Notebooks/Step1.CreateOneCIFFilePerBiologicalAssembly.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "fcc80ba7",
   "metadata": {},
   "source": [
    "# 1. Clean Structures and Create one CIFF file per Biological Assembly"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "37b09ec8",
   "metadata": {},
   "source": [
    "## What is the goal of this notebook? \n",
    "\n",
    "This notebook achieves 2 goals:\n",
    "\n",
    "1. The first step 'cleans' the CIF files we downloaded in step 0. This step will remove some of the **data names** \n",
    "and **data blocks** included in the raw CIF files. A new directory 'clean_bank' is created in this step.\n",
    "\n",
    "\n",
    "2. The second step will create a new CIF files for each [biological assembly](https://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/biological-assemblies#Anchor-BioUnit) present in any structure. Each new structure will be saved with the suffix +0x.cif (where x is the number of the biological assembly). This step also standardizes the **data names** and **data blocks**. In particular how the coordinate portion of the file is printed.\n"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "fb5c24aa",
   "metadata": {},
   "source": [
    "## Import library and create working directory"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "90edccb0",
   "metadata": {},
   "outputs": [],
   "source": [
    "from PDBClean import pdbclean_io, pdbutils, cleanutils"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "101c2903",
   "metadata": {},
   "outputs": [],
   "source": [
    "# Path to project directory\n",
    "PROJDIR=\"./TIM/\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "71d410ed",
   "metadata": {},
   "outputs": [],
   "source": [
    "# Create directory where we will stored the 'clean' cif files.\n",
    "pdbclean_io.check_project(projdir=PROJDIR, level='clean_bank')"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "f3503582",
   "metadata": {},
   "source": [
    "## Clean CIF files (standardize data blocks)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "3dbc8c16",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1/244]: 7rpn.cif\n",
      "[2/244]: 2v2d.cif\n",
      "[3/244]: 4poc.cif\n",
      "[4/244]: 5zfx.cif\n",
      "[5/244]: 1o5x.cif\n",
      "[6/244]: 4gnj.cif\n",
      "[7/244]: 1ydv.cif\n",
      "[8/244]: 4zvj.cif\n",
      "[9/244]: 4ff7.cif\n",
      "[10/244]: 7qon.cif\n",
      "[11/244]: 1klu.cif\n",
      "[12/244]: 3qsr.cif\n",
      "[13/244]: 4o54.cif\n",
      "[14/244]: 2x1s.cif\n",
      "[15/244]: 3py2.cif\n",
      "[16/244]: 2vfh.cif\n",
      "[17/244]: 1hg3.cif\n",
      "[18/244]: 4obt.cif\n",
      "[19/244]: 6up5.cif\n",
      "[20/244]: 7sx1.cif\n",
      "[21/244]: 4hhp.cif\n",
      "[22/244]: 4o57.cif\n",
      "[23/244]: 1nf0.cif\n",
      "[24/244]: 4iot.cif\n",
      "[25/244]: 5tim.cif\n",
      "[26/244]: 1ml1.cif\n",
      "[27/244]: 2vfi.cif\n",
      "[28/244]: 2x1r.cif\n",
      "[29/244]: 3gvg.cif\n",
      "[30/244]: 1m7p.cif\n",
      "[31/244]: 1aw2.cif\n",
      "[32/244]: 7pek.cif\n",
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      "[34/244]: 4o4v.cif\n",
      "[35/244]: 4o53.cif\n",
      "[36/244]: 1ney.cif\n",
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      "[39/244]: 2y63.cif\n",
      "[40/244]: 5i3k.cif\n",
      "[41/244]: 4jeq.cif\n",
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      "[43/244]: 3qst.cif\n",
      "[44/244]: 5i3j.cif\n",
      "[45/244]: 2y62.cif\n",
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      "[47/244]: 4o52.cif\n",
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      "[49/244]: 4o4w.cif\n",
      "[50/244]: 4pod.cif\n",
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      "[54/244]: 2v2c.cif\n",
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      "[66/244]: 5i3i.cif\n",
      "[67/244]: 2y61.cif\n",
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      "[69/244]: 6nee.cif\n",
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      "[71/244]: 1ssg.cif\n",
      "[72/244]: 2x1t.cif\n",
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      "[111/244]: 1tim.cif\n",
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      "[114/244]: 1if2.cif\n",
      "[115/244]: 5gv4.cif\n",
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      "[118/244]: 2iam.cif\n",
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      "[120/244]: 8tim.cif\n",
      "[121/244]: 2dp3.cif\n",
      "[122/244]: 7rmn.cif\n",
      "[123/244]: 1sw7.cif\n",
      "[124/244]: 3uwu.cif\n",
      "[125/244]: 1tpc.cif\n",
      "[126/244]: 1iig.cif\n",
      "[127/244]: 1yya.cif\n",
      "[128/244]: 3th6.cif\n",
      "[129/244]: 4tim.cif\n",
      "[130/244]: 5brb.cif\n",
      "[131/244]: 4z0j.cif\n",
      "[132/244]: 6nxw.cif\n",
      "[133/244]: 7az9.cif\n",
      "[134/244]: 1wob.cif\n",
      "[135/244]: 1lyx.cif\n",
      "[136/244]: 4y90.cif\n",
      "[137/244]: 1tpb.cif\n",
      "[138/244]: 1tpu.cif\n",
      "[139/244]: 6cg9.cif\n",
      "[140/244]: 2vom.cif\n",
      "[141/244]: 6jox.cif\n",
      "[142/244]: 1tpw.cif\n",
      "[143/244]: 3uwv.cif\n",
      "[144/244]: 7r9b.cif\n",
      "[145/244]: 7rcq.cif\n",
      "[146/244]: 4g1k.cif\n",
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      "[153/244]: 1ag1.cif\n",
      "[154/244]: 1tri.cif\n",
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      "[156/244]: 3uww.cif\n",
      "[157/244]: 6c2g.cif\n",
      "[158/244]: 4unk.cif\n",
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      "[160/244]: 2v5l.cif\n",
      "[161/244]: 1sux.cif\n",
      "[162/244]: 1tpe.cif\n",
      "[163/244]: 1tsi.cif\n",
      "[164/244]: 4y9a.cif\n",
      "[165/244]: 1n55.cif\n",
      "[166/244]: 7qh0.cif\n",
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      "[168/244]: 7abx.cif\n",
      "[169/244]: 6nxq.cif\n",
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      "[171/244]: 7r7m.cif\n",
      "[172/244]: 1sw0.cif\n",
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      "[174/244]: 4unl.cif\n",
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      "[176/244]: 2oma.cif\n",
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      "[178/244]: 2jgq.cif\n",
      "[179/244]: 4ymz.cif\n",
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      "[181/244]: 6nxs.cif\n",
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      "[186/244]: 2jk2.cif\n",
      "[187/244]: 1sw3.cif\n",
      "[188/244]: 1hti.cif\n",
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      "[190/244]: 4bi5.cif\n",
      "[191/244]: 2ven.cif\n",
      "[192/244]: 1spq.cif\n",
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      "[205/244]: 1sq7.cif\n",
      "[206/244]: 5bmw.cif\n",
      "[207/244]: 5i3g.cif\n",
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      "[209/244]: 5i3f.cif\n",
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      "[211/244]: 1ttj.cif\n",
      "[212/244]: 2vel.cif\n",
      "[213/244]: 4e41.cif\n",
      "[214/244]: 7n8u.cif\n",
      "[215/244]: 4bi7.cif\n",
      "[216/244]: 1tmh.cif\n",
      "[217/244]: 1m6j.cif\n",
      "[218/244]: 1mo0.cif\n",
      "[219/244]: 2v0t.cif\n",
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      "[221/244]: 6r8h.cif\n",
      "[222/244]: 1kv5.cif\n",
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      "[224/244]: 1i45.cif\n",
      "[225/244]: 7rde.cif\n",
      "[226/244]: 2vfe.cif\n",
      "[227/244]: 2vei.cif\n",
      "[228/244]: 3pvf.cif\n",
      "[229/244]: 2x2g.cif\n",
      "[230/244]: 2vek.cif\n",
      "[231/244]: 1tcd.cif\n",
      "[232/244]: 2vfg.cif\n",
      "[233/244]: 2v2h.cif\n",
      "[234/244]: 4wje.cif\n",
      "[235/244]: 1qds.cif\n",
      "[236/244]: 4p61.cif\n",
      "[237/244]: 1w0m.cif\n",
      "[238/244]: 2btm.cif\n",
      "[239/244]: 1ypi.cif\n",
      "[240/244]: 5bnk.cif\n",
      "[241/244]: 4rcx.cif\n",
      "[242/244]: 2vff.cif\n",
      "[243/244]: 3pwa.cif\n",
      "[244/244]: 2h6r.cif\n"
     ]
    }
   ],
   "source": [
    "cleanutils.process(projdir=PROJDIR, step='clean', source='raw_bank', target='clean_bank')"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "af89bbd9",
   "metadata": {},
   "source": [
    "## Simplify and Split into Biological Assemblies "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "aa8acf0b",
   "metadata": {},
   "outputs": [],
   "source": [
    "# Create directory to store new structures\n",
    "pdbclean_io.check_project(projdir=PROJDIR, level='simple_bank')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "d481cd0f",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[1/244]: 7rpn.cif\n",
      "[2/244]: 2v2d.cif\n",
      "[3/244]: 4poc.cif\n",
      "[4/244]: 5zfx.cif\n",
      "[5/244]: 1o5x.cif\n",
      "[6/244]: 4gnj.cif\n",
      "[7/244]: 1ydv.cif\n",
      "[8/244]: 4zvj.cif\n",
      "[9/244]: 4ff7.cif\n",
      "[10/244]: 7qon.cif\n",
      "[11/244]: 1klu.cif\n",
      "[12/244]: 3qsr.cif\n",
      "[13/244]: 4o54.cif\n",
      "[14/244]: 2x1s.cif\n",
      "[15/244]: 3py2.cif\n",
      "[16/244]: 2vfh.cif\n",
      "[17/244]: 1hg3.cif\n",
      "[18/244]: 4obt.cif\n",
      "[19/244]: 6up5.cif\n",
      "[20/244]: 7sx1.cif\n",
      "[21/244]: 4hhp.cif\n",
      "[22/244]: 4o57.cif\n",
      "[23/244]: 1nf0.cif\n",
      "[24/244]: 4iot.cif\n",
      "[25/244]: 5tim.cif\n",
      "[26/244]: 1ml1.cif\n",
      "[27/244]: 2vfi.cif\n",
      "[28/244]: 2x1r.cif\n",
      "[29/244]: 3gvg.cif\n",
      "[30/244]: 1m7p.cif\n",
      "[31/244]: 1aw2.cif\n",
      "[32/244]: 7pek.cif\n",
      "[33/244]: 4zz9.cif\n",
      "[34/244]: 4o4v.cif\n",
      "[35/244]: 4o53.cif\n",
      "[36/244]: 1ney.cif\n",
      "[37/244]: 6upf.cif\n",
      "[38/244]: 4mva.cif\n",
      "[39/244]: 2y63.cif\n",
      "[40/244]: 5i3k.cif\n",
      "[41/244]: 4jeq.cif\n",
      "[42/244]: 4owg.cif\n",
      "[43/244]: 3qst.cif\n",
      "[44/244]: 5i3j.cif\n",
      "[45/244]: 2y62.cif\n",
      "[46/244]: 7tim.cif\n",
      "[47/244]: 4o52.cif\n",
      "[48/244]: 6up1.cif\n",
      "[49/244]: 4o4w.cif\n",
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      "[54/244]: 2v2c.cif\n",
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      "[57/244]: 1aw1.cif\n",
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      "[140/244]: 2vom.cif\n",
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      "[145/244]: 7rcq.cif\n",
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      "[155/244]: 1tpv.cif\n",
      "[156/244]: 3uww.cif\n",
      "[157/244]: 6c2g.cif\n",
      "[158/244]: 4unk.cif\n",
      "[159/244]: 6d43.cif\n",
      "[160/244]: 2v5l.cif\n",
      "[161/244]: 1sux.cif\n",
      "[162/244]: 1tpe.cif\n",
      "[163/244]: 1tsi.cif\n",
      "[164/244]: 4y9a.cif\n",
      "[165/244]: 1n55.cif\n",
      "[166/244]: 7qh0.cif\n",
      "[167/244]: 1wyi.cif\n",
      "[168/244]: 7abx.cif\n",
      "[169/244]: 6nxq.cif\n",
      "[170/244]: 4y96.cif\n",
      "[171/244]: 7r7m.cif\n",
      "[172/244]: 1sw0.cif\n",
      "[173/244]: 1tpd.cif\n",
      "[174/244]: 4unl.cif\n",
      "[175/244]: 6tim.cif\n",
      "[176/244]: 2oma.cif\n",
      "[177/244]: 1tpf.cif\n",
      "[178/244]: 2jgq.cif\n",
      "[179/244]: 4ymz.cif\n",
      "[180/244]: 4y8f.cif\n",
      "[181/244]: 6nxs.cif\n",
      "[182/244]: 1r2t.cif\n",
      "[183/244]: 6nxr.cif\n",
      "[184/244]: 7skj.cif\n",
      "[185/244]: 4x22.cif\n",
      "[186/244]: 2jk2.cif\n",
      "[187/244]: 1sw3.cif\n",
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      "[219/244]: 2v0t.cif\n",
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      "[226/244]: 2vfe.cif\n",
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      "[229/244]: 2x2g.cif\n",
      "[230/244]: 2vek.cif\n",
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      "[234/244]: 4wje.cif\n",
      "[235/244]: 1qds.cif\n",
      "[236/244]: 4p61.cif\n",
      "[237/244]: 1w0m.cif\n",
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      "[239/244]: 1ypi.cif\n",
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      "[242/244]: 2vff.cif\n",
      "[243/244]: 3pwa.cif\n",
      "[244/244]: 2h6r.cif\n"
     ]
    }
   ],
   "source": [
    "cleanutils.process(projdir=PROJDIR, step='simplify', source='clean_bank', target='simple_bank')"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "6c5b8e0d",
   "metadata": {},
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "756e588d",
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "13d466a2",
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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