Merge pull request #2 from avrabyt/component-develop

🚀 Specklit - Component - st_speckmol

.gitignore

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+# production
+
+dist
+# misc
+.DS_Store
+
+*.egg-info
+__pycache__

LICENSE

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+MIT License
+
+Copyright (c) 2022 Avra
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

MANIFEST.in

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+

README.md

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 # Specklit
 Speck figures to Streamlit Web App
 
+
+## Installation
+`pip install st-speckmol==0.0.3`
+
+## Example
+
+```
+import streamlit as st
+import glob
+from st_speckmol import spec_plot
+
+# Example files path
+ex_files = glob.glob("examples/*.xyz")
+with st.sidebar:
+    example_xyz = st.selectbox("Select a molecule",ex_files)
+    f = open(example_xyz,"r")
+    example_xyz = f.read()
+
+res = spec_plot(example_xyz)
+
+```
 [![Streamlit App](https://static.streamlit.io/badges/streamlit_badge_black_white.svg)](https://share.streamlit.io/avrabyt/specklit/main/app.py)
 
 ![Speclit demo](https://github.com/avrabyt/Specklit/blob/main/SpeckLit_demo.gif)

app-main.py

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+import streamlit as st
+import glob
+from st_speckmol import spec_plot
+
+# Example files path
+ex_files = glob.glob("examples/*.xyz")
+with st.sidebar:
+    example_xyz = st.selectbox("Select a molecule",ex_files)
+    f = open(example_xyz,"r")
+    example_xyz = f.read()
+
+res = spec_plot(example_xyz)

setup.py

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+import setuptools
+
+setuptools.setup(
+    name="st_speckmol",
+    version="0.0.3",
+    author="Avratanu Biswas",
+    author_email="[email protected]",
+    description="Streamlit component for for Speck molecule visualization.",
+    long_description="Streamlit component for visualizing SPECK molecules - https://github.com/wwwtyro/speck",
+    long_description_content_type="text/plain",
+    url="https://github.com/avrabyt/Specklit",
+    packages=setuptools.find_packages(),
+    include_package_data=True,
+    classifiers=[],
+    python_requires=">=3.6",
+    install_requires=["streamlit >= 0.63", "ipyspeck==0.6.1", "ipywidgets==7.6.3"],
+)

speckmol/funx.py

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+import streamlit.components.v1 as components
+import ipywidgets as widgets
+from ipywidgets import embed
+import ipyspeck
+
+def spec_plot(_xyz, wbox_height="700px", 
+            wbox_width="800px",
+            component_h = 700, 
+            component_w = 800, 
+            scroll = False):
+
+    """ Plots the speckmol molecule using the ipyspeck library and returns 
+        the <class 'ipyspeck.speck.Speck'>.
+    
+    Parameters
+    ----------
+    _xyz : str
+        The xyz string of the molecule.
+    wbox_height : str
+        The height of the widget box.
+    wbox_width : str
+        The width of the widget box.
+    component_h : int
+        The height of the streamlit html component.
+    component_w : int
+        The width of the streamlit html component.
+    scroll : bool
+        If True, the streamlit component will scroll.  
+
+    Returns
+    -------
+    spec_xyz : <class 'ipyspeck.speck.Speck'>
+        The speckmol molecule. spec_xyz.keys() returns the keys of the
+        molecule. For example - spec_xyz.keys() returns ['atomScale',  
+        'bondScale', 'atomShade', 'bondThreshold', 'bondColor', 'atomColor',
+        'outline', 'bonds', 'atomScale', 'atomColor', 'atomScale', 'atomScale]
+        These keys are useful for modifying the molecule.
+
+    """        
+    spec_xyz = ipyspeck.speck.Speck(data=_xyz)
+    widg = widgets.Box([spec_xyz], layout=widgets.Layout(height=wbox_height,width=wbox_width))
+    sc = embed.embed_snippet(widg)
+    html = embed.html_template.format(title="", snippet=sc)
+    components.html(html,height = component_h, width = component_w,scrolling=scroll)
+    return spec_xyz

st_speckmol/__init__.py

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+import streamlit.components.v1 as components
+import ipywidgets as widgets
+from ipywidgets import embed
+import ipyspeck
+
+def spec_plot(_xyz, wbox_height="700px", 
+            wbox_width="800px",
+            component_h = 700, 
+            component_w = 800, 
+            scroll = False):
+
+    """ Plots the speckmol molecule using the ipyspeck library and returns 
+        the <class 'ipyspeck.speck.Speck'>.
+    
+    Parameters
+    ----------
+    _xyz : str
+        The xyz string of the molecule.
+    wbox_height : str
+        The height of the widget box.
+    wbox_width : str
+        The width of the widget box.
+    component_h : int
+        The height of the streamlit html component.
+    component_w : int
+        The width of the streamlit html component.
+    scroll : bool
+        If True, the streamlit component will scroll.  
+
+    Returns
+    -------
+    spec_xyz : <class 'ipyspeck.speck.Speck'>
+        The speckmol molecule. spec_xyz.keys() returns the keys of the
+        molecule. For example - spec_xyz.keys() returns ['atomScale',  
+        'bondScale', 'atomShade', 'bondThreshold', 'bondColor', 'atomColor',
+        'outline', 'bonds', 'atomScale', 'atomColor', 'atomScale', 'atomScale]
+        These keys are useful for modifying the molecule.
+
+    """        
+    # Read the xyz file
+    spec_xyz = ipyspeck.speck.Speck(data = _xyz)
+    # Create the widget box
+    widg = widgets.Box([spec_xyz], layout=widgets.Layout(height=wbox_height,width=wbox_width))
+    # Embed the widget box in the streamlit html component
+    sc = embed.embed_snippet(widg)
+    html = embed.html_template.format(title="", snippet=sc)
+    components.html(html,height = component_h, width = component_w,scrolling=scroll)
+    return spec_xyz