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examples/basic/basic.py

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from gmx_top4py.topology.topology import Topology
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# %% [markdown]
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# # 1. Reading a topology file
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# Let's read the GROMACS topology file 'urea.top' into a 'Topology' object.
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# Let's read the GROMACS topology file 'urea.top' into a `Topology` object.
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# %%
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top_path = Path("urea.top") # path to the topology file
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top = Topology.from_path(top_path) # read the topology file into a Topology object
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# In case of the 'urea.top' example, there are one urea molecule and 1000 solvent molecules.
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# The second paragraph of the printout provides an overview of the topology properties of the selected molecule type. <br>
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#<br>
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# <br>
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# With Moleculetype Urea(1x) with: <br>
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# 8 atoms, <br>
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# 7 bonds, <br>
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# 125 residuetypes <br>
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# <br>
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# In the 'urea.top' file, amber99 force field is used.
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# In the 'urea.top' file, the amber99 force field is used.
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# %% [markdown]
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# ## 1.1. The Topology object
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# An instance of the `Topology` class has the following main attributes:
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# %% [markdown]
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# ### 1.1.1. The moleculetypes attribute
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# The `moleculetypes` attribute is a dictionary where the keys are the names of the molecule types and the values are instances of the `MoleculeType` class.
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# %%
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# In the case of the 'urea.top' example, there are two molecule types: 'SOL' and 'Urea(1x)':
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# %% [markdown]
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# In the case of the 'urea.top' example, there are two molecule types: 'SOL' and 'Urea(1x)':
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# %%
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print(top.moleculetypes)
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# %% [markdown]
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# For example, we can access the topology information of the 'Urea(1x)' molecule type as follows:

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