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showmol(obj,height=500,width=500)

"""Shows the Py3DMOL object.

Parameters
----------
obj: Py3DMOL object
    Already existing Py3DMOL object, which can be created using the makeobj function.
height: Integer, default 500
    Is the height of viwer window.
width: Integer, default 500
    Is the width of wiewer window.

Returns
-------
None.
"""

speck_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.
"""

makeobj(xyz,molformat='mol',style='stick',background='white')

"""
makeobj function accepts a molecule structure in a given format and returns a Py3DMOL molecule object.
Accepted formats are 'mol', 'sdf', 'pdb', 'pqr', 'xyz'.

Parameters
----------
xyz: String
    Is the molecule object
molformat: String, default 'mol'    
    Is the format of the molecule. Accepted formats are 'mol', 'sdf', 'pdb', 'pqr', 'xyz'.
style: String, default 'stick'
    Is the style of the molecule. Can be 'stick', 'sphere', 'cross', 'surface', 'ribbon', 'cartoon'
background: String, default 'white'
    Is the background color of the molecule

Returns
-------
obj: Py3DMOL object
"""

render_pdb(id='7T59')

"""
render_pdb function accepts a PDB ID and returns a Py3DMOL object.

Parameters
----------
id: String, default '7T59'
    Is the PDB ID of the molecule.

Returns
-------
obj: Py3DMOL object
"""

render_pdb_resn(viewer,resn_lst)

"""
render_pdb_resn function accepts a Py3DMOL object and adds a list of PDB resn labels to it.

Parameters
----------
viewer: Py3DMOL object
resn_lst: List
    Is the list of PDB resn of the molecules. Example: ['ALA','ARG',,'LYS','THR','TRP','TYR','VAL']

Returns
-------
obj: Py3DMOL object
"""

render_pdb_resi(viewer,resi_lst)

"""
render_pdb_resi function accepts a Py3DMOL object and adds a list of PDB resi labels to it.

Parameters
----------
viewer: Py3DMOL object
resi_lst: List
    Is the list of PDB resi of the molecules. Example: ['42-44','48','49']

Returns
-------
obj: Py3DMOL object
"""

obj_upload(uploaded_file)

"""
obj_upload function accepts a file uploaded with streamlit file_uploader function and returns a Py3DMOL object.
Accepted formats are 'mol', 'sdf', 'pdb', 'pqr', 'xyz'.
In Streamlit a file can be uploaded with: 
    
    uploaded_file = st.sidebar.file_uploader("Upload PDB file")

Parameters
----------
uploaded_file: File
    Is the PDB, xyz or any supported file of the molecule

Returns
-------
obj: Py3DMOL object
"""

add_model(obj,xyz,molformat='mol',model_style='stick')

"""
Adds a model to an existing Py3DMOL object.

Parameters
----------
obj: Py3DMOL object
    Already existing Py3DMOL object.
xyz: String
    Is the model to be added.
molformat: String, default 'mol'    
    Is the format of the added model
model_style: String, default 'stick'
    Is the style of the added model. Can be 'stick', 'sphere', 'cross', 'surface', 'ribbon', 'cartoon'

Returns
-------
None.
"""

add_hover(obj,backgroundColor='white',fontColor='black')

"""
Adds a hover function to the Py3DMOL object to show the atom name when the mouse hovers over an atom.

Parameters
----------
obj: Py3DMOL object
    Already existing Py3DMOL object, which can be created using the makeobj function.
backgroundColor: String, default 'white'
    Is the background color of the hover text
fontColor: String, default 'black'
    Is the color of the text

Returns
-------
None.
"""

add_box(obj,bxc=[0,0,0],bxd=[10,10,10],boxColor='blue',boxOpacity=0.5)

"""Adds a box to an existing Py3DMOL object.

Parameters
----------
obj: Py3DMOL object 
    Already existing Py3DMOL object, which can be created using the makeobj function.
bxc: List of Integers of len 3, default [0,0,0]
    Are the x,y,z coordinates of the center of the box in Angstroms
bxd: List of Integers of len 3, default [10,10,10]
    Are the x,y,z dimensions of the box in Angstroms
boxColor: String, default 'blue'
    Is the color of the box
boxOpacity: String, default 0.5
    Is the opacity of the box

Returns
-------
None.
"""

add_sphere(obj,spcenter=[0,0,0],radius=10,spColor='blue')

"""Adds a sphere to an existing Py3DMOL object.

Parameters
----------
obj: Py3DMOL object 
    Already existing Py3DMOL object, which can be created using the makeobj function.
spcenter: List of Integers of len 3, default [0,0,0].
    Are the x,y,z coordinates of the center of the sphere in Angstroms
radius: integer, default 10
    Is the radius of the sphere in Angstroms.
spColor: String, default 'blue'
    Is the color of the sphere.

Returns
-------
None.
"""

add_cylinder(obj,start=[0,0,0],end=[0,0,1],cylradius=1,cylColor='blue')

"""Adds a cylinder to an existing Py3DMOL object.

Parameters
----------
obj: Py3DMOL object
    Already existing Py3DMOL object, which can be created using the makeobj function.
start: List of Integers of len 3, default [0,0,0]
    Are the x,y,z coordinates of the start of the cylinder in Angstroms.
end: List of Integers of len 3, default [0,0,1]
    Are the x,y,z coordinates of the end of the cylinder in Angstroms.
cylradius: integer, default 1
    Is the radius of the cylinder in Angstroms.
cylColor: String, default 'blue'
    Is the color of the cylinder.
dashed: Boolean, default True
    True for a cylinder dashed. False for a solid cylinder.

Returns
-------
None.
"""