/// <summary>
/// The actual writing of the output.
/// </summary>
/// <param name="obj"></param>
/// <exception cref="CDKException">could not write RGroup query</exception>
public override void Write(IChemObject obj)
{
if (!(obj is IRGroupQuery))
{
throw new CDKException("Only IRGroupQuery input is accepted.");
}
try
{
IRGroupQuery rGroupQuery = (IRGroupQuery)obj;
string now = DateTime.UtcNow.ToString("MMddyyHHmm", DateTimeFormatInfo.InvariantInfo);
IAtomContainer rootAtc = rGroupQuery.RootStructure;
//Construct header
var rootBlock = new StringBuilder();
string header = "$MDL REV 1 " + now + LSEP + "$MOL" + LSEP + "$HDR" + LSEP
+ " Rgroup query file (RGFile)" + LSEP + " CDK " + now + "2D" + LSEP + LSEP + "$END HDR"
+ LSEP + "$CTAB";
rootBlock.Append(header).Append(LSEP);
//Construct the root structure, the scaffold
string rootCTAB = GetCTAB(rootAtc);
rootCTAB = rootCTAB.Replace(LSEP + "M END" + LSEP, "");
rootBlock.Append(rootCTAB).Append(LSEP);
//Write the root's LOG lines
foreach (var rgrpNum in rGroupQuery.RGroupDefinitions.Keys)
{
RGroupList rgList = rGroupQuery.RGroupDefinitions[rgrpNum];
int restH = rgList.IsRestH ? 1 : 0;
string logLine = "M LOG" + MDLV2000Writer.FormatMDLInt(1, 3) + MDLV2000Writer.FormatMDLInt(rgrpNum, 4)
+ MDLV2000Writer.FormatMDLInt(rgList.RequiredRGroupNumber, 4)
+ MDLV2000Writer.FormatMDLInt(restH, 4) + " " + rgList.Occurrence;
rootBlock.Append(logLine).Append(LSEP);
}
//AAL lines are optional, they are needed for R-atoms with multiple bonds to the root
//for which the order of the attachment points can not be implicitly derived
//from the order in the atom block. See CT spec for more on that.
foreach (var rgroupAtom in rGroupQuery.RootAttachmentPoints.Keys)
{
var rApo = rGroupQuery.RootAttachmentPoints[rgroupAtom];
if (rApo.Count > 1)
{
int prevPos = -1;
int apoIdx = 1;
bool implicitlyOrdered = true;
while (rApo.ContainsKey(apoIdx) && implicitlyOrdered)
{
IAtom partner = rApo[apoIdx].GetOther(rgroupAtom);
for (int atIdx = 0; atIdx < rootAtc.Atoms.Count; atIdx++)
{
if (rootAtc.Atoms[atIdx].Equals(partner))
{
if (atIdx < prevPos)
{
implicitlyOrdered = false;
}
prevPos = atIdx;
break;
}
}
apoIdx++;
}
if (!implicitlyOrdered)
{
StringBuilder aalLine = new StringBuilder("M AAL");
for (int atIdx = 0; atIdx < rootAtc.Atoms.Count; atIdx++)
{
if (rootAtc.Atoms[atIdx].Equals(rgroupAtom))
{
aalLine.Append(MDLV2000Writer.FormatMDLInt((atIdx + 1), 4));
aalLine.Append(MDLV2000Writer.FormatMDLInt(rApo.Count, 3));
apoIdx = 1;
while (rApo.ContainsKey(apoIdx))
{
IAtom partner = rApo[apoIdx].GetOther(rgroupAtom);
for (int a = 0; a < rootAtc.Atoms.Count; a++)
{
if (rootAtc.Atoms[a].Equals(partner))
{
aalLine.Append(MDLV2000Writer.FormatMDLInt(a + 1, 4));
aalLine.Append(MDLV2000Writer.FormatMDLInt(apoIdx, 4));
}
}
apoIdx++;
}
}
}
rootBlock.Append(aalLine.ToString()).Append(LSEP);
}
}
}
rootBlock.Append("M END").Append(LSEP).Append("$END CTAB").Append(LSEP);
//Construct each R-group block
var rgpBlock = new StringBuilder();
foreach (var rgrpNum in rGroupQuery.RGroupDefinitions.Keys)
{
var rgrpList = rGroupQuery.RGroupDefinitions[rgrpNum].RGroups;
if (rgrpList != null && rgrpList.Count != 0)
{
rgpBlock.Append("$RGP").Append(LSEP);;
rgpBlock.Append(MDLV2000Writer.FormatMDLInt(rgrpNum, 4)).Append(LSEP);
foreach (var rgroup in rgrpList)
{
//CTAB block
rgpBlock.Append("$CTAB").Append(LSEP);
string ctab = GetCTAB(rgroup.Group);
ctab = ctab.Replace(LSEP + "M END" + LSEP, "");
rgpBlock.Append(ctab).Append(LSEP);
//The APO line
IAtom firstAttachmentPoint = rgroup.FirstAttachmentPoint;
IAtom secondAttachmentPoint = rgroup.SecondAttachmentPoint;
int apoCount = 0;
if (firstAttachmentPoint != null)
{
var apoLine = new StringBuilder();
for (int atIdx = 0; atIdx < rgroup.Group.Atoms.Count; atIdx++)
{
if (rgroup.Group.Atoms[atIdx].Equals(firstAttachmentPoint))
{
apoLine.Append(MDLV2000Writer.FormatMDLInt((atIdx + 1), 4));
apoCount++;
if (secondAttachmentPoint != null &&
secondAttachmentPoint.Equals(firstAttachmentPoint))
{
apoLine.Append(MDLV2000Writer.FormatMDLInt(3, 4));
}
else
{
apoLine.Append(MDLV2000Writer.FormatMDLInt(1, 4));
}
}
}
if (secondAttachmentPoint != null && !secondAttachmentPoint.Equals(firstAttachmentPoint))
{
for (int atIdx = 0; atIdx < rgroup.Group.Atoms.Count; atIdx++)
{
if (rgroup.Group.Atoms[atIdx].Equals(secondAttachmentPoint))
{
apoCount++;
apoLine.Append(MDLV2000Writer.FormatMDLInt((atIdx + 1), 4));
apoLine.Append(MDLV2000Writer.FormatMDLInt(2, 4));
}
}
}
if (apoCount > 0)
{
apoLine.Insert(0, "M APO" + MDLV2000Writer.FormatMDLInt(apoCount, 3));
rgpBlock.Append(apoLine).Append(LSEP);
}
}
rgpBlock.Append("M END").Append(LSEP);
rgpBlock.Append("$END CTAB").Append(LSEP);
}
rgpBlock.Append("$END RGP").Append(LSEP);
}
}
rgpBlock.Append("$END MOL").Append(LSEP);
writer.Write(rootBlock.ToString());
writer.Write(rgpBlock.ToString());
writer.Flush();
}
catch (IOException e)
{
Console.Error.WriteLine(e.StackTrace);
throw new CDKException("Unexpected exception when writing RGFile" + LSEP + e.Message);
}
}
