PyMolinfo

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PyMolInfo (previously molinfo) is a Python package designed for advanced molecular analysis by converting molecular structures into graph representations. This package enables researchers and chemists to load various molecular file formats, transform them into graphs, and extract valuable information through graph-based methods.

• File Format Support: Load molecular data from multiple file formats, including SDF and JSON (soon).
• Graph Conversion: Transform molecular structures into graph representations for detailed analysis.
• Functional Group Identification: Detect and analyze functional groups within the molecular graph.
• Distance Measurement: Compute distances between atoms and bonds in the molecular graph.
• Bond Angle Calculation: Measure angles between bonds using graph-based methods.

To use PyMolinfo, simply install the package and import it into your Python script. Refer to the example code snippets for a quick start.

Test this package by launching our example notebooks on Binder:

• Load a sdf file: Launch Binder
• Visualize a compound: Launch Binder
• Check and count functional groups: Launch Binder
• Create custom functional groups: Launch Binder

You can use the following code to run PyMolinfo in Google Colab:

• Version 1.6.0: Open In Colab
• Version < 1.6.0: Open In Colab

Install molinfo with pip

 pip install PyMolinfo

For detailed documentation, please visit molinfo.readthedocs.io/en/latest/.

Import package as:

import pyMolinfo as mi
# check version
print(mi.__version__)

• Create a compound

# sdf file
comp1 = mi.compound(sdf_file)
# sdf string
comp1 = mi.compound(sdf_string)
# compound by cid
comp1 = mi.compound_by_cid(241)
# compound by inchi
comp1 = mi.compound_by_inchi('InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H')
# log
# print(comp1)
# pp(comp1.atom_bond_block)
# print("-"*100)
# pp(comp1.atom_bond_block_1d)
# print("-"*100)
# pp(comp1.atom_xyz)
# NOTE: functional groups
print(comp1.functional_groups)

• Create a graph

➡️ Create a graph from a compound:

# NOTE: create graph
graph_comp1 = comp1.create_graph()
print(graph_comp1)

➡️ Create a graph from a sdf file:

# sdf file
sdf_file_name_1 = 'test\Structure2D_COMPOUND_CID_261.sdf'
sdf_file = os.path.join(os.getcwd(), sdf_file_name_1)
# create graph
res = mi.create_graph(sdf_file)
print(type(res))
print(res)

• Display a graph:

# plot_mode: Literal['plotly', 'matplotlib'] = 'plotly
# view graph
mi.view_graph(graph_1)

• Display a compound:

# visualize compound by sdf file
mi.g3d(sdf_file)

🖼️ 1-Naphthaleneacetic acid

1-Naphthaleneacetic-acid

# visualize compound by sdf file
mi.g3d(sdf_file, display_bond_length=True)

🖼️ 1-Naphthaleneacetic acid

1-Naphthaleneacetic-acid

• Check the availability of functional groups:

# check functional groups
res, comp1 = mi.check_functional_group(sdf_file, res_format='dataframe')
print(res)

• Calculate angle/distance between atoms

# distance matrix
res_distance = comp1.distance_matrix(dataframe=True)
print(res_distance)
# distance between two atoms
distance = comp1.distance_atoms(['O1', 'C2'])
print(distance)
# angle between atoms
angle = comp1.angle_atoms(['O1', 'C2', 'H3'])
print(angle)
# dihedral angle
dihedral = comp1.d_angle_atoms(['H6', 'O1', 'C2', 'H3'])
print(dihedral)

To create custom functional groups, you need to define the bonds between atoms using the following format:

[atom1-element][atom1-number][bond-type][atom2-element][atom2-number]

Here are the formats for different bond types:

• Single Bond: Represented as C1-C2 where C1 and C2 are the atoms connected by a single bond.
• Double Bond: Represented as C1=C2 where C1 and C2 are the atoms connected by a double bond.
• Triple Bond: Represented as C1#C2 where C1 and C2 are the atoms connected by a triple bond.

1. Cyanide Group: A cyanide group can be represented as N1#C2.

custom_functional_group = [
 {'cyanide': ["N1#C2"]},
]

2. Custom Functional Group: A custom functional group with a single and a double bond can be represented as N1-C2 and C2=O3.

custom_functional_group = [
 {'custom_fg': ["N1-C2", "C2=O3"]},
]

3. Multiple Functional Groups: You can define multiple functional groups in a list.

custom_functional_group = [
 {'N#C': ["N1#C2"]},
 {'custom_fg': ["N1-C2", "C2-H3"]},
 {'NC=O': ["N1-C2", "C2=O3"]},
]

Once you have defined your custom functional groups, you can create and visualize them as follows:

# create custom graph
custom_g = mi.create_custom_functional_groups(custom_functional_group)
# visualize custom graph
# custom_g.d("cyanide")
# find custom functional groups in a compound
res = mi.check_functional_group(
 sdf_file, functional_groups=[custom_g])
print(res)

For any question, contact me on LinkedIn

@sinagilassi