{ "cells": [ { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "# Subprocess" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## 11/9/2023\n", "\n", "print view\n", "\n", "notebook" ] }, { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [ { "data": { "text/html": [ "\n" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "%%html\n", "" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "# Going Outside the (Python) Box" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Sometimes you need to integrate with programs that don't have a python interface (or you think it would just be easier to use the command line interface).\n", "\n", "Python has a versatile subprocess module for calling and interacting with other programs.\n", "\n", "However, first the venerable system command:" ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ " % Total % Received % Xferd Average Speed Time Time Time Current\n", " Dload Upload Total Spent Left Speed\n", "\r", " 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0\r", "100 152 100 152 0 0 11799 0 --:--:-- --:--:-- --:--:-- 12666\n" ] }, { "data": { "text/plain": [ "0" ] }, "execution_count": 2, "metadata": {}, "output_type": "execute_result" } ], "source": [ "import os\n", "os.system(\"curl http://mscbio2025.csb.pitt.edu -o class.html\")" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "The return value of the system command is the exit code (not what is printed to screen)." ] }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [ { "data": { "text/plain": [ "152" ] }, "execution_count": 3, "metadata": {}, "output_type": "execute_result" } ], "source": [ "f = open('class.html')\n", "len(f.read())" ] }, { "cell_type": "code", "execution_count": 18, "metadata": { "slideshow": { "slide_type": "slide" } }, "outputs": [ { "data": { "text/html": [ "
\n", "\n" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "%%html\n", "
\n", "" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "# subprocess" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "The `subprocess` module replaces the following modules (so don't use them):" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "os.system\n", "os.spawn*\n", "os.popen*\n", "popen2.*\n", "commands.*" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "# subprocess.call" ] }, { "cell_type": "code", "execution_count": 5, "metadata": { "slideshow": { "slide_type": "skip" } }, "outputs": [], "source": [ "ARGS='ls'" ] }, { "cell_type": "code", "execution_count": 6, "metadata": { "slideshow": { "slide_type": "skip" } }, "outputs": [], "source": [ "!mkdir /tmp/empty" ] }, { "cell_type": "code", "execution_count": 7, "metadata": { "slideshow": { "slide_type": "skip" } }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "/tmp/empty\n" ] } ], "source": [ "cd /tmp/empty" ] }, { "cell_type": "code", "execution_count": 8, "metadata": {}, "outputs": [ { "data": { "text/plain": [ "0" ] }, "execution_count": 8, "metadata": {}, "output_type": "execute_result" } ], "source": [ "import subprocess\n", "subprocess.call(ARGS, stdin=None, stdout=None, stderr=None, shell=False)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Run the command described by `ARGS`. Wait for command to complete, then return the returncode attribute.\n", "\n", "
" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "# ARGS" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "`ARGS` specifies the command to call and its arguments. It can either be a **string** or a **list of strings**." ] }, { "cell_type": "code", "execution_count": 9, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\n" ] }, { "data": { "text/plain": [ "0" ] }, "execution_count": 9, "metadata": {}, "output_type": "execute_result" } ], "source": [ "subprocess.call('echo')" ] }, { "cell_type": "code", "execution_count": 10, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "hello\n" ] }, { "data": { "text/plain": [ "0" ] }, "execution_count": 10, "metadata": {}, "output_type": "execute_result" } ], "source": [ "subprocess.call(['echo','hello'])" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "If `shell=False` (default) and `args` is a string, it must be only the name of the program (no arguments). If a list is provided, then the first element is the program name and the remaining elements are the arguments." ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "# shell" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "If (and only if) `shell = True` then the string provided for `args` is parsed *exactly* as if you typed it on the commandline. This means you that:\n", "\n", "* you must escape special characters (e.g. spaces in file names)\n", "* you can use the wildcard '*' character to expand file names\n", "* you can add IO redirection\n", "\n", "If `shell=False` then list arguments must be use and they are passed literally to the program (e.g., it would get '*' for a file name).\n", "\n", "`shell` is `False` by default for security reasons. Consider:\n", "\n", " filename = input(\"What file would you like to display?\\n\")\n", " What file would you like to display?\n", " non_existent; rm -rf / #\n", " subprocess.call(\"cat \" + filename, shell=True) # Uh-oh. This will end badly..." ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "Be default `/bin/sh` is used as the shell. You are probably using `bash`. You can specify what shell to use with the `executable` argument." ] }, { "cell_type": "code", "execution_count": 11, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "/bin/sh\n", "/bin/bash\n" ] }, { "data": { "text/plain": [ "0" ] }, "execution_count": 11, "metadata": {}, "output_type": "execute_result" } ], "source": [ "subprocess.call('echo $0',shell=True) #prints out /bin/sh\n", "subprocess.call('echo $0',executable='/bin/bash',shell=True) #prints out /bin/bash" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "# shell Examples" ] }, { "cell_type": "code", "execution_count": 12, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "ls: cannot access '*': No such file or directory\n" ] }, { "data": { "text/plain": [ "2" ] }, "execution_count": 12, "metadata": {}, "output_type": "execute_result" } ], "source": [ "subprocess.call(['ls','*']) # ls: *: No such file or directory" ] }, { "cell_type": "code", "execution_count": 13, "metadata": {}, "outputs": [], "source": [ "!touch file\\ with\\ spaces" ] }, { "cell_type": "code", "execution_count": 14, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "file with spaces\n", "0\n", "2\n", "file with spaces\n", "0\n", "file with spaces\n", "0\n", "2\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "ls: cannot access 'file': No such file or directory\n", "ls: cannot access 'with': No such file or directory\n", "ls: cannot access 'spaces': No such file or directory\n", "ls: cannot access 'file\\ with\\ spaces': No such file or directory\n" ] } ], "source": [ "#note - ls returns nonzero exit code if can't list any files\n", "print(subprocess.call('ls *',shell=True)) #shows all files\n", "print(subprocess.call('ls file with spaces',shell=True)) #tries to ls three different files\n", "print(subprocess.call('ls file\\ with\\ spaces',shell=True)) #shows single file with spaces in name\n", "print(subprocess.call(['ls','file with spaces'])) #ditto\n", "print(subprocess.call(['ls','file\\ with\\ spaces'])) #fails since it looks for file with backslashes in name" ] }, { "cell_type": "code", "execution_count": 15, "metadata": { "slideshow": { "slide_type": "slide" } }, "outputs": [ { "ename": "FileNotFoundError", "evalue": "[Errno 2] No such file or directory: 'ls *'", "output_type": "error", "traceback": [ "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", "\u001b[0;31mFileNotFoundError\u001b[0m Traceback (most recent call last)", "Cell \u001b[0;32mIn[15], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m \u001b[43msubprocess\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcall\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43mls *\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m)\u001b[49m \u001b[38;5;66;03m#why is this FileNotFoundError?\u001b[39;00m\n", "File \u001b[0;32m/usr/lib/python3.10/subprocess.py:345\u001b[0m, in \u001b[0;36mcall\u001b[0;34m(timeout, *popenargs, **kwargs)\u001b[0m\n\u001b[1;32m 337\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mcall\u001b[39m(\u001b[38;5;241m*\u001b[39mpopenargs, timeout\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mNone\u001b[39;00m, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs):\n\u001b[1;32m 338\u001b[0m \u001b[38;5;250m \u001b[39m\u001b[38;5;124;03m\"\"\"Run command with arguments. Wait for command to complete or\u001b[39;00m\n\u001b[1;32m 339\u001b[0m \u001b[38;5;124;03m timeout, then return the returncode attribute.\u001b[39;00m\n\u001b[1;32m 340\u001b[0m \n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 343\u001b[0m \u001b[38;5;124;03m retcode = call([\"ls\", \"-l\"])\u001b[39;00m\n\u001b[1;32m 344\u001b[0m \u001b[38;5;124;03m \"\"\"\u001b[39;00m\n\u001b[0;32m--> 345\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m \u001b[43mPopen\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mpopenargs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m \u001b[38;5;28;01mas\u001b[39;00m p:\n\u001b[1;32m 346\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[1;32m 347\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m p\u001b[38;5;241m.\u001b[39mwait(timeout\u001b[38;5;241m=\u001b[39mtimeout)\n", "File \u001b[0;32m/usr/lib/python3.10/subprocess.py:971\u001b[0m, in \u001b[0;36mPopen.__init__\u001b[0;34m(self, args, bufsize, executable, stdin, stdout, stderr, preexec_fn, close_fds, shell, cwd, env, universal_newlines, startupinfo, creationflags, restore_signals, start_new_session, pass_fds, user, group, extra_groups, encoding, errors, text, umask, pipesize)\u001b[0m\n\u001b[1;32m 967\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mtext_mode:\n\u001b[1;32m 968\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mstderr \u001b[38;5;241m=\u001b[39m io\u001b[38;5;241m.\u001b[39mTextIOWrapper(\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mstderr,\n\u001b[1;32m 969\u001b[0m encoding\u001b[38;5;241m=\u001b[39mencoding, errors\u001b[38;5;241m=\u001b[39merrors)\n\u001b[0;32m--> 971\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_execute_child\u001b[49m\u001b[43m(\u001b[49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mexecutable\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mpreexec_fn\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mclose_fds\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 972\u001b[0m \u001b[43m \u001b[49m\u001b[43mpass_fds\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mcwd\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43menv\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 973\u001b[0m \u001b[43m \u001b[49m\u001b[43mstartupinfo\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mcreationflags\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mshell\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 974\u001b[0m \u001b[43m \u001b[49m\u001b[43mp2cread\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mp2cwrite\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 975\u001b[0m \u001b[43m \u001b[49m\u001b[43mc2pread\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mc2pwrite\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 976\u001b[0m \u001b[43m \u001b[49m\u001b[43merrread\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43merrwrite\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 977\u001b[0m \u001b[43m \u001b[49m\u001b[43mrestore_signals\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 978\u001b[0m \u001b[43m \u001b[49m\u001b[43mgid\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mgids\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43muid\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mumask\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 979\u001b[0m \u001b[43m \u001b[49m\u001b[43mstart_new_session\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 980\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m:\n\u001b[1;32m 981\u001b[0m \u001b[38;5;66;03m# Cleanup if the child failed starting.\u001b[39;00m\n\u001b[1;32m 982\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m f \u001b[38;5;129;01min\u001b[39;00m \u001b[38;5;28mfilter\u001b[39m(\u001b[38;5;28;01mNone\u001b[39;00m, (\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mstdin, \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mstdout, \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mstderr)):\n", "File \u001b[0;32m/usr/lib/python3.10/subprocess.py:1863\u001b[0m, in \u001b[0;36mPopen._execute_child\u001b[0;34m(self, args, executable, preexec_fn, close_fds, pass_fds, cwd, env, startupinfo, creationflags, shell, p2cread, p2cwrite, c2pread, c2pwrite, errread, errwrite, restore_signals, gid, gids, uid, umask, start_new_session)\u001b[0m\n\u001b[1;32m 1861\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m errno_num \u001b[38;5;241m!=\u001b[39m \u001b[38;5;241m0\u001b[39m:\n\u001b[1;32m 1862\u001b[0m err_msg \u001b[38;5;241m=\u001b[39m os\u001b[38;5;241m.\u001b[39mstrerror(errno_num)\n\u001b[0;32m-> 1863\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m child_exception_type(errno_num, err_msg, err_filename)\n\u001b[1;32m 1864\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m child_exception_type(err_msg)\n", "\u001b[0;31mFileNotFoundError\u001b[0m: [Errno 2] No such file or directory: 'ls *'" ] } ], "source": [ "subprocess.call('ls *') #why is this FileNotFoundError?" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "# Input/Output/Error" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Every process (program) has standard places to write output and read input. \n", "\n", "* stdin - standard input is usually from the keyboard\n", "* stdout - standard output is usually buffered\n", "* stderr - standard error is unbuffered (output immediately)\n", "\n", "On the commandline, you can changes these places with IO redirection (<,>,|). For example:\n", "
\n",
    "    grep Congress cnn.html > congress\n",
    "    wc < congress\n",
    "    grep Congress cnn.html | wc\n",
    "
\n", "When calling external programs from scripts we'll usually want to provide input to the programs and read their output, so we'll have to change these 'places' as well." ] }, { "cell_type": "code", "execution_count": 17, "metadata": { "slideshow": { "slide_type": "slide" } }, "outputs": [ { "data": { "text/html": [ "
\n", "\n" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "%%html\n", "
\n", "" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "# stdin/stdout/stderr" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "stdin, stdout and stderr specify the executed program’s standard input, standard output and standard error file handles, respectively. Valid values are\n", "\n", "* `subprocess.PIPE` - this enables communication between your script and the program\n", "* an existing file object - e.g. created with `open`\n", "* None - the program will default to the existing stdin/stdout/stderr \n", "\n", "**Do no use `subprocess.PIPE` with subprocess.call**" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "# Redirecting to files" ] }, { "cell_type": "code", "execution_count": 20, "metadata": {}, "outputs": [ { "data": { "text/plain": [ "'dump\\n'" ] }, "execution_count": 20, "metadata": {}, "output_type": "execute_result" } ], "source": [ "f = open('dump','w')\n", "subprocess.call('ls',stdout=f)\n", "f = open('dump','r') #this would be a very inefficient way to get the stdout of a program\n", "f.readline()" ] }, { "cell_type": "code", "execution_count": 21, "metadata": {}, "outputs": [ { "data": { "text/plain": [ "2" ] }, "execution_count": 21, "metadata": {}, "output_type": "execute_result" } ], "source": [ "f = open('dump','w')\n", "subprocess.call(['ls','nonexistantfile'],stdout=f,stderr=subprocess.STDOUT) #you can redirect stderr to stdout" ] }, { "cell_type": "code", "execution_count": 22, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "ls: cannot access 'nonexistantfile': No such file or directory\n", "\n" ] } ], "source": [ "print(open('dump').read())" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "# subprocess.check_call" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "`check_call` is identical to `call`, but throws an exception when the called program has a nonzero return value." ] }, { "cell_type": "code", "execution_count": 23, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "ls: cannot access 'missingfile': No such file or directory\n" ] }, { "ename": "CalledProcessError", "evalue": "Command '['ls', 'missingfile']' returned non-zero exit status 2.", "output_type": "error", "traceback": [ "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", "\u001b[0;31mCalledProcessError\u001b[0m Traceback (most recent call last)", "Cell \u001b[0;32mIn[23], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m \u001b[43msubprocess\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcheck_call\u001b[49m\u001b[43m(\u001b[49m\u001b[43m[\u001b[49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43mls\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m,\u001b[49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43mmissingfile\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m]\u001b[49m\u001b[43m)\u001b[49m\n", "File \u001b[0;32m/usr/lib/python3.10/subprocess.py:369\u001b[0m, in \u001b[0;36mcheck_call\u001b[0;34m(*popenargs, **kwargs)\u001b[0m\n\u001b[1;32m 367\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m cmd \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[1;32m 368\u001b[0m cmd \u001b[38;5;241m=\u001b[39m popenargs[\u001b[38;5;241m0\u001b[39m]\n\u001b[0;32m--> 369\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m CalledProcessError(retcode, cmd)\n\u001b[1;32m 370\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;241m0\u001b[39m\n", "\u001b[0;31mCalledProcessError\u001b[0m: Command '['ls', 'missingfile']' returned non-zero exit status 2." ] } ], "source": [ "subprocess.check_call(['ls','missingfile'])" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "# subprocess.check_output" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "
" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "# subprocess.check_output" ] }, { "cell_type": "code", "execution_count": 24, "metadata": {}, "outputs": [ { "data": { "text/plain": [ "b'dump\\nfile with spaces\\n'" ] }, "execution_count": 24, "metadata": {}, "output_type": "execute_result" } ], "source": [ "subprocess.check_output(ARGS, stdin=None, stderr=None, shell=False)" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "Typically, you are calling a program because you want to parse its output. `check_output` provides the easiest way to do this. Its return value is what was written to `stdout`. \n", "\n", "Nonzero return values result in a `CalledProcessError` exception (like `check_call`)." ] }, { "cell_type": "code", "execution_count": 25, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "b'file with spaces\\n'\n" ] } ], "source": [ "files = subprocess.check_output('ls file*',shell=True)\n", "print(files)" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "# subprocess.check_output" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Can redirect `stderr` to `STDOUT`" ] }, { "cell_type": "code", "execution_count": 26, "metadata": {}, "outputs": [ { "data": { "text/plain": [ "b\"ls: cannot access 'non_existent_file': No such file or directory\\n\"" ] }, "execution_count": 26, "metadata": {}, "output_type": "execute_result" } ], "source": [ "subprocess.check_output(\"ls non_existent_file; exit 0\", stderr=subprocess.STDOUT, shell=True)" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "fragment" } }, "source": [ "Why `exit 0`?" ] }, { "cell_type": "code", "execution_count": 27, "metadata": { "slideshow": { "slide_type": "slide" } }, "outputs": [ { "data": { "text/html": [ "
\n", "\n" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "%%html\n", "
\n", "" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "How can we communicate with the program we are launching?" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "
" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "# Popen" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "All the previous functions are just convenience wrappers around the Popen object." ] }, { "cell_type": "code", "execution_count": 28, "metadata": {}, "outputs": [ { "data": { "text/plain": [ "" ] }, "execution_count": 28, "metadata": {}, "output_type": "execute_result" }, { "name": "stdout", "output_type": "stream", "text": [ "dump\n", "file with spaces\n" ] } ], "source": [ "subprocess.Popen(ARGS, stdin=None, stdout=None, stderr=None, shell=False, cwd=None, env=None)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Popen has quite a few optional arguments. Shown are just the most common. \n", "\n", "`cwd` sets the working directory for the process (if `None` defaults to the current working directory of the python script).\n", "\n", "`env` is a dictionary that can be used to define a new set of environment variables.\n", "\n", "*`Popen` is a constructor and returns a `Popen` object.* " ] }, { "cell_type": "code", "execution_count": 29, "metadata": {}, "outputs": [ { "data": { "text/plain": [ "subprocess.Popen" ] }, "execution_count": 29, "metadata": {}, "output_type": "execute_result" }, { "name": "stdout", "output_type": "stream", "text": [ "\n" ] } ], "source": [ "proc = subprocess.Popen('echo')\n", "type(proc)" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "# Popen" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "The python script does **not** wait for the called process to finish before returning.\n", "\n", "We can finally use `PIPE`.\n", "\n", "
" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "# subprocess.PIPE" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "If we set stdin/stdout/stderr to `subprocess.PIPE` then they are available to read/write to in the resulting Popen object." ] }, { "cell_type": "code", "execution_count": 30, "metadata": {}, "outputs": [], "source": [ "proc = subprocess.Popen('ls',stdout=subprocess.PIPE)" ] }, { "cell_type": "code", "execution_count": 31, "metadata": {}, "outputs": [ { "data": { "text/plain": [ "_io.BufferedReader" ] }, "execution_count": 31, "metadata": {}, "output_type": "execute_result" } ], "source": [ "type(proc.stdout)" ] }, { "cell_type": "code", "execution_count": 32, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "b'dump\\n'\n" ] } ], "source": [ "print(proc.stdout.readline())" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "# subprocess.PIPE\n", "\n", "Pipes enable communication between your script and the called program. \n", "\n", "If `stdout/stdin/stderr` is set to `subprocess.PIPE` then that input/output stream of the process is accessible through a file object in the returned object." ] }, { "cell_type": "code", "execution_count": 33, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "b'Hello'\n" ] } ], "source": [ "proc = subprocess.Popen('cat',stdin=subprocess.PIPE,stdout=subprocess.PIPE)\n", "proc.stdin.write(b\"Hello\")\n", "proc.stdin.close()\n", "print(proc.stdout.read())" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "python3 strings are unicode, but most programs need byte strings" ] }, { "cell_type": "code", "execution_count": 34, "metadata": {}, "outputs": [ { "ename": "TypeError", "evalue": "a bytes-like object is required, not 'str'", "output_type": "error", "traceback": [ "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", "\u001b[0;31mTypeError\u001b[0m Traceback (most recent call last)", "Cell \u001b[0;32mIn[34], line 2\u001b[0m\n\u001b[1;32m 1\u001b[0m proc \u001b[38;5;241m=\u001b[39m subprocess\u001b[38;5;241m.\u001b[39mPopen(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mcat\u001b[39m\u001b[38;5;124m'\u001b[39m,stdin\u001b[38;5;241m=\u001b[39msubprocess\u001b[38;5;241m.\u001b[39mPIPE,stdout\u001b[38;5;241m=\u001b[39msubprocess\u001b[38;5;241m.\u001b[39mPIPE)\n\u001b[0;32m----> 2\u001b[0m \u001b[43mproc\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mstdin\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mwrite\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mHello\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m)\u001b[49m\n\u001b[1;32m 3\u001b[0m proc\u001b[38;5;241m.\u001b[39mstdin\u001b[38;5;241m.\u001b[39mclose()\n\u001b[1;32m 4\u001b[0m \u001b[38;5;28mprint\u001b[39m(proc\u001b[38;5;241m.\u001b[39mstdout\u001b[38;5;241m.\u001b[39mread())\n", "\u001b[0;31mTypeError\u001b[0m: a bytes-like object is required, not 'str'" ] } ], "source": [ "proc = subprocess.Popen('cat',stdin=subprocess.PIPE,stdout=subprocess.PIPE)\n", "proc.stdin.write(\"Hello\")\n", "proc.stdin.close()\n", "print(proc.stdout.read())" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "# Unicode (aside)\n", "\n", "Bytes strings (which were the default kinds of string in python2) store each character using a single byte (ASCII, like in the Martian).\n", "\n", "Unicode uses 1 to 6 bytes per a character.\n", "\n", "This allows supports for other languages and the all important emoji." ] }, { "cell_type": "code", "execution_count": 48, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "🦄\n" ] } ], "source": [ "print('\\U0001F984')" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "Converting bytes to string" ] }, { "cell_type": "code", "execution_count": 36, "metadata": {}, "outputs": [ { "data": { "text/plain": [ "'a byte str'" ] }, "execution_count": 36, "metadata": {}, "output_type": "execute_result" } ], "source": [ "b'a byte str'.decode()" ] }, { "cell_type": "code", "execution_count": 37, "metadata": {}, "outputs": [ { "data": { "text/plain": [ "b'a unicode string'" ] }, "execution_count": 37, "metadata": {}, "output_type": "execute_result" } ], "source": [ "'a unicode string'.encode()" ] }, { "cell_type": "code", "execution_count": 40, "metadata": { "slideshow": { "slide_type": "slide" } }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "b'Hello'\n" ] } ], "source": [ "proc = subprocess.Popen('cat',stdin=subprocess.PIPE,stdout=subprocess.PIPE)\n", "proc.stdin.write(b\"Hello\")\n", "proc.stdin.close()\n", "print(proc.stdout.read())" ] }, { "cell_type": "code", "execution_count": 38, "metadata": { "slideshow": { "slide_type": "slide" } }, "outputs": [ { "data": { "text/html": [ "
\n", "\n" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "%%html\n", "
\n", "" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "# Warning!" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "-" } }, "source": [ "*Managing simultaneous input and output is tricky and can easily lead to deadlocks*. \n", "\n", "For example, your script may be blocked waiting for output from the process which is blocked waiting for input.\n", "\n", "\n", "\n" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "# `Popen.communicate(input=None)`" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Interact with process: Send data to stdin. Read data from stdout and stderr, until end-of-file is reached. Wait for process to terminate.\n", "\n", "`input` is a string of data to be provided to stdin (which must be set to `PIPE`). \n", "\n", "Likewise, to receive stdout/stderr, they must be set to `PIPE`.\n", "\n", "This *will not deadlock*. \n", "\n", "99% of the time if you have to both provide input and read output of a subprocess, communicate will do what you need.\n" ] }, { "cell_type": "code", "execution_count": 41, "metadata": {}, "outputs": [], "source": [ "proc = subprocess.Popen(\"awk '{print $1}'\",stdin=subprocess.PIPE,stdout=subprocess.PIPE,stderr=subprocess.PIPE,shell=True)\n", "(out, err) = proc.communicate(b\"x y z\\n1 2 3\\na b c\\n\") #returns tuple of output and error" ] }, { "cell_type": "code", "execution_count": 42, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "x\n", "1\n", "a\n", "\n" ] } ], "source": [ "print(out.decode()) # decode converts a bytes string to a regular unicode string" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "# Interacting with Popen" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "* `Popen.poll()` - check to see if process has terminated\n", "* `Popen.wait()` - wait for process to terminate **Do not use PIPE**\n", "* `Popen.terminate()` - terminate the process (ask nicely)\n", "* `Popen.kill()` - kill the process with extreme prejudice\n", "\n", "Note that if your are generating a large amount of data, `communicate`, which buffers all the data in memory, may not be an option (instead just read from `Popen.stdout`). \n", "\n", "If you need to `PIPE` both `stdin` and `stdout` and can't use `communicate`, be *very* careful about controlling how data is communicated." ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "# Review\n", "\n", "* Just want to run a command?\n", " * `subprocess.call`\n", "* Want the output of the command?\n", " * `subprocess.check_output`\n", "* Don't want to wait for command to finish? \n", " * `subprocess.Popen`\n", "* Need to provide data through stdin?\n", " * `subprocess.Popen`, `stdin=subprocess.PIPE`, `communicate`" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "# Exercise" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "We want to predict the binding affinity of a small molecule to a protein using the program `gnina`. \n", "\n", "For simplicity, run your code starting from this colab:\n", "https://colab.research.google.com/drive/1QYo5QLUE80N_G28PlpYs6OKGddhhd931?usp=sharing" ] }, { "cell_type": "code", "execution_count": 43, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "--2023-11-08 16:58:28-- http://mscbio2025.csb.pitt.edu/files/rec.pdb\n", "Resolving mscbio2025.csb.pitt.edu (mscbio2025.csb.pitt.edu)... 136.142.4.139\n", "Connecting to mscbio2025.csb.pitt.edu (mscbio2025.csb.pitt.edu)|136.142.4.139|:80... connected.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 489908 (478K) [chemical/x-pdb]\n", "Saving to: ‘rec.pdb’\n", "\n", "rec.pdb 100%[===================>] 478.43K --.-KB/s in 0.009s \n", "\n", "2023-11-08 16:58:28 (52.6 MB/s) - ‘rec.pdb’ saved [489908/489908]\n", "\n", "--2023-11-08 16:58:28-- http://mscbio2025.csb.pitt.edu/files/lig.pdb\n", "Resolving mscbio2025.csb.pitt.edu (mscbio2025.csb.pitt.edu)... 136.142.4.139\n", "Connecting to mscbio2025.csb.pitt.edu (mscbio2025.csb.pitt.edu)|136.142.4.139|:80... connected.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 3536 (3.5K) [chemical/x-pdb]\n", "Saving to: ‘lig.pdb’\n", "\n", "lig.pdb 100%[===================>] 3.45K --.-KB/s in 0s \n", "\n", "2023-11-08 16:58:28 (519 MB/s) - ‘lig.pdb’ saved [3536/3536]\n", "\n", "--2023-11-08 16:58:28-- http://mscbio2025.csb.pitt.edu/files/receptor.pdb\n", "Resolving mscbio2025.csb.pitt.edu (mscbio2025.csb.pitt.edu)... 136.142.4.139\n", "Connecting to mscbio2025.csb.pitt.edu (mscbio2025.csb.pitt.edu)|136.142.4.139|:80... connected.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 143208 (140K) [chemical/x-pdb]\n", "Saving to: ‘receptor.pdb’\n", "\n", "receptor.pdb 100%[===================>] 139.85K --.-KB/s in 0.003s \n", "\n", "2023-11-08 16:58:28 (46.2 MB/s) - ‘receptor.pdb’ saved [143208/143208]\n", "\n", "--2023-11-08 16:58:28-- http://mscbio2025.csb.pitt.edu/files/ligs.sdf\n", "Resolving mscbio2025.csb.pitt.edu (mscbio2025.csb.pitt.edu)... 136.142.4.139\n", "Connecting to mscbio2025.csb.pitt.edu (mscbio2025.csb.pitt.edu)|136.142.4.139|:80... connected.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 65619 (64K) [chemical/x-mdl-sdfile]\n", "Saving to: ‘ligs.sdf’\n", "\n", "ligs.sdf 100%[===================>] 64.08K --.-KB/s in 0.001s \n", "\n", "2023-11-08 16:58:28 (44.5 MB/s) - ‘ligs.sdf’ saved [65619/65619]\n", "\n" ] } ], "source": [ "!wget http://mscbio2025.csb.pitt.edu/files/rec.pdb\n", "!wget http://mscbio2025.csb.pitt.edu/files/lig.pdb\n", "!wget http://mscbio2025.csb.pitt.edu/files/receptor.pdb\n", "!wget http://mscbio2025.csb.pitt.edu/files/ligs.sdf" ] }, { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "# Project\n", "\n", "1. Run the command `smina -r rec.pdb -l lig.pdb --minimize` on these files.\n", "Parse the affinity and RMSD and print them on one line.\n", "2. Run the command `smina -r receptor.pdb -l ligs.sdf --minimize`. Parse the affinities and RMSDS.\n", " 1. Plot histograms of both\n", " 2. Plot a scatter plot " ] }, { "cell_type": "code", "execution_count": 44, "metadata": { "slideshow": { "slide_type": "notes" } }, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "/home/dkoes/.local/lib/python3.10/site-packages/matplotlib/projections/__init__.py:63: UserWarning: Unable to import Axes3D. This may be due to multiple versions of Matplotlib being installed (e.g. as a system package and as a pip package). As a result, the 3D projection is not available.\n", " warnings.warn(\"Unable to import Axes3D. This may be due to multiple versions of \"\n", "==============================\n", "*** Open Babel Warning in PerceiveBondOrders\n", " Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders\n", "\n" ] } ], "source": [ "import subprocess, re\n", "import matplotlib.pyplot as plt\n", "import numpy as np\n", "%matplotlib inline\n", "\n", "out = subprocess.check_output('gnina -r receptor.pdb -l ligs.sdf --minimize',shell=True).decode(\"utf-8\") \n", "affinities = np.array(re.findall(r'Affinity: (\\S+)',out),dtype=float)\n", "rmsds = np.array(re.findall(r'RMSD: (\\S+)',out),dtype=float)" ] }, { "cell_type": "code", "execution_count": 45, "metadata": { "slideshow": { "slide_type": "slide" } }, "outputs": [ { "data": { "image/png": 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" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "plt.hist(affinities);" ] }, { "cell_type": "code", "execution_count": 46, "metadata": { "slideshow": { "slide_type": "-" } }, "outputs": [ { "data": { "image/png": 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"text/plain": [ "
" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "plt.hist(rmsds);" ] }, { "cell_type": "code", "execution_count": 47, "metadata": { "slideshow": { "slide_type": "-" } }, "outputs": [ { "data": { "image/png": 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A/e///q8k6a233lJNTY2uvfba4M93796tPn36hLdCAACAEIQ0oHjhwoW6/vrr9fTTT6u6ulrTpk1TZmZm8Od/+MMfdPnll4e9SAAAgPYKeZ2brVu36o9//KO8Xq9uuummZj8fOHCghg8fHtYCAQAAQuGy4uxmUHV1dfJ4PKqtrT3tTUABAIBzhHL+Dqnn5s0332xXuyuvvDKUXwsAABA2IYWbq6++OnhjzLY6fFwul/x+f+crAwAA6ICQwk3Pnj2VkpKiadOm6ZZbblFaWlqk6gIAAOiQkKaCV1dX68EHH1RZWZkuvfRSzZgxQ1u2bFH37t3l8XiCDwAAALuEFG6SkpI0ceJEvfrqq/roo4902WWX6a677lJWVpZ+8pOf6OTJk5GqEwAAoF06PVuqsrJSM2bM0J///GcdPHhQqamp4aotIpgtBQBA7Anl/B1Sz02ThoYGPfnkkyooKFBubq7S0tK0adMmxwcbAABgvpAGFJeXl2vdunV66qmnlJ2drenTp+vpp58m1AAAAMcI6bJUQkKCzj33XE2dOlVDhgxps924cePCUlwkcFkKAIDYE8r5O+RwcyZOX+eGcAMAQOyJ2ArFgUDgjG1OnDgRyq8EAAAIqw4NKG5NQ0ODli9frvPPPz9cvxIAACBkIYWbhoYGFRUVaejQoRoxYoSef/55SdJjjz2mnJwcPfzww5o7d24k6gQAAGiXkC5LLVy4UI8++qgKCgq0ZcsW3XTTTZo+fbreffddLV++XDfddJMSExMjVSsAAMAZhRRunnnmGa1fv17jxo3T9u3bddlll+nkyZN6//33gzfUBAAAsFNIl6U++eST4BTw3Nxcud1uzZ07l2ADAAAcI6Rw4/f7lZSUFHzepUsXnX322WEvCgAAoKNCuixlWZamTZsmt9stSaqvr9esWbP0jW98o1m75557LnwVAgAAhCCkcDN16tRmzydPnhzWYgAAADorpHCzbt26SNUBAAAQFmFbxA8AAMAJCDcAAMAohBsAAGAUwg0AADBKSAOKASfxByyVVx7RgWP1Sk9J1vCcVCUmsKAkAMQ7wg1iUsn2ai16aYeqa+uD2zI9ySoe219jcjNtrAwAYDcuSyHmlGyv1uwN25oFG0ny1dZr9oZtKtlebVNlAAAnINwgpvgDlha9tENWKz9r2rbopR3yB1prAQCIB4QbxJTyyiMtemy+ypJUXVuv8soj0SsKAOAohBvElAPH2g42HWkHADAP4QYxJT0lOaztAADmIdwgpgzPSVWmJ1ltTfh26dSsqeE5qdEsCwDgII4IN6tWrVJ2draSk5OVl5en8vLydu331FNPyeVyafz48ZEtEI6RmOBS8dj+ktQi4DQ9Lx7bn/VuACCO2R5uNm7cqMLCQhUXF2vbtm0aMGCARo8erQMHDpx2v7179+qHP/yhrrjiiihVCqcYk5upRyYPltfT/NKT15OsRyYPZp0bAIhzLsuybJ0zm5eXp2HDhmnlypWSpEAgoKysLM2ZM0fz589vdR+/368rr7xSt956q9566y0dPXpUzz//fLter66uTh6PR7W1terevXu43gZswArFABA/Qjl/27pCcWNjo7Zu3aqioqLgtoSEBBUUFKisrKzN/RYvXqz09HTNmDFDb7311mlfo6GhQQ0NDcHndXV1nS8cjpCY4FL+Bb3sLgMA4DC2XpY6dOiQ/H6/MjIymm3PyMiQz+drdZ+3335ba9eu1Zo1a9r1GkuXLpXH4wk+srKyOl03AABwLtvH3ITi2LFjuuWWW7RmzRqlpaW1a5+ioiLV1tYGH1VVVRGuEgAA2MnWy1JpaWlKTExUTU1Ns+01NTXyer0t2u/evVt79+7V2LFjg9sCgYAkqUuXLtq5c6cuuOCCZvu43W653e4IVA8AAJzI1p6bpKQkDRkyRKWlpcFtgUBApaWlys/Pb9H+4osv1j/+8Q9VVFQEH+PGjdM111yjiooKLjkBAAB7e24kqbCwUFOnTtXQoUM1fPhwrVixQsePH9f06dMlSVOmTFHfvn21dOlSJScnKzc3t9n+PXr0kKQW2wEAQHyyPdxMnDhRBw8e1MKFC+Xz+TRw4ECVlJQEBxnv27dPCQkxNTQIAADYyPZ1bqKNdW4AAIg9oZy/6RIBAABGIdwAAACjEG4AAIBRCDcAAMAohBsAAGAUwg0AADAK4QYAABiFcAMAAIxi+wrFOMUfsFReeUQHjtUrPSVZw3NSlZjgsrssAABiDuHGAUq2V2vRSztUXVsf3JbpSVbx2P4ak5tpY2UAAMQeLkvZrGR7tWZv2NYs2EiSr7ZeszdsU8n2apsqAwAgNhFubOQPWFr00g61dnOvpm2LXtohfyCubv8FAECnEG5sVF55pEWPzVdZkqpr61VeeSR6RQEAEOMINzY6cKztYNORdgAAgHBjq/SU5LC2AwAAhBtbDc9JVaYnWW1N+Hbp1Kyp4Tmp0SwLAICYRrixUWKCS8Vj+0tSi4DT9Lx4bH/WuwEAIASEG5uNyc3UI5MHy+tpfunJ60nWI5MHs84NAAAhYhE/BxiTm6nv9PeyQjEAAGFAuHGIxASX8i/oZXcZAADEPC5LAQAAoxBuAACAUQg3AADAKIQbAABgFMINAAAwCuEGAAAYhXADAACMQrgBAABGIdwAAACjEG4AAIBRCDcAAMAohBsAAGAUwg0AADAK4QYAABiFcAMAAIxCuAEAAEYh3AAAAKMQbgAAgFEINwAAwCiEGwAAYBTCDQAAMArhBgAAGIVwAwAAjEK4AQAARiHcAAAAoxBuAACAUQg3AADAKIQbAABglC52FwDAXP6ApXd3H1bZnkOSXMq/oJe+fX4vJSa47C4NgMEINwAiomR7teY/9w8dPfFlcNvKN3apx1ld9cD3LtWY3EwbqwOcxR+wVF55RAeO1Ss9JVnDc1L5EtAJhBsAYVeyvVqzNmxr9WdHT3ypWRu2afXkwQQcQKf+Xha9tEPVtfXBbZmeZBWP7c/fSAcx5gZAWPkDlu5/8YMztlv00g75A1YUKgKcq2R7tWZv2NYs2EiSr7ZeszdsU8n2apsqi22EG8AQ/oClst2H9ULFfpXtPmxbcCivPCJfXcMZ21XX1qu88kgUKgKcyR+wtOilHWrtL7VpG18COobLUoABnNStfeBY/ZkbdaAtYJryyiMtemy+ytK/vwTkX9AreoUZgJ4bIMY5rVs7PSU5Im0B07Q33PMlIHSEGyCGObFbe3hOqrzd3Wdsl+k5NSMEiFftDfd8CQgd4QaIYaF0a0dLYoJL94/71hnbFY/tz1RXxLXhOanK9CSrrb8Cl/gS0FGEGyCGObVbe0xuplZPHqweZ3Vt8bOeZ3VlGjigU18Eisf2l6QWAafpOV8COoYBxUAMc3K39pjcTH2nv5cVioHTGJObqUcmD24xIcDLOjedQrgBYlhTt7avtr7VcTcunfqQtKtbOzHBpcsvStPlF6XZ8vpALGj6IsAKxeHjiMtSq1atUnZ2tpKTk5WXl6fy8vI2265Zs0ZXXHGFevbsqZ49e6qgoOC07QGT0a0NmCEx4VTP5o0D+yr/Ano3O8v2cLNx40YVFhaquLhY27Zt04ABAzR69GgdOHCg1fabN2/WpEmT9MYbb6isrExZWVkaNWqU9u/fH+XKAWdo6tb2eppfevJ6kvUIY1sAxCGXZVm2Ln2Yl5enYcOGaeXKlZKkQCCgrKwszZkzR/Pnzz/j/n6/Xz179tTKlSs1ZcqUM7avq6uTx+NRbW2tunfv3un6AafgxnsATBbK+dvWMTeNjY3aunWrioqKgtsSEhJUUFCgsrKydv2OEydO6Msvv1RqautjChoaGtTQ8O+l4Ovq6jpXNOBQTd3aABDvbL0sdejQIfn9fmVkZDTbnpGRIZ/P167fMW/ePPXp00cFBQWt/nzp0qXyeDzBR1ZWVqfrBgAAzmX7mJvOeOCBB/TUU0/pD3/4g5KTW5/qWlRUpNra2uCjqqoqylUCAIBosvWyVFpamhITE1VTU9Nse01Njbxe72n3/fnPf64HHnhAr7/+ui677LI227ndbrndZ14KHgAAmMHWnpukpCQNGTJEpaWlwW2BQEClpaXKz89vc7+f/exn+ulPf6qSkhINHTo0GqUCtvMHLJXtPqwXKvarbPfhqN4vCgBiie2L+BUWFmrq1KkaOnSohg8frhUrVuj48eOaPn26JGnKlCnq27evli5dKkl68MEHtXDhQj355JPKzs4Ojs05++yzdfbZZ9v2PoBIKtle3WIF00xWMAWAVtkebiZOnKiDBw9q4cKF8vl8GjhwoEpKSoKDjPft26eEhH93MD3yyCNqbGzU97///Wa/p7i4WPfff380SweiomR7tWZv2NZiBWJfbb1mb9jGWjaIWyx/gLbYvs5NtLHODWKJP2Bp5IN/avPO3023V3h73rV8qCOu0JsZf0I5f8f0bCnAdOWVR9oMNpJkSaqurVd55ZHoFQXYrKk38+t/G029mSXbq22qDE5BuAEc7MCxtoNNR9oBsc4fsLTopR2t3ii2aduil3Yw4D7OEW4AB0tPaX39po62A2IdvZloD8IN4GDDc1KV6UluccfvJi6dGmcwPKf1248ApqE3E+1BuAEcLDHBpeKx/SWpRcBpel48tn9YBhOzjg5iAb2ZaA/bp4IDOL0xuZl6ZPLgFjNDvGGcGcLME8SKpt5MX219q+NummYQ0psZ35gKDsSISK3p0dY6Ok2/mXV04DRN/89Kavb/bXv/n2V9nNgUyvmbcAPH44MoclhHB7Gqo72Nkeyl5LMqskI5f3NZCo7G5ZLICmXmSf4FvaJXGHAGY3Iz9Z3+3pDCRCRX++azylkYUAzHYqGuyGPmCWJZYoJL+Rf00o0D+yr/gl6nDTaRXB+HzyrnIdzAkVioKzqYeYJ4Ean1cfiscibCDRyJhbqig3V0EC8i1UvJZ5UzEW7gSFwuiY5orqMD2ClSvZR8VjkT4QaOxOWS6GlaR8fraf5v6fUkMw0cxohULyWfVc7EbCk4Egt1RVdHZp4AsaSpl3L2hm1yqfX1cTrSS8lnlTPRcwNH4nJJ9IUy8ySecFsKc0Sil5LPKmdiET84GmtHwE78/2emSCy2x/8rkccKxadBuIk9rPoJO3BbCoSKz6rIYoViGKXpcgkQLWdau8SlU2uXfKe/l5MXgvisck7AI9wAwNdwWwpncsqJE61z0qU5wg0AfA1rlziPk06caCmS9+3qCGZLAcDXsHaJs3DvJmdz4i0oCDcA8DXclsI5nHjiRHNOvAUF4QYAvoa1S5zDiSdONOfEy7iEGwBoBbelcAYnnjjRnBMv4zKgGIAxwj2bhttS2M+JJ04058RbUBBuABghUrNpWLvEXk48caK5SN23qzO4LAV0QLzeb8ip75vZNOZi/FNscNplXG6/AIQoXtfbcOr79gcsjXzwT20OOm36Zv/2vGs5AcYwp/7/h+YiudAi95Y6DcINOiNe7zfk5PddtvuwJq1594ztfjfz21xeinGsUBzfuLcUEAHxer8hp79vZtO0zsQgwPgntBfhBmineL3fkNPfN7NpWgrXJRwTAxLiA+EGaKd47SFw+vtmNk1z4brHjxPHuBC20F6EG6Cd4rWHwOnv24nTUO0SrkuITrsJYlNNTgtbcC6mggPtFK/3G4qF9+20aah2CcetCpx4Lyem+iNU9NyECd2l5ovXHoJYed+sJtz+S4P/9/+Hgdb+fZw2xsrpA9rhTISbMKC7NH409RB8/Xh7DT/esfK+4302TXsvDa4v+5fWl/2r1c8pp42xckrY4gtsbCHcdJITr00jsuK1hyBe33csOdPg6q9r7XPKaWOsnBC2+AIbexhz0wlOvDaN6GjqIbhxYF/lX9Arbk7w8fq+Y8XpblXQmtY+p5w2xsrusMV4n9hEuOmEcAzeA4BwamtwdVu+/jnltHs52Rm2+AIbuwg3neCE7lIA+LoxuZl6e961+t3Mb2tK/nnt2uern1NOmn1mZ9jiC2zsYsxNJ9jdXQrEEwZ0huarg6vXl/3rjO2//jnlpDFWdg1o5wts7CLcdAIrowLRwYDO0DWFQV/tF0r9RpI+O94Y8ueUk2af2RG2+AIbuwg3nRAr638AsawzMxLjtbentTDYmlj7nIp22OILbOwi3HRSrKz/AcSi9izgdv+LHygluasOfd7QLMDEa29PW2GwNXxOnR5fYGOXy7KsuBrmXVdXJ4/Ho9raWnXv3j1svzdevyECkVS2+7AmrXk3pH0yPckaNyBTv36zssUJvukv0tT1p/wBSyMf/NNpe2xSv9FVC/7ft+TtzudUe8VrUHaaUM7f9NyEiZOuTQOticUA3pGBmr7aej36ZmWrPzN9uf4zze6RpCPHv5S3ezKfVyFw0uBqtA/hBogDsfrNsyMDNc/UFR3teyNFE7N7IocvsLGFdW4Aw8XyCqtnWsCtM0w8wTO7BziFcAMYLNZXWA31dgKhMPEE77RbJwB2IdwABjNhhdVQbydwJiaf4J126wTALoy5AQxmyhiMrw/oTPuGWz945n3V1LXv7tdN4uEEz/IUAOEGMJpJYzC+PqDz/nGnX3/k9itz9OL71XF5gmd2D+Id4QYwmMkrrLanh+LHYy6J2xM8s3sQz1jEDzBc02wpqfUejlhf0C4W1+8BELpQzt+EGyAOxOo6NwDQhBWKATTDGAwA8YRwA8QJxmAAiBescwMAAIxCuAEAAEZxRLhZtWqVsrOzlZycrLy8PJWXl5+2/TPPPKOLL75YycnJuvTSS/XKK69EqVIAAOB0toebjRs3qrCwUMXFxdq2bZsGDBig0aNH68CBA62237JliyZNmqQZM2bob3/7m8aPH6/x48dr+/btUa4cAAA4ke1TwfPy8jRs2DCtXLlSkhQIBJSVlaU5c+Zo/vz5LdpPnDhRx48f18svvxzc9u1vf1sDBw7U6tWrW7RvaGhQQ0ND8HldXZ2ysrKYCg4AQAwJZSq4rT03jY2N2rp1qwoKCoLbEhISVFBQoLKyslb3KSsra9ZekkaPHt1m+6VLl8rj8QQfWVlZ4XsDAADAcWwNN4cOHZLf71dGRkaz7RkZGfL5fK3u4/P5QmpfVFSk2tra4KOqqio8xQMAAEcyfp0bt9stt9ttdxkAACBKbO25SUtLU2Jiompqapptr6mpkdfrbXUfr9cbUnsAABBfbO25SUpK0pAhQ1RaWqrx48dLOjWguLS0VHfddVer++Tn56u0tFT33HNPcNtrr72m/Pz8dr1m0/jpurq6TtUOAACip+m83a55UJbNnnrqKcvtdluPP/64tWPHDuv222+3evToYfl8PsuyLOuWW26x5s+fH2z/zjvvWF26dLF+/vOfWx9++KFVXFxsde3a1frHP/7RrterqqqydOrmyDx48ODBgwePGHtUVVWd8Vxv+5ibiRMn6uDBg1q4cKF8Pp8GDhyokpKS4KDhffv2KSHh31fPRowYoSeffFL33Xef7r33Xl100UV6/vnnlZub267X69Onj6qqqpSSkiKXK7o3DWyahl5VVcU0dIfiGDkbx8f5OEbOFsvHx7IsHTt2TH369DljW9vXuYknoczRhz04Rs7G8XE+jpGzxcvxsX2FYgAAgHAi3AAAAKMQbqLI7XaruLiYdXccjGPkbBwf5+MYOVu8HB/G3AAAAKPQcwMAAIxCuAEAAEYh3AAAAKMQbgAAgFEINxG0efNmuVyuVh9//etf29zv6quvbtF+1qxZUaw8fnT0GNXX1+vOO+9Ur169dPbZZ2vChAktbuiK8Nm0aZPy8vLUrVs39ezZM3gvurZMmzatxfEcM2ZMdIqNQ6EeH8uytHDhQmVmZqpbt24qKCjQP//5z+gUG4eys7Nb/D088MADp90n1s9Dtt9+wWQjRoxQdXV1s20LFixQaWmphg4detp9Z86cqcWLFwefn3XWWRGpMd519BjNnTtXmzZt0jPPPCOPx6O77rpL3/ve9/TOO+9EuuS48/vf/14zZ87UkiVLdO211+rkyZPavn37GfcbM2aM1q1bF3xu+tRXu3Tk+PzsZz/TL3/5S/32t79VTk6OFixYoNGjR2vHjh1KTk6OUuXxZfHixZo5c2bweUpKyhn3ienzUKg3ukTHNTY2Wr1797YWL1582nZXXXWVdffdd0enKDTTnmN09OhRq2vXrtYzzzwT3Pbhhx9akqyysrJolBk3vvzyS6tv377Wb37zm5D2mzp1qnXjjTdGpigEdeT4BAIBy+v1Wg899FBw29GjRy2322397ne/i0SZce+8886zHn744ZD2ifXzEJeloujFF1/U4cOHNX369DO2feKJJ5SWlqbc3FwVFRXpxIkTUagQ7TlGW7du1ZdffqmCgoLgtosvvljnnnuuysrKolFm3Ni2bZv279+vhIQEDRo0SJmZmbr++uvb1XOzefNmpaenq1+/fpo9e7YOHz4chYrjS0eOT2VlpXw+X7O/H4/Ho7y8PP5+IuiBBx5Qr169NGjQID300EM6efLkGfeJ5fMQl6WiaO3atRo9erTOOeec07a7+eabdd5556lPnz76+9//rnnz5mnnzp167rnnolRp/GrPMfL5fEpKSlKPHj2abc/IyJDP54twhfFlz549kqT7779fy5cvV3Z2tpYtW6arr75aH3/8sVJTU1vdb8yYMfre976nnJwc7d69W/fee6+uv/56lZWVKTExMZpvwWgdOT5NfyMZGRnNtvP3Ezn/9V//pcGDBys1NVVbtmxRUVGRqqurtXz58jb3ifnzkN1dR7Fo3rx5lqTTPj788MNm+1RVVVkJCQnWs88+G/LrlZaWWpKsXbt2hestGC+Sx+iJJ56wkpKSWmwfNmyY9eMf/zis78NU7T0+TzzxhCXJevTRR4P71tfXW2lpadbq1avb/Xq7d++2JFmvv/56JN6OcSJ5fN555x1LkvXpp582237TTTdZ//mf/xnR92WSjnzGNVm7dq3VpUsXq76+vt2vF2vnIXpuOuAHP/iBpk2bdto2559/frPn69atU69evTRu3LiQXy8vL0+StGvXLl1wwQUh7x+PInmMvF6vGhsbdfTo0Wa9NzU1NfJ6vR0tOa609/g0Dfbu379/cLvb7db555+vffv2tfv1zj//fKWlpWnXrl267rrrOlRzPInk8Wn6G6mpqVFmZmZwe01NjQYOHNi5wuNIRz7jmuTl5enkyZPau3ev+vXr167Xi7XzEOGmA3r37q3evXu3u71lWVq3bp2mTJmirl27hvx6FRUVktTsgwCnF8ljNGTIEHXt2lWlpaWaMGGCJGnnzp3at2+f8vPzO1V3vGjv8RkyZIjcbrd27typkSNHSpK+/PJL7d27V+edd167X++TTz7R4cOH+Rtqp0gen5ycHHm9XpWWlgbDTF1dnf7yl79o9uzZYXsPpgv1M+6rKioqlJCQoPT09JD2kWLoPGR311E8eP3119vsIvzkk0+sfv36WX/5y18sy7KsXbt2WYsXL7bee+89q7Ky0nrhhRes888/37ryyiujXXZcCeUYWZZlzZo1yzr33HOtP/3pT9Z7771n5efnW/n5+dEsOW7cfffdVt++fa1XX33V+uijj6wZM2ZY6enp1pEjR4Jt+vXrZz333HOWZVnWsWPHrB/+8IdWWVmZVVlZab3++uvW4MGDrYsuuiikbni0T6jHx7Is64EHHrB69OhhvfDCC9bf//5368Ybb7RycnKsL774wo63YLQtW7ZYDz/8sFVRUWHt3r3b2rBhg9W7d29rypQpwTYmnocIN1EwadIka8SIEa3+rLKy0pJkvfHGG5ZlWda+ffusK6+80kpNTbXcbrd14YUXWj/60Y+s2traKFYcf0I5RpZlWV988YV1xx13WD179rTOOuss6z/+4z+s6urqKFUbXxobG60f/OAHVnp6upWSkmIVFBRY27dvb9ZGkrVu3TrLsizrxIkT1qhRo6zevXtbXbt2tc477zxr5syZls/ns6F684V6fCzr1HTwBQsWWBkZGZbb7bauu+46a+fOnVGuPD5s3brVysvLszwej5WcnGxdcskl1pIlS5oFfRPPQy7LsiwbO44AAADCinVuAACAUQg3AADAKIQbAABgFMINAAAwCuEGAAAYhXADAACMQrgBAABGIdwAAACjEG4AOI5lWbr99tuVmpoql8ulioqKVrddffXVuueee9r9e/fu3RvcF4C5WKEYgG3Kyso0cuRIjRkzRps2bQpu/7//+z/deOON2rx5c/CO3q+99lqLbXV1deratatSUlLa9Xp+v18HDx5UWlqaunTpos2bN+uaa67RZ5991uwO7wBiG3cFB2CbtWvXas6cOVq7dq0+/fRT9enTR5K0e/duZWZmasSIEcG2rW1LTU0N6fUSExPl9XrDUzwAx+KyFABbfP7559q4caNmz56t7373u3r88cclSdOmTdOcOXO0b98+uVwuZWdnt7pNUovLUtnZ2VqyZIluvfVWpaSk6Nxzz9Wvf/3r4M+/ellq7969uuaaayRJPXv2lMvl0rRp07R+/Xr16tVLDQ0NzeodP368brnlloj+mwAID8INAFs8/fTTuvjii9WvXz9NnjxZjz32mCzL0i9+8QstXrxY55xzjqqrq/XXv/611W1tWbZsmYYOHaq//e1vuuOOOzR79mzt3LmzRbusrCz9/ve/lyTt3LlT1dXV+sUvfqGbbrpJfr9fL774YrDtgQMHtGnTJt16663h/4cAEHaEGwC2WLt2rSZPnixJGjNmjGpra/XnP/9ZHo9HKSkpwUtIvXv3bnVbW2644QbdcccduvDCCzVv3jylpaXpjTfeaNEuMTExeFkrPT1dXq9XHo9H3bp1080336x169YF227YsEHnnnuurr766vD+IwCICMINgKjbuXOnysvLNWnSJElSly5dNHHiRK1du7bTv/uyyy4L/rfL5ZLX69WBAwdC+h0zZ87UH//4R+3fv1+S9Pjjj2vatGlyuVydrg9A5DGgGEDUrV27VidPngwOIJZOTf92u91auXJlp353165dmz13uVwKBAIh/Y5BgwZpwIABWr9+vUaNGqUPPvig2WwuAM5GuAEQVSdPntT69eu1bNkyjRo1qtnPxo8fr9/97ndRqyUpKUnSqSniX3fbbbdpxYoV2r9/vwoKCpSVlRW1ugB0DpelAETVyy+/rM8++0wzZsxQbm5us8eECRPCcmmqvc477zy5XC69/PLLOnjwoD7//PPgz26++WZ98sknWrNmDQOJgRhDuAEQVWvXrlVBQYE8Hk+Ln02YMEHvvfee6urqolJL3759tWjRIs2fP18ZGRm66667gj/zeDyaMGGCzj77bI0fPz4q9QAID1YoBoA2XHfddfrWt76lX/7yl3aXAiAEhBsA+JrPPvtMmzdv1ve//33t2LFD/fr1s7skACFgQDEAfM2gQYP02Wef6cEHHyTYADGInhsAAGAUBhQDAACjEG4AAIBRCDcAAMAohBsAAGAUwg0AADAK4QYAABiFcAMAAIxCuAEAAEb5/wDgajncci7VGwAAAABJRU5ErkJggg==", "text/plain": [ "
" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "plt.plot(affinities,rmsds,'o')\n", "plt.xlabel(\"Affinity\")\n", "plt.ylabel(\"RMSD\");" ] } ], "metadata": { "celltoolbar": "Slideshow", "kernelspec": { "display_name": "Python 3 (ipykernel)", "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": "3.10.12" } }, "nbformat": 4, "nbformat_minor": 1 }