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Functionality for calling the InChI library from Java. Requires an appropriate InChI binary on the classpath to use
/**
* JNA-InChI - Library for calling InChI from Java
* Copyright © 2018 Daniel Lowe
*
* This library is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public
* License as published by the Free Software Foundation; either
* version 2.1 of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with this program. If not, see atoms = inchiInput.getAtoms();
int atomCount = atoms.size();
if (atomCount > Short.MAX_VALUE) {
throw new IllegalStateException("InChI is limited to 32767 atoms, input contained " + atomCount + " atoms");
}
List bonds = inchiInput.getBonds();
List stereos = inchiInput.getStereos();
if (stereos.size() > Short.MAX_VALUE) {
throw new IllegalStateException("Too many stereochemistry elements in input");
}
IXA_STATUS_HANDLE logger = IxaFunctions.IXA_STATUS_Create();
IXA_MOL_HANDLE nativeMol = IxaFunctions.IXA_MOL_Create(logger);
IxaFunctions.IXA_MOL_ReserveSpace(logger, nativeMol, atomCount, bonds.size(), stereos.size());
try {
Map atomToNativeAtom = addAtoms(nativeMol, logger, atoms);
addBonds(nativeMol, logger, bonds, atomToNativeAtom);
addStereos(nativeMol, logger, stereos, atomToNativeAtom);
return buildInchi(logger, nativeMol, options);
}
finally {
IxaFunctions.IXA_MOL_Destroy(logger, nativeMol);
IxaFunctions.IXA_STATUS_Destroy(logger);
}
}
private static Map addAtoms(IXA_MOL_HANDLE mol, IXA_STATUS_HANDLE logger, List atoms) {
Map atomToNativeAtom = new HashMap<>();
for (InchiAtom atom : atoms) {
//For performance only call IxaFunctions when values differ from the defaults
IXA_ATOMID nativeAtom = IxaFunctions.IXA_MOL_CreateAtom(logger, mol);
atomToNativeAtom.put(atom, nativeAtom);
if (atom.getX() != 0) {
IxaFunctions.IXA_MOL_SetAtomX(logger, mol, nativeAtom, atom.getX());
}
if (atom.getY() != 0) {
IxaFunctions.IXA_MOL_SetAtomY(logger, mol, nativeAtom, atom.getY());
}
if (atom.getZ() != 0) {
IxaFunctions.IXA_MOL_SetAtomZ(logger, mol, nativeAtom, atom.getZ());
}
String elName = atom.getElName();
if (!elName.equals("C")) {
if (elName.length() > 5) {
throw new IllegalArgumentException("Element name was too long: " + elName);
}
IxaFunctions.IXA_MOL_SetAtomElement(logger, mol, nativeAtom, elName);
}
if (atom.getIsotopicMass() != 0) {
IxaFunctions.IXA_MOL_SetAtomMass(logger, mol, nativeAtom, atom.getIsotopicMass());
}
if (atom.getCharge() != 0) {
IxaFunctions.IXA_MOL_SetAtomCharge(logger, mol, nativeAtom, atom.getCharge());
}
if (atom.getRadical() != InchiRadical.NONE) {
IxaFunctions.IXA_MOL_SetAtomRadical(logger, mol, nativeAtom, atom.getRadical().getCode());
}
if (atom.getImplicitHydrogen() != 0) {
IxaFunctions.IXA_MOL_SetAtomHydrogens(logger, mol, nativeAtom, 0, atom.getImplicitHydrogen());
}
if (atom.getImplicitProtium() != 0) {
IxaFunctions.IXA_MOL_SetAtomHydrogens(logger, mol, nativeAtom, 1, atom.getImplicitProtium());
}
if (atom.getImplicitDeuterium() != 0) {
IxaFunctions.IXA_MOL_SetAtomHydrogens(logger, mol, nativeAtom, 2, atom.getImplicitDeuterium());
}
if (atom.getImplicitTritium() != 0) {
IxaFunctions.IXA_MOL_SetAtomHydrogens(logger, mol, nativeAtom, 3, atom.getImplicitTritium());
}
}
return atomToNativeAtom;
}
private static void addBonds(IXA_MOL_HANDLE mol, IXA_STATUS_HANDLE logger, List bonds, Map atomToNativeAtom) {
for (InchiBond bond : bonds) {
IXA_ATOMID nativeAtom1 = atomToNativeAtom.get(bond.getStart());
IXA_ATOMID nativeAtom2 = atomToNativeAtom.get(bond.getEnd());
if (nativeAtom1 == null || nativeAtom2 == null) {
throw new IllegalStateException("Bond referenced an atom that was not part of the InchiInput");
}
IXA_BONDID nativeBond = IxaFunctions.IXA_MOL_CreateBond(logger, mol, nativeAtom1, nativeAtom2);
InchiBondType bondType = bond.getType();
if (bondType != InchiBondType.SINGLE) {
IxaFunctions.IXA_MOL_SetBondType(logger, mol, nativeBond, bondType.getCode());
}
switch (bond.getStereo()) {
case DOUBLE_EITHER:
//Default is to perceive configuration from 2D coordinates
IxaFunctions.IXA_MOL_SetDblBondConfig(logger, mol, nativeBond, IXA_DBLBOND_CONFIG.IXA_DBLBOND_CONFIG_EITHER);
break;
case SINGLE_1DOWN:
IxaFunctions.IXA_MOL_SetBondWedge(logger, mol, nativeBond, nativeAtom1, IXA_BOND_WEDGE.IXA_BOND_WEDGE_DOWN);
break;
case SINGLE_1EITHER:
IxaFunctions.IXA_MOL_SetBondWedge(logger, mol, nativeBond, nativeAtom1, IXA_BOND_WEDGE.IXA_BOND_WEDGE_EITHER);
break;
case SINGLE_1UP:
IxaFunctions.IXA_MOL_SetBondWedge(logger, mol, nativeBond, nativeAtom1, IXA_BOND_WEDGE.IXA_BOND_WEDGE_UP);
break;
case SINGLE_2DOWN:
IxaFunctions.IXA_MOL_SetBondWedge(logger, mol, nativeBond, nativeAtom2, IXA_BOND_WEDGE.IXA_BOND_WEDGE_DOWN);
break;
case SINGLE_2EITHER:
IxaFunctions.IXA_MOL_SetBondWedge(logger, mol, nativeBond, nativeAtom2, IXA_BOND_WEDGE.IXA_BOND_WEDGE_EITHER);
break;
case SINGLE_2UP:
IxaFunctions.IXA_MOL_SetBondWedge(logger, mol, nativeBond, nativeAtom2, IXA_BOND_WEDGE.IXA_BOND_WEDGE_UP);
break;
case NONE:
break;
}
}
}
private static void addStereos(IXA_MOL_HANDLE nativeMol, IXA_STATUS_HANDLE logger, List stereos, Map atomToNativeAtom) {
for (InchiStereo stereo : stereos) {
InchiStereoType type = stereo.getType();
if (type == InchiStereoType.None) {
continue;
}
InchiAtom[] atomsInCenter = stereo.getAtoms();
IXA_ATOMID vertex1 = getStereoVertex(atomToNativeAtom, atomsInCenter[0]);
IXA_ATOMID vertex2 = getStereoVertex(atomToNativeAtom, atomsInCenter[1]);
IXA_ATOMID vertex3 = getStereoVertex(atomToNativeAtom, atomsInCenter[2]);
IXA_ATOMID vertex4 = getStereoVertex(atomToNativeAtom, atomsInCenter[3]);
IXA_STEREOID center;
switch (type) {
case Tetrahedral:
{
IXA_ATOMID centralAtom = atomToNativeAtom.get(stereo.getCentralAtom());
if (centralAtom == null) {
throw new IllegalStateException("Stereo configuration central atom referenced an atom that does not exist");
}
center = IxaFunctions.IXA_MOL_CreateStereoTetrahedron(logger, nativeMol, centralAtom, vertex1, vertex2, vertex3, vertex4);
break;
}
case Allene:
{
IXA_ATOMID centralAtom = atomToNativeAtom.get(stereo.getCentralAtom());
if (centralAtom == null) {
throw new IllegalStateException("Stereo configuration central atom referenced an atom that does not exist");
}
center = IxaFunctions.IXA_MOL_CreateStereoAntiRectangle(logger, nativeMol, centralAtom, vertex1, vertex2, vertex3, vertex4);
break;
}
case DoubleBond:
{
IXA_BONDID centralBond = IxaFunctions.IXA_MOL_GetCommonBond(logger, nativeMol, vertex2, vertex3);
if (centralBond == null) {
throw new IllegalStateException("Could not find olefin/cumulene central bond");
}
//We intentionally pass dummy values for vertex2/vertex3, as the IXA API doesn't actually need these as long as vertex1 and vertex4 aren't implicit hydrogen
center = IxaFunctions.IXA_MOL_CreateStereoRectangle(logger, nativeMol, centralBond, vertex1, IxaFunctions.IXA_ATOMID_IMPLICIT_H, IxaFunctions.IXA_ATOMID_IMPLICIT_H, vertex4);
break;
}
default:
throw new IllegalStateException("Unexpected InChI stereo type:" + type);
}
byte parity = stereo.getParity().getCode();
IxaFunctions.IXA_MOL_SetStereoParity(logger, nativeMol, center, parity);
}
}
private static IXA_ATOMID getStereoVertex(Map atomToNativeAtom, InchiAtom inchiAtom) {
if (InchiStereo.STEREO_IMPLICIT_H == inchiAtom) {
return IxaFunctions.IXA_ATOMID_IMPLICIT_H;
}
IXA_ATOMID vertex = atomToNativeAtom.get(inchiAtom);
if (vertex == null) {
throw new IllegalStateException("Stereo configuration referenced an atom that does not exist");
}
return vertex;
}
private static InchiOutput buildInchi(IXA_STATUS_HANDLE logger, IXA_MOL_HANDLE nativeMol, InchiOptions options) {
IXA_INCHIBUILDER_HANDLE builder = IxaFunctions.IXA_INCHIBUILDER_Create(logger);
try {
IxaFunctions.IXA_INCHIBUILDER_SetMolecule(logger, builder, nativeMol);
long timeoutMilliSecs = options.getTimeoutMilliSeconds();
if (timeoutMilliSecs != 0) {
IxaFunctions.IXA_INCHIBUILDER_SetOption_Timeout_MilliSeconds(logger, builder, timeoutMilliSecs);
}
for (InchiFlag flag : options.getFlags()) {
switch (flag) {
case AuxNone:
IxaFunctions.IXA_INCHIBUILDER_SetOption(logger, builder, IXA_INCHIBUILDER_OPTION.IXA_INCHIBUILDER_OPTION_AuxNone, true);
break;
case ChiralFlagOFF:
IxaFunctions.IXA_MOL_SetChiral(logger, nativeMol, false);
break;
case ChiralFlagON:
IxaFunctions.IXA_MOL_SetChiral(logger, nativeMol, true);
break;
case DoNotAddH:
IxaFunctions.IXA_INCHIBUILDER_SetOption(logger, builder, IXA_INCHIBUILDER_OPTION.IXA_INCHIBUILDER_OPTION_DoNotAddH, true);
break;
case FixedH:
IxaFunctions.IXA_INCHIBUILDER_SetOption(logger, builder, IXA_INCHIBUILDER_OPTION.IXA_INCHIBUILDER_OPTION_FixedH, true);
break;
case KET:
IxaFunctions.IXA_INCHIBUILDER_SetOption(logger, builder, IXA_INCHIBUILDER_OPTION.IXA_INCHIBUILDER_OPTION_KET, true);
break;
case LargeMolecules:
IxaFunctions.IXA_INCHIBUILDER_SetOption(logger, builder, IXA_INCHIBUILDER_OPTION.IXA_INCHIBUILDER_OPTION_LargeMolecules, true);
break;
case NEWPSOFF:
IxaFunctions.IXA_INCHIBUILDER_SetOption(logger, builder, IXA_INCHIBUILDER_OPTION.IXA_INCHIBUILDER_OPTION_NewPsOff, true);
break;
case OneFiveT:
IxaFunctions.IXA_INCHIBUILDER_SetOption(logger, builder, IXA_INCHIBUILDER_OPTION.IXA_INCHIBUILDER_OPTION_15T, true);
break;
case RecMet:
IxaFunctions.IXA_INCHIBUILDER_SetOption(logger, builder, IXA_INCHIBUILDER_OPTION.IXA_INCHIBUILDER_OPTION_RecMet, true);
break;
case SLUUD:
IxaFunctions.IXA_INCHIBUILDER_SetOption(logger, builder, IXA_INCHIBUILDER_OPTION.IXA_INCHIBUILDER_OPTION_SLUUD, true);
break;
case SNon:
IxaFunctions.IXA_INCHIBUILDER_SetOption_Stereo(logger, builder, IXA_INCHIBUILDER_STEREOOPTION.IXA_INCHIBUILDER_STEREOOPTION_SNon);
break;
case SRac:
IxaFunctions.IXA_INCHIBUILDER_SetOption_Stereo(logger, builder, IXA_INCHIBUILDER_STEREOOPTION.IXA_INCHIBUILDER_STEREOOPTION_SRac);
break;
case SRel:
IxaFunctions.IXA_INCHIBUILDER_SetOption_Stereo(logger, builder, IXA_INCHIBUILDER_STEREOOPTION.IXA_INCHIBUILDER_STEREOOPTION_SRel);
break;
case SUCF:
IxaFunctions.IXA_INCHIBUILDER_SetOption_Stereo(logger, builder, IXA_INCHIBUILDER_STEREOOPTION.IXA_INCHIBUILDER_STEREOOPTION_SUCF);
break;
case SUU:
IxaFunctions.IXA_INCHIBUILDER_SetOption(logger, builder, IXA_INCHIBUILDER_OPTION.IXA_INCHIBUILDER_OPTION_SUU, true);
break;
case SaveOpt:
IxaFunctions.IXA_INCHIBUILDER_SetOption(logger, builder, IXA_INCHIBUILDER_OPTION.IXA_INCHIBUILDER_OPTION_SaveOpt, true);
break;
case WarnOnEmptyStructure:
IxaFunctions.IXA_INCHIBUILDER_SetOption(logger, builder, IXA_INCHIBUILDER_OPTION.IXA_INCHIBUILDER_OPTION_WarnOnEmptyStructure, true);
break;
case NoWarnings:
IxaFunctions.IXA_INCHIBUILDER_SetOption(logger, builder, IXA_INCHIBUILDER_OPTION.IXA_INCHIBUILDER_OPTION_NoWarnings, true);
break;
case LooseTSACheck:
IxaFunctions.IXA_INCHIBUILDER_SetOption(logger, builder, IXA_INCHIBUILDER_OPTION.IXA_INCHIBUILDER_OPTION_LooseTSACheck, true);
break;
case Polymers:
IxaFunctions.IXA_INCHIBUILDER_SetOption(logger, builder, IXA_INCHIBUILDER_OPTION.IXA_INCHIBUILDER_OPTION_Polymers, true);
break;
case Polymers105:
IxaFunctions.IXA_INCHIBUILDER_SetOption(logger, builder, IXA_INCHIBUILDER_OPTION.IXA_INCHIBUILDER_OPTION_Polymers105, true);
break;
case FoldCRU:
IxaFunctions.IXA_INCHIBUILDER_SetOption(logger, builder, IXA_INCHIBUILDER_OPTION.IXA_INCHIBUILDER_OPTION_FoldCRU, true);
break;
case NoFrameShift:
IxaFunctions.IXA_INCHIBUILDER_SetOption(logger, builder, IXA_INCHIBUILDER_OPTION.IXA_INCHIBUILDER_OPTION_NoFrameShift, true);
break;
case NoEdits:
IxaFunctions.IXA_INCHIBUILDER_SetOption(logger, builder, IXA_INCHIBUILDER_OPTION.IXA_INCHIBUILDER_OPTION_NoEdits, true);
break;
case NPZz:
IxaFunctions.IXA_INCHIBUILDER_SetOption(logger, builder, IXA_INCHIBUILDER_OPTION.IXA_INCHIBUILDER_OPTION_NPZZ, true);
break;
case SAtZz:
IxaFunctions.IXA_INCHIBUILDER_SetOption(logger, builder, IXA_INCHIBUILDER_OPTION.IXA_INCHIBUILDER_OPTION_SATZZ, true);
break;
default:
throw new IllegalStateException("Unexpected InChI option flag: " + flag);
}
}
String inchi = IxaFunctions.IXA_INCHIBUILDER_GetInChI(logger, builder);
String auxInfo = IxaFunctions.IXA_INCHIBUILDER_GetAuxInfo(logger, builder);
String log = IxaFunctions.IXA_INCHIBUILDER_GetLog(logger, builder);
InchiStatus status = InchiStatus.SUCCESS;
if (IxaFunctions.IXA_STATUS_HasError(logger)) {
status = InchiStatus.ERROR;
}
else if (IxaFunctions.IXA_STATUS_HasWarning(logger)) {
status = InchiStatus.WARNING;
}
StringBuilder sb = new StringBuilder();
int messageCount = IxaFunctions.IXA_STATUS_GetCount(logger);
for (int i = 0; i < messageCount; i++) {
if (i > 0) {
sb.append("; ");
}
sb.append(IxaFunctions.IXA_STATUS_GetMessage(logger, i));
}
return new InchiOutput(inchi, auxInfo, sb.toString(), log, status);
}
finally {
IxaFunctions.IXA_INCHIBUILDER_Destroy(logger, builder);
}
}
public static InchiOutput molToInchi(String molText) {
return molToInchi(molText, InchiOptions.DEFAULT_OPTIONS);
}
public static InchiOutput molToInchi(String molText, InchiOptions options) {
IXA_STATUS_HANDLE logger = IxaFunctions.IXA_STATUS_Create();
IXA_MOL_HANDLE nativeMol = IxaFunctions.IXA_MOL_Create(logger);
try {
IxaFunctions.IXA_MOL_ReadMolfile(logger, nativeMol, molText);
return buildInchi(logger, nativeMol, options);
}
finally {
IxaFunctions.IXA_MOL_Destroy(logger, nativeMol);
IxaFunctions.IXA_STATUS_Destroy(logger);
}
}
/**
* Converts InChI into InChI for validation purposes.
* It may also be used to filter out specific layers.
* For instance, SNon would remove the stereochemical layer.
* Omitting FixedH and/or RecMet would remove Fixed-H or Reconnected layers.
* @param inchi
* @param options
* @return
*/
public static InchiOutput inchiToInchi(String inchi, InchiOptions options) {
IXA_STATUS_HANDLE logger = IxaFunctions.IXA_STATUS_Create();
IXA_MOL_HANDLE nativeMol = IxaFunctions.IXA_MOL_Create(logger);
try {
IxaFunctions.IXA_MOL_ReadInChI(logger, nativeMol, inchi);
return buildInchi(logger, nativeMol, options);
}
finally {
IxaFunctions.IXA_MOL_Destroy(logger, nativeMol);
IxaFunctions.IXA_STATUS_Destroy(logger);
}
}
public static InchiKeyOutput inchiToInchiKey(String inchi){
byte[] inchiKeyBytes = new byte[28];
byte[] szXtra1Bytes = new byte[65];
byte[] szXtra2Bytes = new byte[65];
InchiKeyStatus ret = InchiKeyStatus.of(InchiLibrary.GetINCHIKeyFromINCHI(inchi, 1, 1, inchiKeyBytes, szXtra1Bytes, szXtra2Bytes));
String inchiKeyStr = new String(inchiKeyBytes, StandardCharsets.UTF_8).trim();
String szXtra1 = new String(szXtra1Bytes, StandardCharsets.UTF_8).trim();
String szXtra2 = new String(szXtra2Bytes, StandardCharsets.UTF_8).trim();
return new InchiKeyOutput(inchiKeyStr, ret, szXtra1, szXtra2);
}
/**
* Check if the string represents a valid InChI/StdInChI
* If strict is true, try to perform InChI2InChI conversion; returns success if a resulting InChI string exactly matches source.
* Be cautious: the result may be too strict, i.e. a 'false alarm', due to imperfection of conversion.
* @param inchi
* @param strict if false, just briefly check for proper layout (prefix, version, etc.)
* @return InchiCheckStatus
*/
public static InchiCheckStatus checkInchi(String inchi, boolean strict) {
return InchiCheckStatus.of(InchiLibrary.CheckINCHI(inchi, strict));
}
/**
* Check if the string represents valid InChIKey
* @param inchiKey
* @return InchiKeyCheckStatus
*/
public static InchiKeyCheckStatus checkInchiKey(String inchiKey) {
return InchiKeyCheckStatus.of(InchiLibrary.CheckINCHIKey(inchiKey));
}
/**
* Creates the input data structure for InChI generation out of the auxiliary information (AuxInfo)
* string produced by previous InChI generator calls
* @param auxInfo contains ASCIIZ string of InChI output for a single structure or only the AuxInfo line
* @param doNotAddH if true then InChI will not be allowed to add implicit H
* @param diffUnkUndfStereo if true, use different labels for unknown and undefined stereo
* @return
*/
public static InchiInputFromAuxinfoOutput getInchiInputFromAuxInfo(String auxInfo, boolean doNotAddH, boolean diffUnkUndfStereo) {
tagINCHI_Input pInp = new tagINCHI_Input();
tagInchiInpData input = new tagInchiInpData(pInp);
try {
InchiStatus status = getInchiStatus(InchiLibrary.Get_inchi_Input_FromAuxInfo(auxInfo, doNotAddH, diffUnkUndfStereo, input));
InchiInput inchiInput = new InchiInput();
tagINCHI_Input populatedInput = input.pInp;
if (populatedInput.num_atoms > 0) {
tagInchiAtom[] nativeAtoms = new tagInchiAtom[populatedInput.num_atoms];
populatedInput.atom.toArray(nativeAtoms);
nativeToJavaAtoms(inchiInput, nativeAtoms);
nativeToJavaBonds(inchiInput, nativeAtoms);
}
if (populatedInput.num_stereo0D > 0) {
tagINCHIStereo0D[] nativeStereos = new tagINCHIStereo0D[populatedInput.num_stereo0D];
populatedInput.stereo0D.toArray(nativeStereos);
nativeToJavaStereos(inchiInput, nativeStereos);
}
String message = toString(input.szErrMsg);
Boolean chiralFlag = null;
if (input.bChiral == 1) {
chiralFlag = true;
}
else if (input.bChiral == 2) {
chiralFlag = false;
}
return new InchiInputFromAuxinfoOutput(inchiInput, chiralFlag, message, status);
}
finally {
InchiLibrary.Free_inchi_Input(pInp);
input.clear();
}
}
public static InchiInputFromInchiOutput getInchiInputFromInchi(String inchi) {
return getInchiInputFromInchi(inchi, InchiOptions.DEFAULT_OPTIONS);
}
public static InchiInputFromInchiOutput getInchiInputFromInchi(String inchi, InchiOptions options) {
tagINCHI_InputINCHI input = new tagINCHI_InputINCHI(inchi, options.toString());
tagINCHI_OutputStruct output = new tagINCHI_OutputStruct();
try {
InchiStatus status = getInchiStatus(InchiLibrary.GetStructFromINCHI(input, output));
InchiInput inchiInput = new InchiInput();
if (output.num_atoms > 0) {
tagInchiAtom[] nativeAtoms = new tagInchiAtom[output.num_atoms];
output.atom.toArray(nativeAtoms);
nativeToJavaAtoms(inchiInput, nativeAtoms);
nativeToJavaBonds(inchiInput, nativeAtoms);
}
if (output.num_stereo0D > 0) {
tagINCHIStereo0D[] nativeStereos = new tagINCHIStereo0D[output.num_stereo0D];
output.stereo0D.toArray(nativeStereos);
nativeToJavaStereos(inchiInput, nativeStereos);
}
String message = output.szMessage;
String log = output.szLog;
NativeLong[] nativeFlags = output.WarningFlags;//This is a flattened multi-dimensional array, unflatten as we convert
long[][] warningFlags = new long[2][2];
for (int i = 0; i < nativeFlags.length; i++) {
long val = nativeFlags[i].longValue();
switch (i) {
case 0:
warningFlags[0][0] = val;
break;
case 1:
warningFlags[0][1] = val;
break;
case 2:
warningFlags[1][0] = val;
break;
case 3:
warningFlags[1][1] = val;
break;
default:
break;
}
}
return new InchiInputFromInchiOutput(inchiInput, message, log, status, warningFlags);
}
finally {
InchiLibrary.FreeStructFromINCHI(output);
input.clear();
}
}
private static void nativeToJavaAtoms(InchiInput inchiInput, tagInchiAtom[] nativeAtoms) {
for (int i = 0, numAtoms = nativeAtoms.length; i < numAtoms; i++) {
tagInchiAtom nativeAtom = nativeAtoms[i];
InchiAtom atom = new InchiAtom(toString(nativeAtom.elname));
atom.setX(nativeAtom.x);
atom.setY(nativeAtom.y);
atom.setZ(nativeAtom.z);
atom.setImplicitHydrogen(nativeAtom.num_iso_H[0]);
atom.setImplicitProtium(nativeAtom.num_iso_H[1]);
atom.setImplicitDeuterium(nativeAtom.num_iso_H[2]);
atom.setImplicitTritium(nativeAtom.num_iso_H[3]);
atom.setIsotopicMass(nativeAtom.isotopic_mass);
atom.setRadical(InchiRadical.of(nativeAtom.radical));
atom.setCharge(nativeAtom.charge);
inchiInput.addAtom(atom);
}
}
private static void nativeToJavaBonds(InchiInput inchiInput, tagInchiAtom[] nativeAtoms) {
int numAtoms = nativeAtoms.length;
boolean[] seenAtoms = new boolean[numAtoms];
for (int i = 0; i < numAtoms; i++) {
tagInchiAtom nativeAtom = nativeAtoms[i];
int numBonds = nativeAtom.num_bonds;
if (numBonds > 0) {
InchiAtom atom = inchiInput.getAtom(i);
for (int j = 0; j < numBonds; j++) {
int neighborIdx = nativeAtom.neighbor[j];
if (seenAtoms[neighborIdx]) {
//Only add each bond once
continue;
}
InchiAtom neighbor = inchiInput.getAtom(neighborIdx);
InchiBondType bondType = InchiBondType.of(nativeAtom.bond_type[j]);
InchiBondStereo bondStereo = InchiBondStereo.of(nativeAtom.bond_stereo[j]);
inchiInput.addBond(new InchiBond(atom, neighbor, bondType, bondStereo));
}
}
seenAtoms[i] = true;
}
}
private static void nativeToJavaStereos(InchiInput inchiInput, tagINCHIStereo0D[] nativeStereos) {
for (tagINCHIStereo0D nativeStereo : nativeStereos) {
InchiAtom[] atoms = new InchiAtom[4];
//idxToAtom will give null for -1 input (implicit hydrogen)
for (int i = 0; i < 4; i++) {
int idx = nativeStereo.neighbor[i];
atoms[i] = idx >=0 ? inchiInput.getAtom(idx) : null;
}
InchiAtom centralAtom = nativeStereo.central_atom >=0 ? inchiInput.getAtom(nativeStereo.central_atom) : null;
InchiStereoType stereoType = InchiStereoType.of(nativeStereo.type);
InchiStereoParity parity = InchiStereoParity.of(nativeStereo.parity);
inchiInput.addStereo(new InchiStereo(atoms, centralAtom, stereoType, parity));
}
}
private static InchiStatus getInchiStatus(int ret) {
switch (ret) {
case tagRetValGetINCHI.inchi_Ret_OKAY:/* Success; no errors or warnings*/
return InchiStatus.SUCCESS;
case tagRetValGetINCHI.inchi_Ret_EOF:/* no structural data has been provided */
case tagRetValGetINCHI.inchi_Ret_WARNING:/* Success; warning(s) issued*/
return InchiStatus.WARNING;
case tagRetValGetINCHI.inchi_Ret_ERROR:/* Error: no InChI has been created */
case tagRetValGetINCHI.inchi_Ret_FATAL:/* Severe error: no InChI has been created (typically, memory allocation failure) */
case tagRetValGetINCHI.inchi_Ret_UNKNOWN:/* Unknown program error */
case tagRetValGetINCHI.inchi_Ret_BUSY:/* Previous call to InChI has not returned yet*/
return InchiStatus.ERROR;
default:
return InchiStatus.ERROR;
}
}
private static String toString(byte[] cstr) {
StringBuilder sb = new StringBuilder(cstr.length);
for (int i = 0; i < cstr.length; i++) {
char ch = (char) cstr[i];
if (ch == '\0') {
break;
}
sb.append(ch);
}
return sb.toString();
}
}
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