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added an option to draw legend in free energy profile graphs
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‎doc/metadynminer/index.html

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<head>
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<title>metadynminer API documentation</title>
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<meta name="description" content="Metadynminer is a package designed to help you analyse output HILLS files from PLUMED metadynamics simulations …" />
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<style media="print">@media print{#sidebar h1{page-break-before:always}.source{display:none}}@media print{*{background:transparent !important;color:#000 !important;box-shadow:none !important;text-shadow:none !important}a[href]:after{content:" (" attr(href) ")";font-size:90%}a[href][title]:after{content:none}abbr[title]:after{content:" (" attr(title) ")"}.ir a:after,a[href^="javascript:"]:after,a[href^="#"]:after{content:""}pre,blockquote{border:1px solid #999;page-break-inside:avoid}thead{display:table-header-group}tr,img{page-break-inside:avoid}img{max-width:100% !important}@page{margin:0.5cm}p,h2,h3{orphans:3;widows:3}h1,h2,h3,h4,h5,h6{page-break-after:avoid}}</style>
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<script>window.addEventListener('DOMContentLoaded', () => hljs.initHighlighting())</script>
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</head>
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<body>
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<main>
@@ -116,7 +118,7 @@ <h1 class="title">Package <code>metadynminer</code></h1>
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&#34;&#34;&#34;
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name = &#34;metadynminer&#34;
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__version__ = &#34;0.4.0&#34;
121+
__version__ = &#34;0.5.0&#34;
120122
__author__ = &#39;Jan Beránek&#39;
121123

122124
__pdoc__ = {}
@@ -2339,7 +2341,7 @@ <h1 class="title">Package <code>metadynminer</code></h1>
23392341
plt.clabel(cont, levels = np.arange(0, (vmax + 0.01), contours_spacing))
23402342

23412343
if self.minima.shape[0] == 1:
2342-
background = cmap((float(self.minima.iloc[1])-vmin)/(vmax-vmin))
2344+
background = cmap((float(self.minima.iloc[0,1])-vmin)/(vmax-vmin))
23432345
luma = background[0]*0.2126+background[1]*0.7152+background[3]*0.0722
23442346
if luma &gt; 0.6 and not color_set:
23452347
color = &#34;black&#34;
@@ -2746,7 +2748,7 @@ <h1 class="title">Package <code>metadynminer</code></h1>
27462748
else:
27472749
print(&#34;Fes object doesn&#39;t have supported number of CVs.&#34;)
27482750

2749-
def plot(self, png_name=None, image_size=[10,7], xlabel=None, ylabel=None, label_size=12, cmap=&#34;jet&#34;):
2751+
def plot(self, png_name=None, image_size=[10,7], xlabel=None, ylabel=None, label_size=12, cmap=&#34;jet&#34;, legend=True):
27502752
&#34;&#34;&#34;
27512753
Visualization function for free energy profiles.
27522754

@@ -2769,6 +2771,8 @@ <h1 class="title">Package <code>metadynminer</code></h1>
27692771
* label_size (default=12) = size of labels
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27712773
* cmap (default=&#34;jet&#34;) = matplotlib colormap used for coloring the line of the minima
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2775+
* legend (default=True) = whether there should be a matplotlib&#39;s legend in the graph
27722776
&#34;&#34;&#34;
27732777

27742778
plt.figure(figsize=(image_size[0],image_size[1]))
@@ -2789,6 +2793,8 @@ <h1 class="title">Package <code>metadynminer</code></h1>
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plt.ylabel(&#39;free energy difference (kJ/mol)&#39;, size=label_size)
27902794
else:
27912795
plt.ylabel(ylabel, size=label_size)
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if legend:
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plt.legend(self.minima.iloc[:,0], loc=&#34;lower right&#34;)
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if png_name != None:
27932799
plt.savefig(png_name)</code></pre>
27942800
</details>
@@ -3083,7 +3089,7 @@ <h2 class="section-title" id="header-classes">Classes</h2>
30833089
else:
30843090
print(&#34;Fes object doesn&#39;t have supported number of CVs.&#34;)
30853091

3086-
def plot(self, png_name=None, image_size=[10,7], xlabel=None, ylabel=None, label_size=12, cmap=&#34;jet&#34;):
3092+
def plot(self, png_name=None, image_size=[10,7], xlabel=None, ylabel=None, label_size=12, cmap=&#34;jet&#34;, legend=True):
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&#34;&#34;&#34;
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Visualization function for free energy profiles.
30893095

@@ -3106,6 +3112,8 @@ <h2 class="section-title" id="header-classes">Classes</h2>
31063112
* label_size (default=12) = size of labels
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31083114
* cmap (default=&#34;jet&#34;) = matplotlib colormap used for coloring the line of the minima
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3116+
* legend (default=True) = whether there should be a matplotlib&#39;s legend in the graph
31093117
&#34;&#34;&#34;
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31113119
plt.figure(figsize=(image_size[0],image_size[1]))
@@ -3126,6 +3134,8 @@ <h2 class="section-title" id="header-classes">Classes</h2>
31263134
plt.ylabel(&#39;free energy difference (kJ/mol)&#39;, size=label_size)
31273135
else:
31283136
plt.ylabel(ylabel, size=label_size)
3137+
if legend:
3138+
plt.legend(self.minima.iloc[:,0], loc=&#34;lower right&#34;)
31293139
if png_name != None:
31303140
plt.savefig(png_name)</code></pre>
31313141
</details>
@@ -3344,7 +3354,7 @@ <h3>Methods</h3>
33443354
</details>
33453355
</dd>
33463356
<dt id="metadynminer.FEProfile.plot"><code class="name flex">
3347-
<span>def <span class="ident">plot</span></span>(<span>self, png_name=None, image_size=[10, 7], xlabel=None, ylabel=None, label_size=12, cmap='jet')</span>
3357+
<span>def <span class="ident">plot</span></span>(<span>self, png_name=None, image_size=[10, 7], xlabel=None, ylabel=None, label_size=12, cmap='jet', legend=True)</span>
33483358
</code></dt>
33493359
<dd>
33503360
<div class="desc"><p>Visualization function for free energy profiles. </p>
@@ -3370,12 +3380,15 @@ <h2 id="parameters">Parameters</h2>
33703380
<li>
33713381
<p>cmap (default="jet") = matplotlib colormap used for coloring the line of the minima</p>
33723382
</li>
3383+
<li>
3384+
<p>legend (default=True) = whether there should be a matplotlib's legend in the graph</p>
3385+
</li>
33733386
</ul></div>
33743387
<details class="source">
33753388
<summary>
33763389
<span>Expand source code</span>
33773390
</summary>
3378-
<pre><code class="python">def plot(self, png_name=None, image_size=[10,7], xlabel=None, ylabel=None, label_size=12, cmap=&#34;jet&#34;):
3391+
<pre><code class="python">def plot(self, png_name=None, image_size=[10,7], xlabel=None, ylabel=None, label_size=12, cmap=&#34;jet&#34;, legend=True):
33793392
&#34;&#34;&#34;
33803393
Visualization function for free energy profiles.
33813394

@@ -3398,6 +3411,8 @@ <h2 id="parameters">Parameters</h2>
33983411
* label_size (default=12) = size of labels
33993412

34003413
* cmap (default=&#34;jet&#34;) = matplotlib colormap used for coloring the line of the minima
3414+
3415+
* legend (default=True) = whether there should be a matplotlib&#39;s legend in the graph
34013416
&#34;&#34;&#34;
34023417

34033418
plt.figure(figsize=(image_size[0],image_size[1]))
@@ -3418,6 +3433,8 @@ <h2 id="parameters">Parameters</h2>
34183433
plt.ylabel(&#39;free energy difference (kJ/mol)&#39;, size=label_size)
34193434
else:
34203435
plt.ylabel(ylabel, size=label_size)
3436+
if legend:
3437+
plt.legend(self.minima.iloc[:,0], loc=&#34;lower right&#34;)
34213438
if png_name != None:
34223439
plt.savefig(png_name)</code></pre>
34233440
</details>
@@ -6578,7 +6595,7 @@ <h3>Methods</h3>
65786595
plt.clabel(cont, levels = np.arange(0, (vmax + 0.01), contours_spacing))
65796596

65806597
if self.minima.shape[0] == 1:
6581-
background = cmap((float(self.minima.iloc[1])-vmin)/(vmax-vmin))
6598+
background = cmap((float(self.minima.iloc[0,1])-vmin)/(vmax-vmin))
65826599
luma = background[0]*0.2126+background[1]*0.7152+background[3]*0.0722
65836600
if luma &gt; 0.6 and not color_set:
65846601
color = &#34;black&#34;
@@ -7426,7 +7443,7 @@ <h3>Methods</h3>
74267443
plt.clabel(cont, levels = np.arange(0, (vmax + 0.01), contours_spacing))
74277444

74287445
if self.minima.shape[0] == 1:
7429-
background = cmap((float(self.minima.iloc[1])-vmin)/(vmax-vmin))
7446+
background = cmap((float(self.minima.iloc[0,1])-vmin)/(vmax-vmin))
74307447
luma = background[0]*0.2126+background[1]*0.7152+background[3]*0.0722
74317448
if luma &gt; 0.6 and not color_set:
74327449
color = &#34;black&#34;
@@ -7544,9 +7561,7 @@ <h4><code><a title="metadynminer.Minima" href="#metadynminer.Minima">Minima</a><
75447561
</nav>
75457562
</main>
75467563
<footer id="footer">
7547-
<p>Generated by <a href="https://pdoc3.github.io/pdoc"><cite>pdoc</cite> 0.8.1</a>.</p>
7564+
<p>Generated by <a href="https://pdoc3.github.io/pdoc" title="pdoc: Python API documentation generator"><cite>pdoc</cite> 0.10.0</a>.</p>
75487565
</footer>
7549-
<script src="https://cdnjs.cloudflare.com/ajax/libs/highlight.js/9.12.0/highlight.min.js"></script>
7550-
<script>hljs.initHighlightingOnLoad()</script>
75517566
</body>
75527567
</html>

‎metadynminer/__init__.py

Lines changed: 6 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -56,7 +56,7 @@
5656
"""
5757

5858
name = "metadynminer"
59-
__version__ = "0.4.2"
59+
__version__ = "0.5.0"
6060
__author__ = 'Jan Beránek'
6161

6262
__pdoc__ = {}
@@ -2686,7 +2686,7 @@ def makefeprofile(self, hills):
26862686
else:
26872687
print("Fes object doesn't have supported number of CVs.")
26882688

2689-
def plot(self, png_name=None, image_size=[10,7], xlabel=None, ylabel=None, label_size=12, cmap="jet"):
2689+
def plot(self, png_name=None, image_size=[10,7], xlabel=None, ylabel=None, label_size=12, cmap="jet", legend=True):
26902690
"""
26912691
Visualization function for free energy profiles.
26922692
@@ -2709,6 +2709,8 @@ def plot(self, png_name=None, image_size=[10,7], xlabel=None, ylabel=None, label
27092709
* label_size (default=12) = size of labels
27102710
27112711
* cmap (default="jet") = matplotlib colormap used for coloring the line of the minima
2712+
2713+
* legend (default=True) = whether there should be a matplotlib's legend in the graph
27122714
"""
27132715

27142716
plt.figure(figsize=(image_size[0],image_size[1]))
@@ -2729,5 +2731,7 @@ def plot(self, png_name=None, image_size=[10,7], xlabel=None, ylabel=None, label
27292731
plt.ylabel('free energy difference (kJ/mol)', size=label_size)
27302732
else:
27312733
plt.ylabel(ylabel, size=label_size)
2734+
if legend:
2735+
plt.legend(self.minima.iloc[:,0], loc="lower right")
27322736
if png_name != None:
27332737
plt.savefig(png_name)

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