public bool ContainsAllBitsOf(HasseFingerprint F)
{
BitArray fp2 = ((HasseFingerprint)F).fp;
//todo: think is this good choice:
// for now think F is null nad has no bits then all fp "contains null"
// if (fp2 == null) return true;
for (int i = 0; i < fp.Count; i++)
{
if (fp2[i] == true)
{
if (fp[i] != true) return false;
}
}
/*
BitArray this_clone = new BitArray(fp);
this_clone.Not(); //zeroes become ones
this_clone.And(fp2); // a one at any position results in false
foreach (bool bit in this_clone )
{
if (bit==true) return false;
}
*/
return true;
}
public bool ContainsAllBitsOf(HasseFingerprint F)
{
BitArray fp2 = ((HasseFingerprint)F).fp;
//todo: think is this good choice:
// for now think F is null nad has no bits then all fp "contains null"
// if (fp2 == null) return true;
for (int i = 0; i < fp.Count; i++)
{
if (fp2[i] == true)
{
if (fp[i] != true)
{
return(false);
}
}
}
/*
* BitArray this_clone = new BitArray(fp);
* this_clone.Not(); //zeroes become ones
* this_clone.And(fp2); // a one at any position results in false
* foreach (bool bit in this_clone )
* {
* if (bit==true) return false;
* }
*/
return(true);
}
public FingerprintChemHasseNode(string StrMolecule, HasseNodeTypes ElementType, string debugInfo)
: base(ElementType, debugInfo)
{
ChemObject = new IndigoChemistry();
if (ElementType == HasseNodeTypes.ROOT)
{
this.keystring = "0";
}
else if (Convert.ToBoolean(ElementType & HasseNodeTypes.FRAGMENT)) // is fragment
{
// molecule = null;
hFingerprint = ChemObject.GetEmptyHasseFingerPrint();
hFingerprint.FromHex(StrMolecule);
base.size = hFingerprint.bitCount;
this.keystring = StrMolecule;
return;
}
else
{
ChemObject.InitMolecule(StrMolecule);
this.keystring = ChemObject.keystr;
_isvalid = ChemObject.ChemistryIsValid;
hFingerprint = ChemObject.GetHasseFingerPrint();
base.size = hFingerprint.bitCount;
}
}
public FingerprintChemHasseNode(string StrMolecule, HasseNodeTypes ElementType, string debugInfo)
: base(ElementType, debugInfo)
{
ChemObject = new IndigoChemistry();
if (ElementType == HasseNodeTypes.ROOT)
{
this.keystring = "0";
}
else if (Convert.ToBoolean(ElementType & HasseNodeTypes.FRAGMENT)) // is fragment
{
// molecule = null;
hFingerprint = ChemObject.GetEmptyHasseFingerPrint();
hFingerprint.FromHex(StrMolecule);
base.size = hFingerprint.bitCount;
this.keystring = StrMolecule;
return;
}
else
{
ChemObject.InitMolecule(StrMolecule);
this.keystring = ChemObject.keystr;
_isvalid = ChemObject.ChemistryIsValid;
hFingerprint = ChemObject.GetHasseFingerPrint();
base.size = hFingerprint.bitCount;
}
}
public override bool GetMaxCommonFragments(
HasseNode Node1, HasseNode Node2,
bool dbg, HasseFragmentInsertionQueue NewFragmentList,
int MinimumOverlap)
{
string debugInfo = "";
HasseFingerprint fp1 = ((FingerprintChemHasseNode)Node1).hFingerprint;
HasseFingerprint fp1_clone = fp1.CloneHasseFingerprint();
HasseFingerprint fp2 = ((FingerprintChemHasseNode)Node2).hFingerprint;
fp1_clone.AndBits(fp2);
if (fp1_clone.bitCount >= MinimumOverlap)
{
string strMCS = fp1_clone.ToHex();
HasseFingerprint test = new HasseFingerprint();
test.FromHex(strMCS);
NewFragmentList.Add(
new HasseNode[1] {
this
}, // this is lower than new frag
new HasseNode[2] {
Node1, Node2
}, // those are higher than new frag
strMCS, // string to use for new node creation later
debugInfo, HasseNode.HasseNodeTypes.FRAGMENT | HasseNode.HasseNodeTypes.MAX_COMMON_FRAGMENT, // type of frag
null // this new frag is not associated with a single edge
);
return(true);
}
return(false);
}
public HasseFingerprint CloneHasseFingerprint()
{
BitArray bits = new BitArray(fp); //copies values
HasseFingerprint chp = new HasseFingerprint();
chp.fp = bits;
chp.bitCount = this.bitCount;
return chp;
}
public HasseFingerprint CloneHasseFingerprint()
{
BitArray bits = new BitArray(fp); //copies values
HasseFingerprint chp = new HasseFingerprint();
chp.fp = bits;
chp.bitCount = this.bitCount;
return(chp);
}
public void Minus(HasseFingerprint FP)
{
// do this AND (NOT that)
BitArray fpx = new BitArray(FP.fp);
fpx.Not();
fp.And(fpx);
this.bitCount = this.CountBits();
}
public void AddBitsOf(HasseFingerprint F)
{
BitArray fp2 = ((HasseFingerprint)F).fp;
if (fp == null)
{
fp = new System.Collections.BitArray(fp2);
}
else
{
fp.Or(fp2);
}
this.bitCount = this.CountBits();
}
public ChemHasseNode(IndigoChemistry mol, HasseNodeTypes ElementType, string debugInfo)
: base(ElementType, debugInfo)
{
if (ElementType == HasseNodeTypes.ROOT)
{
// molecule = null;
this.keystring = "{}";
return;
}
ChemObject = mol;
this.keystring = ChemObject.keystr;
_isvalid = ChemObject.ChemistryIsValid;
base.size = ChemObject.heavyAtomCount;
hFingerprint = ChemObject.GetHasseFingerPrint();
}
public bool IsLargerThan(HasseFingerprint F)
{
// if (HasAllBits == true) System.Diagnostics.Debugger.Break();
if (this.bitCount <= F.bitCount)
{
return(false); // this must be larger
}
bool HasAllBits = ContainsAllBitsOf(F);
if (HasAllBits)
{
return(true);
}
return(false);
}
public void AddBitsOf(HasseFingerprint F)
{
BitArray fp2 = ((HasseFingerprint)F).fp;
if (fp == null)
{
fp = new System.Collections.BitArray(fp2);
}
else
{
fp.Or(fp2);
}
this.bitCount = this.CountBits();
}
public FingerprintChemHasseNode(IndigoChemistry mol, HasseNodeTypes ElementType, string debugInfo)
: base(ElementType, debugInfo)
{
if (ElementType == HasseNodeTypes.ROOT)
{
// molecule = null;
this.keystring = "";
return;
}
ChemObject = mol;
this.keystring = ChemObject.keystr;
_isvalid = ChemObject.ChemistryIsValid;
base.size = ChemObject.heavyAtomCount;
hFingerprint = ChemObject.GetHasseFingerPrint();
}
public ChemHasseNode(string StrMolecule, HasseNodeTypes ElementType, string debugInfo)
: base(ElementType, debugInfo)
{
ChemObject = new IndigoChemistry();
if (ElementType == HasseNodeTypes.ROOT)
{
this.keystring = "{}";
}
else
{
ChemObject.InitMolecule(StrMolecule);
this.keystring = ChemObject.keystr;
_isvalid = ChemObject.ChemistryIsValid;
base.size = ChemObject.heavyAtomCount;
hFingerprint = ChemObject.GetHasseFingerPrint();
}
}
public ChemHasseNode(string StrMolecule, HasseNodeTypes ElementType, string debugInfo)
: base(ElementType, debugInfo)
{
ChemObject = new IndigoChemistry();
if (ElementType == HasseNodeTypes.ROOT)
{
this.keystring = "{}";
}
else
{
ChemObject.InitMolecule(StrMolecule);
this.keystring = ChemObject.keystr;
_isvalid = ChemObject.ChemistryIsValid;
base.size = ChemObject.heavyAtomCount;
hFingerprint = ChemObject.GetHasseFingerPrint();
}
}
public override string[] GetDifferenceString(HasseNode LargerNode)
{
if (this.NodeType == HasseNodeTypes.ROOT)
{
return(new string[] { });
}
else
{
string buf;
HasseFingerprint fp = this.hFingerprint;
HasseFingerprint fpclone = fp.CloneHasseFingerprint();
fpclone.Minus(((FingerprintChemHasseNode )LargerNode).hFingerprint);
buf = fpclone.ToHex();
return(new string[] { buf });
}
return(ChemObject.GetDifferenceString(LargerNode));
}
public override bool GetMaxCommonFragments(
HasseNode Node1, HasseNode Node2,
bool dbg, HasseFragmentInsertionQueue NewFragmentList,
int MinimumOverlap)
{
string debugInfo = "";
HasseFingerprint fp1 = ((FingerprintChemHasseNode)Node1).hFingerprint;
HasseFingerprint fp1_clone = fp1.CloneHasseFingerprint();
HasseFingerprint fp2 = ((FingerprintChemHasseNode)Node2).hFingerprint;
fp1_clone.AndBits(fp2);
if(fp1_clone.bitCount >= MinimumOverlap ){
string strMCS = fp1_clone.ToHex();
HasseFingerprint test = new HasseFingerprint();
test.FromHex(strMCS);
NewFragmentList.Add(
new HasseNode[1] { this }, // this is lower than new frag
new HasseNode[2] { Node1, Node2 }, // those are higher than new frag
strMCS, // string to use for new node creation later
debugInfo, HasseNode.HasseNodeTypes.FRAGMENT | HasseNode.HasseNodeTypes.MAX_COMMON_FRAGMENT, // type of frag
null // this new frag is not associated with a single edge
);
return true;
}
return false;
}
public void AndBits(HasseFingerprint FP)
{
fp.And(FP.fp);
this.bitCount = this.CountBits();
}
public bool ContainsFingerprintOf(HasseFingerprint fp )
{
return hFingerprint.ContainsAllBitsOf(fp);
}
public bool ContainsFingerprintOf(HasseFingerprint fp)
{
return(hFingerprint.ContainsAllBitsOf(fp));
}
public void AndBits(HasseFingerprint FP)
{
fp.And(FP.fp );
this.bitCount = this.CountBits();
}
public bool IsLargerThan(HasseFingerprint F)
{
// if (HasAllBits == true) System.Diagnostics.Debugger.Break();
if (this.bitCount <= F.bitCount) return false; // this must be larger
bool HasAllBits = ContainsAllBitsOf(F);
if (HasAllBits ) return true;
return false;
}
public void Minus(HasseFingerprint FP)
{
// do this AND (NOT that)
BitArray fpx= new BitArray (FP.fp);
fpx.Not ();
fp.And(fpx);
this.bitCount = this.CountBits();
}
