if (mol.getAtomAromaticity(v) == ATOM_AROMATIC &&
atom_number == ELEM_C && atom.charge == 0 && atom.radical == 0)
{
// Do not set number of implicit hydrogens here as InChI throws an exception on
// the molecule B1=CB=c2cc3B=CC=c3cc12
;
}
else
// set -1 to tell InChI add implicit hydrogens automatically
hcount = mol.getImplicitH_NoThrow(v, -1);
}
atom.num_iso_H[0] = hcount;
}
// Process cis-trans bonds
for (int e = mol.edgeBegin(); e != mol.edgeEnd(); e = mol.edgeNext(e))
{
if (mol.cis_trans.getParity(e) == 0)
continue;
int subst[4];
mol.cis_trans.getSubstituents_All(e, subst);
const Edge &edge = mol.getEdge(e);
inchi_Stereo0D &st = stereo.push();
// Write it as
// #0 - #1 = #2 - #3
st.neighbor[0] = mapping[subst[0]];
st.neighbor[1] = mapping[edge.beg];
st.neighbor[2] = mapping[edge.end];
st.neighbor[3] = mapping[subst[2]];
if (mol.cis_trans.getParity(e) == MoleculeCisTrans::CIS)
st.parity = INCHI_PARITY_ODD;
else
st.parity = INCHI_PARITY_EVEN;
st.central_atom = NO_ATOM;
st.type = INCHI_StereoType_DoubleBond;
}
// Process tetrahedral stereocenters
for (int i = mol.stereocenters.begin(); i != mol.stereocenters.end(); i = mol.stereocenters.next(i))
{
int v = mol.stereocenters.getAtomIndex(i);
int type, group, pyramid[4];
mol.stereocenters.get(v, type, group, pyramid);
if (type == MoleculeStereocenters::ATOM_ANY)
continue;
for (int i = 0; i < 4; i++)
if (pyramid[i] != -1)
pyramid[i] = mapping[pyramid[i]];
inchi_Stereo0D &st = stereo.push();
/*
4 neighbors
X neighbor[4] : {#W, #X, #Y, #Z}
| central_atom: #A
W--A--Y type : INCHI_StereoType_Tetrahedral
|
Z
parity: if (X,Y,Z) are clockwize when seen from W then parity is 'e' otherwise 'o'
Example (see AXYZW above): if W is above the plane XYZ then parity = 'e'
3 neighbors
Y Y neighbor[4] : {#A, #X, #Y, #Z}
/ / central_atom: #A
X--A (e.g. O=S ) type : INCHI_StereoType_Tetrahedral
\ \
Z Z
*/
int offset = 0;
if (pyramid[3] == -1)
offset = 1;
st.neighbor[offset] = mapping[pyramid[0]];
st.neighbor[offset + 1] = mapping[pyramid[1]];
st.neighbor[offset + 2] = mapping[pyramid[2]];
if (offset == 0)
st.neighbor[3] = mapping[pyramid[3]];
else
st.neighbor[0] = mapping[v];
st.parity = INCHI_PARITY_ODD;
if (offset != 0)
st.parity = INCHI_PARITY_ODD;
else
st.parity = INCHI_PARITY_EVEN;
st.central_atom = mapping[v];
st.type = INCHI_StereoType_Tetrahedral;
}
input.atom = atoms.ptr();
input.num_atoms = atoms.size();
input.stereo0D = stereo.ptr();
input.num_stereo0D = stereo.size();
input.szOptions = options.ptr();
}
void CanonicalSmilesSaver::saveMolecule (Molecule &mol_) const
{
if (mol_.vertexCount() < 1)
return;
QS_DEF(Array<int>, ignored);
QS_DEF(Array<int>, order);
QS_DEF(Array<int>, ranks);
QS_DEF(Molecule, mol);
int i;
if (mol_.repeating_units.size() > 0)
throw Error("can not canonicalize a polymer");
// Detect hydrogens configuration if aromatic but not ambiguous
bool found_invalid_h = false;
for (i = mol_.vertexBegin(); i != mol_.vertexEnd(); i = mol_.vertexNext(i))
{
if (mol_.isRSite(i) || mol_.isPseudoAtom(i))
continue;
if (mol_.getImplicitH_NoThrow(i, -1) == -1)
found_invalid_h = true;
}
if (found_invalid_h)
{
AromaticityOptions options;
options.method = AromaticityOptions::GENERIC;
options.unique_dearomatization = true;
MoleculeDearomatizer::restoreHydrogens(mol_, options);
}
mol.clone(mol_, 0, 0);
// TODO: canonicalize allenes properly
mol.allene_stereo.clear();
ignored.clear_resize(mol.vertexEnd());
ignored.zerofill();
for (i = mol.vertexBegin(); i < mol.vertexEnd(); i = mol.vertexNext(i))
if (mol.convertableToImplicitHydrogen(i))
ignored[i] = 1;
for (i = mol.edgeBegin(); i != mol.edgeEnd(); i = mol.edgeNext(i))
if (mol.getBondTopology(i) == TOPOLOGY_RING && mol.cis_trans.getParity(i) != 0)
{
// we save cis/trans ring bonds into SMILES, but only those who
// do not participate in bigger ring systems
const Edge &edge = mol.getEdge(i);
if (mol.getAtomRingBondsCount(edge.beg) != 2 ||
mol.getAtomRingBondsCount(edge.end) != 2)
{
mol.cis_trans.setParity(i, 0);
continue;
}
// also, discard the cis-trans bonds that have been converted to aromatic
const Vertex &beg = mol.getVertex(edge.beg);
const Vertex &end = mol.getVertex(edge.end);
bool have_singlebond_beg = false;
bool have_singlebond_end = false;
int j;
for (j = beg.neiBegin(); j != beg.neiEnd(); j = beg.neiNext(j))
if (mol.getBondOrder(beg.neiEdge(j)) == BOND_SINGLE)
have_singlebond_beg = true;
for (j = end.neiBegin(); j != end.neiEnd(); j = end.neiNext(j))
if (mol.getBondOrder(end.neiEdge(j)) == BOND_SINGLE)
have_singlebond_end = true;
if (!have_singlebond_beg || !have_singlebond_end)
{
mol.cis_trans.setParity(i, 0);
continue;
}
}
MoleculeAutomorphismSearch of;
of.detect_invalid_cistrans_bonds = find_invalid_stereo;
of.detect_invalid_stereocenters = find_invalid_stereo;
of.find_canonical_ordering = true;
of.ignored_vertices = ignored.ptr();
of.process(mol);
of.getCanonicalNumbering(order);
for (i = mol.edgeBegin(); i != mol.edgeEnd(); i = mol.edgeNext(i))
if (mol.cis_trans.getParity(i) != 0 && of.invalidCisTransBond(i))
mol.cis_trans.setParity(i, 0);
for (i = mol.vertexBegin(); i != mol.vertexEnd(); i = mol.vertexNext(i))
if (mol.stereocenters.getType(i) > MoleculeStereocenters::ATOM_ANY && of.invalidStereocenter(i))
mol.stereocenters.remove(i);
ranks.clear_resize(mol.vertexEnd());
for (i = 0; i < order.size(); i++)
ranks[order[i]] = i;
SmilesSaver saver(_output);
saver.ignore_invalid_hcount = false;
saver.vertex_ranks = ranks.ptr();
saver.ignore_hydrogens = true;
saver.canonize_chiralities = true;
saver.saveMolecule(mol);
}
void MoleculeAutomorphismSearch::_calculateHydrogensAndDegree (Molecule &mol)
{
_hcount.clear_resize(mol.vertexEnd());
_degree.clear_resize(mol.vertexEnd());
_degree.zerofill();
for (int i = mol.vertexBegin(); i != mol.vertexEnd(); i = mol.vertexNext(i))
{
if (mol.isRSite(i) || mol.isPseudoAtom(i) || mol.isTemplateAtom(i))
_hcount[i] = 0;
else
_hcount[i] = mol.getImplicitH_NoThrow(i, -1);
if (_hcount[i] < 0)
{
if (mol.getAtomAromaticity(i) == ATOM_AROMATIC)
{
if (mol.getAtomNumber(i) == ELEM_C && mol.getAtomCharge(i) == 0)
{
if (mol.getVertex(i).degree() == 3)
_hcount[i] = 0;
else if (mol.getVertex(i).degree() == 2)
_hcount[i] = 1;
}
else if (mol.getAtomNumber(i) == ELEM_O && mol.getAtomCharge(i) == 0)
_hcount[i] = 0;
else
{
if (!allow_undefined)
// This code will throw an error with a good explanation
_hcount[i] = mol.getImplicitH(i);
else
// Make number of hydrogens unique in order to make such atoms unique
_hcount[i] = 101 + i;
}
}
else
{
// Number of atoms are underfined, but all the properties like
// connectivity, charge, and etc., and this mean that such
// atoms are comparable even.
// For example, this cis-trans bond is invalid even if the number
// of hydrogens are undefined: CC=C(N(C)=O)N(C)=O
_hcount[i] = 100; // Any big number.
// Later this number can be increased including neighbour hydrogens,
// and this is correct, because nitrogens in these molecules are different:
// C[N](C)=O and [H][N]([H])(C)(C)=O
}
}
const Vertex &vertex = mol.getVertex(i);
_degree[i] = 0;
if (ignored_vertices != 0 && ignored_vertices[i])
continue;
for (int j = vertex.neiBegin(); j != vertex.neiEnd(); j = vertex.neiNext(j))
{
if (mol.getAtomNumber(vertex.neiVertex(j)) == ELEM_H &&
mol.getAtomIsotope(vertex.neiVertex(j)) == 0)
_hcount[i]++;
if (ignored_vertices == 0 || ignored_vertices[vertex.neiVertex(j)] == 0)
_degree[i]++;
}
}
// Compute independent components if the canonical ordering is not required
_independent_component_index.clear_resize(mol.vertexEnd());
if (!find_canonical_ordering)
{
// We can mark different connected components as independent
GraphDecomposer decomposer(mol);
decomposer.decompose();
_independent_component_index.copy(decomposer.getDecomposition());
}
else
_independent_component_index.fffill();
}
