Usage:
./extract_frames_from_dcd.py file.pdb file.dcd outfile.dcd frame_list_file.txt
The frame_list_file.txt
is an ASCII file containing one frame id per line,
starting from 0. Repetitions of frames are allowed and will be kept in the
output file. The order of the frames will be preserved in the output DCD file.
If the list of frames is not given as a file, the standard input is read
instead. This feature is conveninant to pipe from awk, for example:
awk '{print $3}' some_text_file.txt | ./extract_frames_from_dcd.py file.pdb file.dcd outfile.dcd
<!DOCTYPE html>
<html>
<head>
<meta http-equiv="Content-type" content="text/html; charset=utf-8">
<meta http-equiv="Content-Security-Policy" content="default-src 'none'; style-src 'unsafe-inline'; img-src data:; connect-src 'self'">
<title>Site not found · GitHub Pages</title>
<style type="text/css" media="screen">
body {
background-color: #f1f1f1;
margin: 0;
font-family: "Helvetica Neue", Helvetica, Arial, sans-serif;
}
.container { margin: 50px auto 40px auto; width: 600px; text-align: center; }
a { color: #4183c4; text-decoration: none; }
a:hover { text-decoration: underline; }
h1 { width: 800px; position:relative; left: -100px; letter-spacing: -1px; line-height: 60px; font-size: 60px; font-weight: 100; margin: 0px 0 50px 0; text-shadow: 0 1px 0 #fff; }
p { color: rgba(0, 0, 0, 0.5); margin: 20px 0; line-height: 1.6; }
ul { list-style: none; margin: 25px 0; padding: 0; }
li { display: table-cell; font-weight: bold; width: 1%; }
.logo { display: inline-block; margin-top: 35px; }
.logo-img-2x { display: none; }
@media
only screen and (-webkit-min-device-pixel-ratio: 2),
only screen and ( min--moz-device-pixel-ratio: 2),
only screen and ( -o-min-device-pixel-ratio: 2/1),
only screen and ( min-device-pixel-ratio: 2),
only screen and ( min-resolution: 192dpi),
only screen and ( min-resolution: 2dppx) {
.logo-img-1x { display: none; }
.logo-img-2x { display: inline-block; }
}
#suggestions {
margin-top: 35px;
color: #ccc;
}
#suggestions a {
color: #666666;
font-weight: 200;
font-size: 14px;
margin: 0 10px;
}
</style>
</head>
<body>
<div class="container">
<h1>404</h1>
<p><strong>There isn't a GitHub Pages site here.</strong></p>
<p>
If you're trying to publish one,
<a href="https://help.github.com/pages/">read the full documentation</a>
to learn how to set up <strong>GitHub Pages</strong>
for your repository, organization, or user account.
</p>
<div id="suggestions">
<a href="https://githubstatus.com">GitHub Status</a> —
<a href="https://twitter.com/githubstatus">@githubstatus</a>
</div>
<a href="/" class="logo logo-img-1x">
<img width="32" height="32" title="" alt="" src="data:image/png;base64,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">
</a>
<a href="/" class="logo logo-img-2x">
<img width="32" height="32" title="" alt="" src="data:image/png;base64,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">
</a>
</div>
</body>
</html>
If you want to ask me a question or leave me a message add @bougui505 in your comment.