From a957ce43af4a5fa7827213bdbc535d304e237fe4 Mon Sep 17 00:00:00 2001 From: Pavol Juhas Date: Tue, 22 Oct 2013 14:46:59 -0400 Subject: [PATCH 01/22] Turn off Jekyll processing at github web server. This is necessary for hosting the directories that start with underscore. --- .nojekyll | 0 1 file changed, 0 insertions(+), 0 deletions(-) create mode 100644 .nojekyll diff --git a/.nojekyll b/.nojekyll new file mode 100644 index 0000000..e69de29 From 8173c631e1683381427a549ba94cdd70b994349a Mon Sep 17 00:00:00 2001 From: Pavol Juhas Date: Fri, 31 Jan 2014 18:39:40 -0500 Subject: [PATCH 02/22] List of exclude patterns for rsync. 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When it is not found, a full rebuild will be done. +config: cc4ed54e22d4fb3c05d6df8a57159cac +tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/_sources/index.txt b/_sources/index.txt new file mode 100644 index 0000000..97b8fdc --- /dev/null +++ b/_sources/index.txt @@ -0,0 +1,50 @@ +.. _manual-index: + +#################################################### +PyObjCryst documentation +#################################################### + +Software version |release|. + +Last updated |today|. + +.. include:: ../../../README.txt + +=================== +Disclaimer +=================== + +.. include:: ../../../LICENSE.txt + +================ +Acknowledgments +================ + +Developers +----------- + +PyObjCryst is developed and maintained by + +.. literalinclude:: ../../../AUTHORS.txt + +Funding +----------- + +This software was developed as part of the Distributed Data Analysis of Neutron +Scattering Experiments (DANSE) project funded by the US National Science +Foundation under grant DMR-0520547. More information on DANSE can be found at +http://danse.us. 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ful: '', + ness: '' + }; + + var c = "[^aeiou]"; // consonant + var v = "[aeiouy]"; // vowel + var C = c + "[^aeiouy]*"; // consonant sequence + var V = v + "[aeiou]*"; // vowel sequence + + var mgr0 = "^(" + C + ")?" + V + C; // [C]VC... is m>0 + var meq1 = "^(" + C + ")?" + V + C + "(" + V + ")?$"; // [C]VC[V] is m=1 + var mgr1 = "^(" + C + ")?" + V + C + V + C; // [C]VCVC... is m>1 + var s_v = "^(" + C + ")?" + v; // vowel in stem + + this.stemWord = function (w) { + var stem; + var suffix; + var firstch; + var origword = w; + + if (w.length < 3) + return w; + + var re; + var re2; + var re3; + var re4; + + firstch = w.substr(0,1); + if (firstch == "y") + w = firstch.toUpperCase() + w.substr(1); + + // Step 1a + re = /^(.+?)(ss|i)es$/; + re2 = /^(.+?)([^s])s$/; + + if (re.test(w)) + w = w.replace(re,"$1$2"); + else if (re2.test(w)) + w = w.replace(re2,"$1$2"); + + // Step 1b + re = /^(.+?)eed$/; + re2 = /^(.+?)(ed|ing)$/; + if (re.test(w)) { + var fp = re.exec(w); + re = new RegExp(mgr0); + if (re.test(fp[1])) { + re = /.$/; + w = w.replace(re,""); + } + } + else if (re2.test(w)) { + var fp = re2.exec(w); + stem = fp[1]; + re2 = new RegExp(s_v); + if (re2.test(stem)) { + w = stem; + re2 = /(at|bl|iz)$/; + re3 = new RegExp("([^aeiouylsz])\\1$"); + re4 = new RegExp("^" + C + v + "[^aeiouwxy]$"); + if (re2.test(w)) + w = w + "e"; + else if (re3.test(w)) { + re = /.$/; + w = w.replace(re,""); + } + else if (re4.test(w)) + w = w + "e"; + } + } + + // Step 1c + re = /^(.+?)y$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = new RegExp(s_v); + if (re.test(stem)) + w = stem + "i"; + } + + // Step 2 + re = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + suffix = fp[2]; + re = new RegExp(mgr0); + if (re.test(stem)) + w = stem + step2list[suffix]; + } + + // Step 3 + re = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + suffix = fp[2]; + re = new RegExp(mgr0); + if (re.test(stem)) + w = stem + step3list[suffix]; + } + + // Step 4 + re = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/; + re2 = /^(.+?)(s|t)(ion)$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = new RegExp(mgr1); + if (re.test(stem)) + w = stem; + } + else if (re2.test(w)) { + var fp = re2.exec(w); + stem = fp[1] + fp[2]; + re2 = new RegExp(mgr1); + if (re2.test(stem)) + w = stem; + } + + // Step 5 + re = /^(.+?)e$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = new RegExp(mgr1); + re2 = new RegExp(meq1); + re3 = new RegExp("^" + C + v + "[^aeiouwxy]$"); + if (re.test(stem) || (re2.test(stem) && !(re3.test(stem)))) + w = stem; + } + re = /ll$/; + re2 = new RegExp(mgr1); + if (re.test(w) && re2.test(w)) { + re = /.$/; + w = w.replace(re,""); + } + + // and turn initial Y back to y + if (firstch == "y") + w = firstch.toLowerCase() + w.substr(1); + return w; + } +} + + + +/** + * Simple result scoring code. + */ +var Scorer = { + // Implement the following function to further tweak the score for each result + // The function takes a result array [filename, title, anchor, descr, score] + // and returns the new score. + /* + score: function(result) { + return result[4]; + }, + */ + + // query matches the full name of an object + objNameMatch: 11, + // or matches in the last dotted part of the object name + objPartialMatch: 6, + // Additive scores depending on the priority of the object + objPrio: {0: 15, // used to be importantResults + 1: 5, // used to be objectResults + 2: -5}, // used to be unimportantResults + // Used when the priority is not in the mapping. + objPrioDefault: 0, + + // query found in title + title: 15, + // query found in terms + term: 5 +}; + + +/** + * Search Module + */ +var Search = { + + _index : null, + _queued_query : null, + _pulse_status : -1, + + init : function() { + var params = $.getQueryParameters(); + if (params.q) { + var query = params.q[0]; + $('input[name="q"]')[0].value = query; + this.performSearch(query); + } + }, + + loadIndex : function(url) { + $.ajax({type: "GET", url: url, data: null, + dataType: "script", cache: true, + complete: function(jqxhr, textstatus) { + if (textstatus != "success") { + document.getElementById("searchindexloader").src = url; + } + }}); + }, + + setIndex : function(index) { + var q; + this._index = index; + if ((q = this._queued_query) !== null) { + this._queued_query = null; + Search.query(q); + } + }, + + hasIndex : function() { + return this._index !== null; + }, + + deferQuery : function(query) { + this._queued_query = query; + }, + + stopPulse : function() { + this._pulse_status = 0; + }, + + startPulse : function() { + if (this._pulse_status >= 0) + return; + function pulse() { + var i; + Search._pulse_status = (Search._pulse_status + 1) % 4; + var dotString = ''; + for (i = 0; i < Search._pulse_status; i++) + dotString += '.'; + Search.dots.text(dotString); + if (Search._pulse_status > -1) + window.setTimeout(pulse, 500); + } + pulse(); + }, + + /** + * perform a search for something (or wait until index is loaded) + */ + performSearch : function(query) { + // create the required interface elements + this.out = $('#search-results'); + this.title = $('

' + _('Searching') + '

').appendTo(this.out); + this.dots = $('').appendTo(this.title); + this.status = $('

').appendTo(this.out); + this.output = $('
'); + } + // Prettify the comment rating. + comment.pretty_rating = comment.rating + ' point' + + (comment.rating == 1 ? '' : 's'); + // Make a class (for displaying not yet moderated comments differently) + comment.css_class = comment.displayed ? '' : ' moderate'; + // Create a div for this comment. + var context = $.extend({}, opts, comment); + var div = $(renderTemplate(commentTemplate, context)); + + // If the user has voted on this comment, highlight the correct arrow. + if (comment.vote) { + var direction = (comment.vote == 1) ? 'u' : 'd'; + div.find('#' + direction + 'v' + comment.id).hide(); + div.find('#' + direction + 'u' + comment.id).show(); + } + + if (opts.moderator || comment.text != '[deleted]') { + div.find('a.reply').show(); + if (comment.proposal_diff) + div.find('#sp' + comment.id).show(); + if (opts.moderator && !comment.displayed) + div.find('#cm' + comment.id).show(); + if (opts.moderator || (opts.username == comment.username)) + div.find('#dc' + comment.id).show(); + } + return div; + } + + /** + * A simple template renderer. Placeholders such as <%id%> are replaced + * by context['id'] with items being escaped. Placeholders such as <#id#> + * are not escaped. + */ + function renderTemplate(template, context) { + var esc = $(document.createElement('div')); + + function handle(ph, escape) { + var cur = context; + $.each(ph.split('.'), function() { + cur = cur[this]; + }); + return escape ? esc.text(cur || "").html() : cur; + } + + return template.replace(/<([%#])([\w\.]*)\1>/g, function() { + return handle(arguments[2], arguments[1] == '%' ? true : false); + }); + } + + /** Flash an error message briefly. */ + function showError(message) { + $(document.createElement('div')).attr({'class': 'popup-error'}) + .append($(document.createElement('div')) + .attr({'class': 'error-message'}).text(message)) + .appendTo('body') + .fadeIn("slow") + .delay(2000) + .fadeOut("slow"); + } + + /** Add a link the user uses to open the comments popup. */ + $.fn.comment = function() { + return this.each(function() { + var id = $(this).attr('id').substring(1); + var count = COMMENT_METADATA[id]; + var title = count + ' comment' + (count == 1 ? '' : 's'); + var image = count > 0 ? opts.commentBrightImage : opts.commentImage; + var addcls = count == 0 ? ' nocomment' : ''; + $(this) + .append( + $(document.createElement('a')).attr({ + href: '#', + 'class': 'sphinx-comment-open' + addcls, + id: 'ao' + id + }) + .append($(document.createElement('img')).attr({ + src: image, + alt: 'comment', + title: title + })) + .click(function(event) { + event.preventDefault(); + show($(this).attr('id').substring(2)); + }) + ) + .append( + $(document.createElement('a')).attr({ + href: '#', + 'class': 'sphinx-comment-close hidden', + id: 'ah' + id + }) + .append($(document.createElement('img')).attr({ + src: opts.closeCommentImage, + alt: 'close', + title: 'close' + })) + .click(function(event) { + event.preventDefault(); + hide($(this).attr('id').substring(2)); + }) + ); + }); + }; + + var opts = { + processVoteURL: '/_process_vote', + addCommentURL: '/_add_comment', + getCommentsURL: '/_get_comments', + acceptCommentURL: '/_accept_comment', + deleteCommentURL: '/_delete_comment', + commentImage: '/static/_static/comment.png', + closeCommentImage: '/static/_static/comment-close.png', + loadingImage: '/static/_static/ajax-loader.gif', + commentBrightImage: '/static/_static/comment-bright.png', + upArrow: '/static/_static/up.png', + downArrow: '/static/_static/down.png', + upArrowPressed: '/static/_static/up-pressed.png', + downArrowPressed: '/static/_static/down-pressed.png', + voting: false, + moderator: false + }; + + if (typeof COMMENT_OPTIONS != "undefined") { + opts = jQuery.extend(opts, COMMENT_OPTIONS); + } + + var popupTemplate = '\ +
\ +

\ + Sort by:\ + best rated\ + newest\ + oldest\ +

\ +
Comments
\ +
\ + loading comments...
\ +
    \ +
    \ +

    Add a comment\ + (markup):

    \ +
    \ + reStructured text markup: *emph*, **strong**, \ + ``code``, \ + code blocks: :: and an indented block after blank line
    \ +
    \ + \ +

    \ + \ + Propose a change ▹\ + \ + \ + Propose a change ▿\ + \ +

    \ + \ + \ + \ + \ + \ +
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    '; + + var commentTemplate = '\ +
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    \ + \ + \ + \ + \ + \ + \ +
    \ +
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    \ +

    \ + <%username%>\ + <%pretty_rating%>\ + <%time.delta%>\ +

    \ +
    <#text#>
    \ +

    \ + \ + reply ▿\ + proposal ▹\ + proposal ▿\ + \ + \ +

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    +<#proposal_diff#>\
    +        
    \ +
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      \ + '; + + var replyTemplate = '\ +
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    • '; + + $(document).ready(function() { + init(); + }); +})(jQuery); + +$(document).ready(function() { + // add comment anchors for all paragraphs that are commentable + $('.sphinx-has-comment').comment(); + + // highlight search words in search results + $("div.context").each(function() { + var params = $.getQueryParameters(); + var terms = (params.q) ? params.q[0].split(/\s+/) : []; + var result = $(this); + $.each(terms, function() { + result.highlightText(this.toLowerCase(), 'highlighted'); + }); + }); + + // directly open comment window if requested + var anchor = document.location.hash; + if (anchor.substring(0, 9) == '#comment-') { + $('#ao' + anchor.substring(9)).click(); + document.location.hash = '#s' + anchor.substring(9); + } +}); diff --git a/genindex-all.html b/genindex-all.html new file mode 100644 index 0000000..12abe85 --- /dev/null +++ b/genindex-all.html @@ -0,0 +1,98 @@ + + + + + + + + + Index — PyObjCryst 1.0b2-17 documentation + + + + + + + + + + + + + + +
      +
      +
      +
      + + +

      Index

      + +
      + +
      + + +
      +
      +
      +
      +
      + +

      Index

      +

      + +

      Full index on one page

      + + + + + +
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      + + + + \ No newline at end of file diff --git a/genindex.html b/genindex.html new file mode 100644 index 0000000..97a60b5 --- /dev/null +++ b/genindex.html @@ -0,0 +1,102 @@ + + + + + + + + Index — PyObjCryst 1.0b2-17 documentation + + + + + + + + + + + + + + +
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      +
      +
      +
      + +
      +

      PyObjCryst documentation¶

      +

      Software version 1.0b2-17.

      +

      Last updated January 31, 2014.

      +

      PyObjCryst - Python bindings to ObjCryst++ Object-Oriented Crystallographic Library

      +

      The documentation for this release of PyObjCryst can be found on-line at +http://docs.danse.us/diffraction/pyobjcryst-beta1/.

      +
      +

      Disclaimer¶

      +

      This program is part of the DiffPy and DANSE open-source projects at Columbia +University and is available subject to the conditions and terms laid out below.

      +

      Copyright © 2009-2010, Trustees of Columbia University in the City of New York, +all rights reserved.

      +

      For more information please visit the diffpy web-page at http://diffpy.org or +email Prof. Simon Billinge at sb2896@columbia.edu.

      +

      Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met:

      +
      +
        +
      • Redistributions of source code must retain the above copyright notice, this +list of conditions and the following disclaimer.
      • +
      • Redistributions in binary form must reproduce the above copyright notice, +this list of conditions and the following disclaimer in the documentation +and/or other materials provided with the distribution.
      • +
      • Neither the names of COLUMBIA UNIVERSITY, MICHIGAN STATE UNIVERSITY nor the +names of their contributors may be used to endorse or promote products +derived from this software without specific prior written permission.
      • +
      +
      +

      THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS “AS IS” AND +ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED +WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE +FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, +OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

      +
      +
      +

      Acknowledgments¶

      +
      +

      Developers¶

      +

      PyObjCryst is developed and maintained by

      +
      Chris Farrow
      +Pavol Juhas
      +
      +
      +
      +
      +

      Funding¶

      +

      This software was developed as part of the Distributed Data Analysis of Neutron +Scattering Experiments (DANSE) project funded by the US National Science +Foundation under grant DMR-0520547. More information on DANSE can be found at +http://danse.us. Any opinions, findings, and conclusions or recommendations +expressed in this material are those of the author(s) and do not necessarily +reflect the views of the respective funding bodies.

      +
      +
      +
      +

      Installation¶

      +
      +

      Dependencies¶

      +

      The following programs must be installed on your system before you can install +PyObjCryst.

      +
      +
      Python >= 2.5, < 3.0
      +
      +
      +
      python-setuptools >= 0.6c9
      +
      +
      +
      Boost C++ libraries >= 1.35
      +
      +
      +
      ObjCryst++ (see below)
      +
      +
      +
      +
      +
      +

      Installing ObjCryst++¶

      +

      We provide a SCons build script and ObjCryst++ source bundle to make it easier +to build ObjCryst++ and its dependencies (cctbx and newmat) as a shared +library. This requires SCons (http://www.scons.org) to be installed on your +computer. Here’s how to install.

      +
      +

      1. Download ObjCryst-latest.tar.gz from http://dev.danse.us/packages/ to the +directory containing INSTALL.txt

      +
      > wget http://dev.danse.us/packages/ObjCryst-latest.tar.gz
      +
      +
      +
        +
      1. Extract the archive to the libobjcryst directory

        +
        > tar xzvf ObjCryst-latest.tar.gz -C libobjcryst
        +
        +
        +
      2. +
      3. From the libobjcryst directory run the following command

        +
        > scons build=fast install
        +
        +
        +

        This will build and install the shared libraries, and header files to +standard system-dependent locations. Run scons -h for other installation +options.

        +
      4. +
      +
      +

      This build method has been tested on Linux platforms with recent GNU and Intel +C++ compilers.

      +

      Once you have done this, you can install PyObjCryst as instructed below.

      +
      +
      +

      Installing PyObjCryst¶

      +

      To install PyObjCryst, you must have ObjCryst++ installed as a shared library +(see above). Once this is done, type the following from the command line from +the directory containing INSTALL.txt

      +
      > python setup.py install
      +
      +
      +

      For installation options, type

      +
      > python setup.py --help install
      +
      +
      +
      +
      +
      +

      API¶

      +

      The API for PyObjCryst is at <http://docs.danse.us/diffraction/pyobjcrystapi-beta1/>.

      +
      +
      + + +
      +
      +
      +
      +
      +

      Table Of Contents

      + + +

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      + + + +
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      +
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When it is not found, a full rebuild will be done. -config: cc4ed54e22d4fb3c05d6df8a57159cac -tags: 645f666f9bcd5a90fca523b33c5a78b7 +config: 17145d9d4e75007530ae98ed1d26ef3a +tags: fbb0d17656682115ca4d033fb2f83ba1 diff --git a/_sources/api/modules.txt b/_sources/api/modules.txt new file mode 100644 index 0000000..6860350 --- /dev/null +++ b/_sources/api/modules.txt @@ -0,0 +1,7 @@ +pyobjcryst +========== + +.. toctree:: + :maxdepth: 4 + + pyobjcryst diff --git a/_sources/api/pyobjcryst.tests.txt b/_sources/api/pyobjcryst.tests.txt new file mode 100644 index 0000000..fbcc215 --- /dev/null +++ b/_sources/api/pyobjcryst.tests.txt @@ -0,0 +1,91 @@ +tests Package +============= + +:mod:`tests` Package +-------------------- + +.. automodule:: pyobjcryst.tests + :members: + :undoc-members: + :show-inheritance: + +:mod:`pyobjcrysttest` Module +---------------------------- + +.. automodule:: pyobjcryst.tests.pyobjcrysttest + :members: + :undoc-members: + :show-inheritance: + +:mod:`pyobjcrysttestutils` Module +--------------------------------- + +.. automodule:: pyobjcryst.tests.pyobjcrysttestutils + :members: + :undoc-members: + :show-inheritance: + +:mod:`run` Module +----------------- + +.. automodule:: pyobjcryst.tests.run + :members: + :undoc-members: + :show-inheritance: + +:mod:`testcif` Module +--------------------- + +.. automodule:: pyobjcryst.tests.testcif + :members: + :undoc-members: + :show-inheritance: + +:mod:`testclocks` Module +------------------------ + +.. automodule:: pyobjcryst.tests.testclocks + :members: + :undoc-members: + :show-inheritance: + +:mod:`testconverters` Module +---------------------------- + +.. automodule:: pyobjcryst.tests.testconverters + :members: + :undoc-members: + :show-inheritance: + +:mod:`testcrystal` Module +------------------------- + +.. automodule:: pyobjcryst.tests.testcrystal + :members: + :undoc-members: + :show-inheritance: + +:mod:`testmolecule` Module +-------------------------- + +.. automodule:: pyobjcryst.tests.testmolecule + :members: + :undoc-members: + :show-inheritance: + +:mod:`testrefinableobj` Module +------------------------------ + +.. automodule:: pyobjcryst.tests.testrefinableobj + :members: + :undoc-members: + :show-inheritance: + +:mod:`testutils` Module +----------------------- + +.. automodule:: pyobjcryst.tests.testutils + :members: + :undoc-members: + :show-inheritance: + diff --git a/_sources/api/pyobjcryst.txt b/_sources/api/pyobjcryst.txt new file mode 100644 index 0000000..6320c73 --- /dev/null +++ b/_sources/api/pyobjcryst.txt @@ -0,0 +1,138 @@ +pyobjcryst Package +================== + +:mod:`pyobjcryst` Package +------------------------- + +.. automodule:: pyobjcryst.__init__ + :members: + :undoc-members: + :show-inheritance: + +:mod:`atom` Module +------------------ + +.. automodule:: pyobjcryst.atom + :members: + :undoc-members: + :show-inheritance: + +:mod:`crystal` Module +--------------------- + +.. automodule:: pyobjcryst.crystal + :members: + :undoc-members: + :show-inheritance: + +:mod:`general` Module +--------------------- + +.. automodule:: pyobjcryst.general + :members: + :undoc-members: + :show-inheritance: + +:mod:`io` Module +---------------- + +.. automodule:: pyobjcryst.io + :members: + :undoc-members: + :show-inheritance: + +:mod:`molecule` Module +---------------------- + +.. automodule:: pyobjcryst.molecule + :members: + :undoc-members: + :show-inheritance: + +:mod:`polyhedron` Module +------------------------ + +.. automodule:: pyobjcryst.polyhedron + :members: + :undoc-members: + :show-inheritance: + +:mod:`refinableobj` Module +-------------------------- + +.. automodule:: pyobjcryst.refinableobj + :members: + :undoc-members: + :show-inheritance: + +:mod:`scatterer` Module +----------------------- + +.. automodule:: pyobjcryst.scatterer + :members: + :undoc-members: + :show-inheritance: + +:mod:`scatteringpower` Module +----------------------------- + +.. automodule:: pyobjcryst.scatteringpower + :members: + :undoc-members: + :show-inheritance: + +:mod:`scatteringpowersphere` Module +----------------------------------- + +.. automodule:: pyobjcryst.scatteringpowersphere + :members: + :undoc-members: + :show-inheritance: + +:mod:`spacegroup` Module +------------------------ + +.. automodule:: pyobjcryst.spacegroup + :members: + :undoc-members: + :show-inheritance: + +:mod:`unitcell` Module +---------------------- + +.. automodule:: pyobjcryst.unitcell + :members: + :undoc-members: + :show-inheritance: + +:mod:`utils` Module +------------------- + +.. automodule:: pyobjcryst.utils + :members: + :undoc-members: + :show-inheritance: + +:mod:`version` Module +--------------------- + +.. automodule:: pyobjcryst.version + :members: + :undoc-members: + :show-inheritance: + +:mod:`zscatterer` Module +------------------------ + +.. automodule:: pyobjcryst.zscatterer + :members: + :undoc-members: + :show-inheritance: + +Subpackages +----------- + +.. toctree:: + + pyobjcryst.tests + diff --git a/_sources/index.txt b/_sources/index.txt index 97b8fdc..af675e3 100644 --- a/_sources/index.txt +++ b/_sources/index.txt @@ -8,7 +8,11 @@ Software version |release|. Last updated |today|. -.. include:: ../../../README.txt +PyObjCryst - Python bindings to ObjCryst++ Object-Oriented Crystallographic Library + +The documentation for this release of PyObjCryst can be found on-line at + + http://diffpy.github.io/doc/pyobjcryst/ =================== Disclaimer @@ -27,24 +31,18 @@ PyObjCryst is developed and maintained by .. literalinclude:: ../../../AUTHORS.txt -Funding ------------ - -This software was developed as part of the Distributed Data Analysis of Neutron -Scattering Experiments (DANSE) project funded by the US National Science -Foundation under grant DMR-0520547. More information on DANSE can be found at -http://danse.us. Any opinions, findings, and conclusions or recommendations -expressed in this material are those of the author(s) and do not necessarily -reflect the views of the respective funding bodies. - ====================================== Installation ====================================== -.. include:: ../../../INSTALL.txt +.. include:: install.rst ====================================== API ====================================== -The API for PyObjCryst is at . +.. toctree:: + :maxdepth: 3 + + api/modules.rst +* :ref:`genindex` diff --git a/_sources/install.txt b/_sources/install.txt new file mode 100644 index 0000000..fa250f1 --- /dev/null +++ b/_sources/install.txt @@ -0,0 +1,78 @@ +REQUIREMENTS + +The diffpy.srreal requires Python 2.6 or 2.7 and the following software: + + setuptools -- tools for installing Python packages + scons -- software constructions tool (1.0 or later) + python-dev -- header files for interfacing Python with C + libboost-dev -- Boost C++ libraries development files (1.43 or later) + ObjCryst++ -- Object-Oriented Crystallographic Library + +Some of the required software may be available in the system package manager, +for example, on Ubuntu Linux the dependencies can be installed as: + + sudo apt-get install \ + python-setuptools scons build-essential python-dev libboost-dev + +For Mac OS X machine with the MacPorts package manager one could do + + sudo port install \ + python27 py27-setuptools scons boost + +When installing with MacPorts, make sure the MacPorts bin directory is the +first in the system PATH and that python27 is selected as the default +Python version in MacPorts: + + sudo port select --set python python27 + +For other required packages see their respective web pages for installation +instructions. + +INSTALLATION + +The easiest option is to use the latest DiffPy-CMI release bundle from +http://www.diffpy.org/, which comes with pyobjcryst and all other +dependencies included. + +If you prefer to install from sources: + +Installing ObjCryst++ + +We provide a SCons build script and ObjCryst++ source bundle to make it easier +to build ObjCryst++ and its dependencies (cctbx and newmat) as a shared +library. This requires SCons (http://www.scons.org) to be installed on your +computer. Here's how to install. + + 1. Download ObjCryst-latest.tar.gz from http://dev.danse.us/packages/ to the + directory containing INSTALL.txt :: + + > wget http://dev.danse.us/packages/ObjCryst-latest.tar.gz + + 2. Extract the archive to the libobjcryst directory :: + + > tar xzvf ObjCryst-latest.tar.gz -C libobjcryst + + 3. From the libobjcryst directory run the following command :: + + > scons build=fast install + + This will build and install the shared libraries, and header files to + standard system-dependent locations. Run `scons -h` for other installation + options. + +This build method has been tested on Linux platforms with recent GNU and Intel +C++ compilers. + +Once you have done this, you can install PyObjCryst as instructed below. + +Installing PyObjCryst + +To install PyObjCryst, you must have ObjCryst++ installed as a shared library +(see above). Once this is done, type the following from the command line from +the directory containing README.txt :: + +> python setup.py install + +For installation options, type :: + +> python setup.py --help install \ No newline at end of file diff --git a/_static/basic.css b/_static/basic.css index c959cf0..43e8baf 100644 --- a/_static/basic.css +++ b/_static/basic.css @@ -4,7 +4,7 @@ * * Sphinx stylesheet -- basic theme. * - * :copyright: Copyright 2007-2013 by the Sphinx team, see AUTHORS. + * :copyright: Copyright 2007-2011 by the Sphinx team, see AUTHORS. * :license: BSD, see LICENSE for details. * */ @@ -89,7 +89,6 @@ div.sphinxsidebar #searchbox input[type="submit"] { img { border: 0; - max-width: 100%; } /* -- search page ----------------------------------------------------------- */ @@ -402,6 +401,10 @@ dl.glossary dt { margin: 0; } +.refcount { + color: #060; +} + .optional { font-size: 1.3em; } diff --git a/_static/default.css b/_static/default.css index 6b1243e..7833719 100644 --- a/_static/default.css +++ b/_static/default.css @@ -4,7 +4,7 @@ * * Sphinx stylesheet -- default theme. * - * :copyright: Copyright 2007-2013 by the Sphinx team, see AUTHORS. + * :copyright: Copyright 2007-2011 by the Sphinx team, see AUTHORS. * :license: BSD, see LICENSE for details. * */ diff --git a/_static/doctools.js b/_static/doctools.js index 2036e5f..d4619fd 100644 --- a/_static/doctools.js +++ b/_static/doctools.js @@ -4,7 +4,7 @@ * * Sphinx JavaScript utilities for all documentation. * - * :copyright: Copyright 2007-2013 by the Sphinx team, see AUTHORS. + * :copyright: Copyright 2007-2011 by the Sphinx team, see AUTHORS. * :license: BSD, see LICENSE for details. * */ @@ -32,7 +32,7 @@ if (!window.console || !console.firebug) { */ jQuery.urldecode = function(x) { return decodeURIComponent(x).replace(/\+/g, ' '); -}; +} /** * small helper function to urlencode strings @@ -61,6 +61,18 @@ jQuery.getQueryParameters = function(s) { return result; }; +/** + * small function to check if an array contains + * a given item. + */ +jQuery.contains = function(arr, item) { + for (var i = 0; i < arr.length; i++) { + if (arr[i] == item) + return true; + } + return false; +}; + /** * highlight a given string on a jquery object by wrapping it in * span elements with the given class name. @@ -168,9 +180,6 @@ var Documentation = { var terms = (params.highlight) ? 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      ').text(excerpt); + $.each(hlwords, function() { + rv = rv.highlightText(this, 'highlighted'); + }); + return rv; +} + /** * Porter Stemmer @@ -193,38 +220,6 @@ var Stemmer = function() { } - -/** - * Simple result scoring code. - */ -var Scorer = { - // Implement the following function to further tweak the score for each result - // The function takes a result array [filename, title, anchor, descr, score] - // and returns the new score. - /* - score: function(result) { - return result[4]; - }, - */ - - // query matches the full name of an object - objNameMatch: 11, - // or matches in the last dotted part of the object name - objPartialMatch: 6, - // Additive scores depending on the priority of the object - objPrio: {0: 15, // used to be importantResults - 1: 5, // used to be objectResults - 2: -5}, // used to be unimportantResults - // Used when the priority is not in the mapping. - objPrioDefault: 0, - - // query found in title - title: 15, - // query found in terms - term: 5 -}; - - /** * Search Module */ @@ -244,13 +239,8 @@ var Search = { }, loadIndex : function(url) { - $.ajax({type: "GET", url: url, data: null, - dataType: "script", cache: true, - complete: function(jqxhr, textstatus) { - if (textstatus != "success") { - document.getElementById("searchindexloader").src = url; - } - }}); + $.ajax({type: "GET", url: url, data: null, success: null, + dataType: "script", cache: true}); }, setIndex : function(index) { @@ -278,20 +268,19 @@ var Search = { if (this._pulse_status >= 0) return; function pulse() { - var i; Search._pulse_status = (Search._pulse_status + 1) % 4; var dotString = ''; - for (i = 0; i < Search._pulse_status; i++) + for (var i = 0; i < Search._pulse_status; i++) dotString += '.'; Search.dots.text(dotString); if (Search._pulse_status > -1) window.setTimeout(pulse, 500); - } + }; pulse(); }, /** - * perform a search for something (or wait until index is loaded) + * perform a search for something */ performSearch : function(query) { // create the required interface elements @@ -311,46 +300,41 @@ var Search = { this.deferQuery(query); }, - /** - * execute search (requires search index to be loaded) - */ query : function(query) { - var i; - var stopwords = ["a","and","are","as","at","be","but","by","for","if","in","into","is","it","near","no","not","of","on","or","such","that","the","their","then","there","these","they","this","to","was","will","with"]; + var stopwords = ["and","then","into","it","as","are","in","if","for","no","there","their","was","is","be","to","that","but","they","not","such","with","by","a","on","these","of","will","this","near","the","or","at"]; - // stem the searchterms and add them to the correct list + // Stem the searchterms and add them to the correct list var stemmer = new Stemmer(); var searchterms = []; var excluded = []; var hlterms = []; var tmp = query.split(/\s+/); var objectterms = []; - for (i = 0; i < tmp.length; i++) { - if (tmp[i] !== "") { + for (var i = 0; i < tmp.length; i++) { + if (tmp[i] != "") { objectterms.push(tmp[i].toLowerCase()); } - if ($u.indexOf(stopwords, tmp[i].toLowerCase()) != -1 || tmp[i].match(/^\d+$/) || - tmp[i] === "") { + if ($u.indexOf(stopwords, tmp[i]) != -1 || tmp[i].match(/^\d+$/) || + tmp[i] == "") { // skip this "word" continue; } // stem the word - var word = stemmer.stemWord(tmp[i].toLowerCase()); - var toAppend; + var word = stemmer.stemWord(tmp[i]).toLowerCase(); // select the correct list if (word[0] == '-') { - toAppend = excluded; + var toAppend = excluded; word = word.substr(1); } else { - toAppend = searchterms; + var toAppend = searchterms; hlterms.push(tmp[i].toLowerCase()); } // only add if not already in the list - if (!$u.contains(toAppend, word)) + if (!$.contains(toAppend, word)) toAppend.push(word); - } + }; var highlightstring = '?highlight=' + $.urlencode(hlterms.join(" ")); // console.debug('SEARCH: searching for:'); @@ -358,51 +342,89 @@ var Search = { // console.info('excluded: ', excluded); // prepare search + var filenames = this._index.filenames; + var titles = this._index.titles; var terms = this._index.terms; - var titleterms = this._index.titleterms; - - // array of [filename, title, anchor, descr, score] - var results = []; + var fileMap = {}; + var files = null; + // different result priorities + var importantResults = []; + var objectResults = []; + var regularResults = []; + var unimportantResults = []; $('#search-progress').empty(); // lookup as object - for (i = 0; i < objectterms.length; i++) { - var others = [].concat(objectterms.slice(0, i), - objectterms.slice(i+1, objectterms.length)); - results = results.concat(this.performObjectSearch(objectterms[i], others)); + for (var i = 0; i < objectterms.length; i++) { + var others = [].concat(objectterms.slice(0,i), + objectterms.slice(i+1, objectterms.length)) + var results = this.performObjectSearch(objectterms[i], others); + // Assume first word is most likely to be the object, + // other words more likely to be in description. + // Therefore put matches for earlier words first. + // (Results are eventually used in reverse order). + objectResults = results[0].concat(objectResults); + importantResults = results[1].concat(importantResults); + unimportantResults = results[2].concat(unimportantResults); } - // lookup as search terms in fulltext - results = results.concat(this.performTermsSearch(searchterms, excluded, terms, Scorer.term)) - .concat(this.performTermsSearch(searchterms, excluded, titleterms, Scorer.title)); - - // let the scorer override scores with a custom scoring function - if (Scorer.score) { - for (i = 0; i < results.length; i++) - results[i][4] = Scorer.score(results[i]); + // perform the search on the required terms + for (var i = 0; i < searchterms.length; i++) { + var word = searchterms[i]; + // no match but word was a required one + if ((files = terms[word]) == null) + break; + if (files.length == undefined) { + files = [files]; + } + // create the mapping + for (var j = 0; j < files.length; j++) { + var file = files[j]; + if (file in fileMap) + fileMap[file].push(word); + else + fileMap[file] = [word]; + } } - // now sort the results by score (in opposite order of appearance, since the - // display function below uses pop() to retrieve items) and then - // alphabetically - results.sort(function(a, b) { - var left = a[4]; - var right = b[4]; - if (left > right) { - return 1; - } else if (left < right) { - return -1; - } else { - // same score: sort alphabetically - left = a[1].toLowerCase(); - right = b[1].toLowerCase(); - return (left > right) ? -1 : ((left < right) ? 1 : 0); + // now check if the files don't contain excluded terms + for (var file in fileMap) { + var valid = true; + + // check if all requirements are matched + if (fileMap[file].length != searchterms.length) + continue; + + // ensure that none of the excluded terms is in the + // search result. + for (var i = 0; i < excluded.length; i++) { + if (terms[excluded[i]] == file || + $.contains(terms[excluded[i]] || [], file)) { + valid = false; + break; + } } + + // if we have still a valid result we can add it + // to the result list + if (valid) + regularResults.push([filenames[file], titles[file], '', null]); + } + + // delete unused variables in order to not waste + // memory until list is retrieved completely + delete filenames, titles, terms; + + // now sort the regular results descending by title + regularResults.sort(function(a, b) { + var left = a[1].toLowerCase(); + var right = b[1].toLowerCase(); + return (left > right) ? -1 : ((left < right) ? 1 : 0); }); - // for debugging - //Search.lastresults = results.slice(); // a copy - //console.info('search results:', Search.lastresults); + // combine all results + var results = unimportantResults.concat(regularResults) + .concat(objectResults).concat(importantResults); // print the results var resultCount = results.length; @@ -411,7 +433,7 @@ var Search = { if (results.length) { var item = results.pop(); var listItem = $('
    • '); - if (DOCUMENTATION_OPTIONS.FILE_SUFFIX === '') { + if (DOCUMENTATION_OPTIONS.FILE_SUFFIX == '') { // dirhtml builder var dirname = item[0] + '/'; if (dirname.match(/\/index\/$/)) { @@ -435,18 +457,16 @@ var Search = { displayNextItem(); }); } else if (DOCUMENTATION_OPTIONS.HAS_SOURCE) { - $.ajax({url: DOCUMENTATION_OPTIONS.URL_ROOT + '_sources/' + item[0] + '.txt', - dataType: "text", - complete: function(jqxhr, textstatus) { - var data = jqxhr.responseText; - if (data !== '') { - listItem.append(Search.makeSearchSummary(data, searchterms, hlterms)); - } - Search.output.append(listItem); - listItem.slideDown(5, function() { - displayNextItem(); - }); - }}); + $.get(DOCUMENTATION_OPTIONS.URL_ROOT + '_sources/' + + item[0] + '.txt', function(data) { + if (data != '') { + listItem.append($.makeSearchSummary(data, searchterms, hlterms)); + Search.output.append(listItem); + } + listItem.slideDown(5, function() { + displayNextItem(); + }); + }, "text"); } else { // no source available, just display title Search.output.append(listItem); @@ -469,32 +489,20 @@ var Search = { displayNextItem(); }, - /** - * search for object names - */ performObjectSearch : function(object, otherterms) { var filenames = this._index.filenames; var objects = this._index.objects; var objnames = this._index.objnames; var titles = this._index.titles; - var i; - var results = []; + var importantResults = []; + var objectResults = []; + var unimportantResults = []; for (var prefix in objects) { for (var name in objects[prefix]) { var fullname = (prefix ? prefix + '.' : '') + name; if (fullname.toLowerCase().indexOf(object) > -1) { - var score = 0; - var parts = fullname.split('.'); - // check for different match types: exact matches of full name or - // "last name" (i.e. last dotted part) - if (fullname == object || parts[parts.length - 1] == object) { - score += Scorer.objNameMatch; - // matches in last name - } else if (parts[parts.length - 1].indexOf(object) > -1) { - score += Scorer.objPartialMatch; - } var match = objects[prefix][name]; var objname = objnames[match[1]][2]; var title = titles[match[0]]; @@ -504,7 +512,7 @@ var Search = { var haystack = (prefix + ' ' + name + ' ' + objname + ' ' + title).toLowerCase(); var allfound = true; - for (i = 0; i < otherterms.length; i++) { + for (var i = 0; i < otherterms.length; i++) { if (haystack.indexOf(otherterms[i]) == -1) { allfound = false; break; @@ -515,107 +523,37 @@ var Search = { } } var descr = objname + _(', in ') + title; - - var anchor = match[3]; - if (anchor === '') + anchor = match[3]; + if (anchor == '') anchor = fullname; else if (anchor == '-') anchor = objnames[match[1]][1] + '-' + fullname; - // add custom score for some objects according to scorer - if (Scorer.objPrio.hasOwnProperty(match[2])) { - score += Scorer.objPrio[match[2]]; - } else { - score += Scorer.objPrioDefault; + result = [filenames[match[0]], fullname, '#'+anchor, descr]; + switch (match[2]) { + case 1: objectResults.push(result); break; + case 0: importantResults.push(result); break; + case 2: unimportantResults.push(result); break; } - results.push([filenames[match[0]], fullname, '#'+anchor, descr, score]); } } } - return results; - }, - - /** - * search for full-text terms in the index - */ - performTermsSearch : function(searchterms, excluded, terms, score) { - var filenames = this._index.filenames; - var titles = this._index.titles; - - var i, j, file, files; - var fileMap = {}; - var results = []; - - // perform the search on the required terms - for (i = 0; i < searchterms.length; i++) { - var word = searchterms[i]; - // no match but word was a required one - if ((files = terms[word]) === undefined) - break; - if (files.length === undefined) { - files = [files]; - } - // create the mapping - for (j = 0; j < files.length; j++) { - file = files[j]; - if (file in fileMap) - fileMap[file].push(word); - else - fileMap[file] = [word]; - } - } - - // now check if the files don't contain excluded terms - for (file in fileMap) { - var valid = true; - - // check if all requirements are matched - if (fileMap[file].length != searchterms.length) - continue; - - // ensure that none of the excluded terms is in the search result - for (i = 0; i < excluded.length; i++) { - if (terms[excluded[i]] == file || - $u.contains(terms[excluded[i]] || [], file)) { - valid = false; - break; - } - } - - // if we have still a valid result we can add it to the result list - if (valid) { - results.push([filenames[file], titles[file], '', null, score]); - } - } - return results; - }, + // sort results descending + objectResults.sort(function(a, b) { + return (a[1] > b[1]) ? -1 : ((a[1] < b[1]) ? 1 : 0); + }); - /** - * helper function to return a node containing the - * search summary for a given text. keywords is a list - * of stemmed words, hlwords is the list of normal, unstemmed - * words. the first one is used to find the occurance, the - * latter for highlighting it. - */ - makeSearchSummary : function(text, keywords, hlwords) { - var textLower = text.toLowerCase(); - var start = 0; - $.each(keywords, function() { - var i = textLower.indexOf(this.toLowerCase()); - if (i > -1) - start = i; + importantResults.sort(function(a, b) { + return (a[1] > b[1]) ? -1 : ((a[1] < b[1]) ? 1 : 0); }); - start = Math.max(start - 120, 0); - var excerpt = ((start > 0) ? '...' : '') + - $.trim(text.substr(start, 240)) + - ((start + 240 - text.length) ? '...' : ''); - var rv = $('
      ').text(excerpt); - $.each(hlwords, function() { - rv = rv.highlightText(this, 'highlighted'); + + unimportantResults.sort(function(a, b) { + return (a[1] > b[1]) ? -1 : ((a[1] < b[1]) ? 1 : 0); }); - return rv; + + return [importantResults, objectResults, unimportantResults] } -}; +} $(document).ready(function() { Search.init(); diff --git a/_static/sidebar.js b/_static/sidebar.js index 874a890..a45e192 100644 --- a/_static/sidebar.js +++ b/_static/sidebar.js @@ -16,20 +16,12 @@ * Once the browser is closed the cookie is deleted and the position * reset to the default (expanded). * - * :copyright: Copyright 2007-2013 by the Sphinx team, see AUTHORS. + * :copyright: Copyright 2007-2011 by the Sphinx team, see AUTHORS. * :license: BSD, see LICENSE for details. * */ $(function() { - - - - - - - - // global elements used by the functions. // the 'sidebarbutton' element is defined as global after its // creation, in the add_sidebar_button function @@ -142,7 +134,7 @@ $(function() { var items = document.cookie.split(';'); 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      +
      +
      +
      + +
      +

      pyobjcryst Package¶

      +
      +

      pyobjcryst Package¶

      +

      Python wrapping of ObjCryst++.

      +

      Objects are wrapped according to their header file in the ObjCryst source.

      +

      See the online ObjCryst++ documentation (http://vincefn.net/ObjCryst/).

      +
      +
      Modules
      +
      atom – Wrapping of Atom.h +crystal – Wrapping of Crystal.h +general – Wrapping of General.h +io – Wrapping of IO.h +molecule – Wrapping of Molecule.h +polyhedron – Wrapping of Polyhedron.h +refinableobj – Wrapping of RefinableObj.h +scatterer – Wrapping of Scatterer.h +scatteringpower – Wrapping of ScatteringPower.h +scatteringpowersphere – Wrapping of ScatteringPowerSphere.h +spacegroup – Wrapping of SpaceGroup.h +unitcell – Wrapping of UnitCell.h +zscatterer – Wrapping of ZScatterer.h
      +
      +

      General Changes +- C++ methods that can return const or non-const objects return non-const

      +
      +
      objects in python.
      +
        +
      • Classes with a Print() method have the output of this method exposed in the +__str__ python method. Thus, obj.Print() == print obj.
      • +
      • CrystVector and CrystMatrix are converted to numpy arrays.
      • +
      • Indexing methods raise IndexError when index is out of bounds.
      • +
      +

      See the modules’ documentation for specific changes.

      +
      +
      +

      atom Module¶

      +

      Python wrapping of Atom.h

      +

      See the online ObjCryst++ documentation (http://vincefn.net/ObjCryst/).

      +

      Changes from ObjCryst::Atom +- The default constructor has been disabled. When not followed-up by Init, it

      +
      +
      will cause segmentation faults, even if it is printed.
      +
      +
      +

      crystal Module¶

      +

      Python wrapping of Crystal.h.

      +

      See the online ObjCryst++ documentation (http://vincefn.net/ObjCryst/).

      +

      Changes from ObjCryst::Crystal +- CIFOutput accepts a python file-like object +- CalcDynPopCorr is not enabled, as the API states that this is for internal

      +
      +
      use only.
      +

      Other Changes +- CreateCrystalFromCIF is placed here instead of in a seperate CIF module. This

      +
      +
      method accepts a python file rather than a CIF object.
      +
      +
      +

      general Module¶

      +

      Python wrapping of things from General.h.

      +

      See the online ObjCryst++ documentation (http://vincefn.net/ObjCryst/).

      +
      +
      +

      io Module¶

      +

      Python wrapping of IO.h

      +

      See the online ObjCryst++ documentation (http://vincefn.net/ObjCryst/).

      +

      Changes from ObjCryst::XMLCrystTag +- The istream constructor of XMLCrystTag is not wrapped.

      +
      +
      +

      molecule Module¶

      +

      Python wrapping of Molecule.h

      +

      See the online ObjCryst++ documentation (http://vincefn.net/ObjCryst/).

      +

      Changes from ObjCryst::Molecule +- The public data are not wrapped. +- Added __getitem__ access for MolAtoms. +- AddAtom returns the added MolAtom +- AddBond returns the added MolBond +- AddBondAngle returns the added MolBondAngle +- AddDihedralAngle returns the added MolDihedralAngle +- RemoveAtom returns None, has an indexed version +- RemoveBond returns None, has an indexed version +- RemoveBondAngle returns None, has an indexed version +- RemoveDihedralAngle returns None, has an indexed version +- RemoveRigidGroup returns None +- Added GetNbAtoms +- Added GetNbBonds +- Added GetNbBondAngles +- Added GetNbDihedralAngles +- Added GetNbRigidGroups +- Added GetBond +- Added GetBondAngle +- Added GetDihedralAngle +- Added GetRigidGroup +- FindBond returns the bond if found, None otherwise +- FindBondAngle returns the bond angle if found, None otherwise +- FindDihedralAngle returns the dihedral angle if found, None otherwise +- FindAtom is identical to GetAtom. +- FlipAtomGroup is not wrapped. +- FlipGroup, RotorGroup and StretchModeGroup are not wrapped. +- StretchMode getters are not wrapped +- Quaternion ordinates Q0, Q1, Q2 and Q3 wrapped as properties.

      +

      Changes from ObjCryst::MolAtom +- Wrapped as a to-python converter only (no constructor) +- File IO is disabled +- X, Y and Z are wrapped as properties rather than methods.

      +

      Changes from ObjCryst::MolBondAngle +- Wrapped as a to-python converter only (no constructor) +- Added __getitem__ access for MolAtoms. +- File IO is disabled +- GetDeriv and CalcGradient are not wrapped. +- Angle0, AngleDelta and AngleSigma are wrapped as properties rather than

      +
      +
      methods.
      +
        +
      • IsFlexible and SetFlexible are not wrapped, as they are not implemented in +the library.
      • +
      +

      Changes from ObjCryst::MolDihedralAngle +- Wrapped as a to-python converter only (no constructor) +- Added __getitem__ access for MolAtoms.

      +

      Changes from ObjCryst::Quaternion +- IO is not wrapped +- Q0, Q1, Q2 and Q3 are wrapped as properties, rather than functions. +- RotateVector overloaded to return tuple of the mutated arguments.

      +

      Changes from ObjCryst::RigidGroup +- RigidGroup is wrapped to have python-set methods rather than stl::set

      +
      +
      methods.
      +
      +
      +

      polyhedron Module¶

      +

      Python wrapping of Polyhedron.h

      +

      See the online ObjCryst++ documentation (http://vincefn.net/ObjCryst/).

      +
      +
      +

      refinableobj Module¶

      +

      Python wrapping of RefinableObj.h

      +

      See the online ObjCryst++ documentation (http://vincefn.net/ObjCryst/).

      +

      Changes from ObjCryst::RefinableObj +- XMLOutput and XMLInput accept python file-like objects. +- GetPar that takes a const double* is not exposed, as it is designed for

      +
      +
      internal use.
      +
        +
      • GetParamSet returns a copy of the internal data so that no indirect +manipulation can take place from python.
      • +
      • SetDeleteRefParInDestructor(false) is called in the constructors of the +python class and the parameter accessors.
      • +
      • SetDeleteRefParInDestructor is not exposed.
      • +
      • RemovePar is overloaded to return None.
      • +
      +

      Changes from ObjCryst::RefinablePar +- The constructor has been changed to accept a double, rather than a pointer to

      +
      +
      a double.
      +
        +
      • The copy and default constructors and Init are not wrapped in order to avoid +memory corruption. Since boost cannot implicitly handle double* object, a +wrapper class had to be created. However, this wrapper class cannot be used +to convert RefinablePar objected created in c++. Thus, +ObjCryst::RefinablePar objects created in c++ are passed into python as +instances of _RefinablePar, which is a python wrapper around +ObjCryst::RefinablePar. The RefinablePar python class is a wrapper around +the C++ class PyRefinablePar, which manages its own double*. These python +classes are interchangable once instantiated, so users should not notice.
      • +
      • XML input/output are not exposed.
      • +
      +

      Changes from ObjCryst::RefinableObjClock +- operator= is wrapped as the SetEqual method

      +
      +
      a.SetEqual(b) -> a = b
      +

      Changes from ObjCryst::ObjRegistry +- DeleteAll not wrapped +- GetObj(const unsigned int i) not wrapped. Documentation says that this is

      +
      +
      for internal use only.
      +

      Changes from ObjCryst::Restraint +- The default and copy constructors are not wrapped, nor is Init. +- GetType returns a non-const reference to the RefParType. This should be a

      +
      +
      no-no, but RefParType has no mutating methods, so this should no lead to +trouble.
      +
        +
      • XML input/output are not exposed.
      • +
      +
      +
      +

      scatterer Module¶

      +

      Python wrapping of Scatterer.h

      +

      See the online ObjCryst++ documentation (http://vincefn.net/ObjCryst/).

      +

      Changes from ObjCryst::Scatterer +- C++ methods that can return const or non-const objects return non-const

      +
      +
      objects in python.
      +
        +
      • Operator string() is not exposed.
      • +
      • Internal use only methods have not been exposed.
      • +
      • InitRefParList is not exposed, as it is not used inside of Scatterer.
      • +
      • GetClockScattCompList is exposed using a workaround, because it is not +implemented in the library.
      • +
      • Methods related to visualization are not exposed.
      • +
      +
      +
      +

      scatteringpower Module¶

      +

      Python wrapping of ScatteringPower.h

      +

      See the online ObjCryst++ documentation (http://vincefn.net/ObjCryst/).

      +

      Changes from ObjCryst::ScatteringComponent +- Added attributes X, Y, Z, Occupancy to conform to MolAtom.

      +

      Changes from ObjCryst::ScatteringComponentList +- Wrapped as a to-python converter only (no constructor)

      +
      +
      +

      scatteringpowersphere Module¶

      +

      Python wrapping of ScatteringPowerSphere.h

      +

      See the online ObjCryst++ documentation (http://vincefn.net/ObjCryst/).

      +
      +
      +

      spacegroup Module¶

      +

      Python wrapping of SpaceGroup.h.

      +

      See the online ObjCryst++ documentation (http://vincefn.net/ObjCryst/).

      +
      +
      +

      unitcell Module¶

      +

      Python wrapping of UnitCell.h

      +

      See the online ObjCryst++ documentation (http://vincefn.net/ObjCryst/).

      +
      +
      +

      utils Module¶

      +

      Utilities for crystals.

      +
      +
      +pyobjcryst.utils.crystalToDiffpyStructure(crystal)¶
      +

      Create a diffpy.Structure.Structure from a crystal.

      +

      This requires diffpy.Structure to be installed. This uses file IO transfer +data, so there is some inherent precision loss.

      +

      Note that the resulting structure will be in P1 symmetry.

      +
      + +
      +
      +pyobjcryst.utils.expandSymmetry(crystal)¶
      +

      Expand a crystal to P1 symmetry.

      +

      This requires diffpy.Structure to be installed. This uses file IO transfer +data, so there is some inherent precision loss.

      +

      This returns a new structure.

      +
      + +
      +
      +pyobjcryst.utils.moleculeFromDiffpyStructure(crystal, stru)¶
      +

      Create and return a molecule from a diffpy.Structure object.

      +
      + +
      +
      +pyobjcryst.utils.printxyz(crystal)¶
      +

      Print a crystal in xyz format.

      +
      + +
      +
      +pyobjcryst.utils.putAtomsInMolecule(crystal, alist=None, name=None)¶
      +

      Place atoms from a crystal into a molecule inside the crystal.

      +

      Selected atoms are put into a new Molecule object, which is then placed +inside of the Crystal. The atoms are then removed from the crystal. The +molecule is placed at the center of mass of the moved atoms.

      +

      crystal – The crystal containing the atoms. +alist – A list of indices or names identifying the atoms. If alist is

      +
      +
      None (default), all atoms from the crystal are placed into a +molecule.
      +
      +
      name – A name for the molecule. If name is None (default), the name
      +
      m_cname will be given, where cname is substituted for the +crystal’s name.
      +
      +

      Raises TypeError if idxlist identifies a non-atom.

      +
      + +
      +
      +pyobjcryst.utils.writexyz(crystal, filename)¶
      +

      Write a crystal to an xyz file.

      +
      + +
      +
      +

      version Module¶

      +

      Definition of __version__, __date__, __gitsha__ for pyobjcryst.

      +
      +
      +

      zscatterer Module¶

      +

      Python wrapping of Zscatterer.

      +

      See the online ObjCryst++ documentation (http://vincefn.net/ObjCryst/).

      +

      Changes from ObjCryst::ZAtom +- XMLOutput and Input are not wrapped.

      +

      Changes from ObjCryst++ +- XMLOutput and Input are not wrapped.

      +
      + +
      + + +
      +
      +
      +
      +
      +

      Table Of Contents

      + + +

      Previous topic

      +

      pyobjcryst

      +

      Next topic

      +

      tests Package

      +

      This Page

      + + + +
      +
      +
      +
      + + + + \ No newline at end of file diff --git a/api/pyobjcryst.tests.html b/api/pyobjcryst.tests.html new file mode 100644 index 0000000..4e5d9a2 --- /dev/null +++ b/api/pyobjcryst.tests.html @@ -0,0 +1,904 @@ + + + + + + + + + + tests Package — PyObjCryst 1.0b3-6 documentation + + + + + + + + + + + + + + + + +
      +
      +
      +
      + +
      +

      tests Package¶

      +
      +

      tests Package¶

      +

      Unit tests for pyobjcryst.

      +
      +
      +pyobjcryst.tests.test()¶
      +

      Execute all unit tests for the pyobjcryst package. +Return a unittest TestResult object.

      +
      + +
      +
      +pyobjcryst.tests.testsuite()¶
      +

      Build a unit tests suite for the pyobjcryst package.

      +

      Return a unittest.TestSuite object.

      +
      + +
      +
      +

      pyobjcrysttest Module¶

      +

      Small tests for pyobjcryst.

      +

      To check for memory leaks, run +valgrind –tool=memcheck –leak-check=full /usr/bin/python ./pyobjcrysttest.py

      +
      +
      +pyobjcryst.tests.pyobjcrysttest.getScatterer()¶
      +

      Make a crystal and return scatterer from GetScatt.

      +
      + +
      +
      +pyobjcryst.tests.pyobjcrysttest.makeCrystal(sp, atom)¶
      +
      + +
      +
      +pyobjcryst.tests.pyobjcrysttest.makeScatterer()¶
      +
      + +
      +
      +pyobjcryst.tests.pyobjcrysttest.parTest()¶
      +
      + +
      +
      +pyobjcryst.tests.pyobjcrysttest.test1()¶
      +

      Run some tests.

      +
      + +
      +
      +pyobjcryst.tests.pyobjcrysttest.testCrystalScope()¶
      +

      Test to see if the the crystal survives after it is out of scope.

      +
      + +
      +
      +pyobjcryst.tests.pyobjcrysttest.testMultiAdd()¶
      +

      Test exception for multi-crystal additions.

      +
      + +
      +
      +pyobjcryst.tests.pyobjcrysttest.testRemoveFunctions()¶
      +

      Test the RemoveScatterer and RemoveScatteringPower method.

      +
      + +
      +
      +pyobjcryst.tests.pyobjcrysttest.testScattererScope()¶
      +

      Test when atoms go out of scope before crystal.

      +
      + +
      +
      +

      pyobjcrysttestutils Module¶

      +

      Utilities for tests.

      +
      +
      +pyobjcryst.tests.pyobjcrysttestutils.datafile(filename)¶
      +
      + +
      +
      +pyobjcryst.tests.pyobjcrysttestutils.getScatterer()¶
      +

      Make a crystal and return scatterer from GetScatt.

      +
      + +
      +
      +pyobjcryst.tests.pyobjcrysttestutils.loadcifdata(filename)¶
      +
      + +
      +
      +pyobjcryst.tests.pyobjcrysttestutils.makeC60()¶
      +
      + +
      +
      +pyobjcryst.tests.pyobjcrysttestutils.makeCrystal(sp, atom)¶
      +
      + +
      +
      +pyobjcryst.tests.pyobjcrysttestutils.makeLaMnO3()¶
      +
      + +
      +
      +pyobjcryst.tests.pyobjcrysttestutils.makeMnO6()¶
      +
      + +
      +
      +pyobjcryst.tests.pyobjcrysttestutils.makeScatterer()¶
      +
      + +
      +
      +pyobjcryst.tests.pyobjcrysttestutils.makeScattererAnisotropic()¶
      +
      + +
      +
      +pyobjcryst.tests.pyobjcrysttestutils.toxyz(crystal, filename)¶
      +

      Write a crystal to an xyz file.

      +
      + +
      +
      +

      run Module¶

      +

      Convenience module for executing all unit tests with

      +

      python -m pyobjcryst.tests.run

      +
      +
      +

      testcif Module¶

      +

      Tests for crystal module.

      +
      +
      +class pyobjcryst.tests.testcif.TestCif(methodName='runTest')¶
      +

      Bases: unittest.case.TestCase

      +
      +
      +testBadCif()¶
      +

      Make sure we can read all cif files.

      +
      + +
      +
      +test_Ag_silver_cif()¶
      +

      Check loading of Ag_silver.cif

      +
      + +
      +
      +test_BaTiO3_cif()¶
      +

      Check loading of BaTiO3.cif

      +
      + +
      +
      +test_C_graphite_hex_cif()¶
      +

      Check loading of C_graphite_hex.cif

      +
      + +
      +
      +test_CaF2_fluorite_cif()¶
      +

      Check loading of CaF2_fluorite.cif

      +
      + +
      +
      +test_CaTiO3_cif()¶
      +

      Check loading of CaTiO3.cif and its ADPs.

      +
      + +
      +
      +test_CdSe_cadmoselite_cif()¶
      +

      Check loading of CdSe_cadmoselite.cif

      +
      + +
      +
      +test_CeO2_cif()¶
      +

      Check loading of CeO2.cif

      +
      + +
      +
      +test_NaCl_cif()¶
      +

      Check loading of NaCl.cif

      +
      + +
      +
      +test_Ni_cif()¶
      +

      Check loading of Ni.cif

      +
      + +
      +
      +test_PbS_galena_cif()¶
      +

      Check loading of PbS_galena.cif

      +
      + +
      +
      +test_PbTe_cif()¶
      +

      Check loading of PbTe.cif

      +
      + +
      +
      +test_Si_cif()¶
      +

      Check loading of Si.cif

      +
      + +
      +
      +test_Si_setting2_cif()¶
      +

      Check loading of Si_setting2.cif

      +
      + +
      +
      +test_SrTiO3_tausonite_cif()¶
      +

      Check loading of SrTiO3_tausonite.cif

      +
      + +
      +
      +test_TiO2_anatase_cif()¶
      +

      Check loading of TiO2_anatase.cif

      +
      + +
      +
      +test_TiO2_rutile_cif()¶
      +

      Check loading of TiO2_rutile.cif and its ADP data

      +
      + +
      +
      +test_ZnS_sphalerite_cif()¶
      +

      Check loading of ZnS_sphalerite.cif

      +
      + +
      +
      +test_ZnS_wurtzite_cif()¶
      +

      Check loading of ZnS_wurtzite.cif

      +
      + +
      +
      +test_Zn_zinc_cif()¶
      +

      Check loading of Zn_zinc.cif

      +
      + +
      +
      +test_caffeine_cif()¶
      +

      Check loading of caffeine.cif and the data inside.

      +
      + +
      +
      +test_menthol_cif()¶
      +

      Check loading of menthol.cif

      +
      + +
      +
      +test_paracetamol_cif()¶
      +

      Check loading of paracetamol.cif

      +
      + +
      + +
      +
      +

      testclocks Module¶

      +

      Tests for crystal module.

      +
      +
      +class pyobjcryst.tests.testclocks.TestClocks(methodName='runTest')¶
      +

      Bases: unittest.case.TestCase

      +
      +
      +testClockIncrement()¶
      +

      Make sure that clocks increment properly.

      +
      + +
      + +
      +
      +

      testconverters Module¶

      +

      Test the converters.

      +

      This verifies results from tests built into the _registerconverters module.

      +
      +
      +class pyobjcryst.tests.testconverters.TestConverters(methodName='runTest')¶
      +

      Bases: unittest.case.TestCase

      +
      +
      +testMatrix()¶
      +
      + +
      +
      +testVector()¶
      +
      + +
      + +
      +
      +

      testcrystal Module¶

      +

      Tests for crystal module.

      +
      +
      +class pyobjcryst.tests.testcrystal.TestCrystal(methodName='runTest')¶
      +

      Bases: unittest.case.TestCase

      +
      +
      +testCrystalScope()¶
      +

      Test to see if the the crystal survives after it is out of scope.

      +
      + +
      +
      +testDummyAtom()¶
      +

      Test dummy atoms.

      +
      + +
      +
      +testEmbedding()¶
      +

      Test integrity of mutually-embedded objects.

      +
      + +
      +
      +testGetScatterer()¶
      +

      Test GetScatterer.

      +
      + +
      +
      +testGetScatteringComponentList()¶
      +

      Test the RemoveScatterer and RemoveScatteringPower method.

      +
      + +
      +
      +testNullData()¶
      +

      Make sure we get an error when trying to add or remove Null.

      +
      + +
      +
      +testRemoveFunctions()¶
      +

      Test the RemoveScatterer and RemoveScatteringPower method.

      +
      + +
      +
      +testScattererB()¶
      +

      Test Biso and Bij of scatterer.

      +
      + +
      +
      +testScattererScope()¶
      +

      Test when atoms go out of scope before crystal.

      +
      + +
      + +
      +
      +

      testmolecule Module¶

      +

      Tests for molecule module.

      +
      +
      +class pyobjcryst.tests.testmolecule.TestMolAtom(methodName='runTest')¶
      +

      Bases: unittest.case.TestCase

      +
      +
      +setUp()¶
      +
      + +
      +
      +tearDown()¶
      +
      + +
      +
      +testAccessors()¶
      +
      + +
      + +
      +
      +class pyobjcryst.tests.testmolecule.TestMolBond(methodName='runTest')¶
      +

      Bases: unittest.case.TestCase

      +
      +
      +setUp()¶
      +
      + +
      +
      +tearDown()¶
      +
      + +
      +
      +testAccessors()¶
      +
      + +
      + +
      +
      +class pyobjcryst.tests.testmolecule.TestMolBondAngle(methodName='runTest')¶
      +

      Bases: unittest.case.TestCase

      +
      +
      +setUp()¶
      +
      + +
      +
      +tearDown()¶
      +
      + +
      +
      +testAccessors()¶
      +
      + +
      + +
      +
      +class pyobjcryst.tests.testmolecule.TestMolDihedralAngle(methodName='runTest')¶
      +

      Bases: unittest.case.TestCase

      +
      +
      +setUp()¶
      +
      + +
      +
      +tearDown()¶
      +
      + +
      +
      +testAccessors()¶
      +
      + +
      + +
      +
      +class pyobjcryst.tests.testmolecule.TestMolecule(methodName='runTest')¶
      +

      Bases: unittest.case.TestCase

      +
      +
      +setUp()¶
      +
      + +
      +
      +tearDown()¶
      +
      + +
      +
      +testAddPar()¶
      +

      See if we crash if we add a parameter and delete the molecule.

      +
      + +
      +
      +testAtoms()¶
      +

      Make sure the atoms are there.

      +

      This tests AddAtom by association. +This tests GetAtom.

      +
      + +
      +
      +testBondAngles()¶
      +

      Test the BondAngle accessors.

      +
      + +
      +
      +testBonds()¶
      +

      Test the Bond methods.

      +
      + +
      +
      +testContainment()¶
      +

      Make sure we can still use the molecule if the crystal is out of +scope.

      +
      + +
      +
      +testDihedralAngles()¶
      +

      Test the FindDihedralAngle method.

      +
      + +
      +
      +testManipulation()¶
      +

      Test moving the atoms.

      +
      + +
      +
      +testProperties()¶
      +

      Make sure we can access the python-only properties.

      +
      + +
      +
      +testRigidGroup()¶
      +

      Test adding and manipulating a rigid group.

      +
      + +
      + +
      +
      +class pyobjcryst.tests.testmolecule.TestStretchModeBondAngle(methodName='runTest')¶
      +

      Bases: unittest.case.TestCase

      +
      +
      +setUp()¶
      +
      + +
      +
      +tearDown()¶
      +
      + +
      +
      +testStretchModeBondAngle()¶
      +

      Test the StretchModeBondLength class.

      +
      + +
      + +
      +
      +class pyobjcryst.tests.testmolecule.TestStretchModeBondLength(methodName='runTest')¶
      +

      Bases: unittest.case.TestCase

      +
      +
      +setUp()¶
      +
      + +
      +
      +tearDown()¶
      +
      + +
      +
      +testStretchModeBondLength()¶
      +

      Test the StretchModeBondLength class.

      +
      + +
      + +
      +
      +class pyobjcryst.tests.testmolecule.TestStretchModeTorsion(methodName='runTest')¶
      +

      Bases: unittest.case.TestCase

      +
      +
      +setUp()¶
      +
      + +
      +
      +tearDown()¶
      +
      + +
      +
      +testDummy()¶
      +

      Test adding a dummy atom.

      +
      + +
      +
      +testStretchModeTorsion()¶
      +

      Test the StretchModeBondLength class.

      +
      + +
      + +
      +
      +

      testrefinableobj Module¶

      +

      Tests for refinableobj module.

      +
      +
      +class pyobjcryst.tests.testrefinableobj.TestRefinableObj(methodName='runTest')¶
      +

      Bases: unittest.case.TestCase

      +
      +
      +setUp()¶
      +

      Make a RefinableObj and add some RefinablePars.

      +
      + +
      +
      +tearDown()¶
      +

      Clean up those pesky xml files.

      +

      ObjCryst dumps save state into xml files when an exception is thrown. +Clean those up.

      +
      + +
      +
      +testAddParRefinableObj()¶
      +

      Test adding another object.

      +
      + +
      +
      +testAddParTwice()¶
      +

      Try to add the same parameter twice.

      +

      We could stop this in the bindings, but since RefinableObj doesn’t +delete its parameters in the destructor, it shouldn’t lead to trouble.

      +
      + +
      +
      +testFixUnFix()¶
      +

      Test FixAllPar.

      +
      + +
      +
      +testGetPar()¶
      +

      Test GetPar.

      +
      + +
      +
      +testLimits()¶
      +

      Test the limit-setting functions.

      +
      + +
      +
      +testNames()¶
      +

      Test the naming methods.

      +
      + +
      +
      +testOptimStep()¶
      +

      Test SetGlobalOptimStep.

      +
      + +
      +
      +testParmSets()¶
      +

      Test creation of parameter sets.

      +
      + +
      +
      +testUsedUnUsed()¶
      +

      Test FixAllPar.

      +
      + +
      + +
      +
      +class pyobjcryst.tests.testrefinableobj.TestRefinableObjClock(methodName='runTest')¶
      +

      Bases: unittest.case.TestCase

      +
      +
      +testRelations()¶
      +

      Test clicking!

      +

      Chances are that someone will someday read this code for an example on +how to use clocks. If not, then I’ve wasted my time writing this. +Anyway, clocks are more complex then they appear. This is because +ObjCryst++ has an internal clock that gets incremented whenever any +clock is Clicked. So, one cannot trust that a clock will increment by +only one value when it is clicked. Furthermore, clocks only alert their +parents to a change. So, it is possible to decrease the value of a +parent clock with SetEqual below the values of its children clocks. +Callling Click on the parent or child will restore the proper parent > +child relationship.

      +
      + +
      +
      +testRemoveChild()¶
      +

      Test the RemoveChild method.

      +
      + +
      + +
      +
      +class pyobjcryst.tests.testrefinableobj.TestRefinablePar(methodName='runTest')¶
      +

      Bases: unittest.case.TestCase

      +
      +
      +setUp()¶
      +
      + +
      +
      +testGetType()¶
      +

      See if we can get the proper RefParType from a RefinablePar.

      +
      + +
      +
      +testToFromPython()¶
      +

      See if refinable parameters can be created from within python and +within c++.

      +
      + +
      + +
      +
      +class pyobjcryst.tests.testrefinableobj.TestRestraint(methodName='runTest')¶
      +

      Bases: unittest.case.TestCase

      +
      +
      +testEquality()¶
      +

      See if we get back what we put in.

      +
      + +
      + +
      +
      +

      testutils Module¶

      +

      Tests for crystal module.

      +
      +
      +class pyobjcryst.tests.testutils.TestPutAtomsInMolecule(methodName='runTest')¶
      +

      Bases: unittest.case.TestCase

      +
      + +
      +
      + + +
      +
      +
      +
      +
      +

      Table Of Contents

      + + +

      Previous topic

      +

      pyobjcryst Package

      +

      This Page

      + + + +
      +
      +
      +
      + + + + \ No newline at end of file diff --git a/genindex-C.html b/genindex-C.html new file mode 100644 index 0000000..50163ea --- /dev/null +++ b/genindex-C.html @@ -0,0 +1,120 @@ + + + + + + + + + + + + Index — PyObjCryst 1.0b3-6 documentation + + + + + + + + + + + + + + +
      +
      +
      +
      + + +

      Index – C

      + + + +
      + +
      crystalToDiffpyStructure() (in module pyobjcryst.utils) +
      + +
      + + +
      +
      +
      +
      +
      +

      Index

      +

      C + | D + | E + | G + | L + | M + | P + | S + | T + | W +

      + +

      Full index on one page

      + + + + +
      +
      +
      +
      + + + + \ No newline at end of file diff --git a/genindex-D.html b/genindex-D.html new file mode 100644 index 0000000..43e3e8f --- /dev/null +++ b/genindex-D.html @@ -0,0 +1,120 @@ + + + + + + + + + + + + Index — PyObjCryst 1.0b3-6 documentation + + + + + + + + + + + + + + +
      +
      +
      +
      + + +

      Index – D

      + + + +
      + +
      datafile() (in module pyobjcryst.tests.pyobjcrysttestutils) +
      + +
      + + +
      +
      +
      +
      +
      +

      Index

      +

      C + | D + | E + | G + | L + | M + | P + | S + | T + | W +

      + +

      Full index on one page

      + + + + +
      +
      +
      +
      + + + + \ No newline at end of file diff --git a/genindex-E.html b/genindex-E.html new file mode 100644 index 0000000..7eee9ba --- /dev/null +++ b/genindex-E.html @@ -0,0 +1,120 @@ + + + + + + + + + + + + Index — PyObjCryst 1.0b3-6 documentation + + + + + + + + + + + + + + +
      +
      +
      +
      + + +

      Index – E

      + + + +
      + +
      expandSymmetry() (in module pyobjcryst.utils) +
      + +
      + + +
      +
      +
      +
      +
      +

      Index

      +

      C + | D + | E + | G + | L + | M + | P + | S + | T + | W +

      + +

      Full index on one page

      + + + + +
      +
      +
      +
      + + + + \ No newline at end of file diff --git a/genindex-G.html b/genindex-G.html new file mode 100644 index 0000000..80615a1 --- /dev/null +++ b/genindex-G.html @@ -0,0 +1,126 @@ + + + + + + + + + + + + Index — PyObjCryst 1.0b3-6 documentation + + + + + + + + + + + + + + +
      + +
      +
      +

      Index

      +

      C + | D + | E + | G + | L + | M + | P + | S + | T + | W +

      + +

      Full index on one page

      + + + + +
      +
      +
      +
      + + + + \ No newline at end of file diff --git a/genindex-L.html b/genindex-L.html new file mode 100644 index 0000000..e968390 --- /dev/null +++ b/genindex-L.html @@ -0,0 +1,120 @@ + + + + + + + + + + + + Index — PyObjCryst 1.0b3-6 documentation + + + + + + + + + + + + + + +
      +
      +
      +
      + + +

      Index – L

      + + + +
      + +
      loadcifdata() (in module pyobjcryst.tests.pyobjcrysttestutils) +
      + +
      + + +
      +
      +
      +
      +
      +

      Index

      +

      C + | D + | E + | G + | L + | M + | P + | S + | T + | W +

      + +

      Full index on one page

      + + + + +
      +
      +
      +
      + + + + \ No newline at end of file diff --git a/genindex-M.html b/genindex-M.html new file mode 100644 index 0000000..b9f8862 --- /dev/null +++ b/genindex-M.html @@ -0,0 +1,158 @@ + + + + + + + + + + + + Index — PyObjCryst 1.0b3-6 documentation + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/genindex-P.html b/genindex-P.html new file mode 100644 index 0000000..2c73788 --- /dev/null +++ b/genindex-P.html @@ -0,0 +1,238 @@ + + + + + + + + + + + + Index — PyObjCryst 1.0b3-6 documentation + + + + + + + + + + + + + + +
      + +
      +
      +

      Index

      +

      C + | D + | E + | G + | L + | M + | P + | S + | T + | W +

      + +

      Full index on one page

      + + + + +
      +
      +
      +
      + + + + \ No newline at end of file diff --git a/genindex-S.html b/genindex-S.html new file mode 100644 index 0000000..8859987 --- /dev/null +++ b/genindex-S.html @@ -0,0 +1,158 @@ + + + + + + + + + + + + Index — PyObjCryst 1.0b3-6 documentation + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/genindex-T.html b/genindex-T.html new file mode 100644 index 0000000..470a995 --- /dev/null +++ b/genindex-T.html @@ -0,0 +1,528 @@ + + + + + + + + + + + + Index — PyObjCryst 1.0b3-6 documentation + + + + + + + + + + + + + + +
      +
      +
      +
      + + +

      Index – T

      + + + + +
      + +
      tearDown() (pyobjcryst.tests.testmolecule.TestMolAtom method) +
      + +
      + +
      (pyobjcryst.tests.testmolecule.TestMolBond method) +
      + + +
      (pyobjcryst.tests.testmolecule.TestMolBondAngle method) +
      + + +
      (pyobjcryst.tests.testmolecule.TestMolDihedralAngle method) +
      + + +
      (pyobjcryst.tests.testmolecule.TestMolecule method) +
      + + +
      (pyobjcryst.tests.testmolecule.TestStretchModeBondAngle method) +
      + + +
      (pyobjcryst.tests.testmolecule.TestStretchModeBondLength method) +
      + + +
      (pyobjcryst.tests.testmolecule.TestStretchModeTorsion method) +
      + + +
      (pyobjcryst.tests.testrefinableobj.TestRefinableObj method) +
      + +
      + +
      test() (in module pyobjcryst.tests) +
      + + +
      test1() (in module pyobjcryst.tests.pyobjcrysttest) +
      + + +
      test_Ag_silver_cif() (pyobjcryst.tests.testcif.TestCif method) +
      + + +
      test_BaTiO3_cif() (pyobjcryst.tests.testcif.TestCif method) +
      + + +
      test_C_graphite_hex_cif() (pyobjcryst.tests.testcif.TestCif method) +
      + + +
      test_CaF2_fluorite_cif() (pyobjcryst.tests.testcif.TestCif method) +
      + + +
      test_caffeine_cif() (pyobjcryst.tests.testcif.TestCif method) +
      + + +
      test_CaTiO3_cif() (pyobjcryst.tests.testcif.TestCif method) +
      + + +
      test_CdSe_cadmoselite_cif() (pyobjcryst.tests.testcif.TestCif method) +
      + + +
      test_CeO2_cif() (pyobjcryst.tests.testcif.TestCif method) +
      + + +
      test_menthol_cif() (pyobjcryst.tests.testcif.TestCif method) +
      + + +
      test_NaCl_cif() (pyobjcryst.tests.testcif.TestCif method) +
      + + +
      test_Ni_cif() (pyobjcryst.tests.testcif.TestCif method) +
      + + +
      test_paracetamol_cif() (pyobjcryst.tests.testcif.TestCif method) +
      + + +
      test_PbS_galena_cif() (pyobjcryst.tests.testcif.TestCif method) +
      + + +
      test_PbTe_cif() (pyobjcryst.tests.testcif.TestCif method) +
      + + +
      test_Si_cif() (pyobjcryst.tests.testcif.TestCif method) +
      + + +
      test_Si_setting2_cif() (pyobjcryst.tests.testcif.TestCif method) +
      + + +
      test_SrTiO3_tausonite_cif() (pyobjcryst.tests.testcif.TestCif method) +
      + + +
      test_TiO2_anatase_cif() (pyobjcryst.tests.testcif.TestCif method) +
      + + +
      test_TiO2_rutile_cif() (pyobjcryst.tests.testcif.TestCif method) +
      + + +
      test_Zn_zinc_cif() (pyobjcryst.tests.testcif.TestCif method) +
      + + +
      test_ZnS_sphalerite_cif() (pyobjcryst.tests.testcif.TestCif method) +
      + + +
      test_ZnS_wurtzite_cif() (pyobjcryst.tests.testcif.TestCif method) +
      + + +
      testAccessors() (pyobjcryst.tests.testmolecule.TestMolAtom method) +
      + +
      + +
      (pyobjcryst.tests.testmolecule.TestMolBond method) +
      + + +
      (pyobjcryst.tests.testmolecule.TestMolBondAngle method) +
      + + +
      (pyobjcryst.tests.testmolecule.TestMolDihedralAngle method) +
      + +
      + +
      testAddPar() (pyobjcryst.tests.testmolecule.TestMolecule method) +
      + + +
      testAddParRefinableObj() (pyobjcryst.tests.testrefinableobj.TestRefinableObj method) +
      + + +
      testAddParTwice() (pyobjcryst.tests.testrefinableobj.TestRefinableObj method) +
      + + +
      testAtoms() (pyobjcryst.tests.testmolecule.TestMolecule method) +
      + + +
      testBadCif() (pyobjcryst.tests.testcif.TestCif method) +
      + + +
      testBondAngles() (pyobjcryst.tests.testmolecule.TestMolecule method) +
      + + +
      testBonds() (pyobjcryst.tests.testmolecule.TestMolecule method) +
      + + +
      TestCif (class in pyobjcryst.tests.testcif) +
      + + +
      testClockIncrement() (pyobjcryst.tests.testclocks.TestClocks method) +
      + + +
      TestClocks (class in pyobjcryst.tests.testclocks) +
      + + +
      testContainment() (pyobjcryst.tests.testmolecule.TestMolecule method) +
      + + +
      TestConverters (class in pyobjcryst.tests.testconverters) +
      + + +
      TestCrystal (class in pyobjcryst.tests.testcrystal) +
      + + +
      testCrystalScope() (in module pyobjcryst.tests.pyobjcrysttest) +
      + +
      + +
      (pyobjcryst.tests.testcrystal.TestCrystal method) +
      + +
      + +
      testDihedralAngles() (pyobjcryst.tests.testmolecule.TestMolecule method) +
      + + +
      testDummy() (pyobjcryst.tests.testmolecule.TestStretchModeTorsion method) +
      + + +
      testDummyAtom() (pyobjcryst.tests.testcrystal.TestCrystal method) +
      + +
      + +
      testEmbedding() (pyobjcryst.tests.testcrystal.TestCrystal method) +
      + + +
      testEquality() (pyobjcryst.tests.testrefinableobj.TestRestraint method) +
      + + +
      testFixUnFix() (pyobjcryst.tests.testrefinableobj.TestRefinableObj method) +
      + + +
      testGetPar() (pyobjcryst.tests.testrefinableobj.TestRefinableObj method) +
      + + +
      testGetScatterer() (pyobjcryst.tests.testcrystal.TestCrystal method) +
      + + +
      testGetScatteringComponentList() (pyobjcryst.tests.testcrystal.TestCrystal method) +
      + + +
      testGetType() (pyobjcryst.tests.testrefinableobj.TestRefinablePar method) +
      + + +
      testLimits() (pyobjcryst.tests.testrefinableobj.TestRefinableObj method) +
      + + +
      testManipulation() (pyobjcryst.tests.testmolecule.TestMolecule method) +
      + + +
      testMatrix() (pyobjcryst.tests.testconverters.TestConverters method) +
      + + +
      TestMolAtom (class in pyobjcryst.tests.testmolecule) +
      + + +
      TestMolBond (class in pyobjcryst.tests.testmolecule) +
      + + +
      TestMolBondAngle (class in pyobjcryst.tests.testmolecule) +
      + + +
      TestMolDihedralAngle (class in pyobjcryst.tests.testmolecule) +
      + + +
      TestMolecule (class in pyobjcryst.tests.testmolecule) +
      + + +
      testMultiAdd() (in module pyobjcryst.tests.pyobjcrysttest) +
      + + +
      testNames() (pyobjcryst.tests.testrefinableobj.TestRefinableObj method) +
      + + +
      testNullData() (pyobjcryst.tests.testcrystal.TestCrystal method) +
      + + +
      testOptimStep() (pyobjcryst.tests.testrefinableobj.TestRefinableObj method) +
      + + +
      testParmSets() (pyobjcryst.tests.testrefinableobj.TestRefinableObj method) +
      + + +
      testProperties() (pyobjcryst.tests.testmolecule.TestMolecule method) +
      + + +
      TestPutAtomsInMolecule (class in pyobjcryst.tests.testutils) +
      + + +
      TestRefinableObj (class in pyobjcryst.tests.testrefinableobj) +
      + + +
      TestRefinableObjClock (class in pyobjcryst.tests.testrefinableobj) +
      + + +
      TestRefinablePar (class in pyobjcryst.tests.testrefinableobj) +
      + + +
      testRelations() (pyobjcryst.tests.testrefinableobj.TestRefinableObjClock method) +
      + + +
      testRemoveChild() (pyobjcryst.tests.testrefinableobj.TestRefinableObjClock method) +
      + + +
      testRemoveFunctions() (in module pyobjcryst.tests.pyobjcrysttest) +
      + +
      + +
      (pyobjcryst.tests.testcrystal.TestCrystal method) +
      + +
      + +
      TestRestraint (class in pyobjcryst.tests.testrefinableobj) +
      + + +
      testRigidGroup() (pyobjcryst.tests.testmolecule.TestMolecule method) +
      + + +
      testScattererB() (pyobjcryst.tests.testcrystal.TestCrystal method) +
      + + +
      testScattererScope() (in module pyobjcryst.tests.pyobjcrysttest) +
      + +
      + +
      (pyobjcryst.tests.testcrystal.TestCrystal method) +
      + +
      + +
      TestStretchModeBondAngle (class in pyobjcryst.tests.testmolecule) +
      + + +
      testStretchModeBondAngle() (pyobjcryst.tests.testmolecule.TestStretchModeBondAngle method) +
      + + +
      TestStretchModeBondLength (class in pyobjcryst.tests.testmolecule) +
      + + +
      testStretchModeBondLength() (pyobjcryst.tests.testmolecule.TestStretchModeBondLength method) +
      + + +
      TestStretchModeTorsion (class in pyobjcryst.tests.testmolecule) +
      + + +
      testStretchModeTorsion() (pyobjcryst.tests.testmolecule.TestStretchModeTorsion method) +
      + + +
      testsuite() (in module pyobjcryst.tests) +
      + + +
      testToFromPython() (pyobjcryst.tests.testrefinableobj.TestRefinablePar method) +
      + + +
      testUsedUnUsed() (pyobjcryst.tests.testrefinableobj.TestRefinableObj method) +
      + + +
      testVector() (pyobjcryst.tests.testconverters.TestConverters method) +
      + + +
      toxyz() (in module pyobjcryst.tests.pyobjcrysttestutils) +
      + +
      + + +
      +
      +
      +
      +
      +

      Index

      +

      C + | D + | E + | G + | L + | M + | P + | S + | T + | W +

      + +

      Full index on one page

      + + + + +
      +
      +
      +
      + + + + \ No newline at end of file diff --git a/genindex-W.html b/genindex-W.html new file mode 100644 index 0000000..533e8f9 --- /dev/null +++ b/genindex-W.html @@ -0,0 +1,120 @@ + + + + + + + + + + + + Index — PyObjCryst 1.0b3-6 documentation + + + + + + + + + + + + + + +
      +
      +
      +
      + + +

      Index – W

      + + + +
      + +
      writexyz() (in module pyobjcryst.utils) +
      + +
      + + +
      +
      +
      +
      +
      +

      Index

      +

      C + | D + | E + | G + | L + | M + | P + | S + | T + | W +

      + +

      Full index on one page

      + + + + +
      +
      +
      +
      + + + + \ No newline at end of file diff --git a/genindex-all.html b/genindex-all.html index 12abe85..4295841 100644 --- a/genindex-all.html +++ b/genindex-all.html @@ -1,4 +1,7 @@ + + + @@ -7,15 +10,15 @@ - Index — PyObjCryst 1.0b2-17 documentation + Index — PyObjCryst 1.0b3-6 documentation - + @@ -47,8 +53,726 @@

      Navigation

      Index

      + C + | D + | E + | G + | L + | M + | P + | S + | T + | W
      +

      C

      + + +
      + +
      crystalToDiffpyStructure() (in module pyobjcryst.utils) +
      + +
      + +

      D

      + + +
      + +
      datafile() (in module pyobjcryst.tests.pyobjcrysttestutils) +
      + +
      + +

      E

      + + +
      + +
      expandSymmetry() (in module pyobjcryst.utils) +
      + +
      + +

      G

      + + +
      + +
      getScatterer() (in module pyobjcryst.tests.pyobjcrysttest) +
      + +
      + +
      (in module pyobjcryst.tests.pyobjcrysttestutils) +
      + +
      +
      + +

      L

      + + +
      + +
      loadcifdata() (in module pyobjcryst.tests.pyobjcrysttestutils) +
      + +
      + +

      M

      + + + +
      + +
      makeC60() (in module pyobjcryst.tests.pyobjcrysttestutils) +
      + + +
      makeCrystal() (in module pyobjcryst.tests.pyobjcrysttest) +
      + +
      + +
      (in module pyobjcryst.tests.pyobjcrysttestutils) +
      + +
      + +
      makeLaMnO3() (in module pyobjcryst.tests.pyobjcrysttestutils) +
      + + +
      makeMnO6() (in module pyobjcryst.tests.pyobjcrysttestutils) +
      + +
      + +
      makeScatterer() (in module pyobjcryst.tests.pyobjcrysttest) +
      + +
      + +
      (in module pyobjcryst.tests.pyobjcrysttestutils) +
      + +
      + +
      makeScattererAnisotropic() (in module pyobjcryst.tests.pyobjcrysttestutils) +
      + + +
      moleculeFromDiffpyStructure() (in module pyobjcryst.utils) +
      + +
      + +

      P

      + + + +
      + +
      parTest() (in module pyobjcryst.tests.pyobjcrysttest) +
      + + +
      printxyz() (in module pyobjcryst.utils) +
      + + +
      putAtomsInMolecule() (in module pyobjcryst.utils) +
      + + +
      pyobjcryst.__init__ (module) +
      + + +
      pyobjcryst.atom (module) +
      + + +
      pyobjcryst.crystal (module) +
      + + +
      pyobjcryst.general (module) +
      + + +
      pyobjcryst.io (module) +
      + + +
      pyobjcryst.molecule (module) +
      + + +
      pyobjcryst.polyhedron (module) +
      + + +
      pyobjcryst.refinableobj (module) +
      + + +
      pyobjcryst.scatterer (module) +
      + + +
      pyobjcryst.scatteringpower (module) +
      + + +
      pyobjcryst.scatteringpowersphere (module) +
      + + +
      pyobjcryst.spacegroup (module) +
      + +
      + +
      pyobjcryst.tests (module) +
      + + +
      pyobjcryst.tests.pyobjcrysttest (module) +
      + + +
      pyobjcryst.tests.pyobjcrysttestutils (module) +
      + + +
      pyobjcryst.tests.run (module) +
      + + +
      pyobjcryst.tests.testcif (module) +
      + + +
      pyobjcryst.tests.testclocks (module) +
      + + +
      pyobjcryst.tests.testconverters (module) +
      + + +
      pyobjcryst.tests.testcrystal (module) +
      + + +
      pyobjcryst.tests.testmolecule (module) +
      + + +
      pyobjcryst.tests.testrefinableobj (module) +
      + + +
      pyobjcryst.tests.testutils (module) +
      + + +
      pyobjcryst.unitcell (module) +
      + + +
      pyobjcryst.utils (module) +
      + + +
      pyobjcryst.version (module) +
      + + +
      pyobjcryst.zscatterer (module) +
      + +
      + +

      S

      + + +
      + +
      setUp() (pyobjcryst.tests.testmolecule.TestMolAtom method) +
      + +
      + +
      (pyobjcryst.tests.testmolecule.TestMolBond method) +
      + + +
      (pyobjcryst.tests.testmolecule.TestMolBondAngle method) +
      + + +
      (pyobjcryst.tests.testmolecule.TestMolDihedralAngle method) +
      + + +
      (pyobjcryst.tests.testmolecule.TestMolecule method) +
      + + +
      (pyobjcryst.tests.testmolecule.TestStretchModeBondAngle method) +
      + + +
      (pyobjcryst.tests.testmolecule.TestStretchModeBondLength method) +
      + + +
      (pyobjcryst.tests.testmolecule.TestStretchModeTorsion method) +
      + + +
      (pyobjcryst.tests.testrefinableobj.TestRefinableObj method) +
      + + +
      (pyobjcryst.tests.testrefinableobj.TestRefinablePar method) +
      + +
      +
      + +

      T

      + + + +
      + +
      tearDown() (pyobjcryst.tests.testmolecule.TestMolAtom method) +
      + +
      + +
      (pyobjcryst.tests.testmolecule.TestMolBond method) +
      + + +
      (pyobjcryst.tests.testmolecule.TestMolBondAngle method) +
      + + +
      (pyobjcryst.tests.testmolecule.TestMolDihedralAngle method) +
      + + +
      (pyobjcryst.tests.testmolecule.TestMolecule method) +
      + + +
      (pyobjcryst.tests.testmolecule.TestStretchModeBondAngle method) +
      + + +
      (pyobjcryst.tests.testmolecule.TestStretchModeBondLength method) +
      + + +
      (pyobjcryst.tests.testmolecule.TestStretchModeTorsion method) +
      + + +
      (pyobjcryst.tests.testrefinableobj.TestRefinableObj method) +
      + +
      + +
      test() (in module pyobjcryst.tests) +
      + + +
      test1() (in module pyobjcryst.tests.pyobjcrysttest) +
      + + +
      test_Ag_silver_cif() (pyobjcryst.tests.testcif.TestCif method) +
      + + +
      test_BaTiO3_cif() (pyobjcryst.tests.testcif.TestCif method) +
      + + +
      test_C_graphite_hex_cif() (pyobjcryst.tests.testcif.TestCif method) +
      + + +
      test_CaF2_fluorite_cif() (pyobjcryst.tests.testcif.TestCif method) +
      + + +
      test_caffeine_cif() (pyobjcryst.tests.testcif.TestCif method) +
      + + +
      test_CaTiO3_cif() (pyobjcryst.tests.testcif.TestCif method) +
      + + +
      test_CdSe_cadmoselite_cif() (pyobjcryst.tests.testcif.TestCif method) +
      + + +
      test_CeO2_cif() (pyobjcryst.tests.testcif.TestCif method) +
      + + +
      test_menthol_cif() (pyobjcryst.tests.testcif.TestCif method) +
      + + +
      test_NaCl_cif() (pyobjcryst.tests.testcif.TestCif method) +
      + + +
      test_Ni_cif() (pyobjcryst.tests.testcif.TestCif method) +
      + + +
      test_paracetamol_cif() (pyobjcryst.tests.testcif.TestCif method) +
      + + +
      test_PbS_galena_cif() (pyobjcryst.tests.testcif.TestCif method) +
      + + +
      test_PbTe_cif() (pyobjcryst.tests.testcif.TestCif method) +
      + + +
      test_Si_cif() (pyobjcryst.tests.testcif.TestCif method) +
      + + +
      test_Si_setting2_cif() (pyobjcryst.tests.testcif.TestCif method) +
      + + +
      test_SrTiO3_tausonite_cif() (pyobjcryst.tests.testcif.TestCif method) +
      + + +
      test_TiO2_anatase_cif() (pyobjcryst.tests.testcif.TestCif method) +
      + + +
      test_TiO2_rutile_cif() (pyobjcryst.tests.testcif.TestCif method) +
      + + +
      test_Zn_zinc_cif() (pyobjcryst.tests.testcif.TestCif method) +
      + + +
      test_ZnS_sphalerite_cif() (pyobjcryst.tests.testcif.TestCif method) +
      + + +
      test_ZnS_wurtzite_cif() (pyobjcryst.tests.testcif.TestCif method) +
      + + +
      testAccessors() (pyobjcryst.tests.testmolecule.TestMolAtom method) +
      + +
      + +
      (pyobjcryst.tests.testmolecule.TestMolBond method) +
      + + +
      (pyobjcryst.tests.testmolecule.TestMolBondAngle method) +
      + + +
      (pyobjcryst.tests.testmolecule.TestMolDihedralAngle method) +
      + +
      + +
      testAddPar() (pyobjcryst.tests.testmolecule.TestMolecule method) +
      + + +
      testAddParRefinableObj() (pyobjcryst.tests.testrefinableobj.TestRefinableObj method) +
      + + +
      testAddParTwice() (pyobjcryst.tests.testrefinableobj.TestRefinableObj method) +
      + + +
      testAtoms() (pyobjcryst.tests.testmolecule.TestMolecule method) +
      + + +
      testBadCif() (pyobjcryst.tests.testcif.TestCif method) +
      + + +
      testBondAngles() (pyobjcryst.tests.testmolecule.TestMolecule method) +
      + + +
      testBonds() (pyobjcryst.tests.testmolecule.TestMolecule method) +
      + + +
      TestCif (class in pyobjcryst.tests.testcif) +
      + + +
      testClockIncrement() (pyobjcryst.tests.testclocks.TestClocks method) +
      + + +
      TestClocks (class in pyobjcryst.tests.testclocks) +
      + + +
      testContainment() (pyobjcryst.tests.testmolecule.TestMolecule method) +
      + + +
      TestConverters (class in pyobjcryst.tests.testconverters) +
      + + +
      TestCrystal (class in pyobjcryst.tests.testcrystal) +
      + + +
      testCrystalScope() (in module pyobjcryst.tests.pyobjcrysttest) +
      + +
      + +
      (pyobjcryst.tests.testcrystal.TestCrystal method) +
      + +
      + +
      testDihedralAngles() (pyobjcryst.tests.testmolecule.TestMolecule method) +
      + + +
      testDummy() (pyobjcryst.tests.testmolecule.TestStretchModeTorsion method) +
      + + +
      testDummyAtom() (pyobjcryst.tests.testcrystal.TestCrystal method) +
      + +
      + +
      testEmbedding() (pyobjcryst.tests.testcrystal.TestCrystal method) +
      + + +
      testEquality() (pyobjcryst.tests.testrefinableobj.TestRestraint method) +
      + + +
      testFixUnFix() (pyobjcryst.tests.testrefinableobj.TestRefinableObj method) +
      + + +
      testGetPar() (pyobjcryst.tests.testrefinableobj.TestRefinableObj method) +
      + + +
      testGetScatterer() (pyobjcryst.tests.testcrystal.TestCrystal method) +
      + + +
      testGetScatteringComponentList() (pyobjcryst.tests.testcrystal.TestCrystal method) +
      + + +
      testGetType() (pyobjcryst.tests.testrefinableobj.TestRefinablePar method) +
      + + +
      testLimits() (pyobjcryst.tests.testrefinableobj.TestRefinableObj method) +
      + + +
      testManipulation() (pyobjcryst.tests.testmolecule.TestMolecule method) +
      + + +
      testMatrix() (pyobjcryst.tests.testconverters.TestConverters method) +
      + + +
      TestMolAtom (class in pyobjcryst.tests.testmolecule) +
      + + +
      TestMolBond (class in pyobjcryst.tests.testmolecule) +
      + + +
      TestMolBondAngle (class in pyobjcryst.tests.testmolecule) +
      + + +
      TestMolDihedralAngle (class in pyobjcryst.tests.testmolecule) +
      + + +
      TestMolecule (class in pyobjcryst.tests.testmolecule) +
      + + +
      testMultiAdd() (in module pyobjcryst.tests.pyobjcrysttest) +
      + + +
      testNames() (pyobjcryst.tests.testrefinableobj.TestRefinableObj method) +
      + + +
      testNullData() (pyobjcryst.tests.testcrystal.TestCrystal method) +
      + + +
      testOptimStep() (pyobjcryst.tests.testrefinableobj.TestRefinableObj method) +
      + + +
      testParmSets() (pyobjcryst.tests.testrefinableobj.TestRefinableObj method) +
      + + +
      testProperties() (pyobjcryst.tests.testmolecule.TestMolecule method) +
      + + +
      TestPutAtomsInMolecule (class in pyobjcryst.tests.testutils) +
      + + +
      TestRefinableObj (class in pyobjcryst.tests.testrefinableobj) +
      + + +
      TestRefinableObjClock (class in pyobjcryst.tests.testrefinableobj) +
      + + +
      TestRefinablePar (class in pyobjcryst.tests.testrefinableobj) +
      + + +
      testRelations() (pyobjcryst.tests.testrefinableobj.TestRefinableObjClock method) +
      + + +
      testRemoveChild() (pyobjcryst.tests.testrefinableobj.TestRefinableObjClock method) +
      + + +
      testRemoveFunctions() (in module pyobjcryst.tests.pyobjcrysttest) +
      + +
      + +
      (pyobjcryst.tests.testcrystal.TestCrystal method) +
      + +
      + +
      TestRestraint (class in pyobjcryst.tests.testrefinableobj) +
      + + +
      testRigidGroup() (pyobjcryst.tests.testmolecule.TestMolecule method) +
      + + +
      testScattererB() (pyobjcryst.tests.testcrystal.TestCrystal method) +
      + + +
      testScattererScope() (in module pyobjcryst.tests.pyobjcrysttest) +
      + +
      + +
      (pyobjcryst.tests.testcrystal.TestCrystal method) +
      + +
      + +
      TestStretchModeBondAngle (class in pyobjcryst.tests.testmolecule) +
      + + +
      testStretchModeBondAngle() (pyobjcryst.tests.testmolecule.TestStretchModeBondAngle method) +
      + + +
      TestStretchModeBondLength (class in pyobjcryst.tests.testmolecule) +
      + + +
      testStretchModeBondLength() (pyobjcryst.tests.testmolecule.TestStretchModeBondLength method) +
      + + +
      TestStretchModeTorsion (class in pyobjcryst.tests.testmolecule) +
      + + +
      testStretchModeTorsion() (pyobjcryst.tests.testmolecule.TestStretchModeTorsion method) +
      + + +
      testsuite() (in module pyobjcryst.tests) +
      + + +
      testToFromPython() (pyobjcryst.tests.testrefinableobj.TestRefinablePar method) +
      + + +
      testUsedUnUsed() (pyobjcryst.tests.testrefinableobj.TestRefinableObj method) +
      + + +
      testVector() (pyobjcryst.tests.testconverters.TestConverters method) +
      + + +
      toxyz() (in module pyobjcryst.tests.pyobjcrysttestutils) +
      + +
      + +

      W

      + + +
      + +
      writexyz() (in module pyobjcryst.utils) +
      + +
      + @@ -58,7 +782,17 @@

      Index

      Index

      -

      +

      C + | D + | E + | G + | L + | M + | P + | S + | T + | W +

      Full index on one page

      @@ -87,12 +821,15 @@

      Navigation

    • index
    • -
    • PyObjCryst 1.0b2-17 documentation »
    • +
    • + modules |
    • +
    • PyObjCryst 1.0b3-6 documentation »
    • \ No newline at end of file diff --git a/genindex.html b/genindex.html index 97a60b5..21e5946 100644 --- a/genindex.html +++ b/genindex.html @@ -1,3 +1,5 @@ + + @@ -6,15 +8,15 @@ - Index — PyObjCryst 1.0b2-17 documentation + Index — PyObjCryst 1.0b3-6 documentation - + @@ -48,7 +53,17 @@

      Index

      Index pages by letter:

      -

      +

      C + | D + | E + | G + | L + | M + | P + | S + | T + | W +

      Full index on one page (can be huge)

      @@ -62,7 +77,17 @@

      Index

      Index

      -

      +

      C + | D + | E + | G + | L + | M + | P + | S + | T + | W +

      Full index on one page

      @@ -91,12 +116,15 @@

      Navigation

    • index
    • -
    • PyObjCryst 1.0b2-17 documentation »
    • +
    • + modules |
    • +
    • PyObjCryst 1.0b3-6 documentation »
    • \ No newline at end of file diff --git a/index.html b/index.html index e183fab..18158e3 100644 --- a/index.html +++ b/index.html @@ -1,3 +1,5 @@ + + @@ -6,15 +8,15 @@ - PyObjCryst documentation — PyObjCryst 1.0b2-17 documentation + PyObjCryst documentation — PyObjCryst 1.0b3-6 documentation - + + @@ -44,11 +53,12 @@

      Navigation

      PyObjCryst documentation¶

      -

      Software version 1.0b2-17.

      -

      Last updated January 31, 2014.

      +

      Software version 1.0b3-6.

      +

      Last updated February 10, 2014.

      PyObjCryst - Python bindings to ObjCryst++ Object-Oriented Crystallographic Library

      -

      The documentation for this release of PyObjCryst can be found on-line at -http://docs.danse.us/diffraction/pyobjcryst-beta1/.

      +

      The documentation for this release of PyObjCryst can be found on-line at

      +
      +

      Disclaimer¶

      This program is part of the DiffPy and DANSE open-source projects at Columbia @@ -87,52 +97,51 @@

      Acknowledgments

      Developers¶

      PyObjCryst is developed and maintained by

      -
      Chris Farrow
      -Pavol Juhas
      -
      -
      +
      Pavol Juhas
      +Chris Farrow
      +Simon J.L. Billinge
      +
      -
      -

      Funding¶

      -

      This software was developed as part of the Distributed Data Analysis of Neutron -Scattering Experiments (DANSE) project funded by the US National Science -Foundation under grant DMR-0520547. More information on DANSE can be found at -http://danse.us. Any opinions, findings, and conclusions or recommendations -expressed in this material are those of the author(s) and do not necessarily -reflect the views of the respective funding bodies.

      Installation¶

      -
      -

      Dependencies¶

      -

      The following programs must be installed on your system before you can install -PyObjCryst.

      -
      -
      Python >= 2.5, < 3.0
      -
      -
      -
      python-setuptools >= 0.6c9
      -
      -
      -
      Boost C++ libraries >= 1.35
      -
      -
      -
      ObjCryst++ (see below)
      -
      -
      +

      REQUIREMENTS

      +

      The diffpy.srreal requires Python 2.6 or 2.7 and the following software:

      +
      +
      setuptools – tools for installing Python packages +scons – software constructions tool (1.0 or later) +python-dev – header files for interfacing Python with C +libboost-dev – Boost C++ libraries development files (1.43 or later) +ObjCryst++ – Object-Oriented Crystallographic Library
      +

      Some of the required software may be available in the system package manager, +for example, on Ubuntu Linux the dependencies can be installed as:

      +
      +
      +
      sudo apt-get install
      +
      python-setuptools scons build-essential python-dev libboost-dev
      -
      -
      -

      Installing ObjCryst++¶

      +
      +

      For Mac OS X machine with the MacPorts package manager one could do

      +
      +
      +
      sudo port install
      +
      python27 py27-setuptools scons boost
      +
      +
      +

      When installing with MacPorts, make sure the MacPorts bin directory is the +first in the system PATH and that python27 is selected as the default +Python version in MacPorts:

      +
      +
      sudo port select –set python python27
      +

      For other required packages see their respective web pages for installation +instructions.

      +

      INSTALLATION

      +

      The easiest option is to use the latest DiffPy-CMI release bundle from +http://www.diffpy.org/, which comes with pyobjcryst and all other +dependencies included.

      +

      If you prefer to install from sources:

      +

      Installing ObjCryst++

      We provide a SCons build script and ObjCryst++ source bundle to make it easier to build ObjCryst++ and its dependencies (cctbx and newmat) as a shared library. This requires SCons (http://www.scons.org) to be installed on your @@ -140,18 +149,15 @@

      Installing ObjCryst++

      1. Download ObjCryst-latest.tar.gz from http://dev.danse.us/packages/ to the directory containing INSTALL.txt

      -
      > wget http://dev.danse.us/packages/ObjCryst-latest.tar.gz
      -
      +
      > wget http://dev.danse.us/packages/ObjCryst-latest.tar.gz
      1. Extract the archive to the libobjcryst directory

        -
        > tar xzvf ObjCryst-latest.tar.gz -C libobjcryst
        -
        +
        > tar xzvf ObjCryst-latest.tar.gz -C libobjcryst
      2. From the libobjcryst directory run the following command

        -
        > scons build=fast install
        -
        +
        > scons build=fast install

        This will build and install the shared libraries, and header files to standard system-dependent locations. Run scons -h for other installation @@ -162,24 +168,48 @@

        Installing ObjCryst++This build method has been tested on Linux platforms with recent GNU and Intel C++ compilers.

        Once you have done this, you can install PyObjCryst as instructed below.

        -

        -
        -

        Installing PyObjCryst¶

        +

        Installing PyObjCryst

        To install PyObjCryst, you must have ObjCryst++ installed as a shared library (see above). Once this is done, type the following from the command line from -the directory containing INSTALL.txt

        -
        > python setup.py install
        -
        +the directory containing README.txt

        +
        > python setup.py install

        For installation options, type

        -
        > python setup.py --help install
        -
        -
        +
        > python setup.py --help install
        @@ -195,20 +225,19 @@

        Table Of Contents

      3. Disclaimer
      4. Acknowledgments
      5. -
      6. Installation
      7. +

        Next topic

        +

        pyobjcryst

        This Page

    • index
    • -
    • PyObjCryst 1.0b2-17 documentation »
    • +
    • + modules |
    • +
    • + next |
    • +
    • PyObjCryst 1.0b3-6 documentation »
    • \ No newline at end of file diff --git a/install.html b/install.html new file mode 100644 index 0000000..1993965 --- /dev/null +++ b/install.html @@ -0,0 +1,167 @@ + + + + + + + + + + <no title> — PyObjCryst 1.0b3-6 documentation + + + + + + + + + + + + + + +
      +
      +
      +
      + +

      REQUIREMENTS

      +

      The diffpy.srreal requires Python 2.6 or 2.7 and the following software:

      +
      +
      setuptools – tools for installing Python packages +scons – software constructions tool (1.0 or later) +python-dev – header files for interfacing Python with C +libboost-dev – Boost C++ libraries development files (1.43 or later) +ObjCryst++ – Object-Oriented Crystallographic Library
      +

      Some of the required software may be available in the system package manager, +for example, on Ubuntu Linux the dependencies can be installed as:

      +
      +
      +
      sudo apt-get install
      +
      python-setuptools scons build-essential python-dev libboost-dev
      +
      +
      +

      For Mac OS X machine with the MacPorts package manager one could do

      +
      +
      +
      sudo port install
      +
      python27 py27-setuptools scons boost
      +
      +
      +

      When installing with MacPorts, make sure the MacPorts bin directory is the +first in the system PATH and that python27 is selected as the default +Python version in MacPorts:

      +
      +
      sudo port select –set python python27
      +

      For other required packages see their respective web pages for installation +instructions.

      +

      INSTALLATION

      +

      The easiest option is to use the latest DiffPy-CMI release bundle from +http://www.diffpy.org/, which comes with pyobjcryst and all other +dependencies included.

      +

      If you prefer to install from sources:

      +

      Installing ObjCryst++

      +

      We provide a SCons build script and ObjCryst++ source bundle to make it easier +to build ObjCryst++ and its dependencies (cctbx and newmat) as a shared +library. This requires SCons (http://www.scons.org) to be installed on your +computer. Here’s how to install.

      +
      +

      1. Download ObjCryst-latest.tar.gz from http://dev.danse.us/packages/ to the +directory containing INSTALL.txt

      +
      > wget http://dev.danse.us/packages/ObjCryst-latest.tar.gz
      +
      +
        +
      1. Extract the archive to the libobjcryst directory

        +
        > tar xzvf ObjCryst-latest.tar.gz -C libobjcryst
        +
        +
      2. +
      3. From the libobjcryst directory run the following command

        +
        > scons build=fast install
        +
        +

        This will build and install the shared libraries, and header files to +standard system-dependent locations. Run scons -h for other installation +options.

        +
      4. +
      +
      +

      This build method has been tested on Linux platforms with recent GNU and Intel +C++ compilers.

      +

      Once you have done this, you can install PyObjCryst as instructed below.

      +

      Installing PyObjCryst

      +

      To install PyObjCryst, you must have ObjCryst++ installed as a shared library +(see above). Once this is done, type the following from the command line from +the directory containing README.txt

      +
      > python setup.py install
      +
      +

      For installation options, type

      +
      > python setup.py --help install
      +
      + + +
      +
      +
      +
      +
      +

      This Page

      + + + +
      +
      +
      +
      + + + + \ No newline at end of file diff --git a/objects.inv b/objects.inv index 110820ba6cc5fb381d57cf18469e8308649eb420..07cbb856aea32276e8b78c8ca1ec5c4853da30b4 100644 GIT binary patch delta 1627 zcmV-h2Bi7<0l*EALIX1`Hjzd;f4y7JbJ{u(zW1+S=Jgt0lg{+eTjDgG%!I%c@(#Ut zge|aIS#l-0iSyS#$>xUv8?bl9g#=q#Nvqv&zg>w`#!STYZJchRYS*Gmyd%)b4iLWm>_db?Gunzf81vz#b2uI4#O5@WoXuWMSDi3v&32~XldIAIGd(3649lS zc?Q=wm(gzxH%E{JCK1&Onh7y71?%)&mpD0_Fl2(6Fzh*_RB{@*PGBQp3(z`pyNZZ% z4xY$4E9wBB<@e)(;H0!OWOQ2EaAv=ZB)^j)z7@-Atq~_$53Y|)f9^cFQ)`RLszD?K1$C)^Vg9>c{$lrGRCN7fs_A;XVOl)l3&|VWagI_a=~* zoHF4!DpVKygWOu6e;#UTUNWfUgMFN`&T(lm7S z27ABitAzkgBVWC4L|lMhJ+QYIVL#Aq%eg`#Il5i#Xc+7kO=z5w-?RptKs0XfIS(o+ zK>}uPhp9wIW7D~f27NVFsXoh%TZw)YqZwM(1Fn`ynE z0JO<66RON|lN5O+UTy04f%)}O@AEV*`VG{;@XNBcj0OjHP($HyG6FD^!zyQgPsN17O@@HO z-VgJ-3R%~Ie_Flo^fgN_V8p zX?!oC%u`oR#>vLLu*QRW*3r3RSKoh%Y51Be^Nt0``vW|a0JUy+0o=km+i9t*fjL|| z!r+#6fA;5p&s+(aaEyX<)0Gx@J=#7bmf4oCzx~OHr5OeGE^gW5hzOSD6@vK3TuW(I z5f6!FxNrovmiDVf$fpa~^_l9Vt)h$w@%|VY{g%#Y99tE6F-2fRsDQ%>oHW+U5%Vqw zu|DFL&Jw~Y*70$>zfY7k6J;3HK9Bj3!o#^|f2cU2?kGz~N>n%XhROnV$`25eI+;RJ z<>ORvBm7n{EseD;7J0}Ef^exwmN@4~=v#jWsV2Ts)=b{B#Ud-LP34iv73gH`;4WQ< zS-tz=5jER&EoSmT$#ha!ogqdbuX#e*;+dpd@u}yW^ZV7sr0#P%Cj~g^ ze;xg_URnREi!s2mX;V_*3Bk$(%eDOO>TbA3iN?^8nZb77597Qa3Gf<7=(Pvb zFArLXu&$^6>lf|N6J z?SC(~0y7`nhqu_33I6mr~aLF;ZVvOy4ph;%SjuO#!Na zXa2RjqZMs%|2~RHQH)Gm0 Zh}RLUAYnWPom92{uC?9f{|BeZhUuYkGnoJY delta 136 zcmV;30C)eu4fz3(LIg4`F*lJ#I(f^@Psz+nNv%*QE=jSR3RD}>RsIp*)f`G*IR4xEwG)NwDLP5j; diff --git a/py-modindex.html b/py-modindex.html new file mode 100644 index 0000000..489bb87 --- /dev/null +++ b/py-modindex.html @@ -0,0 +1,247 @@ + + + + + + + + + + Python Module Index — PyObjCryst 1.0b3-6 documentation + + + + + + + + + + + + + + + + + +
      +
      +
      +
      + + +

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          + pyobjcryst.tests.testrefinableobj +
          + pyobjcryst.tests.testutils +
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      + + + + \ No newline at end of file diff --git a/search.html b/search.html index 439863f..1295c22 100644 --- a/search.html +++ b/search.html @@ -1,3 +1,5 @@ + + @@ -6,15 +8,15 @@ - Search — PyObjCryst 1.0b2-17 documentation + Search — PyObjCryst 1.0b3-6 documentation - + - - @@ -41,7 +41,10 @@

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| 10 +++++----- genindex-W.html | 10 +++++----- genindex-all.html | 10 +++++----- genindex.html | 10 +++++----- index.html | 15 ++++++--------- install.html | 10 +++++----- objects.inv | Bin 1728 -> 1705 bytes py-modindex.html | 10 +++++----- search.html | 10 +++++----- searchindex.js | 2 +- 23 files changed, 98 insertions(+), 105 deletions(-) diff --git a/.buildinfo b/.buildinfo index d2de10b..062d905 100644 --- a/.buildinfo +++ b/.buildinfo @@ -1,4 +1,4 @@ # Sphinx build info version 1 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. -config: 17145d9d4e75007530ae98ed1d26ef3a +config: 34b3881e8ed15f25052a9394b72c62f4 tags: fbb0d17656682115ca4d033fb2f83ba1 diff --git a/_sources/index.txt b/_sources/index.txt index af675e3..a070a50 100644 --- a/_sources/index.txt +++ b/_sources/index.txt @@ -10,10 +10,6 @@ Last updated |today|. PyObjCryst - Python bindings to ObjCryst++ Object-Oriented Crystallographic Library -The documentation for this release of PyObjCryst can be found on-line at - - http://diffpy.github.io/doc/pyobjcryst/ - =================== Disclaimer =================== diff --git a/api/modules.html b/api/modules.html index 7d002bf..434dc46 100644 --- a/api/modules.html +++ b/api/modules.html @@ -8,7 +8,7 @@ - pyobjcryst — PyObjCryst 1.0b3-6 documentation + pyobjcryst — PyObjCryst 1.0b3-7 documentation @@ -16,7 +16,7 @@ - + @@ -46,7 +46,7 @@

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    • diff --git a/genindex-C.html b/genindex-C.html index 50163ea..f61e35f 100644 --- a/genindex-C.html +++ b/genindex-C.html @@ -10,7 +10,7 @@ - Index — PyObjCryst 1.0b3-6 documentation + Index — PyObjCryst 1.0b3-7 documentation @@ -18,7 +18,7 @@ - + @@ -109,7 +109,7 @@

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      Navigation

      PyObjCryst documentation¶

      -

      Software version 1.0b3-6.

      +

      Software version 1.0b3-7.

      Last updated February 10, 2014.

      PyObjCryst - Python bindings to ObjCryst++ Object-Oriented Crystallographic Library

      -

      The documentation for this release of PyObjCryst can be found on-line at

      -
      -

      Disclaimer¶

      This program is part of the DiffPy and DANSE open-source projects at Columbia @@ -272,7 +269,7 @@

      Navigation

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      Navigation

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    • PyObjCryst 1.0b3-6 documentation »
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    • @@ -76,21 +76,7 @@

      pyobjcrystutils Module
    • version Module
    • zscatterer Module
    • -
    • Subpackages @@ -148,7 +134,7 @@

      Navigation

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    • @@ -362,21 +358,7 @@

      pyobjcryst

      Subpackages¶

      @@ -417,9 +399,6 @@

      Table Of Contents

      Previous topic

      pyobjcryst

      -

      Next topic

      -

      tests Package

      This Page

    • modules |
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    • pyobjcryst »
    • diff --git a/api/pyobjcryst.tests.html b/api/pyobjcryst.tests.html deleted file mode 100644 index 2a486dd..0000000 --- a/api/pyobjcryst.tests.html +++ /dev/null @@ -1,904 +0,0 @@ - - - - - - - - - - tests Package — PyObjCryst 1.0b3-7 documentation - - - - - - - - - - - - - - - - -
      -
      -
      -
      - -
      -

      tests Package¶

      -
      -

      tests Package¶

      -

      Unit tests for pyobjcryst.

      -
      -
      -pyobjcryst.tests.test()¶
      -

      Execute all unit tests for the pyobjcryst package. -Return a unittest TestResult object.

      -
      - -
      -
      -pyobjcryst.tests.testsuite()¶
      -

      Build a unit tests suite for the pyobjcryst package.

      -

      Return a unittest.TestSuite object.

      -
      - -
      -
      -

      pyobjcrysttest Module¶

      -

      Small tests for pyobjcryst.

      -

      To check for memory leaks, run -valgrind –tool=memcheck –leak-check=full /usr/bin/python ./pyobjcrysttest.py

      -
      -
      -pyobjcryst.tests.pyobjcrysttest.getScatterer()¶
      -

      Make a crystal and return scatterer from GetScatt.

      -
      - -
      -
      -pyobjcryst.tests.pyobjcrysttest.makeCrystal(sp, atom)¶
      -
      - -
      -
      -pyobjcryst.tests.pyobjcrysttest.makeScatterer()¶
      -
      - -
      -
      -pyobjcryst.tests.pyobjcrysttest.parTest()¶
      -
      - -
      -
      -pyobjcryst.tests.pyobjcrysttest.test1()¶
      -

      Run some tests.

      -
      - -
      -
      -pyobjcryst.tests.pyobjcrysttest.testCrystalScope()¶
      -

      Test to see if the the crystal survives after it is out of scope.

      -
      - -
      -
      -pyobjcryst.tests.pyobjcrysttest.testMultiAdd()¶
      -

      Test exception for multi-crystal additions.

      -
      - -
      -
      -pyobjcryst.tests.pyobjcrysttest.testRemoveFunctions()¶
      -

      Test the RemoveScatterer and RemoveScatteringPower method.

      -
      - -
      -
      -pyobjcryst.tests.pyobjcrysttest.testScattererScope()¶
      -

      Test when atoms go out of scope before crystal.

      -
      - -
      -
      -

      pyobjcrysttestutils Module¶

      -

      Utilities for tests.

      -
      -
      -pyobjcryst.tests.pyobjcrysttestutils.datafile(filename)¶
      -
      - -
      -
      -pyobjcryst.tests.pyobjcrysttestutils.getScatterer()¶
      -

      Make a crystal and return scatterer from GetScatt.

      -
      - -
      -
      -pyobjcryst.tests.pyobjcrysttestutils.loadcifdata(filename)¶
      -
      - -
      -
      -pyobjcryst.tests.pyobjcrysttestutils.makeC60()¶
      -
      - -
      -
      -pyobjcryst.tests.pyobjcrysttestutils.makeCrystal(sp, atom)¶
      -
      - -
      -
      -pyobjcryst.tests.pyobjcrysttestutils.makeLaMnO3()¶
      -
      - -
      -
      -pyobjcryst.tests.pyobjcrysttestutils.makeMnO6()¶
      -
      - -
      -
      -pyobjcryst.tests.pyobjcrysttestutils.makeScatterer()¶
      -
      - -
      -
      -pyobjcryst.tests.pyobjcrysttestutils.makeScattererAnisotropic()¶
      -
      - -
      -
      -pyobjcryst.tests.pyobjcrysttestutils.toxyz(crystal, filename)¶
      -

      Write a crystal to an xyz file.

      -
      - -
      -
      -

      run Module¶

      -

      Convenience module for executing all unit tests with

      -

      python -m pyobjcryst.tests.run

      -
      -
      -

      testcif Module¶

      -

      Tests for crystal module.

      -
      -
      -class pyobjcryst.tests.testcif.TestCif(methodName='runTest')¶
      -

      Bases: unittest.case.TestCase

      -
      -
      -testBadCif()¶
      -

      Make sure we can read all cif files.

      -
      - -
      -
      -test_Ag_silver_cif()¶
      -

      Check loading of Ag_silver.cif

      -
      - -
      -
      -test_BaTiO3_cif()¶
      -

      Check loading of BaTiO3.cif

      -
      - -
      -
      -test_C_graphite_hex_cif()¶
      -

      Check loading of C_graphite_hex.cif

      -
      - -
      -
      -test_CaF2_fluorite_cif()¶
      -

      Check loading of CaF2_fluorite.cif

      -
      - -
      -
      -test_CaTiO3_cif()¶
      -

      Check loading of CaTiO3.cif and its ADPs.

      -
      - -
      -
      -test_CdSe_cadmoselite_cif()¶
      -

      Check loading of CdSe_cadmoselite.cif

      -
      - -
      -
      -test_CeO2_cif()¶
      -

      Check loading of CeO2.cif

      -
      - -
      -
      -test_NaCl_cif()¶
      -

      Check loading of NaCl.cif

      -
      - -
      -
      -test_Ni_cif()¶
      -

      Check loading of Ni.cif

      -
      - -
      -
      -test_PbS_galena_cif()¶
      -

      Check loading of PbS_galena.cif

      -
      - -
      -
      -test_PbTe_cif()¶
      -

      Check loading of PbTe.cif

      -
      - -
      -
      -test_Si_cif()¶
      -

      Check loading of Si.cif

      -
      - -
      -
      -test_Si_setting2_cif()¶
      -

      Check loading of Si_setting2.cif

      -
      - -
      -
      -test_SrTiO3_tausonite_cif()¶
      -

      Check loading of SrTiO3_tausonite.cif

      -
      - -
      -
      -test_TiO2_anatase_cif()¶
      -

      Check loading of TiO2_anatase.cif

      -
      - -
      -
      -test_TiO2_rutile_cif()¶
      -

      Check loading of TiO2_rutile.cif and its ADP data

      -
      - -
      -
      -test_ZnS_sphalerite_cif()¶
      -

      Check loading of ZnS_sphalerite.cif

      -
      - -
      -
      -test_ZnS_wurtzite_cif()¶
      -

      Check loading of ZnS_wurtzite.cif

      -
      - -
      -
      -test_Zn_zinc_cif()¶
      -

      Check loading of Zn_zinc.cif

      -
      - -
      -
      -test_caffeine_cif()¶
      -

      Check loading of caffeine.cif and the data inside.

      -
      - -
      -
      -test_menthol_cif()¶
      -

      Check loading of menthol.cif

      -
      - -
      -
      -test_paracetamol_cif()¶
      -

      Check loading of paracetamol.cif

      -
      - -
      - -
      -
      -

      testclocks Module¶

      -

      Tests for crystal module.

      -
      -
      -class pyobjcryst.tests.testclocks.TestClocks(methodName='runTest')¶
      -

      Bases: unittest.case.TestCase

      -
      -
      -testClockIncrement()¶
      -

      Make sure that clocks increment properly.

      -
      - -
      - -
      -
      -

      testconverters Module¶

      -

      Test the converters.

      -

      This verifies results from tests built into the _registerconverters module.

      -
      -
      -class pyobjcryst.tests.testconverters.TestConverters(methodName='runTest')¶
      -

      Bases: unittest.case.TestCase

      -
      -
      -testMatrix()¶
      -
      - -
      -
      -testVector()¶
      -
      - -
      - -
      -
      -

      testcrystal Module¶

      -

      Tests for crystal module.

      -
      -
      -class pyobjcryst.tests.testcrystal.TestCrystal(methodName='runTest')¶
      -

      Bases: unittest.case.TestCase

      -
      -
      -testCrystalScope()¶
      -

      Test to see if the the crystal survives after it is out of scope.

      -
      - -
      -
      -testDummyAtom()¶
      -

      Test dummy atoms.

      -
      - -
      -
      -testEmbedding()¶
      -

      Test integrity of mutually-embedded objects.

      -
      - -
      -
      -testGetScatterer()¶
      -

      Test GetScatterer.

      -
      - -
      -
      -testGetScatteringComponentList()¶
      -

      Test the RemoveScatterer and RemoveScatteringPower method.

      -
      - -
      -
      -testNullData()¶
      -

      Make sure we get an error when trying to add or remove Null.

      -
      - -
      -
      -testRemoveFunctions()¶
      -

      Test the RemoveScatterer and RemoveScatteringPower method.

      -
      - -
      -
      -testScattererB()¶
      -

      Test Biso and Bij of scatterer.

      -
      - -
      -
      -testScattererScope()¶
      -

      Test when atoms go out of scope before crystal.

      -
      - -
      - -
      -
      -

      testmolecule Module¶

      -

      Tests for molecule module.

      -
      -
      -class pyobjcryst.tests.testmolecule.TestMolAtom(methodName='runTest')¶
      -

      Bases: unittest.case.TestCase

      -
      -
      -setUp()¶
      -
      - -
      -
      -tearDown()¶
      -
      - -
      -
      -testAccessors()¶
      -
      - -
      - -
      -
      -class pyobjcryst.tests.testmolecule.TestMolBond(methodName='runTest')¶
      -

      Bases: unittest.case.TestCase

      -
      -
      -setUp()¶
      -
      - -
      -
      -tearDown()¶
      -
      - -
      -
      -testAccessors()¶
      -
      - -
      - -
      -
      -class pyobjcryst.tests.testmolecule.TestMolBondAngle(methodName='runTest')¶
      -

      Bases: unittest.case.TestCase

      -
      -
      -setUp()¶
      -
      - -
      -
      -tearDown()¶
      -
      - -
      -
      -testAccessors()¶
      -
      - -
      - -
      -
      -class pyobjcryst.tests.testmolecule.TestMolDihedralAngle(methodName='runTest')¶
      -

      Bases: unittest.case.TestCase

      -
      -
      -setUp()¶
      -
      - -
      -
      -tearDown()¶
      -
      - -
      -
      -testAccessors()¶
      -
      - -
      - -
      -
      -class pyobjcryst.tests.testmolecule.TestMolecule(methodName='runTest')¶
      -

      Bases: unittest.case.TestCase

      -
      -
      -setUp()¶
      -
      - -
      -
      -tearDown()¶
      -
      - -
      -
      -testAddPar()¶
      -

      See if we crash if we add a parameter and delete the molecule.

      -
      - -
      -
      -testAtoms()¶
      -

      Make sure the atoms are there.

      -

      This tests AddAtom by association. -This tests GetAtom.

      -
      - -
      -
      -testBondAngles()¶
      -

      Test the BondAngle accessors.

      -
      - -
      -
      -testBonds()¶
      -

      Test the Bond methods.

      -
      - -
      -
      -testContainment()¶
      -

      Make sure we can still use the molecule if the crystal is out of -scope.

      -
      - -
      -
      -testDihedralAngles()¶
      -

      Test the FindDihedralAngle method.

      -
      - -
      -
      -testManipulation()¶
      -

      Test moving the atoms.

      -
      - -
      -
      -testProperties()¶
      -

      Make sure we can access the python-only properties.

      -
      - -
      -
      -testRigidGroup()¶
      -

      Test adding and manipulating a rigid group.

      -
      - -
      - -
      -
      -class pyobjcryst.tests.testmolecule.TestStretchModeBondAngle(methodName='runTest')¶
      -

      Bases: unittest.case.TestCase

      -
      -
      -setUp()¶
      -
      - -
      -
      -tearDown()¶
      -
      - -
      -
      -testStretchModeBondAngle()¶
      -

      Test the StretchModeBondLength class.

      -
      - -
      - -
      -
      -class pyobjcryst.tests.testmolecule.TestStretchModeBondLength(methodName='runTest')¶
      -

      Bases: unittest.case.TestCase

      -
      -
      -setUp()¶
      -
      - -
      -
      -tearDown()¶
      -
      - -
      -
      -testStretchModeBondLength()¶
      -

      Test the StretchModeBondLength class.

      -
      - -
      - -
      -
      -class pyobjcryst.tests.testmolecule.TestStretchModeTorsion(methodName='runTest')¶
      -

      Bases: unittest.case.TestCase

      -
      -
      -setUp()¶
      -
      - -
      -
      -tearDown()¶
      -
      - -
      -
      -testDummy()¶
      -

      Test adding a dummy atom.

      -
      - -
      -
      -testStretchModeTorsion()¶
      -

      Test the StretchModeBondLength class.

      -
      - -
      - -
      -
      -

      testrefinableobj Module¶

      -

      Tests for refinableobj module.

      -
      -
      -class pyobjcryst.tests.testrefinableobj.TestRefinableObj(methodName='runTest')¶
      -

      Bases: unittest.case.TestCase

      -
      -
      -setUp()¶
      -

      Make a RefinableObj and add some RefinablePars.

      -
      - -
      -
      -tearDown()¶
      -

      Clean up those pesky xml files.

      -

      ObjCryst dumps save state into xml files when an exception is thrown. -Clean those up.

      -
      - -
      -
      -testAddParRefinableObj()¶
      -

      Test adding another object.

      -
      - -
      -
      -testAddParTwice()¶
      -

      Try to add the same parameter twice.

      -

      We could stop this in the bindings, but since RefinableObj doesn’t -delete its parameters in the destructor, it shouldn’t lead to trouble.

      -
      - -
      -
      -testFixUnFix()¶
      -

      Test FixAllPar.

      -
      - -
      -
      -testGetPar()¶
      -

      Test GetPar.

      -
      - -
      -
      -testLimits()¶
      -

      Test the limit-setting functions.

      -
      - -
      -
      -testNames()¶
      -

      Test the naming methods.

      -
      - -
      -
      -testOptimStep()¶
      -

      Test SetGlobalOptimStep.

      -
      - -
      -
      -testParmSets()¶
      -

      Test creation of parameter sets.

      -
      - -
      -
      -testUsedUnUsed()¶
      -

      Test FixAllPar.

      -
      - -
      - -
      -
      -class pyobjcryst.tests.testrefinableobj.TestRefinableObjClock(methodName='runTest')¶
      -

      Bases: unittest.case.TestCase

      -
      -
      -testRelations()¶
      -

      Test clicking!

      -

      Chances are that someone will someday read this code for an example on -how to use clocks. If not, then I’ve wasted my time writing this. -Anyway, clocks are more complex then they appear. This is because -ObjCryst++ has an internal clock that gets incremented whenever any -clock is Clicked. So, one cannot trust that a clock will increment by -only one value when it is clicked. Furthermore, clocks only alert their -parents to a change. So, it is possible to decrease the value of a -parent clock with SetEqual below the values of its children clocks. -Callling Click on the parent or child will restore the proper parent > -child relationship.

      -
      - -
      -
      -testRemoveChild()¶
      -

      Test the RemoveChild method.

      -
      - -
      - -
      -
      -class pyobjcryst.tests.testrefinableobj.TestRefinablePar(methodName='runTest')¶
      -

      Bases: unittest.case.TestCase

      -
      -
      -setUp()¶
      -
      - -
      -
      -testGetType()¶
      -

      See if we can get the proper RefParType from a RefinablePar.

      -
      - -
      -
      -testToFromPython()¶
      -

      See if refinable parameters can be created from within python and -within c++.

      -
      - -
      - -
      -
      -class pyobjcryst.tests.testrefinableobj.TestRestraint(methodName='runTest')¶
      -

      Bases: unittest.case.TestCase

      -
      -
      -testEquality()¶
      -

      See if we get back what we put in.

      -
      - -
      - -
      -
      -

      testutils Module¶

      -

      Tests for crystal module.

      -
      -
      -class pyobjcryst.tests.testutils.TestPutAtomsInMolecule(methodName='runTest')¶
      -

      Bases: unittest.case.TestCase

      -
      - -
      -
      - - -
      -
      -
      -
      -
      -

      Table Of Contents

      - - -

      Previous topic

      -

      pyobjcryst Package

      -

      This Page

      - - - -
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      - - - - \ No newline at end of file diff --git a/genindex-C.html b/genindex-C.html index f61e35f..7aae35c 100644 --- a/genindex-C.html +++ b/genindex-C.html @@ -10,7 +10,7 @@ - Index — PyObjCryst 1.0b3-7 documentation + Index — PyObjCryst 1.0b3-15 documentation @@ -18,7 +18,7 @@ - + @@ -69,14 +69,9 @@

      Index – C

      Index

      C - | D | E - | G - | L | M | P - | S - | T | W

      @@ -109,7 +104,7 @@

      Navigation

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