rdkit/Docs/Notebooks/FingerprintGenerators.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Fingerprint Generators"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Creating and using a fingerprint generator\n",
    "\n",
    "Fingerprint generators can be created by using the functions that return the type of generator desired."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "{541731: 1, 574497: 1, 574498: 1, 590881: 1, 590882: 1, 590945: 1, 1590306: 3, 1590307: 3, 1590369: 1, 1590370: 2, 1590401: 2, 1590402: 1, 1592354: 1, 1592355: 2}\n"
     ]
    }
   ],
   "source": [
    "from rdkit import Chem\n",
    "from rdkit.Chem import rdFingerprintGenerator\n",
    "\n",
    "mol = Chem.MolFromSmiles('CC(O)C(O)(O)C')\n",
    "generator = rdFingerprintGenerator.GetAtomPairGenerator()\n",
    "fingerprint = generator.GetSparseCountFingerprint(mol)\n",
    "non_zero = fingerprint.GetNonzeroElements()\n",
    "\n",
    "print(non_zero)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "We can set the parameters for the fingerprint while creating the generator for it."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "{574497: 1, 574498: 1, 590881: 1, 590882: 1, 590945: 1, 1590306: 3, 1590369: 1, 1590370: 2, 1590401: 2, 1590402: 1, 1592354: 1}\n"
     ]
    }
   ],
   "source": [
    "generator = rdFingerprintGenerator.GetAtomPairGenerator(minDistance = 1, maxDistance = 2, includeChirality = False)\n",
    "fingerprint = generator.GetSparseCountFingerprint(mol)\n",
    "non_zero = fingerprint.GetNonzeroElements()\n",
    "\n",
    "print(non_zero)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "We can provide the molecule dependent arguments while creating the fingerprint."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "{574497: 1, 574498: 1, 590945: 1, 1590369: 1, 1590370: 2}\n",
      "{590881: 1, 590882: 1, 1590306: 2, 1590401: 1, 1590402: 1}\n"
     ]
    }
   ],
   "source": [
    "fingerprint = generator.GetSparseCountFingerprint(mol, fromAtoms = [1])\n",
    "non_zero = fingerprint.GetNonzeroElements()\n",
    "\n",
    "print(non_zero)\n",
    "\n",
    "fingerprint = generator.GetSparseCountFingerprint(mol, ignoreAtoms = [1, 5])\n",
    "non_zero = fingerprint.GetNonzeroElements()\n",
    "\n",
    "print(non_zero)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Types of fingerprint generators\n",
    "\n",
    "Currently 4 fingerprint types are supported by fingerprint generators"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Atom pair {541731: 1, 574497: 1, 574498: 1, 590881: 1, 590882: 1, 590945: 1, 1590306: 3, 1590307: 3, 1590369: 1, 1590370: 2, 1590401: 2, 1590402: 1, 1592354: 1, 1592355: 2}\n",
      "Morgan {864662311: 3, 1542631284: 2, 1542633699: 1, 1741045729: 1, 2245273601: 1, 2245277810: 1, 2246728737: 2, 2782665878: 1, 2927183216: 1, 3537119515: 1, 3537123720: 1}\n",
      "RDKitFingerprint {398441839: 4, 561308092: 2, 623990427: 1, 1524090560: 6, 1606685044: 2, 1636471275: 3, 1753257252: 1, 1940446997: 2, 2332326087: 1, 2880661462: 1, 2911990635: 1, 3060973103: 1, 3083228099: 1, 3473416248: 3, 3743603664: 1, 3768818763: 1, 3977409745: 3, 4274652475: 3, 4275705116: 3, 4279989780: 2}\n",
      "TopologicalTorsion {4303897120: 1, 12893570080: 1, 12893831712: 2, 12893831776: 2}\n"
     ]
    }
   ],
   "source": [
    "generator = rdFingerprintGenerator.GetAtomPairGenerator()\n",
    "fingerprint = generator.GetSparseCountFingerprint(mol)\n",
    "non_zero = fingerprint.GetNonzeroElements()\n",
    "\n",
    "print(\"Atom pair\", non_zero)\n",
    "\n",
    "generator = rdFingerprintGenerator.GetMorganGenerator(radius = 3)\n",
    "fingerprint = generator.GetSparseCountFingerprint(mol)\n",
    "non_zero = fingerprint.GetNonzeroElements()\n",
    "\n",
    "print(\"Morgan\", non_zero)\n",
    "\n",
    "generator = rdFingerprintGenerator.GetRDKitFPGenerator()\n",
    "fingerprint = generator.GetSparseCountFingerprint(mol)\n",
    "non_zero = fingerprint.GetNonzeroElements()\n",
    "\n",
    "print(\"RDKitFingerprint\", non_zero)\n",
    "\n",
    "generator = rdFingerprintGenerator.GetTopologicalTorsionGenerator()\n",
    "fingerprint = generator.GetSparseCountFingerprint(mol)\n",
    "non_zero = fingerprint.GetNonzeroElements()\n",
    "\n",
    "print(\"TopologicalTorsion\", non_zero)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Invariant generators\n",
    "\n",
    "It is possible to use a custom invariant generators while creating fingerprints. Invariant generators provide values to be used as invariants for each atom or bond in the molecule and these values affect the generated fingerprint."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "RDKitFingerprint {1940446997: 1, 4275705116: 2}\n",
      "RDKitFingerprint {578931652: 1, 2298572045: 2}\n"
     ]
    }
   ],
   "source": [
    "simpleMol = Chem.MolFromSmiles('CCC')\n",
    "\n",
    "generator = rdFingerprintGenerator.GetRDKitFPGenerator()\n",
    "fingerprint = generator.GetSparseCountFingerprint(simpleMol)\n",
    "non_zero = fingerprint.GetNonzeroElements()\n",
    "\n",
    "print(\"RDKitFingerprint\", non_zero)\n",
    "\n",
    "atomInvariantsGen = rdFingerprintGenerator.GetAtomPairAtomInvGen()\n",
    "\n",
    "generator = rdFingerprintGenerator.GetRDKitFPGenerator(atomInvariantsGenerator = atomInvariantsGen)\n",
    "fingerprint = generator.GetSparseCountFingerprint(simpleMol)\n",
    "non_zero = fingerprint.GetNonzeroElements()\n",
    "\n",
    "print(\"RDKitFingerprint\", non_zero)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Currently available invariants generators are:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Morgan with AtomPairAtomInvGen {33: 2, 35: 1, 36: 1, 97: 3, 523835848: 1, 618975071: 1, 2343097318: 1, 3205489706: 2, 3205489717: 1, 3205494725: 1, 3205494778: 1}\n",
      "Morgan with MorganAtomInvGen {864662311: 3, 1542631284: 2, 1542633699: 1, 1741045729: 1, 2245273601: 1, 2245277810: 1, 2246728737: 2, 2782665878: 1, 2927183216: 1, 3537119515: 1, 3537123720: 1}\n",
      "Morgan with MorganFeatureAtomInvGen {0: 4, 3: 3, 614176407: 1, 792807483: 1, 3205495869: 2, 3205496825: 3, 3208860345: 1}\n",
      "Morgan with RDKitAtomInvGen {12: 4, 16: 3, 165450225: 1, 608338133: 1, 2705297134: 1, 3205492925: 3, 3205493174: 2}\n",
      "Morgan with MorganBondInvGen {864662311: 3, 1542631284: 2, 1542633699: 1, 1741045729: 1, 2245273601: 1, 2245277810: 1, 2246728737: 2, 2782665878: 1, 2927183216: 1, 3537119515: 1, 3537123720: 1}\n"
     ]
    }
   ],
   "source": [
    "atomInvariantsGen = rdFingerprintGenerator.GetAtomPairAtomInvGen()\n",
    "\n",
    "generator = rdFingerprintGenerator.GetMorganGenerator(radius = 3, atomInvariantsGenerator = atomInvariantsGen)\n",
    "fingerprint = generator.GetSparseCountFingerprint(mol)\n",
    "non_zero = fingerprint.GetNonzeroElements()\n",
    "\n",
    "print(\"Morgan with AtomPairAtomInvGen\", non_zero)\n",
    "\n",
    "atomInvariantsGen = rdFingerprintGenerator.GetMorganAtomInvGen()\n",
    "\n",
    "generator = rdFingerprintGenerator.GetMorganGenerator(radius = 3, atomInvariantsGenerator = atomInvariantsGen)\n",
    "fingerprint = generator.GetSparseCountFingerprint(mol)\n",
    "non_zero = fingerprint.GetNonzeroElements()\n",
    "\n",
    "# Default for Morgan FP\n",
    "print(\"Morgan with MorganAtomInvGen\", non_zero)\n",
    "\n",
    "atomInvariantsGen = rdFingerprintGenerator.GetMorganFeatureAtomInvGen()\n",
    "\n",
    "generator = rdFingerprintGenerator.GetMorganGenerator(radius = 3, atomInvariantsGenerator = atomInvariantsGen)\n",
    "fingerprint = generator.GetSparseCountFingerprint(mol)\n",
    "non_zero = fingerprint.GetNonzeroElements()\n",
    "\n",
    "print(\"Morgan with MorganFeatureAtomInvGen\", non_zero)\n",
    "\n",
    "atomInvariantsGen = rdFingerprintGenerator.GetRDKitAtomInvGen()\n",
    "\n",
    "generator = rdFingerprintGenerator.GetMorganGenerator(radius = 3, atomInvariantsGenerator = atomInvariantsGen)\n",
    "fingerprint = generator.GetSparseCountFingerprint(mol)\n",
    "non_zero = fingerprint.GetNonzeroElements()\n",
    "\n",
    "print(\"Morgan with RDKitAtomInvGen\", non_zero)\n",
    "\n",
    "bondInvariantsGen = rdFingerprintGenerator.GetMorganBondInvGen()\n",
    "\n",
    "generator = rdFingerprintGenerator.GetMorganGenerator(radius = 3, bondInvariantsGenerator = bondInvariantsGen)\n",
    "fingerprint = generator.GetSparseCountFingerprint(mol)\n",
    "non_zero = fingerprint.GetNonzeroElements()\n",
    "\n",
    "# Default for Morgan FP\n",
    "print(\"Morgan with MorganBondInvGen\", non_zero)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Custom Invariants\n",
    "\n",
    "It is also possible to provide custom invariants instead of using a invariants generator"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "{541730: 1, 558113: 2}\n",
      "{16417: 2, 16418: 1}\n"
     ]
    }
   ],
   "source": [
    "\n",
    "generator = rdFingerprintGenerator.GetAtomPairGenerator()\n",
    "fingerprint = generator.GetSparseCountFingerprint(simpleMol)\n",
    "non_zero = fingerprint.GetNonzeroElements()\n",
    "\n",
    "print(non_zero)\n",
    "\n",
    "customAtomInvariants = [1, 1, 1]\n",
    "fingerprint = generator.GetSparseCountFingerprint(simpleMol, customAtomInvariants = customAtomInvariants)\n",
    "non_zero = fingerprint.GetNonzeroElements()\n",
    "\n",
    "print(non_zero)\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Convenience functions"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Bulk fingerprint"
   ]
  }
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