\n"
]
}
],
"source": [
"with open(os.path.join(data_path, '1OLG.pdb'), 'r') as f:\n",
" print(type(f))"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Python has a wonderful keyword, `with`. This keyword enables **context management**. Upon entry into a `with` block, variables have certain meaning. In this case, the variable `f` has the meaning of an open file, an instance of the `_io.TextIOWrapper` class. Upon exit, certain operations take place. For file objects created by opening them, the file is automatically closed upon exit, **even if there is an error**. This is important. If your program raises an exception before you have a chance to close the file, it won't get closed and you could be in trouble. If you use context management, the file will still get closed. So here is an important tip:\n",
"\n",
"\n",
"\n",
"Use context management using `with` when working with files.\n",
" \n",
"
\n",
"\n",
"Let's focus for a moment on the variable `f` in the above code cell. It is a Python `file` object, which has methods and attributes, just like any other object. We'll explore those in a moment, but first, let's look at how we opened the file. The first argument to `open()` is a string that has the name of the file, with the full path if necessary. The second argument is a string that says what we will be doing with the file. I.e., are we reading or writing to the file? The possible strings for this second argument are\n",
"\n",
"|string | meaning|\n",
"|:------|:-------|\n",
"|`'r'` | open a text file for reading|\n",
"|`'w'` | create and open a text file for writing|\n",
"|`'a'` | append an existing text file|\n",
"|`'r+'`| open a text file for reading and writing|\n",
"|append `'b'` to any of the above | same as above, except for binary files|\n",
"\n",
"We will mostly be working with text files in the bootcamp, so the first three are the most useful. A big warning, though....\n",
"\n",
"\n",
"\n",
"Trying to open an existing file with `'w'` will wipe it out and create a new file.\n",
" \n",
"
"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Reading data out of the file with file object methods\n",
"\n",
"We will focus on the methods `f.read()` and `f.readlines()`. What do they do?\n",
"\n",
"|method | task|\n",
"|:------|:-------|\n",
"|`f.read()` | Read the entire contents of the file into a string|\n",
"|`f.readlines()` | Read the entire file into a list with each item being a string representing a line|\n",
"\n",
"First, we'll try using the first method to get a single string with the entire contents of the file."
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"'HEADER ANTI-ONCOGENE 13-JUN-94 1OLG \\nTITLE HIGH-RESOLUTION SOLUTION STRUCTURE OF THE OLIGOMERIZATION \\nTITLE 2 DOMAIN OF P53 BY MULTI-DIMENSIONAL NMR \\nCOMPND MOL_ID: 1; \\nCOMPND 2 MOLECULE: TUMOR SUPPRESSOR P53 (OLIGOMERIZATION DOMAIN); \\nCOMPND 3 CHAIN: A, B, C, D; \\nCOMPND 4 ENGINEERED: YES \\nSOURCE MOL_ID: 1; \\nSOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; \\nSOURCE 3 ORGANISM_COMMON: HUMAN; \\nSOURCE 4 ORGANISM_TAXID: 9606 \\nKEYWDS ANTI-ONCOGENE \\nEXPDTA SOLUTION NMR '"
]
},
"execution_count": 3,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# Read file into string\n",
"with open('../data/1OLG.pdb', 'r') as f:\n",
" f_str = f.read()\n",
"\n",
"# Let's look at the first 1000 characters\n",
"f_str[:1000]"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"We see lots of `\\n`, which signifies a new line. The backslash is known as an **escape character**, meaning that the `n` after it does not signify the letter n, but that `\\n` together means a new line.\n",
"\n",
"Now, let's try reading it in as a list."
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"['HEADER ANTI-ONCOGENE 13-JUN-94 1OLG \\n',\n",
" 'TITLE HIGH-RESOLUTION SOLUTION STRUCTURE OF THE OLIGOMERIZATION \\n',\n",
" 'TITLE 2 DOMAIN OF P53 BY MULTI-DIMENSIONAL NMR \\n',\n",
" 'COMPND MOL_ID: 1; \\n',\n",
" 'COMPND 2 MOLECULE: TUMOR SUPPRESSOR P53 (OLIGOMERIZATION DOMAIN); \\n',\n",
" 'COMPND 3 CHAIN: A, B, C, D; \\n',\n",
" 'COMPND 4 ENGINEERED: YES \\n',\n",
" 'SOURCE MOL_ID: 1; \\n',\n",
" 'SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; \\n',\n",
" 'SOURCE 3 ORGANISM_COMMON: HUMAN; \\n']"
]
},
"execution_count": 4,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# Read contents of the file in as a list\n",
"with open('../data/1OLG.pdb', 'r') as f:\n",
" f_list = f.readlines()\n",
"\n",
"# Look at the list (first ten entries)\n",
"f_list[:10]"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"We see that each entry is a line, including the newline character. To look at lines in files, the `rstrip()` method for strings can come it handy. It strips all whitespace, including newlines, from the end of a string."
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"'HEADER ANTI-ONCOGENE 13-JUN-94 1OLG'"
]
},
"execution_count": 5,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"f_list[0].rstrip()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Reading line-by-line\n",
"\n",
"What if we do not want to read the entire file into a list? For example, if a file is several gigabytes, we do not want to spend all of our RAM storing a list. Instead, we can read it line-by-line. Conveniently, the file object can be used as an iterator."
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"HEADER ANTI-ONCOGENE 13-JUN-94 1OLG\n",
"TITLE HIGH-RESOLUTION SOLUTION STRUCTURE OF THE OLIGOMERIZATION\n",
"TITLE 2 DOMAIN OF P53 BY MULTI-DIMENSIONAL NMR\n",
"COMPND MOL_ID: 1;\n",
"COMPND 2 MOLECULE: TUMOR SUPPRESSOR P53 (OLIGOMERIZATION DOMAIN);\n",
"COMPND 3 CHAIN: A, B, C, D;\n",
"COMPND 4 ENGINEERED: YES\n",
"SOURCE MOL_ID: 1;\n",
"SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;\n",
"SOURCE 3 ORGANISM_COMMON: HUMAN;\n",
"SOURCE 4 ORGANISM_TAXID: 9606\n"
]
}
],
"source": [
"# Print the first ten lines of the file\n",
"with open('../data/1OLG.pdb', 'r') as f:\n",
" for i, line in enumerate(f):\n",
" print(line.rstrip())\n",
" if i >= 10:\n",
" break"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Alternatively, we can use the method `f.readline()` to read a single line in the file and return it as a string."
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"HEADER ANTI-ONCOGENE 13-JUN-94 1OLG\n",
"TITLE HIGH-RESOLUTION SOLUTION STRUCTURE OF THE OLIGOMERIZATION\n",
"TITLE 2 DOMAIN OF P53 BY MULTI-DIMENSIONAL NMR\n",
"COMPND MOL_ID: 1;\n",
"COMPND 2 MOLECULE: TUMOR SUPPRESSOR P53 (OLIGOMERIZATION DOMAIN);\n",
"COMPND 3 CHAIN: A, B, C, D;\n",
"COMPND 4 ENGINEERED: YES\n",
"SOURCE MOL_ID: 1;\n",
"SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;\n",
"SOURCE 3 ORGANISM_COMMON: HUMAN;\n"
]
}
],
"source": [
"# Print the first ten lines of the file\n",
"with open('../data/1OLG.pdb', 'r') as f:\n",
" i = 0\n",
" while i < 10:\n",
" print(f.readline().rstrip())\n",
" i += 1"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Each subsequent call to `f.readline()` reads in the next line of the file. (Remember, as we read through a file, we keep moving forward in the bytes of the file and we have to use `f.seek()` to rewind.)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Writing to a file\n",
"\n",
"Writing to a file has similar syntax. We already saw how to open a file for writing. Again, context management is useful. However, before trying to open a file, we should check to make sure a file of the same name does not exist before opening it. The `os.path` module is useful. The function `os.path.isfile()` function checks to see if a file exists."
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"True"
]
},
"execution_count": 8,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"os.path.isfile('../data/1OLG.pdb')"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Now that we know how to check existence of a file so we do not overwrite it, we can open and write a file."
]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {},
"outputs": [
{
"ename": "RuntimeError",
"evalue": "knowledge.txt already exists.",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mRuntimeError\u001b[0m Traceback (most recent call last)",
"\u001b[0;32m\u001b[0m in \u001b[0;36m\u001b[0;34m\u001b[0m\n\u001b[1;32m 1\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mos\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mpath\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0misfile\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'knowledge.txt'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 2\u001b[0;31m \u001b[0;32mraise\u001b[0m \u001b[0mRuntimeError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'knowledge.txt already exists.'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 3\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 4\u001b[0m \u001b[0;32mwith\u001b[0m \u001b[0mopen\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'knowledge.txt'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m'w'\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mas\u001b[0m \u001b[0mf\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 5\u001b[0m \u001b[0mf\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mwrite\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"...as we know, there are known knowns;\"\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;31mRuntimeError\u001b[0m: knowledge.txt already exists."
]
}
],
"source": [
"if os.path.isfile('knowledge.txt'):\n",
" raise RuntimeError('knowledge.txt already exists.')\n",
"\n",
"with open('knowledge.txt', 'w') as f:\n",
" f.write(\"...as we know, there are known knowns;\")\n",
" f.write(\"there are things we know we know.\")\n",
" f.write(\"We also know there are known unknowns;\")\n",
" f.write(\"that is to say we know there are some things we do not know.\")\n",
" f.write(\"But there are also unknown unknowns,\")\n",
" f.write(\"the ones we don't know we don't know.\")"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Note that we can use the `f.write()` method to write strings to a file. Let's look at the file contents."
]
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"...as we know, there are known knowns;\n",
"there are things we know we know.\n",
"We also know there are known unknowns;\n",
"that is to say we know there are some things we do not know.\n",
"But there are also unknown unknowns,\n",
"the ones we don't know we don't know."
]
}
],
"source": [
"!cat knowledge.txt"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Ah! There are no newlines! When writing to a file, unlike when you use the `print()` function, you must include the newline characters. Let's try again, intentionally obliterating our first attempt."
]
},
{
"cell_type": "code",
"execution_count": 11,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"...as we know, there are known knowns;\n",
"there are things we know we know.\n",
"We also know there are known unknowns;\n",
"that is to say we know there are some things we do not know.\n",
"But there are also unknown unknowns,\n",
"the ones we don't know we don't know."
]
}
],
"source": [
"with open('knowledge.txt', 'w') as f:\n",
" f.write(\"...as we know, there are known knowns;\\n\")\n",
" f.write(\"there are things we know we know.\\n\")\n",
" f.write(\"We also know there are known unknowns;\\n\")\n",
" f.write(\"that is to say we know there are some things we do not know.\\n\")\n",
" f.write(\"But there are also unknown unknowns,\\n\")\n",
" f.write(\"the ones we don't know we don't know.\")\n",
" \n",
"!cat knowledge.txt"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"That's better. Note also that `f.write()` **only** takes strings as arguments. You cannot pass numbers. They must be converted to strings first."
]
},
{
"cell_type": "code",
"execution_count": 12,
"metadata": {},
"outputs": [
{
"ename": "TypeError",
"evalue": "write() argument must be str, not float",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mTypeError\u001b[0m Traceback (most recent call last)",
"\u001b[0;32m\u001b[0m in \u001b[0;36m\u001b[0;34m\u001b[0m\n\u001b[1;32m 2\u001b[0m \u001b[0;32mwith\u001b[0m \u001b[0mopen\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'gimme_phi.txt'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m'w'\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mas\u001b[0m \u001b[0mf\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 3\u001b[0m \u001b[0mf\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mwrite\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'The golden ratio is φ = '\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 4\u001b[0;31m \u001b[0mf\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mwrite\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;36m1.61803398875\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
"\u001b[0;31mTypeError\u001b[0m: write() argument must be str, not float"
]
}
],
"source": [
"# This will result in an exception\n",
"with open('gimme_phi.txt', 'w') as f:\n",
" f.write('The golden ratio is φ = ')\n",
" f.write(1.61803398875)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Yup. It must be a string. Let's try again."
]
},
{
"cell_type": "code",
"execution_count": 13,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"The golden ratio is φ = 1.61803399"
]
}
],
"source": [
"with open('gimme_phi.txt', 'w') as f:\n",
" f.write('The golden ratio is φ = ')\n",
" f.write('{phi:.8f}'.format(phi=1.61803398875))\n",
"\n",
"!cat gimme_phi.txt"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"That works!"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## An exercise: extract atomic coordinates for first chain in tetramer\n",
"\n",
"As an example on how to do file I/O, we will take the PDB file and extract only the `ATOM` records for the first chain of the tetramer and write only those entries to a new file.\n",
"\n",
"It is useful to know that according to the [PDB format specification](http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM), column 21 in the `ATOM` entry gives the ID of the chain.\n",
"\n",
"We also conveniently use the fact that we can have multiple files open in our `with` block, separating them with commas."
]
},
{
"cell_type": "code",
"execution_count": 14,
"metadata": {},
"outputs": [],
"source": [
"with open('../data/1OLG.pdb', 'r') as f, open('atoms_chain_A.txt', 'w') as f_out:\n",
" # Put the ATOM lines from chain A in new file\n",
" for line in f:\n",
" if len(line) > 21 and line[:4] == 'ATOM' and line[21] == 'A':\n",
" f_out.write(line)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Let's see how we did!"
]
},
{
"cell_type": "code",
"execution_count": 15,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"ATOM 1 N LYS A 319 18.634 25.437 10.685 1.00 4.81 N \n",
"ATOM 2 CA LYS A 319 17.984 25.295 9.354 1.00 4.32 C \n",
"ATOM 3 C LYS A 319 18.160 23.876 8.818 1.00 3.74 C \n",
"ATOM 4 O LYS A 319 19.259 23.441 8.537 1.00 3.67 O \n",
"ATOM 5 CB LYS A 319 18.609 26.282 8.371 1.00 4.67 C \n",
"ATOM 6 CG LYS A 319 18.003 26.056 6.986 1.00 5.15 C \n",
"ATOM 7 CD LYS A 319 16.476 26.057 7.091 1.00 5.90 C \n",
"ATOM 8 CE LYS A 319 16.014 27.341 7.784 1.00 6.51 C \n",
"ATOM 9 NZ LYS A 319 16.388 28.518 6.952 1.00 7.33 N \n",
"ATOM 10 H1 LYS A 319 18.414 24.606 11.281 1.00 5.09 H \n"
]
}
],
"source": [
"!head -10 atoms_chain_A.txt"
]
},
{
"cell_type": "code",
"execution_count": 16,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"ATOM 689 HD2 PRO A 359 0.183 25.663 13.542 1.00 4.71 H \n",
"ATOM 690 HD3 PRO A 359 0.246 23.956 13.062 1.00 4.53 H \n",
"ATOM 691 N GLY A 360 -3.984 26.791 10.832 1.00 5.45 N \n",
"ATOM 692 CA GLY A 360 -4.489 28.138 10.445 1.00 5.95 C \n",
"ATOM 693 C GLY A 360 -5.981 28.236 10.765 1.00 6.77 C \n",
"ATOM 694 O GLY A 360 -6.401 27.621 11.732 1.00 7.24 O \n",
"ATOM 695 OXT GLY A 360 -6.679 28.924 10.039 1.00 7.15 O \n",
"ATOM 696 H GLY A 360 -4.589 26.020 10.828 1.00 5.72 H \n",
"ATOM 697 HA2 GLY A 360 -3.950 28.896 10.995 1.00 5.99 H \n",
"ATOM 698 HA3 GLY A 360 -4.341 28.288 9.386 1.00 6.05 H \n"
]
}
],
"source": [
"!tail -10 atoms_chain_A.txt"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Nice!"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Finding files and with glob\n",
"\n",
"In the above snippet of code, we extracted all atom records from a PDB file. We might want to do this (or some other operation) for many files. For example, the directory `~/git/data/` has four PDB files in it. For the present discussion, let's say we want to pull the sequence of chain A out of each PDB file.\n",
"\n",
"The `glob` module from the standard library enables us to get a list of all files that match a pattern. In our case, we want all files matching `data/*.pdb`, where `*` is a **wild card character**, meaning that any matches of characters where `*` appears are allowed. Let's see what `glob.glob()` gives us."
]
},
{
"cell_type": "code",
"execution_count": 17,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"['../data/1OLG.pdb',\n",
" '../data/1J6Z.pdb',\n",
" '../data/1FAG.pdb',\n",
" '../data/2ERK.pdb']"
]
},
"execution_count": 17,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"file_list = glob.glob('../data/*.pdb')\n",
"\n",
"file_list"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"We have the four PDB files. We can now loop over them and pull out the sequences."
]
},
{
"cell_type": "code",
"execution_count": 18,
"metadata": {},
"outputs": [],
"source": [
"# Dictionary to hold sequences\n",
"seqs = {}\n",
"\n",
"# Loop through all matching files\n",
"for file_name in file_list:\n",
" # Extract PDB ID\n",
" pdb_id = file_name[file_name.rfind('/')+1:file_name.rfind('.')]\n",
" \n",
" # Initialize sequence string, which we build as we go along\n",
" seq = ''\n",
" with open(file_name, 'r') as f:\n",
" for line in f:\n",
" if len(line) > 11 and line[:6] == 'SEQRES' and line[11] == 'A':\n",
" seq += line[19:].rstrip() + ' '\n",
"\n",
" # Build sequence with dash-joined three letter codes\n",
" seq = '-'.join(seq.split())\n",
"\n",
" # Store in the dictionary\n",
" seqs[pdb_id] = seq"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Let's take a look at what we got. We'll look at actin."
]
},
{
"cell_type": "code",
"execution_count": 19,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"'ASP-GLU-ASP-GLU-THR-THR-ALA-LEU-VAL-CYS-ASP-ASN-GLY-SER-GLY-LEU-VAL-LYS-ALA-GLY-PHE-ALA-GLY-ASP-ASP-ALA-PRO-ARG-ALA-VAL-PHE-PRO-SER-ILE-VAL-GLY-ARG-PRO-ARG-HIS-GLN-GLY-VAL-MET-VAL-GLY-MET-GLY-GLN-LYS-ASP-SER-TYR-VAL-GLY-ASP-GLU-ALA-GLN-SER-LYS-ARG-GLY-ILE-LEU-THR-LEU-LYS-TYR-PRO-ILE-GLU-HIC-GLY-ILE-ILE-THR-ASN-TRP-ASP-ASP-MET-GLU-LYS-ILE-TRP-HIS-HIS-THR-PHE-TYR-ASN-GLU-LEU-ARG-VAL-ALA-PRO-GLU-GLU-HIS-PRO-THR-LEU-LEU-THR-GLU-ALA-PRO-LEU-ASN-PRO-LYS-ALA-ASN-ARG-GLU-LYS-MET-THR-GLN-ILE-MET-PHE-GLU-THR-PHE-ASN-VAL-PRO-ALA-MET-TYR-VAL-ALA-ILE-GLN-ALA-VAL-LEU-SER-LEU-TYR-ALA-SER-GLY-ARG-THR-THR-GLY-ILE-VAL-LEU-ASP-SER-GLY-ASP-GLY-VAL-THR-HIS-ASN-VAL-PRO-ILE-TYR-GLU-GLY-TYR-ALA-LEU-PRO-HIS-ALA-ILE-MET-ARG-LEU-ASP-LEU-ALA-GLY-ARG-ASP-LEU-THR-ASP-TYR-LEU-MET-LYS-ILE-LEU-THR-GLU-ARG-GLY-TYR-SER-PHE-VAL-THR-THR-ALA-GLU-ARG-GLU-ILE-VAL-ARG-ASP-ILE-LYS-GLU-LYS-LEU-CYS-TYR-VAL-ALA-LEU-ASP-PHE-GLU-ASN-GLU-MET-ALA-THR-ALA-ALA-SER-SER-SER-SER-LEU-GLU-LYS-SER-TYR-GLU-LEU-PRO-ASP-GLY-GLN-VAL-ILE-THR-ILE-GLY-ASN-GLU-ARG-PHE-ARG-CYS-PRO-GLU-THR-LEU-PHE-GLN-PRO-SER-PHE-ILE-GLY-MET-GLU-SER-ALA-GLY-ILE-HIS-GLU-THR-THR-TYR-ASN-SER-ILE-MET-LYS-CYS-ASP-ILE-ASP-ILE-ARG-LYS-ASP-LEU-TYR-ALA-ASN-ASN-VAL-MET-SER-GLY-GLY-THR-THR-MET-TYR-PRO-GLY-ILE-ALA-ASP-ARG-MET-GLN-LYS-GLU-ILE-THR-ALA-LEU-ALA-PRO-SER-THR-MET-LYS-ILE-LYS-ILE-ILE-ALA-PRO-PRO-GLU-ARG-LYS-TYR-SER-VAL-TRP-ILE-GLY-GLY-SER-ILE-LEU-ALA-SER-LEU-SER-THR-PHE-GLN-GLN-MET-TRP-ILE-THR-LYS-GLN-GLU-TYR-ASP-GLU-ALA-GLY-PRO-SER-ILE-VAL-HIS-ARG-LYS-CYS-PHE'"
]
},
"execution_count": 19,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"seqs['1J6Z']"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Computing environment"
]
},
{
"cell_type": "code",
"execution_count": 20,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"CPython 3.8.3\n",
"IPython 7.16.1\n",
"\n",
"jupyterlab 2.1.5\n"
]
}
],
"source": [
"%load_ext watermark\n",
"%watermark -v -p jupyterlab"
]
}
],
"metadata": {
"anaconda-cloud": {},
"kernelspec": {
"display_name": "Python 3",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.8.3"
}
},
"nbformat": 4,
"nbformat_minor": 4
}