<html>
<head>
<meta http-equiv="Content-Type" content="text/html;
charset=windows-1252">
</head>
<body>
<p>FYI, readcif doesn't build the molecular data structures, it just
parses (mm)CIF files quickly. That is, it's the foundation that
you would need to build a mmCIF reader.<br>
</p>
<p> -- Greg<br>
</p>
<div class="moz-cite-prefix">On 7/6/2021 11:07 AM, Eric Pettersen
via ChimeraX-users wrote:<br>
</div>
<blockquote type="cite"
cite="mid:EBEB40E5-119E-4C3B-8825-44B61DEFF338@cgl.ucsf.edu">
<meta http-equiv="Content-Type" content="text/html;
charset=windows-1252">
If the <i class="">only</i><span style="font-style: normal;"
class=""> thing you need ChimeraX for is to read/parse mmCIF </span>files,
we do package that part as a separate library: <a
href="https://github.com/RBVI/readcif" class=""
moz-do-not-send="true">GitHub - RBVI/readcif: A fast C++ CIF and
mmCIF parser</a>
<div class=""><br class="">
</div>
<div class="">
<div class="">--Eric</div>
<div class=""><br class="">
</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Eric
Pettersen</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>UCSF
Computer Graphics Lab</div>
</div>
<div class=""><br class="">
<div><br class="">
<blockquote type="cite" class="">
<div class="">On Jul 6, 2021, at 11:01 AM, Tom Goddard via
ChimeraX-users <<a
href="mailto:chimerax-users@cgl.ucsf.edu" class=""
moz-do-not-send="true">chimerax-users@cgl.ucsf.edu</a>>
wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<meta http-equiv="Content-Type" content="text/html;
charset=windows-1252" class="">
<div style="word-wrap: break-word; -webkit-nbsp-mode:
space; line-break: after-white-space;" class="">Hi
James,
<div class=""><br class="">
</div>
<div class=""> The ChimeraX Python modules have not
been packaged to be used outside the ChimeraX
application. I have tried making a chimerax module
that can be installed in any Python (with the right
version for binary compatibility) where all its Python
capabilities can be used without needing the
application user interface. But we have not
distributed that, it has lots of problems. We have
put it into two grant proposals to get funding for it
but one proposal was not funded and the other we are
still waiting to hear about.</div>
<div class=""><br class="">
</div>
<div class=""> In theory it shouldn't be hard to reuse
specific parts of ChimeraX, for instance reading mmCIF
files. That is in the mmcif ChimeraX Python module.</div>
<div class=""><br class="">
</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span><a
href="https://github.com/RBVI/ChimeraX/tree/develop/src/bundles/mmcif"
class="" moz-do-not-send="true">https://github.com/RBVI/ChimeraX/tree/develop/src/bundles/mmcif</a><br
class="">
<div class=""><br class="">
</div>
<div class="">But that needs various other ChimeraX
modules (atomstruct, element, pyinstance,
pdbconnect, readcif, logger, arrays) listed in the
mmcif bundle_info.xml file</div>
<div class=""><br class="">
</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span><a
href="https://github.com/RBVI/ChimeraX/blob/develop/src/bundles/mmcif/bundle_info.xml"
class="" moz-do-not-send="true">https://github.com/RBVI/ChimeraX/blob/develop/src/bundles/mmcif/bundle_info.xml</a></div>
<div class=""><br class="">
</div>
<div class="">and those in turn require some other
ChimeraX Python modules. ChimeraX contains hundreds
of Python modules, so how will you figure out which
ones you need? The easy solution is to take them
all. But there are more problems, because the
ChimeraX application initializes many of the
modules, for instance, letting the atomic data
structures module know where the residue template
files are located. So you also need to figure that
out. These many obstacles are why we proposed
funding to make the code more usable without running
the ChimeraX application -- it will be a good bit of
work.</div>
<div class=""><br class="">
</div>
<div class=""> So the standard solution is instead to
just run your processing scripts with the ChimeraX
application from the command-line</div>
<div class=""><br class="">
</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>chimerax
--nogui myscript.py</div>
<div class=""><br class="">
</div>
<div class=""> For compiling ChimeraX you must be
using old ChimeraX source code (your example is
fetching Python 3.7 but ChimeraX has used Python 3.8
for the last 9 months). The current ChimeraX build
does not fetch third party libraries with rsync, it
uses https and curl and does not need a password.
So use the current ChimeraX source from github and
you should not have that problem.</div>
<div class=""><br class="">
</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span><a
href="https://github.com/RBVI/ChimeraX" class=""
moz-do-not-send="true">https://github.com/RBVI/ChimeraX</a></div>
<div class=""><br class="">
</div>
<div class=""> Tom</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
<blockquote type="cite" class="">
<div class="">On Jul 3, 2021, at 5:51 AM, James
Loy via ChimeraX-users <<a
href="mailto:chimerax-users@cgl.ucsf.edu"
class="" moz-do-not-send="true">chimerax-users@cgl.ucsf.edu</a>>
wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div dir="ltr" class="">Hello!
<div class=""><br class="">
</div>
<div class="">Thank you for creating such an
amazing piece of software!</div>
<div class=""><br class="">
</div>
<div class="">I'm trying to use portions of
ChimeraX for part of a CIF file processing
pipeline. In order to automate the process,
I'm building a docker image that has
ChimeraX installed. Ideally, we would like
to use the pieces of ChimeraX we need by
importing the relevant python modules. Is
this possible? If so, must I build ChimeraX
from source?</div>
<div class=""><br class="">
</div>
<div class="">Additionally, I have tried
several times to build v1.1.1 from source
and I have not been able to. I am always
prompted for a password when trying to rsync
the dependencies:</div>
<div class="">
<div style="margin: 0px;
font-variant-numeric: normal;
font-variant-east-asian: normal;
font-stretch: normal; font-size: 12px;
line-height: normal; font-family:
JuliaMono; background-color: rgba(242,
242, 206, 0.94);" class=""><span
class="gmail-s1"
style="font-variant-ligatures:no-common-ligatures">/bin/sh
-c 'rsync -a $1 .' -- <a
href="http://plato.cgl.ucsf.edu"
class="" moz-do-not-send="true">plato.cgl.ucsf.edu</a>:/usr/local/projects/chimerax/www/data/prereqs/python/Python-3.7.8.tar.xz</span></div>
<div style="margin: 0px;
font-variant-numeric: normal;
font-variant-east-asian: normal;
font-stretch: normal; font-size: 12px;
line-height: normal; font-family:
JuliaMono; background-color: rgba(242,
242, 206, 0.94);" class=""><span
class="gmail-s1"
style="font-variant-ligatures:no-common-ligatures"><a
href="mailto:user@plato.cgl.ucsf.edu"
class="" moz-do-not-send="true">user@plato.cgl.ucsf.edu</a>'s
password:</span></div>
</div>
<div class="">In order to build from source,
do I need to register somewhere to get
credentials?</div>
<div class=""><br class="">
</div>
<div class="">Just to be clear, this CIF file
processing pipeline is for academic (UT
Austin) use, not commercial.</div>
<div class=""><br class="">
</div>
<div class="">Thanks in advance!</div>
<div class="">James<br class="">
-- <br class="">
<div dir="ltr" class="gmail_signature"
data-smartmail="gmail_signature">
<div dir="ltr" class="">
<div class="">
<div dir="ltr" class="">
<div class="">James Loy, Ph. D.</div>
<div class="">614.915.9792<br
class="">
</div>
<div class=""><a
href="https://www.linkedin.com/in/james-m-loy-ph-d-ba2256a/"
target="_blank" class=""
moz-do-not-send="true">LinkedIn</a><br
class="">
</div>
</div>
</div>
</div>
</div>
</div>
</div>
_______________________________________________<br
class="">
ChimeraX-users mailing list<br class="">
<a href="mailto:ChimeraX-users@cgl.ucsf.edu"
class="" moz-do-not-send="true">ChimeraX-users@cgl.ucsf.edu</a><br
class="">
Manage subscription:<br class="">
<a class="moz-txt-link-freetext" href="https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</a><br class="">
</div>
</blockquote>
</div>
<br class="">
</div>
</div>
_______________________________________________<br
class="">
ChimeraX-users mailing list<br class="">
<a href="mailto:ChimeraX-users@cgl.ucsf.edu" class=""
moz-do-not-send="true">ChimeraX-users@cgl.ucsf.edu</a><br
class="">
Manage subscription:<br class="">
<a class="moz-txt-link-freetext" href="https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</a><br
class="">
</div>
</blockquote>
</div>
<br class="">
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<pre class="moz-quote-pre" wrap="">_______________________________________________
ChimeraX-users mailing list
<a class="moz-txt-link-abbreviated" href="mailto:ChimeraX-users@cgl.ucsf.edu">ChimeraX-users@cgl.ucsf.edu</a>
Manage subscription:
<a class="moz-txt-link-freetext" href="https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</a>
</pre>
</blockquote>
</body>
</html>