Notebooks/Step2.2.AssignMolIDToEntitiesFoindInCIFfiles2.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "1a9e8a53",
   "metadata": {},
   "source": [
    "# Assign MolID to the entities found in the CIF files (2) "
   ]
  },
  {
   "cell_type": "markdown",
   "id": "bcec58a5",
   "metadata": {},
   "source": [
    "## What is the goal of this notebook?\n",
    "\n",
    "This is a continuation from `Assign MolID to the entities found in the CIF files (1)`.\n",
    "In this notebook we will show what happens when you assign the same name to different chains, because you want to concatenate them. For example, if you want to make all the waters or ions be in the same chain. \n",
    "\n",
    "**Note:** Make sure to run part 1 of this step in advance."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "3771f378",
   "metadata": {},
   "outputs": [],
   "source": [
    "## First, import library and setup directories"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "05789e90",
   "metadata": {},
   "outputs": [],
   "source": [
    "from PDBClean import pdbclean_io"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "ee726354",
   "metadata": {},
   "outputs": [],
   "source": [
    "PROJDIR=\"./TIM/\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "2fa40724",
   "metadata": {},
   "outputs": [],
   "source": [
    "pdbclean_io.check_project(projdir=PROJDIR, action='create', level='simple_bank_sub2')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "968b5aae",
   "metadata": {},
   "outputs": [],
   "source": [
    "# Let's copy the same structures we selected on step 2.1 \n",
    "\n",
    "! cp $PROJDIR/simple_bank_sub/*cif $PROJDIR/simple_bank_sub2/"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "afbff1c4",
   "metadata": {},
   "outputs": [],
   "source": [
    "pdbclean_io.check_project(projdir=PROJDIR, action='create', level='standard_MolID_bank2')"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "abfe9d89",
   "metadata": {},
   "source": [
    "### Running PDBClean_MolID_CIF.py\n",
    "\n",
    "Remember that the way to run this script in the terminal is as following:\n",
    "\n",
    "> PDBClean_MolID_CIF.py `{Input Directory}` `{Output Directory}`\n",
    "\n",
    "The input directory contains the structures that we generated in Step 1. The output directory is where the new structures will be stored. "
   ]
  },
  {
   "cell_type": "markdown",
   "id": "db035e81",
   "metadata": {},
   "source": [
    "### Renaming MolID, how to choose a name? \n",
    "\n",
    "This is a personal decision. You can decide how name each entity. In part 2.1 we assigned a different MolID to each entity, as shown in the table below:\n",
    "\n",
    "| New MolID | ENTITIES |\n",
    "|---|:---|\n",
    "| A | 1:TRIOSEPHOSPHATE ISOMERASE SYNONYM TRIOSE-PHOSPHATE ISOMERASE, TIM: |\n",
    "| B | 1:SN-GLYCEROL-3-PHOSPHATE: |\n",
    "| C | 1:SN-GLYCEROL-1-PHOSPHATE: |\n",
    "| D,E | 2:GLYCEROL: |\n",
    "| F,G | 2:WATER: |\n",
    "| H,I | 2:TRIOSEPHOSPHATE ISOMERASE: |\n",
    "| J | 1:PHOSPHATE ION: |\n",
    "| K,L | 2:2-PHOSPHOGLYCOLIC ACID: | \n",
    "\n",
    "\n",
    "For this example, let's try assigning the same MolID to different entities: \n",
    "\n",
    "| New MolID | ENTITIES |\n",
    "|---|:---|\n",
    "| A | 1:TRIOSEPHOSPHATE ISOMERASE SYNONYM TRIOSE-PHOSPHATE ISOMERASE, TIM: |\n",
    "| D | 1:SN-GLYCEROL-3-PHOSPHATE: |\n",
    "| D | 1:SN-GLYCEROL-1-PHOSPHATE: |\n",
    "| D,D | 2:GLYCEROL: |\n",
    "| C,C | 2:WATER: |\n",
    "| A,B | 2:TRIOSEPHOSPHATE ISOMERASE: |\n",
    "| D | 1:PHOSPHATE ION: |\n",
    "| D,D | 2:2-PHOSPHOGLYCOLIC ACID: | \n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "6dcca91c",
   "metadata": {
    "scrolled": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Reading: ./TIM//simple_bank_sub2/2y62+00.cif  (1 of 6)\n",
      "Reading: ./TIM//simple_bank_sub2/1ag1+00.cif  (2 of 6)\n",
      "Reading: ./TIM//simple_bank_sub2/1aw1+04.cif  (3 of 6)\n",
      "Reading: ./TIM//simple_bank_sub2/1aw1+02.cif  (4 of 6)\n",
      "Reading: ./TIM//simple_bank_sub2/1aw1+03.cif  (5 of 6)\n",
      "Reading: ./TIM//simple_bank_sub2/1aw1+01.cif  (6 of 6)\n",
      "PDBClean MolID Conversion Build Menu\n",
      "             Select one of the following options to proceed:\n",
      "             1) Show full conversion\n",
      "             2) Show only unassigned conversions\n",
      "             3) Enter input file\n",
      "             4) Search MolID to add chain ID conversion\n",
      "             5) Go entry by entry to add chain ID conversion\n",
      "             6) Remove a chain ID conversion\n",
      "             A) Track changes (original_chain_name:new_chain:entity:file_name)\n",
      "          \n",
      "Option Number: 1:TRIOSEPHOSPHATE ISOMERASE SYNONYM TRIOSE-PHOSPHATE ISOMERASE, TIM:\n",
      "1:SN-GLYCEROL-3-PHOSPHATE:\n",
      "1:SN-GLYCEROL-1-PHOSPHATE:\n",
      "2:GLYCEROL:\n",
      "2:WATER:\n",
      "2:TRIOSEPHOSPHATE ISOMERASE:\n",
      "1:PHOSPHATE ION:\n",
      "2:2-PHOSPHOGLYCOLIC ACID:\n",
      "You need to accept 8 entity conversions\n",
      "You need to accept 12 total chain conversions\n",
      "PDBClean MolID Conversion Build Menu\n",
      "             Select one of the following options to proceed:\n",
      "             1) Show full conversion\n",
      "             2) Show only unassigned conversions\n",
      "             3) Enter input file\n",
      "             4) Search MolID to add chain ID conversion\n",
      "             5) Go entry by entry to add chain ID conversion\n",
      "             6) Remove a chain ID conversion\n",
      "             A) Track changes (original_chain_name:new_chain:entity:file_name)\n",
      "          \n",
      "Option Number: Enter chain IDs for each of the following MolID.\n",
      "Comma separated, no spaces\n",
      "TRIOSEPHOSPHATE ISOMERASE SYNONYM TRIOSE-PHOSPHATE ISOMERASE, TIM:SN-GLYCEROL-3-PHOSPHATE:SN-GLYCEROL-1-PHOSPHATE:GLYCEROL:WATER:TRIOSEPHOSPHATE ISOMERASE:PHOSPHATE ION:2-PHOSPHOGLYCOLIC ACID:Congratulations! You have successfully constructed your\n",
      "                 conversion templates. You can proceed to the next section\n",
      "                 by selection option 7 or, continue to edit your conversion\n",
      "                 template through this menu\n",
      "              \n",
      "PDBClean MolID Conversion Build Menu\n",
      "             Select one of the following options to proceed:\n",
      "             1) Show full conversion\n",
      "             2) Show only unassigned conversions\n",
      "             3) Enter input file\n",
      "             4) Search MolID to add chain ID conversion\n",
      "             5) Go entry by entry to add chain ID conversion\n",
      "             6) Remove a chain ID conversion\n",
      "             A) Track changes (original_chain_name:new_chain:entity:file_name)\n",
      "          \n",
      "    7) Continue to next step of curation\n",
      "Option Number: PDBClean Concatenations Menu\n",
      "                 -------------------------------\n",
      "                 This menu appeared because you have assigned the same chain name to two (or more) entities.\n",
      "                 Note that this will concatenate the entities. So you need to either re-assign chain names,\n",
      "                 or ACCEPT concatenations.\n",
      "\n",
      "                 Note: All proposed concatenations must be accepted (by running option 4 or 5) before the curation can\n",
      "                 be completed.\n",
      "\n",
      "                 Before you do anything, we suggest to choose option 2, so you know which concatenations have not\n",
      "                 been accepted. It will also give you the proper format of the input for option 3.\n",
      "\n",
      "                 If you are sure that all the concatenations are correct. Option 5 will accept all of them. They \n",
      "                 will be printed to screen as they are being accepted. \n",
      "\n",
      "                 Select one of the following options to proceed:\n",
      "                 1) Show all conversions\n",
      "                 2) Show only unaccepted concatenations\n",
      "                 3) Search and modify destination chainIDs of proposed concatenations\n",
      "                 4) Accept proposed concatenation one by one\n",
      "                    (Repeat this step until finalizing option appears)\n",
      "                 5) Accept ALL (BE CAREFUL, make sure you agree with all concatenations)\n",
      "              \n",
      "Option Number: ./TIM//simple_bank_sub2/2y62+00.cif:SN-GLYCEROL-3-PHOSPHATE:B:D:1\n",
      "./TIM//simple_bank_sub2/2y62+00.cif:SN-GLYCEROL-1-PHOSPHATE:C:D:2\n",
      "./TIM//simple_bank_sub2/2y62+00.cif:GLYCEROL:D:D:3\n",
      "./TIM//simple_bank_sub2/2y62+00.cif:GLYCEROL:E:D:4\n",
      "./TIM//simple_bank_sub2/1ag1+00.cif:WATER:D:C:1\n",
      "./TIM//simple_bank_sub2/1ag1+00.cif:WATER:E:C:2\n",
      "./TIM//simple_bank_sub2/1aw1+04.cif:2-PHOSPHOGLYCOLIC ACID:O:D:1\n",
      "./TIM//simple_bank_sub2/1aw1+04.cif:2-PHOSPHOGLYCOLIC ACID:P:D:2\n",
      "./TIM//simple_bank_sub2/1aw1+04.cif:WATER:W:C:1\n",
      "./TIM//simple_bank_sub2/1aw1+04.cif:WATER:X:C:2\n",
      "./TIM//simple_bank_sub2/1aw1+02.cif:2-PHOSPHOGLYCOLIC ACID:K:D:1\n",
      "./TIM//simple_bank_sub2/1aw1+02.cif:2-PHOSPHOGLYCOLIC ACID:L:D:2\n",
      "./TIM//simple_bank_sub2/1aw1+02.cif:WATER:S:C:1\n",
      "./TIM//simple_bank_sub2/1aw1+02.cif:WATER:T:C:2\n",
      "./TIM//simple_bank_sub2/1aw1+03.cif:2-PHOSPHOGLYCOLIC ACID:M:D:1\n",
      "./TIM//simple_bank_sub2/1aw1+03.cif:2-PHOSPHOGLYCOLIC ACID:N:D:2\n",
      "./TIM//simple_bank_sub2/1aw1+03.cif:WATER:U:C:1\n",
      "./TIM//simple_bank_sub2/1aw1+03.cif:WATER:V:C:2\n",
      "./TIM//simple_bank_sub2/1aw1+01.cif:2-PHOSPHOGLYCOLIC ACID:I:D:1\n",
      "./TIM//simple_bank_sub2/1aw1+01.cif:2-PHOSPHOGLYCOLIC ACID:J:D:2\n",
      "./TIM//simple_bank_sub2/1aw1+01.cif:WATER:Q:C:1\n",
      "./TIM//simple_bank_sub2/1aw1+01.cif:WATER:R:C:2\n",
      "You need to accept 22 concatenations\n",
      "PDBClean Concatenations Menu\n",
      "                 -------------------------------\n",
      "                 This menu appeared because you have assigned the same chain name to two (or more) entities.\n",
      "                 Note that this will concatenate the entities. So you need to either re-assign chain names,\n",
      "                 or ACCEPT concatenations.\n",
      "\n",
      "                 Note: All proposed concatenations must be accepted (by running option 4 or 5) before the curation can\n",
      "                 be completed.\n",
      "\n",
      "                 Before you do anything, we suggest to choose option 2, so you know which concatenations have not\n",
      "                 been accepted. It will also give you the proper format of the input for option 3.\n",
      "\n",
      "                 If you are sure that all the concatenations are correct. Option 5 will accept all of them. They \n",
      "                 will be printed to screen as they are being accepted. \n",
      "\n",
      "                 Select one of the following options to proceed:\n",
      "                 1) Show all conversions\n",
      "                 2) Show only unaccepted concatenations\n",
      "                 3) Search and modify destination chainIDs of proposed concatenations\n",
      "                 4) Accept proposed concatenation one by one\n",
      "                    (Repeat this step until finalizing option appears)\n",
      "                 5) Accept ALL (BE CAREFUL, make sure you agree with all concatenations)\n",
      "              \n",
      "Option Number: "
     ]
    }
   ],
   "source": [
    "! echo '2\\n5\\nA\\nD\\nD\\nD,D\\nC,C\\nA,B\\nD\\nD,D\\n7\\n2\\nQUIT\\n' | PDBClean_MolID_CIF.py $PROJDIR/simple_bank_sub2 $PROJDIR/standard_MolID_bank2"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "dd0f37da",
   "metadata": {},
   "source": [
    "## A pause to explain what is going on:\n",
    "\n",
    "Notice that a new menu appears when we assign the same MolID to more than one entity. We need to either give a new MolID to the entities, or accept a concatenation. We want to guarantee that you did not assign the same MolID by mistake, so you need to approve each case one by one. \n",
    "\n",
    "In the cell above, we chose option `2) Show only unaccepted concatenations`. Let's take a look at the output:\n",
    "\n",
    "`\n",
    "./TIM//simple_bank_sub2/2y62+00.cif:SN-GLYCEROL-3-PHOSPHATE:B:D:1\n",
    "./TIM//simple_bank_sub2/2y62+00.cif:SN-GLYCEROL-1-PHOSPHATE:C:D:2\n",
    "./TIM//simple_bank_sub2/2y62+00.cif:GLYCEROL:D:D:3\n",
    "./TIM//simple_bank_sub2/2y62+00.cif:GLYCEROL:E:D:4\n",
    "./TIM//simple_bank_sub2/1ag1+00.cif:WATER:D:C:1\n",
    "./TIM//simple_bank_sub2/1ag1+00.cif:WATER:E:C:2\n",
    "./TIM//simple_bank_sub2/1aw1+04.cif:2-PHOSPHOGLYCOLIC ACID:O:D:1\n",
    "./TIM//simple_bank_sub2/1aw1+04.cif:2-PHOSPHOGLYCOLIC ACID:P:D:2\n",
    "./TIM//simple_bank_sub2/1aw1+04.cif:WATER:W:C:1\n",
    "./TIM//simple_bank_sub2/1aw1+04.cif:WATER:X:C:2\n",
    "./TIM//simple_bank_sub2/1aw1+02.cif:2-PHOSPHOGLYCOLIC ACID:K:D:1\n",
    "./TIM//simple_bank_sub2/1aw1+02.cif:2-PHOSPHOGLYCOLIC ACID:L:D:2\n",
    "./TIM//simple_bank_sub2/1aw1+02.cif:WATER:S:C:1\n",
    "./TIM//simple_bank_sub2/1aw1+02.cif:WATER:T:C:2\n",
    "./TIM//simple_bank_sub2/1aw1+03.cif:2-PHOSPHOGLYCOLIC ACID:M:D:1\n",
    "./TIM//simple_bank_sub2/1aw1+03.cif:2-PHOSPHOGLYCOLIC ACID:N:D:2\n",
    "./TIM//simple_bank_sub2/1aw1+03.cif:WATER:U:C:1\n",
    "./TIM//simple_bank_sub2/1aw1+03.cif:WATER:V:C:2\n",
    "./TIM//simple_bank_sub2/1aw1+01.cif:2-PHOSPHOGLYCOLIC ACID:I:D:1\n",
    "./TIM//simple_bank_sub2/1aw1+01.cif:2-PHOSPHOGLYCOLIC ACID:J:D:2\n",
    "./TIM//simple_bank_sub2/1aw1+01.cif:WATER:Q:C:1\n",
    "./TIM//simple_bank_sub2/1aw1+01.cif:WATER:R:C:2\n",
    "You need to accept 22 concatenations\n",
    "`\n",
    "\n",
    "Notice that the format is: \n",
    "\n",
    "`file name` : `entity` : `New MolID we just assigned`: `order of entity with same MolID in CIF file`\n",
    "\n",
    "To continue running the script, you will need to accept each of these concatenations. For this notebook we only show how to accept three of the proposed concatenations. We recommend doing this step on the terminal, and approve each concatenation one by one. \n",
    "\n",
    "Choosing menu `4) Accept proposed concatenation one by one` will print one of the concatenations that stills need to be approved.A new menu will appear, we need to choose option `2) Accept planned concatenation`. This will bring us back to the concatenation menu. We need to repeat this step (choose option 4, and then 2), until the finalize option appears. \n",
    "\n",
    "Even though it is beneficial to check each merge one by one, it can be very tedious (in the case of ions, users would have to approve hundreds of merges), so we also provide the option to accept all the merges automatically `5) Accept ALL`. PDBCleanV2 will still print all merges to the screen, so users can verify that everything is fine.\n",
    "\n",
    "Once all concatenations have been accepted, an option to finalize the curation will appear.\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "7821c381",
   "metadata": {
    "scrolled": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Reading: ./TIM//simple_bank_sub2/2y62+00.cif  (1 of 6)\n",
      "Reading: ./TIM//simple_bank_sub2/1ag1+00.cif  (2 of 6)\n",
      "Reading: ./TIM//simple_bank_sub2/1aw1+04.cif  (3 of 6)\n",
      "Reading: ./TIM//simple_bank_sub2/1aw1+02.cif  (4 of 6)\n",
      "Reading: ./TIM//simple_bank_sub2/1aw1+03.cif  (5 of 6)\n",
      "Reading: ./TIM//simple_bank_sub2/1aw1+01.cif  (6 of 6)\n",
      "PDBClean MolID Conversion Build Menu\n",
      "             Select one of the following options to proceed:\n",
      "             1) Show full conversion\n",
      "             2) Show only unassigned conversions\n",
      "             3) Enter input file\n",
      "             4) Search MolID to add chain ID conversion\n",
      "             5) Go entry by entry to add chain ID conversion\n",
      "             6) Remove a chain ID conversion\n",
      "             A) Track changes (original_chain_name:new_chain:entity:file_name)\n",
      "          \n",
      "Option Number: 1:TRIOSEPHOSPHATE ISOMERASE SYNONYM TRIOSE-PHOSPHATE ISOMERASE, TIM:\n",
      "1:SN-GLYCEROL-3-PHOSPHATE:\n",
      "1:SN-GLYCEROL-1-PHOSPHATE:\n",
      "2:GLYCEROL:\n",
      "2:WATER:\n",
      "2:TRIOSEPHOSPHATE ISOMERASE:\n",
      "1:PHOSPHATE ION:\n",
      "2:2-PHOSPHOGLYCOLIC ACID:\n",
      "You need to accept 8 entity conversions\n",
      "You need to accept 12 total chain conversions\n",
      "PDBClean MolID Conversion Build Menu\n",
      "             Select one of the following options to proceed:\n",
      "             1) Show full conversion\n",
      "             2) Show only unassigned conversions\n",
      "             3) Enter input file\n",
      "             4) Search MolID to add chain ID conversion\n",
      "             5) Go entry by entry to add chain ID conversion\n",
      "             6) Remove a chain ID conversion\n",
      "             A) Track changes (original_chain_name:new_chain:entity:file_name)\n",
      "          \n",
      "Option Number: Enter chain IDs for each of the following MolID.\n",
      "Comma separated, no spaces\n",
      "TRIOSEPHOSPHATE ISOMERASE SYNONYM TRIOSE-PHOSPHATE ISOMERASE, TIM:SN-GLYCEROL-3-PHOSPHATE:SN-GLYCEROL-1-PHOSPHATE:GLYCEROL:WATER:TRIOSEPHOSPHATE ISOMERASE:PHOSPHATE ION:2-PHOSPHOGLYCOLIC ACID:Congratulations! You have successfully constructed your\n",
      "                 conversion templates. You can proceed to the next section\n",
      "                 by selection option 7 or, continue to edit your conversion\n",
      "                 template through this menu\n",
      "              \n",
      "PDBClean MolID Conversion Build Menu\n",
      "             Select one of the following options to proceed:\n",
      "             1) Show full conversion\n",
      "             2) Show only unassigned conversions\n",
      "             3) Enter input file\n",
      "             4) Search MolID to add chain ID conversion\n",
      "             5) Go entry by entry to add chain ID conversion\n",
      "             6) Remove a chain ID conversion\n",
      "             A) Track changes (original_chain_name:new_chain:entity:file_name)\n",
      "          \n",
      "    7) Continue to next step of curation\n",
      "Option Number: PDBClean Concatenations Menu\n",
      "                 -------------------------------\n",
      "                 This menu appeared because you have assigned the same chain name to two (or more) entities.\n",
      "                 Note that this will concatenate the entities. So you need to either re-assign chain names,\n",
      "                 or ACCEPT concatenations.\n",
      "\n",
      "                 Note: All proposed concatenations must be accepted (by running option 4 or 5) before the curation can\n",
      "                 be completed.\n",
      "\n",
      "                 Before you do anything, we suggest to choose option 2, so you know which concatenations have not\n",
      "                 been accepted. It will also give you the proper format of the input for option 3.\n",
      "\n",
      "                 If you are sure that all the concatenations are correct. Option 5 will accept all of them. They \n",
      "                 will be printed to screen as they are being accepted. \n",
      "\n",
      "                 Select one of the following options to proceed:\n",
      "                 1) Show all conversions\n",
      "                 2) Show only unaccepted concatenations\n",
      "                 3) Search and modify destination chainIDs of proposed concatenations\n",
      "                 4) Accept proposed concatenation one by one\n",
      "                    (Repeat this step until finalizing option appears)\n",
      "                 5) Accept ALL (BE CAREFUL, make sure you agree with all concatenations)\n",
      "              \n",
      "Option Number: ./TIM//simple_bank_sub2/2y62+00.cif:SN-GLYCEROL-3-PHOSPHATE:B:D:1\n",
      "Select one of the following options to proceed:\n",
      "                         1) Perform new search\n",
      "                         2) Accept planned concatenation\n",
      "                      \n",
      "./TIM//simple_bank_sub2/2y62+00.cif:SN-GLYCEROL-1-PHOSPHATE:C:D:2\n",
      "Select one of the following options to proceed:\n",
      "                         1) Perform new search\n",
      "                         2) Accept planned concatenation\n",
      "                      \n",
      "./TIM//simple_bank_sub2/2y62+00.cif:GLYCEROL:D:D:3\n",
      "Select one of the following options to proceed:\n",
      "                         1) Perform new search\n",
      "                         2) Accept planned concatenation\n",
      "                      \n",
      "./TIM//simple_bank_sub2/2y62+00.cif:GLYCEROL:E:D:4\n",
      "Select one of the following options to proceed:\n",
      "                         1) Perform new search\n",
      "                         2) Accept planned concatenation\n",
      "                      \n",
      "./TIM//simple_bank_sub2/1ag1+00.cif:WATER:D:C:1\n",
      "Select one of the following options to proceed:\n",
      "                         1) Perform new search\n",
      "                         2) Accept planned concatenation\n",
      "                      \n",
      "./TIM//simple_bank_sub2/1ag1+00.cif:WATER:E:C:2\n",
      "Select one of the following options to proceed:\n",
      "                         1) Perform new search\n",
      "                         2) Accept planned concatenation\n",
      "                      \n",
      "./TIM//simple_bank_sub2/1aw1+04.cif:2-PHOSPHOGLYCOLIC ACID:O:D:1\n",
      "Select one of the following options to proceed:\n",
      "                         1) Perform new search\n",
      "                         2) Accept planned concatenation\n",
      "                      \n",
      "./TIM//simple_bank_sub2/1aw1+04.cif:2-PHOSPHOGLYCOLIC ACID:P:D:2\n",
      "Select one of the following options to proceed:\n",
      "                         1) Perform new search\n",
      "                         2) Accept planned concatenation\n",
      "                      \n",
      "./TIM//simple_bank_sub2/1aw1+04.cif:WATER:W:C:1\n",
      "Select one of the following options to proceed:\n",
      "                         1) Perform new search\n",
      "                         2) Accept planned concatenation\n",
      "                      \n",
      "./TIM//simple_bank_sub2/1aw1+04.cif:WATER:X:C:2\n",
      "Select one of the following options to proceed:\n",
      "                         1) Perform new search\n",
      "                         2) Accept planned concatenation\n",
      "                      \n",
      "./TIM//simple_bank_sub2/1aw1+02.cif:2-PHOSPHOGLYCOLIC ACID:K:D:1\n",
      "Select one of the following options to proceed:\n",
      "                         1) Perform new search\n",
      "                         2) Accept planned concatenation\n",
      "                      \n",
      "./TIM//simple_bank_sub2/1aw1+02.cif:2-PHOSPHOGLYCOLIC ACID:L:D:2\n",
      "Select one of the following options to proceed:\n",
      "                         1) Perform new search\n",
      "                         2) Accept planned concatenation\n",
      "                      \n",
      "./TIM//simple_bank_sub2/1aw1+02.cif:WATER:S:C:1\n",
      "Select one of the following options to proceed:\n",
      "                         1) Perform new search\n",
      "                         2) Accept planned concatenation\n",
      "                      \n",
      "./TIM//simple_bank_sub2/1aw1+02.cif:WATER:T:C:2\n",
      "Select one of the following options to proceed:\n",
      "                         1) Perform new search\n",
      "                         2) Accept planned concatenation\n",
      "                      \n",
      "./TIM//simple_bank_sub2/1aw1+03.cif:2-PHOSPHOGLYCOLIC ACID:M:D:1\n",
      "Select one of the following options to proceed:\n",
      "                         1) Perform new search\n",
      "                         2) Accept planned concatenation\n",
      "                      \n",
      "./TIM//simple_bank_sub2/1aw1+03.cif:2-PHOSPHOGLYCOLIC ACID:N:D:2\n",
      "Select one of the following options to proceed:\n",
      "                         1) Perform new search\n",
      "                         2) Accept planned concatenation\n",
      "                      \n",
      "./TIM//simple_bank_sub2/1aw1+03.cif:WATER:U:C:1\n",
      "Select one of the following options to proceed:\n",
      "                         1) Perform new search\n",
      "                         2) Accept planned concatenation\n",
      "                      \n",
      "./TIM//simple_bank_sub2/1aw1+03.cif:WATER:V:C:2\n",
      "Select one of the following options to proceed:\n",
      "                         1) Perform new search\n",
      "                         2) Accept planned concatenation\n",
      "                      \n",
      "./TIM//simple_bank_sub2/1aw1+01.cif:2-PHOSPHOGLYCOLIC ACID:I:D:1\n",
      "Select one of the following options to proceed:\n",
      "                         1) Perform new search\n",
      "                         2) Accept planned concatenation\n",
      "                      \n",
      "./TIM//simple_bank_sub2/1aw1+01.cif:2-PHOSPHOGLYCOLIC ACID:J:D:2\n",
      "Select one of the following options to proceed:\n",
      "                         1) Perform new search\n",
      "                         2) Accept planned concatenation\n",
      "                      \n",
      "./TIM//simple_bank_sub2/1aw1+01.cif:WATER:Q:C:1\n",
      "Select one of the following options to proceed:\n",
      "                         1) Perform new search\n",
      "                         2) Accept planned concatenation\n",
      "                      \n",
      "./TIM//simple_bank_sub2/1aw1+01.cif:WATER:R:C:2\n",
      "Select one of the following options to proceed:\n",
      "                         1) Perform new search\n",
      "                         2) Accept planned concatenation\n",
      "                      \n",
      "0\n",
      "Congratulations! You have successfully constructed your\n",
      "                     conversion templates.You can proceed to the next section\n",
      "                     by selection option 6 or, continue to edit your conversion\n",
      "                     template through this menu\n",
      "                  \n",
      "PDBClean Concatenations Menu\n",
      "                 -------------------------------\n",
      "                 This menu appeared because you have assigned the same chain name to two (or more) entities.\n",
      "                 Note that this will concatenate the entities. So you need to either re-assign chain names,\n",
      "                 or ACCEPT concatenations.\n",
      "\n",
      "                 Note: All proposed concatenations must be accepted (by running option 4 or 5) before the curation can\n",
      "                 be completed.\n",
      "\n",
      "                 Before you do anything, we suggest to choose option 2, so you know which concatenations have not\n",
      "                 been accepted. It will also give you the proper format of the input for option 3.\n",
      "\n",
      "                 If you are sure that all the concatenations are correct. Option 5 will accept all of them. They \n",
      "                 will be printed to screen as they are being accepted. \n",
      "\n",
      "                 Select one of the following options to proceed:\n",
      "                 1) Show all conversions\n",
      "                 2) Show only unaccepted concatenations\n",
      "                 3) Search and modify destination chainIDs of proposed concatenations\n",
      "                 4) Accept proposed concatenation one by one\n",
      "                    (Repeat this step until finalizing option appears)\n",
      "                 5) Accept ALL (BE CAREFUL, make sure you agree with all concatenations)\n",
      "              \n",
      "    6) Finalize Curation\n",
      "Option Number: Finalizing Curation ...\n"
     ]
    }
   ],
   "source": [
    "! echo \"2\\n5\\nA\\nD\\nD\\nD,D\\nC,C\\nA,B\\nD\\nD,D\\n7\\n5\\n6\" | PDBClean_MolID_CIF.py $PROJDIR/simple_bank_sub2 $PROJDIR/standard_MolID_bank2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "a65e7eaa",
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "PDBCleanV2",
   "language": "python",
   "name": "pdbcleanv2"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.10.5"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 5
}