{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# SpecLibFasta usage"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "%reload_ext autoreload\n",
    "%autoreload 2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "from alphabase.protein.fasta import SpecLibFasta"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Proteins from a dict (or loaded from fasta files)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "prot1 = 'MABCDESTKAFGHIJKLMNOPQRAFGHIJK'\n",
    "prot2 = 'AFGHIJKLMNOPQR'\n",
    "protein_dict = {\n",
    "    'xx': {\n",
    "        'protein_id': 'xx',\n",
    "        'gene_name': '',\n",
    "        'sequence': prot1\n",
    "    },\n",
    "    'yy': {\n",
    "        'protein_id': 'yy',\n",
    "        'gene_name': 'gene',\n",
    "        'sequence': prot2\n",
    "    }\n",
    "}"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "`alphabase.protein.fasta.SpecLibFasta.get_peptides_from_protein_dict` will digest a protein dict into a peptide dataframe. \n",
    "\n",
    "`alphabase.protein.fasta.SpecLibFasta.get_peptides_from_fasta` will digest a fasta file or a fasta list into a peptide dataframe. "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>sequence</th>\n",
       "      <th>protein_idxes</th>\n",
       "      <th>miss_cleavage</th>\n",
       "      <th>is_prot_nterm</th>\n",
       "      <th>is_prot_cterm</th>\n",
       "      <th>mods</th>\n",
       "      <th>mod_sites</th>\n",
       "      <th>nAA</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>AFGHIJK</td>\n",
       "      <td>0;1</td>\n",
       "      <td>0</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>LMNOPQR</td>\n",
       "      <td>0;1</td>\n",
       "      <td>0</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>ABCDESTK</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>8</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>MABCDESTK</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>9</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>AFGHIJKLMNOPQR</td>\n",
       "      <td>0;1</td>\n",
       "      <td>1</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>14</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>LMNOPQRAFGHIJK</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>14</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>ABCDESTKAFGHIJK</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>15</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>MABCDESTKAFGHIJK</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>16</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>AFGHIJKLMNOPQRAFGHIJK</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>21</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>ABCDESTKAFGHIJKLMNOPQR</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>22</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>MABCDESTKAFGHIJKLMNOPQR</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>23</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                   sequence protein_idxes  miss_cleavage  is_prot_nterm  \\\n",
       "0                   AFGHIJK           0;1              0           True   \n",
       "1                   LMNOPQR           0;1              0          False   \n",
       "2                  ABCDESTK             0              0           True   \n",
       "3                 MABCDESTK             0              0           True   \n",
       "4            AFGHIJKLMNOPQR           0;1              1           True   \n",
       "5            LMNOPQRAFGHIJK             0              1          False   \n",
       "6           ABCDESTKAFGHIJK             0              1           True   \n",
       "7          MABCDESTKAFGHIJK             0              1           True   \n",
       "8     AFGHIJKLMNOPQRAFGHIJK             0              2          False   \n",
       "9    ABCDESTKAFGHIJKLMNOPQR             0              2           True   \n",
       "10  MABCDESTKAFGHIJKLMNOPQR             0              2           True   \n",
       "\n",
       "    is_prot_cterm mods mod_sites  nAA  \n",
       "0            True                   7  \n",
       "1            True                   7  \n",
       "2           False                   8  \n",
       "3           False                   9  \n",
       "4            True                  14  \n",
       "5            True                  14  \n",
       "6           False                  15  \n",
       "7           False                  16  \n",
       "8            True                  21  \n",
       "9           False                  22  \n",
       "10          False                  23  "
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "fasta_lib = SpecLibFasta(\n",
    "    ['b_z1','y_z1'], I_to_L=False, decoy='pseudo_reverse',\n",
    "    var_mods=['Acetyl@Protein_N-term', 'Oxidation@M'],\n",
    "    fix_mods=['Carbamidomethyl@C'],\n",
    ")\n",
    "# fasta_lib.get_peptides_from_fasta(fasta_files)\n",
    "fasta_lib.get_peptides_from_protein_dict(protein_dict)\n",
    "fasta_lib.precursor_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>protein_id</th>\n",
       "      <th>gene_name</th>\n",
       "      <th>sequence</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>xx</td>\n",
       "      <td></td>\n",
       "      <td>MABCDESTKAFGHIJKLMNOPQRAFGHIJK</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>yy</td>\n",
       "      <td>gene</td>\n",
       "      <td>AFGHIJKLMNOPQR</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "  protein_id gene_name                        sequence\n",
       "0         xx            MABCDESTKAFGHIJKLMNOPQRAFGHIJK\n",
       "1         yy      gene                  AFGHIJKLMNOPQR"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "fasta_lib.protein_df"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "We can also append the protein names to precursor_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
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       "\n",
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       "\n",
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>sequence</th>\n",
       "      <th>protein_idxes</th>\n",
       "      <th>miss_cleavage</th>\n",
       "      <th>is_prot_nterm</th>\n",
       "      <th>is_prot_cterm</th>\n",
       "      <th>mods</th>\n",
       "      <th>mod_sites</th>\n",
       "      <th>nAA</th>\n",
       "      <th>proteins</th>\n",
       "      <th>genes</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>AFGHIJK</td>\n",
       "      <td>0;1</td>\n",
       "      <td>0</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>7</td>\n",
       "      <td>xx;yy</td>\n",
       "      <td>gene</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>LMNOPQR</td>\n",
       "      <td>0;1</td>\n",
       "      <td>0</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>7</td>\n",
       "      <td>xx;yy</td>\n",
       "      <td>gene</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>ABCDESTK</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>8</td>\n",
       "      <td>xx</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>MABCDESTK</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>9</td>\n",
       "      <td>xx</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>AFGHIJKLMNOPQR</td>\n",
       "      <td>0;1</td>\n",
       "      <td>1</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>14</td>\n",
       "      <td>xx;yy</td>\n",
       "      <td>gene</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>LMNOPQRAFGHIJK</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>14</td>\n",
       "      <td>xx</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>ABCDESTKAFGHIJK</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>15</td>\n",
       "      <td>xx</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>MABCDESTKAFGHIJK</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>16</td>\n",
       "      <td>xx</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>AFGHIJKLMNOPQRAFGHIJK</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>21</td>\n",
       "      <td>xx</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>ABCDESTKAFGHIJKLMNOPQR</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>22</td>\n",
       "      <td>xx</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>MABCDESTKAFGHIJKLMNOPQR</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>23</td>\n",
       "      <td>xx</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                   sequence protein_idxes  miss_cleavage  is_prot_nterm  \\\n",
       "0                   AFGHIJK           0;1              0           True   \n",
       "1                   LMNOPQR           0;1              0          False   \n",
       "2                  ABCDESTK             0              0           True   \n",
       "3                 MABCDESTK             0              0           True   \n",
       "4            AFGHIJKLMNOPQR           0;1              1           True   \n",
       "5            LMNOPQRAFGHIJK             0              1          False   \n",
       "6           ABCDESTKAFGHIJK             0              1           True   \n",
       "7          MABCDESTKAFGHIJK             0              1           True   \n",
       "8     AFGHIJKLMNOPQRAFGHIJK             0              2          False   \n",
       "9    ABCDESTKAFGHIJKLMNOPQR             0              2           True   \n",
       "10  MABCDESTKAFGHIJKLMNOPQR             0              2           True   \n",
       "\n",
       "    is_prot_cterm mods mod_sites  nAA proteins genes  \n",
       "0            True                   7    xx;yy  gene  \n",
       "1            True                   7    xx;yy  gene  \n",
       "2           False                   8       xx        \n",
       "3           False                   9       xx        \n",
       "4            True                  14    xx;yy  gene  \n",
       "5            True                  14       xx        \n",
       "6           False                  15       xx        \n",
       "7           False                  16       xx        \n",
       "8            True                  21       xx        \n",
       "9           False                  22       xx        \n",
       "10          False                  23       xx        "
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "fasta_lib.append_protein_name()\n",
    "fasta_lib.precursor_df"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "If we have our own precursor_df loaded by psm_readers, we can directly assign it to fasta_lib. \n",
    "\n",
    "``` python\n",
    "fasta_lib._precursor_df = precursor_df\n",
    "```\n",
    "Thus, we can still use SpecLibFasta functionalities for this precursor_df."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Add modifications including both var_mods (`Acetyl@Protein_N-term`, `Oxidation@M`, see initialzation of fasta_lib) and fix_mods (`Carbamidomethyl@C`) into the precursor_df."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
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       "\n",
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>sequence</th>\n",
       "      <th>mods</th>\n",
       "      <th>mod_sites</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>AFGHIJK</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>AFGHIJK</td>\n",
       "      <td>Acetyl@Protein_N-term</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>LMNOPQR</td>\n",
       "      <td>Oxidation@M</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>LMNOPQR</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>ABCDESTK</td>\n",
       "      <td>Carbamidomethyl@C</td>\n",
       "      <td>3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>ABCDESTK</td>\n",
       "      <td>Acetyl@Protein_N-term;Carbamidomethyl@C</td>\n",
       "      <td>0;3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>MABCDESTK</td>\n",
       "      <td>Oxidation@M;Carbamidomethyl@C</td>\n",
       "      <td>1;4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>MABCDESTK</td>\n",
       "      <td>Carbamidomethyl@C</td>\n",
       "      <td>4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>MABCDESTK</td>\n",
       "      <td>Acetyl@Protein_N-term;Oxidation@M;Carbamidomet...</td>\n",
       "      <td>0;1;4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>MABCDESTK</td>\n",
       "      <td>Acetyl@Protein_N-term;Carbamidomethyl@C</td>\n",
       "      <td>0;4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>AFGHIJKLMNOPQR</td>\n",
       "      <td>Oxidation@M</td>\n",
       "      <td>9</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>AFGHIJKLMNOPQR</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>AFGHIJKLMNOPQR</td>\n",
       "      <td>Acetyl@Protein_N-term;Oxidation@M</td>\n",
       "      <td>0;9</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>AFGHIJKLMNOPQR</td>\n",
       "      <td>Acetyl@Protein_N-term</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14</th>\n",
       "      <td>LMNOPQRAFGHIJK</td>\n",
       "      <td>Oxidation@M</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>LMNOPQRAFGHIJK</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>16</th>\n",
       "      <td>ABCDESTKAFGHIJK</td>\n",
       "      <td>Carbamidomethyl@C</td>\n",
       "      <td>3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17</th>\n",
       "      <td>ABCDESTKAFGHIJK</td>\n",
       "      <td>Acetyl@Protein_N-term;Carbamidomethyl@C</td>\n",
       "      <td>0;3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18</th>\n",
       "      <td>MABCDESTKAFGHIJK</td>\n",
       "      <td>Oxidation@M;Carbamidomethyl@C</td>\n",
       "      <td>1;4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>19</th>\n",
       "      <td>MABCDESTKAFGHIJK</td>\n",
       "      <td>Carbamidomethyl@C</td>\n",
       "      <td>4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20</th>\n",
       "      <td>MABCDESTKAFGHIJK</td>\n",
       "      <td>Acetyl@Protein_N-term;Oxidation@M;Carbamidomet...</td>\n",
       "      <td>0;1;4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>21</th>\n",
       "      <td>MABCDESTKAFGHIJK</td>\n",
       "      <td>Acetyl@Protein_N-term;Carbamidomethyl@C</td>\n",
       "      <td>0;4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>22</th>\n",
       "      <td>AFGHIJKLMNOPQRAFGHIJK</td>\n",
       "      <td>Oxidation@M</td>\n",
       "      <td>9</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>23</th>\n",
       "      <td>AFGHIJKLMNOPQRAFGHIJK</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>24</th>\n",
       "      <td>ABCDESTKAFGHIJKLMNOPQR</td>\n",
       "      <td>Oxidation@M;Carbamidomethyl@C</td>\n",
       "      <td>17;3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>25</th>\n",
       "      <td>ABCDESTKAFGHIJKLMNOPQR</td>\n",
       "      <td>Carbamidomethyl@C</td>\n",
       "      <td>3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>26</th>\n",
       "      <td>ABCDESTKAFGHIJKLMNOPQR</td>\n",
       "      <td>Acetyl@Protein_N-term;Oxidation@M;Carbamidomet...</td>\n",
       "      <td>0;17;3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>27</th>\n",
       "      <td>ABCDESTKAFGHIJKLMNOPQR</td>\n",
       "      <td>Acetyl@Protein_N-term;Carbamidomethyl@C</td>\n",
       "      <td>0;3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>28</th>\n",
       "      <td>MABCDESTKAFGHIJKLMNOPQR</td>\n",
       "      <td>Oxidation@M;Carbamidomethyl@C</td>\n",
       "      <td>1;4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>29</th>\n",
       "      <td>MABCDESTKAFGHIJKLMNOPQR</td>\n",
       "      <td>Oxidation@M;Carbamidomethyl@C</td>\n",
       "      <td>18;4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>30</th>\n",
       "      <td>MABCDESTKAFGHIJKLMNOPQR</td>\n",
       "      <td>Oxidation@M;Oxidation@M;Carbamidomethyl@C</td>\n",
       "      <td>1;18;4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>31</th>\n",
       "      <td>MABCDESTKAFGHIJKLMNOPQR</td>\n",
       "      <td>Carbamidomethyl@C</td>\n",
       "      <td>4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>32</th>\n",
       "      <td>MABCDESTKAFGHIJKLMNOPQR</td>\n",
       "      <td>Acetyl@Protein_N-term;Oxidation@M;Carbamidomet...</td>\n",
       "      <td>0;1;4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>33</th>\n",
       "      <td>MABCDESTKAFGHIJKLMNOPQR</td>\n",
       "      <td>Acetyl@Protein_N-term;Oxidation@M;Carbamidomet...</td>\n",
       "      <td>0;18;4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>34</th>\n",
       "      <td>MABCDESTKAFGHIJKLMNOPQR</td>\n",
       "      <td>Acetyl@Protein_N-term;Oxidation@M;Oxidation@M;...</td>\n",
       "      <td>0;1;18;4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>35</th>\n",
       "      <td>MABCDESTKAFGHIJKLMNOPQR</td>\n",
       "      <td>Acetyl@Protein_N-term;Carbamidomethyl@C</td>\n",
       "      <td>0;4</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                   sequence  \\\n",
       "0                   AFGHIJK   \n",
       "1                   AFGHIJK   \n",
       "2                   LMNOPQR   \n",
       "3                   LMNOPQR   \n",
       "4                  ABCDESTK   \n",
       "5                  ABCDESTK   \n",
       "6                 MABCDESTK   \n",
       "7                 MABCDESTK   \n",
       "8                 MABCDESTK   \n",
       "9                 MABCDESTK   \n",
       "10           AFGHIJKLMNOPQR   \n",
       "11           AFGHIJKLMNOPQR   \n",
       "12           AFGHIJKLMNOPQR   \n",
       "13           AFGHIJKLMNOPQR   \n",
       "14           LMNOPQRAFGHIJK   \n",
       "15           LMNOPQRAFGHIJK   \n",
       "16          ABCDESTKAFGHIJK   \n",
       "17          ABCDESTKAFGHIJK   \n",
       "18         MABCDESTKAFGHIJK   \n",
       "19         MABCDESTKAFGHIJK   \n",
       "20         MABCDESTKAFGHIJK   \n",
       "21         MABCDESTKAFGHIJK   \n",
       "22    AFGHIJKLMNOPQRAFGHIJK   \n",
       "23    AFGHIJKLMNOPQRAFGHIJK   \n",
       "24   ABCDESTKAFGHIJKLMNOPQR   \n",
       "25   ABCDESTKAFGHIJKLMNOPQR   \n",
       "26   ABCDESTKAFGHIJKLMNOPQR   \n",
       "27   ABCDESTKAFGHIJKLMNOPQR   \n",
       "28  MABCDESTKAFGHIJKLMNOPQR   \n",
       "29  MABCDESTKAFGHIJKLMNOPQR   \n",
       "30  MABCDESTKAFGHIJKLMNOPQR   \n",
       "31  MABCDESTKAFGHIJKLMNOPQR   \n",
       "32  MABCDESTKAFGHIJKLMNOPQR   \n",
       "33  MABCDESTKAFGHIJKLMNOPQR   \n",
       "34  MABCDESTKAFGHIJKLMNOPQR   \n",
       "35  MABCDESTKAFGHIJKLMNOPQR   \n",
       "\n",
       "                                                 mods mod_sites  \n",
       "0                                                                \n",
       "1                               Acetyl@Protein_N-term         0  \n",
       "2                                         Oxidation@M         2  \n",
       "3                                                                \n",
       "4                                   Carbamidomethyl@C         3  \n",
       "5             Acetyl@Protein_N-term;Carbamidomethyl@C       0;3  \n",
       "6                       Oxidation@M;Carbamidomethyl@C       1;4  \n",
       "7                                   Carbamidomethyl@C         4  \n",
       "8   Acetyl@Protein_N-term;Oxidation@M;Carbamidomet...     0;1;4  \n",
       "9             Acetyl@Protein_N-term;Carbamidomethyl@C       0;4  \n",
       "10                                        Oxidation@M         9  \n",
       "11                                                               \n",
       "12                  Acetyl@Protein_N-term;Oxidation@M       0;9  \n",
       "13                              Acetyl@Protein_N-term         0  \n",
       "14                                        Oxidation@M         2  \n",
       "15                                                               \n",
       "16                                  Carbamidomethyl@C         3  \n",
       "17            Acetyl@Protein_N-term;Carbamidomethyl@C       0;3  \n",
       "18                      Oxidation@M;Carbamidomethyl@C       1;4  \n",
       "19                                  Carbamidomethyl@C         4  \n",
       "20  Acetyl@Protein_N-term;Oxidation@M;Carbamidomet...     0;1;4  \n",
       "21            Acetyl@Protein_N-term;Carbamidomethyl@C       0;4  \n",
       "22                                        Oxidation@M         9  \n",
       "23                                                               \n",
       "24                      Oxidation@M;Carbamidomethyl@C      17;3  \n",
       "25                                  Carbamidomethyl@C         3  \n",
       "26  Acetyl@Protein_N-term;Oxidation@M;Carbamidomet...    0;17;3  \n",
       "27            Acetyl@Protein_N-term;Carbamidomethyl@C       0;3  \n",
       "28                      Oxidation@M;Carbamidomethyl@C       1;4  \n",
       "29                      Oxidation@M;Carbamidomethyl@C      18;4  \n",
       "30          Oxidation@M;Oxidation@M;Carbamidomethyl@C    1;18;4  \n",
       "31                                  Carbamidomethyl@C         4  \n",
       "32  Acetyl@Protein_N-term;Oxidation@M;Carbamidomet...     0;1;4  \n",
       "33  Acetyl@Protein_N-term;Oxidation@M;Carbamidomet...    0;18;4  \n",
       "34  Acetyl@Protein_N-term;Oxidation@M;Oxidation@M;...  0;1;18;4  \n",
       "35            Acetyl@Protein_N-term;Carbamidomethyl@C       0;4  "
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "fasta_lib.add_modifications()\n",
    "fasta_lib.precursor_df[['sequence','mods','mod_sites']]"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "`alphabase.protein.fasta.SpecLibFasta.add_additional_modifications` is specially designed for `Phospho`, as it may generate thousands of peptidoforms for a peptide with multiple phospho sites. "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>sequence</th>\n",
       "      <th>protein_idxes</th>\n",
       "      <th>miss_cleavage</th>\n",
       "      <th>is_prot_nterm</th>\n",
       "      <th>is_prot_cterm</th>\n",
       "      <th>mods</th>\n",
       "      <th>mod_sites</th>\n",
       "      <th>nAA</th>\n",
       "      <th>proteins</th>\n",
       "      <th>genes</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>AFGHIJK</td>\n",
       "      <td>0;1</td>\n",
       "      <td>0</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>7</td>\n",
       "      <td>xx;yy</td>\n",
       "      <td>gene</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>AFGHIJK</td>\n",
       "      <td>0;1</td>\n",
       "      <td>0</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>Acetyl@Protein_N-term</td>\n",
       "      <td>0</td>\n",
       "      <td>7</td>\n",
       "      <td>xx;yy</td>\n",
       "      <td>gene</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>LMNOPQR</td>\n",
       "      <td>0;1</td>\n",
       "      <td>0</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>Oxidation@M</td>\n",
       "      <td>2</td>\n",
       "      <td>7</td>\n",
       "      <td>xx;yy</td>\n",
       "      <td>gene</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>LMNOPQR</td>\n",
       "      <td>0;1</td>\n",
       "      <td>0</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>7</td>\n",
       "      <td>xx;yy</td>\n",
       "      <td>gene</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>ABCDESTK</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>Carbamidomethyl@C;Phospho@S</td>\n",
       "      <td>3;6</td>\n",
       "      <td>8</td>\n",
       "      <td>xx</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>79</th>\n",
       "      <td>MABCDESTKAFGHIJKLMNOPQR</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>Acetyl@Protein_N-term;Oxidation@M;Oxidation@M;...</td>\n",
       "      <td>0;1;18;4;8</td>\n",
       "      <td>23</td>\n",
       "      <td>xx</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>80</th>\n",
       "      <td>MABCDESTKAFGHIJKLMNOPQR</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>Acetyl@Protein_N-term;Oxidation@M;Oxidation@M;...</td>\n",
       "      <td>0;1;18;4</td>\n",
       "      <td>23</td>\n",
       "      <td>xx</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>81</th>\n",
       "      <td>MABCDESTKAFGHIJKLMNOPQR</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>Acetyl@Protein_N-term;Carbamidomethyl@C;Phospho@S</td>\n",
       "      <td>0;4;7</td>\n",
       "      <td>23</td>\n",
       "      <td>xx</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>82</th>\n",
       "      <td>MABCDESTKAFGHIJKLMNOPQR</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>Acetyl@Protein_N-term;Carbamidomethyl@C;Phospho@T</td>\n",
       "      <td>0;4;8</td>\n",
       "      <td>23</td>\n",
       "      <td>xx</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>83</th>\n",
       "      <td>MABCDESTKAFGHIJKLMNOPQR</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>Acetyl@Protein_N-term;Carbamidomethyl@C</td>\n",
       "      <td>0;4</td>\n",
       "      <td>23</td>\n",
       "      <td>xx</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>84 rows × 10 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                   sequence protein_idxes  miss_cleavage  is_prot_nterm  \\\n",
       "0                   AFGHIJK           0;1              0           True   \n",
       "1                   AFGHIJK           0;1              0           True   \n",
       "2                   LMNOPQR           0;1              0          False   \n",
       "3                   LMNOPQR           0;1              0          False   \n",
       "4                  ABCDESTK             0              0           True   \n",
       "..                      ...           ...            ...            ...   \n",
       "79  MABCDESTKAFGHIJKLMNOPQR             0              2           True   \n",
       "80  MABCDESTKAFGHIJKLMNOPQR             0              2           True   \n",
       "81  MABCDESTKAFGHIJKLMNOPQR             0              2           True   \n",
       "82  MABCDESTKAFGHIJKLMNOPQR             0              2           True   \n",
       "83  MABCDESTKAFGHIJKLMNOPQR             0              2           True   \n",
       "\n",
       "    is_prot_cterm                                               mods  \\\n",
       "0            True                                                      \n",
       "1            True                              Acetyl@Protein_N-term   \n",
       "2            True                                        Oxidation@M   \n",
       "3            True                                                      \n",
       "4           False                        Carbamidomethyl@C;Phospho@S   \n",
       "..            ...                                                ...   \n",
       "79          False  Acetyl@Protein_N-term;Oxidation@M;Oxidation@M;...   \n",
       "80          False  Acetyl@Protein_N-term;Oxidation@M;Oxidation@M;...   \n",
       "81          False  Acetyl@Protein_N-term;Carbamidomethyl@C;Phospho@S   \n",
       "82          False  Acetyl@Protein_N-term;Carbamidomethyl@C;Phospho@T   \n",
       "83          False            Acetyl@Protein_N-term;Carbamidomethyl@C   \n",
       "\n",
       "     mod_sites  nAA proteins genes  \n",
       "0                 7    xx;yy  gene  \n",
       "1            0    7    xx;yy  gene  \n",
       "2            2    7    xx;yy  gene  \n",
       "3                 7    xx;yy  gene  \n",
       "4          3;6    8       xx        \n",
       "..         ...  ...      ...   ...  \n",
       "79  0;1;18;4;8   23       xx        \n",
       "80    0;1;18;4   23       xx        \n",
       "81       0;4;7   23       xx        \n",
       "82       0;4;8   23       xx        \n",
       "83         0;4   23       xx        \n",
       "\n",
       "[84 rows x 10 columns]"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from alphabase.protein.fasta import append_special_modifications\n",
    "fasta_lib._precursor_df = append_special_modifications(\n",
    "    fasta_lib.precursor_df, ['Phospho@S','Phospho@T'],\n",
    "    min_mod_num=0, max_mod_num=1, max_peptidoform_num=100\n",
    ")\n",
    "fasta_lib.precursor_df"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Flexible method to add peptide labeling"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>sequence</th>\n",
       "      <th>protein_idxes</th>\n",
       "      <th>miss_cleavage</th>\n",
       "      <th>is_prot_nterm</th>\n",
       "      <th>is_prot_cterm</th>\n",
       "      <th>mods</th>\n",
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       "      <th>nAA</th>\n",
       "      <th>proteins</th>\n",
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       "      <th>labeling_channel</th>\n",
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       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
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       "      <td>AFGHIJK</td>\n",
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       "      <td></td>\n",
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       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>LMNOPQR</td>\n",
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       "      <td>0</td>\n",
       "      <td>False</td>\n",
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       "      <td>False</td>\n",
       "      <td>Carbamidomethyl@C;Phospho@S</td>\n",
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       "    <tr>\n",
       "      <th>247</th>\n",
       "      <td>MABCDESTKAFGHIJKLMNOPQR</td>\n",
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       "      <td>Acetyl@Protein_N-term;Carbamidomethyl@C;Phosph...</td>\n",
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       "</table>\n",
       "<p>252 rows × 11 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                    sequence protein_idxes  miss_cleavage  is_prot_nterm  \\\n",
       "0                    AFGHIJK           0;1              0           True   \n",
       "1                    AFGHIJK           0;1              0           True   \n",
       "2                    LMNOPQR           0;1              0          False   \n",
       "3                    LMNOPQR           0;1              0          False   \n",
       "4                   ABCDESTK             0              0           True   \n",
       "..                       ...           ...            ...            ...   \n",
       "247  MABCDESTKAFGHIJKLMNOPQR             0              2           True   \n",
       "248  MABCDESTKAFGHIJKLMNOPQR             0              2           True   \n",
       "249  MABCDESTKAFGHIJKLMNOPQR             0              2           True   \n",
       "250  MABCDESTKAFGHIJKLMNOPQR             0              2           True   \n",
       "251  MABCDESTKAFGHIJKLMNOPQR             0              2           True   \n",
       "\n",
       "     is_prot_cterm                                               mods  \\\n",
       "0             True                                                      \n",
       "1             True                              Acetyl@Protein_N-term   \n",
       "2             True                                        Oxidation@M   \n",
       "3             True                                                      \n",
       "4            False                        Carbamidomethyl@C;Phospho@S   \n",
       "..             ...                                                ...   \n",
       "247          False  Acetyl@Protein_N-term;Oxidation@M;Oxidation@M;...   \n",
       "248          False  Acetyl@Protein_N-term;Oxidation@M;Oxidation@M;...   \n",
       "249          False  Acetyl@Protein_N-term;Carbamidomethyl@C;Phosph...   \n",
       "250          False  Acetyl@Protein_N-term;Carbamidomethyl@C;Phosph...   \n",
       "251          False  Acetyl@Protein_N-term;Carbamidomethyl@C;Dimeth...   \n",
       "\n",
       "           mod_sites  nAA proteins genes labeling_channel  \n",
       "0                       7    xx;yy  gene                   \n",
       "1                  0    7    xx;yy  gene                   \n",
       "2                  2    7    xx;yy  gene                   \n",
       "3                       7    xx;yy  gene                   \n",
       "4                3;6    8       xx                         \n",
       "..               ...  ...      ...   ...              ...  \n",
       "247  0;1;18;4;8;9;16   23       xx                      8  \n",
       "248    0;1;18;4;9;16   23       xx                      8  \n",
       "249       0;4;7;9;16   23       xx                      8  \n",
       "250       0;4;8;9;16   23       xx                      8  \n",
       "251         0;4;9;16   23       xx                      8  \n",
       "\n",
       "[252 rows x 11 columns]"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "fasta_lib.add_peptide_labeling({\n",
    "    '': [], # not labelled for reference\n",
    "    '0': ['Dimethyl@Any_N-term','Dimethyl@K'],\n",
    "    '8': ['Dimethyl:2H(6)13C(2)@Any_N-term','Dimethyl:2H(6)13C(2)@K'],\n",
    "})\n",
    "fasta_lib.precursor_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "</table>\n",
       "<p>756 rows × 4 columns</p>\n",
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      ],
      "text/plain": [
       "                    sequence  \\\n",
       "0                    AFGHIJK   \n",
       "1                    AFGHIJK   \n",
       "2                    AFGHIJK   \n",
       "3                    AFGHIJK   \n",
       "4                    AFGHIJK   \n",
       "..                       ...   \n",
       "751  MABCDESTKAFGHIJKLMNOPQR   \n",
       "752  MABCDESTKAFGHIJKLMNOPQR   \n",
       "753  MABCDESTKAFGHIJKLMNOPQR   \n",
       "754  MABCDESTKAFGHIJKLMNOPQR   \n",
       "755  MABCDESTKAFGHIJKLMNOPQR   \n",
       "\n",
       "                                                  mods   mod_sites  charge  \n",
       "0                                                                        2  \n",
       "1                                                                        3  \n",
       "2                                                                        4  \n",
       "3                                Acetyl@Protein_N-term           0       2  \n",
       "4                                Acetyl@Protein_N-term           0       3  \n",
       "..                                                 ...         ...     ...  \n",
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       "754  Acetyl@Protein_N-term;Carbamidomethyl@C;Dimeth...    0;4;9;16       3  \n",
       "755  Acetyl@Protein_N-term;Carbamidomethyl@C;Dimeth...    0;4;9;16       4  \n",
       "\n",
       "[756 rows x 4 columns]"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "fasta_lib.add_charge()\n",
    "fasta_lib.precursor_df[['sequence','mods','mod_sites','charge']]"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Append precursor mz and isotope information"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/Users/wenfengzeng/workspace/alphabase/alphabase/peptide/precursor.py:613: RuntimeWarning: invalid value encountered in divide\n",
      "  precursor_dist /= np.sum(precursor_dist, axis=1, keepdims=True)\n"
     ]
    },
    {
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       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>752</th>\n",
       "      <td>3.000720e+06</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>753</th>\n",
       "      <td>6.001400e+06</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>754</th>\n",
       "      <td>4.000934e+06</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>755</th>\n",
       "      <td>3.000700e+06</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>756 rows × 7 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "     precursor_mz       i_0       i_1       i_2       i_3       i_4  i_5\n",
       "0    3.932371e+02  0.625822  0.285918  0.072883  0.013411  0.001966  0.0\n",
       "1    2.624938e+02  0.625822  0.285918  0.072883  0.013411  0.001966  0.0\n",
       "2    1.971222e+02  0.625822  0.285918  0.072883  0.013411  0.001966  0.0\n",
       "3    4.142423e+02  0.610921  0.292699  0.078690  0.015312  0.002378  0.0\n",
       "4    2.764973e+02  0.610921  0.292699  0.078690  0.015312  0.002378  0.0\n",
       "..            ...       ...       ...       ...       ...       ...  ...\n",
       "751  4.000960e+06       NaN       NaN       NaN       NaN       NaN  NaN\n",
       "752  3.000720e+06       NaN       NaN       NaN       NaN       NaN  NaN\n",
       "753  6.001400e+06       NaN       NaN       NaN       NaN       NaN  NaN\n",
       "754  4.000934e+06       NaN       NaN       NaN       NaN       NaN  NaN\n",
       "755  3.000700e+06       NaN       NaN       NaN       NaN       NaN  NaN\n",
       "\n",
       "[756 rows x 7 columns]"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "fasta_lib.calc_precursor_mz()\n",
    "fasta_lib.calc_precursor_isotope()\n",
    "fasta_lib.precursor_df[['precursor_mz']+[col for col in fasta_lib.precursor_df.columns if col.startswith('i_')]]"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Using `alphabase.spectral_library.base.SpecLibBase.calc_fragment_mz_df` to calculate fragment mz dataframe."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "      <th></th>\n",
       "      <th>b_z1</th>\n",
       "      <th>y_z1</th>\n",
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       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>7.204439e+01</td>\n",
       "      <td>714.429749</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>2.191128e+02</td>\n",
       "      <td>567.361328</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>2.761343e+02</td>\n",
       "      <td>510.339844</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>4.131932e+02</td>\n",
       "      <td>373.280945</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>5.262772e+02</td>\n",
       "      <td>260.196869</td>\n",
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       "    <tr>\n",
       "      <th>...</th>\n",
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       "    <tr>\n",
       "      <th>11911</th>\n",
       "      <td>1.200205e+07</td>\n",
       "      <td>751.420959</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11912</th>\n",
       "      <td>1.200216e+07</td>\n",
       "      <td>637.377991</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11913</th>\n",
       "      <td>1.200240e+07</td>\n",
       "      <td>400.230286</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11914</th>\n",
       "      <td>1.200250e+07</td>\n",
       "      <td>303.177521</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11915</th>\n",
       "      <td>1.200262e+07</td>\n",
       "      <td>175.118958</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>11916 rows × 2 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "               b_z1        y_z1\n",
       "0      7.204439e+01  714.429749\n",
       "1      2.191128e+02  567.361328\n",
       "2      2.761343e+02  510.339844\n",
       "3      4.131932e+02  373.280945\n",
       "4      5.262772e+02  260.196869\n",
       "...             ...         ...\n",
       "11911  1.200205e+07  751.420959\n",
       "11912  1.200216e+07  637.377991\n",
       "11913  1.200240e+07  400.230286\n",
       "11914  1.200250e+07  303.177521\n",
       "11915  1.200262e+07  175.118958\n",
       "\n",
       "[11916 rows x 2 columns]"
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "fasta_lib.calc_fragment_mz_df()\n",
    "fasta_lib.fragment_mz_df"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "`calc_fragment_mz_df()` also generate pointers `frag_start_idx` and `frag_stop_idx` in the precursor_df to locate fragments of each precursor. "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>frag_start_idx</th>\n",
       "      <th>frag_stop_idx</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>0</td>\n",
       "      <td>6</td>\n",
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       "      <th>1</th>\n",
       "      <td>6</td>\n",
       "      <td>12</td>\n",
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       "      <th>2</th>\n",
       "      <td>12</td>\n",
       "      <td>18</td>\n",
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       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>18</td>\n",
       "      <td>24</td>\n",
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       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>24</td>\n",
       "      <td>30</td>\n",
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       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
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       "    <tr>\n",
       "      <th>751</th>\n",
       "      <td>11806</td>\n",
       "      <td>11828</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>752</th>\n",
       "      <td>11828</td>\n",
       "      <td>11850</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>753</th>\n",
       "      <td>11850</td>\n",
       "      <td>11872</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>754</th>\n",
       "      <td>11872</td>\n",
       "      <td>11894</td>\n",
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       "    <tr>\n",
       "      <th>755</th>\n",
       "      <td>11894</td>\n",
       "      <td>11916</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>756 rows × 2 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "     frag_start_idx  frag_stop_idx\n",
       "0                 0              6\n",
       "1                 6             12\n",
       "2                12             18\n",
       "3                18             24\n",
       "4                24             30\n",
       "..              ...            ...\n",
       "751           11806          11828\n",
       "752           11828          11850\n",
       "753           11850          11872\n",
       "754           11872          11894\n",
       "755           11894          11916\n",
       "\n",
       "[756 rows x 2 columns]"
      ]
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "fasta_lib.precursor_df[['frag_start_idx','frag_stop_idx']]"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Note that all fragment ions are stored from peptide's N-terminal to C-terminal, so the b-ions are in the ascending order (from b1 to bn) and y-ions are in the decending order (from yn to y1)."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "      <th></th>\n",
       "      <th>b_z1</th>\n",
       "      <th>y_z1</th>\n",
       "    </tr>\n",
       "  </thead>\n",
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       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>72.044388</td>\n",
       "      <td>714.429749</td>\n",
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       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>219.112808</td>\n",
       "      <td>567.361328</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>276.134277</td>\n",
       "      <td>510.339844</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>413.193176</td>\n",
       "      <td>373.280945</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>526.277222</td>\n",
       "      <td>260.196869</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>639.361328</td>\n",
       "      <td>147.112808</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "          b_z1        y_z1\n",
       "6    72.044388  714.429749\n",
       "7   219.112808  567.361328\n",
       "8   276.134277  510.339844\n",
       "9   413.193176  373.280945\n",
       "10  526.277222  260.196869\n",
       "11  639.361328  147.112808"
      ]
     },
     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "start, end = fasta_lib.precursor_df[['frag_start_idx','frag_stop_idx']].values[1]\n",
    "fasta_lib.fragment_mz_df.iloc[start:end,:]"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Save protein_df, precursor_df, fragment_mz_df, fragment_intensity_df into a hdf file."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [],
   "source": [
    "# fasta_lib.save_hdf('path/to/hdf_file.hdf')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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