From b9819e9932f61e27e358972aca8935559845ade9 Mon Sep 17 00:00:00 2001
From: An Nguyen <caman.nguyenthanh@gmail.com>
Date: Mon, 29 Jul 2024 10:33:06 +0700
Subject: [PATCH 1/2] Update valenceCount from ketcher v2

---
 .../ketcherails/chem/struct_valence.js        | 439 +++++++-----------
 1 file changed, 175 insertions(+), 264 deletions(-)

diff --git a/app/assets/javascripts/ketcherails/chem/struct_valence.js b/app/assets/javascripts/ketcherails/chem/struct_valence.js
index 9805e91..0696e3d 100644
--- a/app/assets/javascripts/ketcherails/chem/struct_valence.js
+++ b/app/assets/javascripts/ketcherails/chem/struct_valence.js
@@ -13,8 +13,7 @@
 if (!window.chem || !chem.Struct)
 	throw new Error("Include MolData.js first");
 
-chem.Struct.prototype.calcConn = function (aid)
-{
+chem.Struct.prototype.calcConn = function (aid) {
 	var conn = 0;
 	var atom = this.atoms.get(aid);
 	var hasAromatic = false;
@@ -47,8 +46,11 @@ chem.Struct.prototype.calcConn = function (aid)
 	return conn;
 };
 
-chem.Struct.Atom.prototype.calcValence = function (conn)
-{
+chem.Struct.Atom.isHeteroAtom = function (label) {
+	return label !== 'C' && label !== 'H';
+}
+
+chem.Struct.Atom.prototype.calcValence = function (connectionCount) {
 	var atom = this;
 	var charge = atom.charge;
 	var label = atom.label;
@@ -56,319 +58,239 @@ chem.Struct.Atom.prototype.calcValence = function (conn)
 		this.implicitH = 0;
 		return true;
 	}
-	var elem = chem.Element.getElementByLabel(label);
-	if (elem == null) {
+	var element = chem.Element.getElementByLabel(label);
+
+	if (element == null) {
 		this.implicitH = 0;
 		return true;
 	}
 
-	var groupno = chem.Element.elements.get(elem).group;
-	var rad = chem.Struct.radicalElectrons(atom.radical);
+	var groupno = chem.Element.elements.get(element).group;
+	var radicalCount = chem.Struct.radicalElectrons(atom.radical);
 
-	var valence = conn;
-	var hyd = 0;
+	var valence = connectionCount;
+	var hydrogenCount = 0;
 	var absCharge = Math.abs(charge);
 
-	if (groupno == 1)
-	{
+	if (groupno == 1) {
 		if (label == 'H' ||
 			label == 'Li' || label == 'Na' || label == 'K' ||
-			label == 'Rb' || label == 'Cs' || label == 'Fr')
-			{
+			label == 'Rb' || label == 'Cs' || label == 'Fr') {
 			valence = 1;
-			hyd = 1 - rad - conn - absCharge;
+			hydrogenCount = 1 - radicalCount - connectionCount - absCharge;
 		}
-	}
-	else if (groupno == 3)
-	{
-		if (label == 'B' || label == 'Al' || label == 'Ga' || label == 'In')
-		{
-			if (charge == -1)
-			{
+	} else if (groupno === 2) {
+		if (
+			connectionCount + radicalCount + absCharge === 2 ||
+			connectionCount + radicalCount + absCharge === 0
+		) {
+			valence = 2;
+		} else hydrogenCount = -1;
+	} else if (groupno === 3) {
+		if (label === 'B' || label === 'Al' || label === 'Ga' || label === 'In') {
+			if (charge === -1) {
 				valence = 4;
-				hyd = 4 - rad - conn;
-			}
-			else
-			{
+				hydrogenCount = 4 - radicalCount - connectionCount;
+			} else {
 				valence = 3;
-				hyd = 3 - rad - conn - absCharge;
+				hydrogenCount = 3 - radicalCount - connectionCount - absCharge;
 			}
-		}
-		else if (label == 'Tl')
-		{
-			if (charge == -1)
-			{
-				if (rad + conn <= 2)
-				{
+		} else if (label === 'Tl') {
+			if (charge === -1) {
+				if (radicalCount + connectionCount <= 2) {
 					valence = 2;
-					hyd = 2 - rad - conn;
-				}
-				else
-				{
+					hydrogenCount = 2 - radicalCount - connectionCount;
+				} else {
 					valence = 4;
-					hyd = 4 - rad - conn;
+					hydrogenCount = 4 - radicalCount - connectionCount;
 				}
-			}
-			else if (charge == -2)
-			{
-				if (rad + conn <= 3)
-				{
+			} else if (charge === -2) {
+				if (radicalCount + connectionCount <= 3) {
 					valence = 3;
-					hyd = 3 - rad - conn;
-				}
-				else
-				{
+					hydrogenCount = 3 - radicalCount - connectionCount;
+				} else {
 					valence = 5;
-					hyd = 5 - rad - conn;
-				}
-			}
-			else
-			{
-				if (rad + conn + absCharge <= 1)
-				{
-					valence = 1;
-					hyd = 1 - rad - conn - absCharge;
-				}
-				else
-				{
-					valence = 3;
-					hyd = 3 - rad - conn - absCharge;
+					hydrogenCount = 5 - radicalCount - connectionCount;
 				}
+			} else if (radicalCount + connectionCount + absCharge <= 1) {
+				valence = 1;
+				hydrogenCount = 1 - radicalCount - connectionCount - absCharge;
+			} else {
+				valence = 3;
+				hydrogenCount = 3 - radicalCount - connectionCount - absCharge;
 			}
 		}
-	}
-	else if (groupno == 4)
-	{
-		if (label == 'C' || label == 'Si' || label == 'Ge')
-		{
+	} else if (groupno === 4) {
+		if (label === 'C' || label === 'Si' || label === 'Ge') {
 			valence = 4;
-			hyd = 4 - rad - conn - absCharge;
-		}
-		else if (label == 'Sn' || label == 'Pb')
-		{
-			if (conn + rad + absCharge <= 2)
-			{
+			hydrogenCount = 4 - radicalCount - connectionCount - absCharge;
+		} else if (label === 'Sn' || label === 'Pb') {
+			if (connectionCount + radicalCount + absCharge <= 2) {
 				valence = 2;
-				hyd = 2 - rad - conn - absCharge;
-			}
-			else
-			{
+				hydrogenCount = 2 - radicalCount - connectionCount - absCharge;
+			} else {
 				valence = 4;
-				hyd = 4 - rad - conn - absCharge;
+				hydrogenCount = 4 - radicalCount - connectionCount - absCharge;
 			}
 		}
-	}
-	else if (groupno == 5)
-	{
-		if (label == 'N' || label == 'P')
-		{
-			if (charge == 1)
-			{
+	} else if (groupno === 5) {
+		if (label === 'N' || label === 'P') {
+			if (charge === 1) {
 				valence = 4;
-				hyd = 4 - rad - conn;
-			}
-			else if (charge == 2)
-			{
+				hydrogenCount = 4 - radicalCount - connectionCount;
+			} else if (charge === 2) {
 				valence = 3;
-				hyd = 3 - rad - conn;
-			}
-			else
-			{
-				if (label == 'N' || rad + conn + absCharge <= 3)
-				{
-					valence = 3;
-					hyd = 3 - rad - conn - absCharge;
-				}
-				else // ELEM_P && rad + conn + absCharge > 3
-				{
-					valence = 5;
-					hyd = 5 - rad - conn - absCharge;
-				}
+				hydrogenCount = 3 - radicalCount - connectionCount;
+			} else if (
+				label === 'N' ||
+				radicalCount + connectionCount + absCharge <= 3
+			) {
+				valence = 3;
+				hydrogenCount = 3 - radicalCount - connectionCount - absCharge;
+			} else {
+				// ELEM_P && rad + conn + absCharge > 3
+				valence = 5;
+				hydrogenCount = 5 - radicalCount - connectionCount - absCharge;
 			}
-		}
-		else if (label == 'Bi' || label == 'Sb' || label == 'As')
-		{
-			if (charge == 1)
-			{
-				if (rad + conn <= 2 && label != 'As')
-				{
+		} else if (label === 'Bi' || label === 'Sb' || label === 'As') {
+			if (charge === 1) {
+				if (radicalCount + connectionCount <= 2 && label !== 'As') {
 					valence = 2;
-					hyd = 2 - rad - conn;
-				}
-				else
-				{
+					hydrogenCount = 2 - radicalCount - connectionCount;
+				} else {
 					valence = 4;
-					hyd = 4 - rad - conn;
+					hydrogenCount = 4 - radicalCount - connectionCount;
 				}
-			}
-			else if (charge == 2)
-			{
+			} else if (charge === 2) {
 				valence = 3;
-				hyd = 3 - rad - conn;
-			}
-			else
-			{
-				if (rad + conn <= 3)
-				{
-					valence = 3;
-					hyd = 3 - rad - conn - absCharge;
-				}
-				else
-				{
-					valence = 5;
-					hyd = 5 - rad - conn - absCharge;
-				}
+				hydrogenCount = 3 - radicalCount - connectionCount;
+			} else if (radicalCount + connectionCount <= 3) {
+				valence = 3;
+				hydrogenCount = 3 - radicalCount - connectionCount - absCharge;
+			} else {
+				valence = 5;
+				hydrogenCount = 5 - radicalCount - connectionCount - absCharge;
 			}
 		}
-	}
-	else if (groupno == 6)
-	{
-		if (label == 'O')
-		{
-			if (charge >= 1)
-			{
+	} else if (groupno === 6) {
+		if (label === 'O') {
+			if (charge >= 1) {
 				valence = 3;
-				hyd = 3 - rad - conn;
-			}
-			else
-			{
+				hydrogenCount = 3 - radicalCount - connectionCount;
+			} else {
 				valence = 2;
-				hyd = 2 - rad - conn - absCharge;
+				hydrogenCount = 2 - radicalCount - connectionCount - absCharge;
 			}
-		}
-		else if (label == 'S' || label == 'Se' || label == 'Po')
-		{
-			if (charge == 1)
-			{
-				if (conn <= 3)
-				{
+		} else if (label === 'S' || label === 'Se' || label === 'Po') {
+			if (charge === 1) {
+				if (connectionCount <= 3) {
 					valence = 3;
-					hyd = 3 - rad - conn;
-				}
-				else
-				{
+					hydrogenCount = 3 - radicalCount - connectionCount;
+				} else {
 					valence = 5;
-					hyd = 5 - rad - conn;
+					hydrogenCount = 5 - radicalCount - connectionCount;
 				}
-			}
-			else
-			{
-				if (conn + rad + absCharge <= 2)
-				{
-					valence = 2;
-					hyd = 2 - rad - conn - absCharge;
-				}
-				else if (conn + rad + absCharge <= 4)
+			} else if (connectionCount + radicalCount + absCharge <= 2) {
+				valence = 2;
+				hydrogenCount = 2 - radicalCount - connectionCount - absCharge;
+			} else if (connectionCount + radicalCount + absCharge <= 4) {
 				// See examples in PubChem
 				// [S] : CID 16684216
 				// [Se]: CID 5242252
 				// [Po]: no example, just following ISIS/Draw logic here
-				{
-					valence = 4;
-					hyd = 4 - rad - conn - absCharge;
-				}
-				else
+				valence = 4;
+				hydrogenCount = 4 - radicalCount - connectionCount - absCharge;
+			} else {
 				// See examples in PubChem
 				// [S] : CID 46937044
 				// [Se]: CID 59786
 				// [Po]: no example, just following ISIS/Draw logic here
-				{
-					valence = 6;
-					hyd = 6 - rad - conn - absCharge;
-				}
+				valence = 6;
+				hydrogenCount = 6 - radicalCount - connectionCount - absCharge;
 			}
-		}
-		else if (label == 'Te')
-		{
-			if (charge == -1)
-			{
-				if (conn <= 2)
-				{
+		} else if (label === 'Te') {
+			if (charge === -1) {
+				if (connectionCount <= 2) {
 					valence = 2;
-					hyd = 2 - rad - conn - absCharge;
+					hydrogenCount = 2 - radicalCount - connectionCount - absCharge;
 				}
-			}
-			else if (charge == 0 || charge == 2)
-			{
-				if (conn <= 2)
-				{
+			} else if (charge === 0 || charge === 2) {
+				if (connectionCount <= 2) {
 					valence = 2;
-					hyd = 2 - rad - conn - absCharge;
-				}
-				else if (conn <= 4)
-				{
+					hydrogenCount = 2 - radicalCount - connectionCount - absCharge;
+				} else if (connectionCount <= 4) {
 					valence = 4;
-					hyd = 4 - rad - conn - absCharge;
-				}
-				else if (charge == 0 && conn <= 6)
-				{
+					hydrogenCount = 4 - radicalCount - connectionCount - absCharge;
+				} else if (charge === 0 && connectionCount <= 6) {
 					valence = 6;
-					hyd = 6 - rad - conn - absCharge;
+					hydrogenCount = 6 - radicalCount - connectionCount - absCharge;
+				} else {
+					hydrogenCount = -1;
 				}
-				else
-					hyd = -1;
 			}
 		}
-	}
-	else if (groupno == 7)
-	{
-		if (label == 'F')
-		{
+	} else if (groupno === 7) {
+		if (label === 'F') {
 			valence = 1;
-			hyd = 1 - rad - conn - absCharge;
-		}
-		else if (label == 'Cl' || label == 'Br' ||
-			label == 'I'  || label == 'At')
-			{
-			if (charge == 1)
-			{
-				if (conn <= 2)
-				{
+			hydrogenCount = 1 - radicalCount - connectionCount - absCharge;
+		} else if (
+			label === 'Cl' ||
+			label === 'Br' ||
+			label === 'I' ||
+			label === 'At'
+		) {
+			if (charge === 1) {
+				if (connectionCount <= 2) {
 					valence = 2;
-					hyd = 2 - rad - conn;
+					hydrogenCount = 2 - radicalCount - connectionCount;
+				} else if (
+					connectionCount === 3 ||
+					connectionCount === 5 ||
+					connectionCount >= 7
+				) {
+					hydrogenCount = -1;
 				}
-				else if (conn == 3 || conn == 5 || conn >= 7)
-					hyd = -1;
-			}
-			else if (charge == 0)
-			{
-				if (conn <= 1)
-				{
+			} else if (charge === 0) {
+				if (connectionCount <= 1) {
 					valence = 1;
-					hyd = 1 - rad - conn;
-				}
-				// While the halogens can have valence 3, they can not have
-				// hydrogens in that case.
-				else if (conn == 2 || conn == 4 || conn == 6)
-				{
-					if (rad == 1)
-					{
-						valence = conn;
-						hyd = 0;
+					hydrogenCount = 1 - radicalCount - connectionCount;
+					// While the halogens can have valence 3, they can not have
+					// hydrogens in that case.
+				} else if (
+					connectionCount === 2 ||
+					connectionCount === 4 ||
+					connectionCount === 6
+				) {
+					if (radicalCount === 1) {
+						valence = connectionCount;
+						hydrogenCount = 0;
+					} else {
+						hydrogenCount = -1; // will throw an error in the end
 					}
-					else
-						hyd = -1; // will throw an error in the end
+				} else if (connectionCount > 7) {
+					hydrogenCount = -1; // will throw an error in the end
 				}
-				else if (conn > 7)
-					hyd = -1; // will throw an error in the end
 			}
 		}
+	} else if (groupno === 8) {
+		if (connectionCount + radicalCount + absCharge === 0) valence = 1;
+		else hydrogenCount = -1;
+	}
+	if (chem.Struct.Atom.isHeteroAtom(label) && this.implicitHCount !== null) {
+		hydrogenCount = this.implicitHCount;
 	}
-
 	this.valence = valence;
-	this.implicitH = hyd;
-	if (this.implicitH < 0)
-	{
-		this.valence = conn;
+	this.implicitH = hydrogenCount;
+	if (this.implicitH < 0) {
+		this.valence = connectionCount;
 		this.implicitH = 0;
 		this.badConn = true;
 		return false;
 	}
 	return true;
-};
+}
 
-chem.Struct.Atom.prototype.calcValenceMinusHyd = function (conn)
-{
+chem.Struct.Atom.prototype.calcValenceMinusHyd = function (conn) {
 	var atom = this;
 	var charge = atom.charge;
 	var label = atom.label;
@@ -383,50 +305,40 @@ chem.Struct.Atom.prototype.calcValenceMinusHyd = function (conn)
 	var groupno = chem.Element.elements.get(elem).group;
 	var rad = chem.Struct.radicalElectrons(atom.radical);
 
-	if (groupno == 3)
-	{
-		if (label == 'B' || label == 'Al' || label == 'Ga' || label == 'In')
-		{
+	if (groupno == 3) {
+		if (label == 'B' || label == 'Al' || label == 'Ga' || label == 'In') {
 			if (charge == -1)
 				if (rad + conn <= 4)
 					return rad + conn;
 		}
 	}
-	else if (groupno == 5)
-	{
-		if (label == 'N' || label == 'P')
-		{
+	else if (groupno == 5) {
+		if (label == 'N' || label == 'P') {
 			if (charge == 1)
 				return rad + conn;
 			if (charge == 2)
 				return rad + conn;
 		}
-		else if (label == 'Sb' || label == 'Bi' || label == 'As')
-		{
+		else if (label == 'Sb' || label == 'Bi' || label == 'As') {
 			if (charge == 1)
 				return rad + conn;
 			else if (charge == 2)
 				return rad + conn;
 		}
 	}
-	else if (groupno == 6)
-	{
-		if (label == 'O')
-		{
+	else if (groupno == 6) {
+		if (label == 'O') {
 			if (charge >= 1)
 				return rad + conn;
 		}
-		else if (label == 'S'  || label == 'Se' || label == 'Po')
-		{
+		else if (label == 'S' || label == 'Se' || label == 'Po') {
 			if (charge == 1)
 				return rad + conn;
 		}
 	}
-	else if (groupno == 7)
-	{
+	else if (groupno == 7) {
 		if (label == 'Cl' || label == 'Br' ||
-			label == 'I'  || label == 'At')
-			{
+			label == 'I' || label == 'At') {
 			if (charge == 1)
 				return rad + conn;
 		}
@@ -435,8 +347,7 @@ chem.Struct.Atom.prototype.calcValenceMinusHyd = function (conn)
 	return rad + conn + Math.abs(charge);
 };
 
-chem.Struct.prototype.calcImplicitHydrogen = function (aid)
-{
+chem.Struct.prototype.calcImplicitHydrogen = function (aid) {
 	var conn = this.calcConn(aid);
 	var atom = this.atoms.get(aid);
 	atom.badConn = false;

From cdb6c0b1ac6fd5e5aa1aa8d88b0353e205e11af1 Mon Sep 17 00:00:00 2001
From: An Nguyen <caman.nguyenthanh@gmail.com>
Date: Fri, 2 Aug 2024 09:08:47 +0700
Subject: [PATCH 2/2] Update calcImplicitHydrogen

---
 .../ketcherails/chem/struct_valence.js        | 149 +++++++++---------
 1 file changed, 77 insertions(+), 72 deletions(-)

diff --git a/app/assets/javascripts/ketcherails/chem/struct_valence.js b/app/assets/javascripts/ketcherails/chem/struct_valence.js
index 0696e3d..2fa64c0 100644
--- a/app/assets/javascripts/ketcherails/chem/struct_valence.js
+++ b/app/assets/javascripts/ketcherails/chem/struct_valence.js
@@ -13,13 +13,12 @@
 if (!window.chem || !chem.Struct)
 	throw new Error("Include MolData.js first");
 
-chem.Struct.prototype.calcConn = function (aid) {
-	var conn = 0;
-	var atom = this.atoms.get(aid);
-	var hasAromatic = false;
-	for (var i = 0; i < atom.neighbors.length; ++i) {
-		var hb = this.halfBonds.get(atom.neighbors[i]);
-		var bond = this.bonds.get(hb.bid);
+chem.Struct.prototype.calcConn = function (atom) {
+	let conn = 0;
+	for (let i = 0; i < atom.neighbors.length; ++i) {
+		const hb = this.halfBonds.get(atom.neighbors[i]);
+		const bond = this.bonds.get(hb.bid);
+
 		switch (bond.type) {
 			case chem.Struct.BOND.TYPE.SINGLE:
 				conn += 1;
@@ -31,19 +30,13 @@ chem.Struct.prototype.calcConn = function (aid) {
 				conn += 3;
 				break;
 			case chem.Struct.BOND.TYPE.AROMATIC:
-				conn += 1;
-				hasAromatic = true;
-				break;
-			case chem.Struct.BOND.TYPE.COORDINATION:
-				// conn += 0;
-				break;
+				if (atom.neighbors.length === 1) return [-1, true];
+				return [atom.neighbors.length, true];
 			default:
-				return -1;
+				return [-1, false];
 		}
 	}
-	if (hasAromatic)
-		conn += 1;
-	return conn;
+	return [conn, false];
 };
 
 chem.Struct.Atom.isHeteroAtom = function (label) {
@@ -291,56 +284,41 @@ chem.Struct.Atom.prototype.calcValence = function (connectionCount) {
 }
 
 chem.Struct.Atom.prototype.calcValenceMinusHyd = function (conn) {
-	var atom = this;
-	var charge = atom.charge;
-	var label = atom.label;
-	var elem = chem.Element.getElementByLabel(label);
-	if (elem == null)
-		throw new Error("Element " + label + " unknown");
-	if (elem < 0) { // query atom, skip
+	const charge = this.charge || 0;
+	const label = this.label;
+	const element = chem.Element.getElementByLabel(this.label);
+	if (!element) {
+		// query atom, skip
 		this.implicitH = 0;
-		return null;
+		return 0;
 	}
 
-	var groupno = chem.Element.elements.get(elem).group;
-	var rad = chem.Struct.radicalElectrons(atom.radical);
+	const groupno = chem.Element.elements.get(elem).group;
+	const rad = chem.Struct.radicalElectrons(this.radical);
 
-	if (groupno == 3) {
-		if (label == 'B' || label == 'Al' || label == 'Ga' || label == 'In') {
-			if (charge == -1)
-				if (rad + conn <= 4)
-					return rad + conn;
-		}
-	}
-	else if (groupno == 5) {
-		if (label == 'N' || label == 'P') {
-			if (charge == 1)
-				return rad + conn;
-			if (charge == 2)
-				return rad + conn;
-		}
-		else if (label == 'Sb' || label == 'Bi' || label == 'As') {
-			if (charge == 1)
-				return rad + conn;
-			else if (charge == 2)
-				return rad + conn;
+	if (groupno === 3) {
+		if (label === 'B' || label === 'Al' || label === 'Ga' || label === 'In') {
+			if (charge === -1) {
+				if (rad + conn <= 4) return rad + conn;
+			}
 		}
-	}
-	else if (groupno == 6) {
-		if (label == 'O') {
-			if (charge >= 1)
-				return rad + conn;
+	} else if (groupno === 5) {
+		if (label === 'N' || label === 'P') {
+			if (charge === 1) return rad + conn;
+			if (charge === 2) return rad + conn;
+		} else if (label === 'Sb' || label === 'Bi' || label === 'As') {
+			if (charge === 1) return rad + conn;
+			else if (charge === 2) return rad + conn;
 		}
-		else if (label == 'S' || label == 'Se' || label == 'Po') {
-			if (charge == 1)
-				return rad + conn;
+	} else if (groupno === 6) {
+		if (label === 'O') {
+			if (charge >= 1) return rad + conn;
+		} else if (label === 'S' || label === 'Se' || label === 'Po') {
+			if (charge === 1) return rad + conn;
 		}
-	}
-	else if (groupno == 7) {
-		if (label == 'Cl' || label == 'Br' ||
-			label == 'I' || label == 'At') {
-			if (charge == 1)
-				return rad + conn;
+	} else if (groupno === 7) {
+		if (label === 'Cl' || label === 'Br' || label === 'I' || label === 'At') {
+			if (charge === 1) return rad + conn;
 		}
 	}
 
@@ -348,24 +326,51 @@ chem.Struct.Atom.prototype.calcValenceMinusHyd = function (conn) {
 };
 
 chem.Struct.prototype.calcImplicitHydrogen = function (aid) {
-	var conn = this.calcConn(aid);
-	var atom = this.atoms.get(aid);
+	const atom = this.atoms.get(aid);
+	const charge = atom.charge || 0;
+	const [conn, isAromatic] = this.calcConn(atom);
+	let correctConn = conn;
 	atom.badConn = false;
-	if (conn < 0 || atom.isQuery()) {
+
+	if (isAromatic) {
+		if (atom.label === 'C' && charge === 0) {
+			if (conn === 3) {
+				atom.implicitH = - chem.Struct.radicalElectrons(atom.radical);
+				return;
+			}
+			if (conn === 2) {
+				atom.implicitH = 1 - chem.Struct.radicalElectrons(atom.radical);
+				return;
+			}
+		} else if (
+			(atom.label === 'O' && charge === 0) ||
+			(atom.label === 'N' && charge === 0 && conn === 3) ||
+			(atom.label === 'N' && charge === 1 && conn === 3) ||
+			(atom.label === 'S' && charge === 0 && conn === 3) ||
+			!atom.implicitH
+		) {
+			atom.implicitH = 0;
+			return;
+		} else if (!atom.hasImplicitH) {
+			correctConn++;
+		}
+	}
+
+	if (correctConn < 0 || atom.isQuery() || atom.attachmentPoints) {
 		atom.implicitH = 0;
 		return;
 	}
+
 	if (atom.explicitValence >= 0) {
-		var elem = chem.Element.getElementByLabel(atom.label);
-		atom.implicitH = 0;
-		if (elem != null) {
-			atom.implicitH = atom.explicitValence - atom.calcValenceMinusHyd(conn);
-			if (atom.implicitH < 0) {
-				atom.implicitH = 0;
-				atom.badConn = true;
-			}
+		const elem = chem.Element.getElementByLabel(atom.label);
+		atom.implicitH = elem
+			? atom.explicitValence - atom.calcValenceMinusHyd(correctConn)
+			: 0;
+		if (atom.implicitH < 0) {
+			atom.implicitH = 0;
+			atom.badConn = true;
 		}
 	} else {
-		atom.calcValence(conn);
+		atom.calcValence(correctConn);
 	}
 };