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<!DOCTYPE html>
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<section id="pygromos-package">
<h1>pygromos package<a class="headerlink" href="#pygromos-package" title="Permalink to this headline">¶</a></h1>
<section id="subpackages">
<h2>Subpackages<a class="headerlink" href="#subpackages" title="Permalink to this headline">¶</a></h2>
<div class="toctree-wrapper compound">
<ul>
<li class="toctree-l1"><a class="reference internal" href="pygromos.analysis.html">pygromos.analysis package</a><ul>
<li class="toctree-l2"><a class="reference internal" href="pygromos.analysis.html#submodules">Submodules</a></li>
<li class="toctree-l2"><a class="reference internal" href="pygromos.analysis.html#module-pygromos.analysis.coordinate_analysis">pygromos.analysis.coordinate_analysis module</a></li>
<li class="toctree-l2"><a class="reference internal" href="pygromos.analysis.html#module-pygromos.analysis.energy_analysis">pygromos.analysis.energy_analysis module</a></li>
<li class="toctree-l2"><a class="reference internal" href="pygromos.analysis.html#module-pygromos.analysis.error_estimate">pygromos.analysis.error_estimate module</a></li>
<li class="toctree-l2"><a class="reference internal" href="pygromos.analysis.html#module-pygromos.analysis.free_energy_calculation">pygromos.analysis.free_energy_calculation module</a></li>
<li class="toctree-l2"><a class="reference internal" href="pygromos.analysis.html#module-pygromos.analysis">Module contents</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="pygromos.data.html">pygromos.data package</a><ul>
<li class="toctree-l2"><a class="reference internal" href="pygromos.data.html#subpackages">Subpackages</a><ul>
<li class="toctree-l3"><a class="reference internal" href="pygromos.data.ene_ana_libs.html">pygromos.data.ene_ana_libs package</a><ul>
<li class="toctree-l4"><a class="reference internal" href="pygromos.data.ene_ana_libs.html#module-pygromos.data.ene_ana_libs">Module contents</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="pygromos.data.ff.html">pygromos.data.ff package</a><ul>
<li class="toctree-l4"><a class="reference internal" href="pygromos.data.ff.html#subpackages">Subpackages</a></li>
<li class="toctree-l4"><a class="reference internal" href="pygromos.data.ff.html#submodules">Submodules</a></li>
<li class="toctree-l4"><a class="reference internal" href="pygromos.data.ff.html#module-pygromos.data.ff.addAtomType">pygromos.data.ff.addAtomType module</a></li>
<li class="toctree-l4"><a class="reference internal" href="pygromos.data.ff.html#module-pygromos.data.ff.atomType">pygromos.data.ff.atomType module</a></li>
<li class="toctree-l4"><a class="reference internal" href="pygromos.data.ff.html#module-pygromos.data.ff">Module contents</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="pygromos.data.simulation_parameters_templates.html">pygromos.data.simulation_parameters_templates package</a><ul>
<li class="toctree-l4"><a class="reference internal" href="pygromos.data.simulation_parameters_templates.html#module-pygromos.data.simulation_parameters_templates">Module contents</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="pygromos.data.solvent_coordinates.html">pygromos.data.solvent_coordinates package</a><ul>
<li class="toctree-l4"><a class="reference internal" href="pygromos.data.solvent_coordinates.html#module-pygromos.data.solvent_coordinates">Module contents</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="pygromos.data.topology_templates.html">pygromos.data.topology_templates package</a><ul>
<li class="toctree-l4"><a class="reference internal" href="pygromos.data.topology_templates.html#module-pygromos.data.topology_templates">Module contents</a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="pygromos.data.html#module-pygromos.data">Module contents</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="pygromos.files.html">pygromos.files package</a><ul>
<li class="toctree-l2"><a class="reference internal" href="pygromos.files.html#subpackages">Subpackages</a><ul>
<li class="toctree-l3"><a class="reference internal" href="pygromos.files.blocks.html">pygromos.files.blocks package</a><ul>
<li class="toctree-l4"><a class="reference internal" href="pygromos.files.blocks.html#submodules">Submodules</a></li>
<li class="toctree-l4"><a class="reference internal" href="pygromos.files.blocks.html#module-pygromos.files.blocks.coord_blocks">pygromos.files.blocks.coord_blocks module</a></li>
<li class="toctree-l4"><a class="reference internal" href="pygromos.files.blocks.html#module-pygromos.files.blocks.imd_blocks">pygromos.files.blocks.imd_blocks module</a></li>
<li class="toctree-l4"><a class="reference internal" href="pygromos.files.blocks.html#module-pygromos.files.blocks.miscBlocks">pygromos.files.blocks.miscBlocks module</a></li>
<li class="toctree-l4"><a class="reference internal" href="pygromos.files.blocks.html#module-pygromos.files.blocks.mtb_blocks">pygromos.files.blocks.mtb_blocks module</a></li>
<li class="toctree-l4"><a class="reference internal" href="pygromos.files.blocks.html#module-pygromos.files.blocks.pertubation_blocks">pygromos.files.blocks.pertubation_blocks module</a></li>
<li class="toctree-l4"><a class="reference internal" href="pygromos.files.blocks.html#module-pygromos.files.blocks.qmmm_blocks">pygromos.files.blocks.qmmm_blocks module</a></li>
<li class="toctree-l4"><a class="reference internal" href="pygromos.files.blocks.html#module-pygromos.files.blocks.replica_exchange_blocks">pygromos.files.blocks.replica_exchange_blocks module</a></li>
<li class="toctree-l4"><a class="reference internal" href="pygromos.files.blocks.html#module-pygromos.files.blocks.topology_blocks">pygromos.files.blocks.topology_blocks module</a></li>
<li class="toctree-l4"><a class="reference internal" href="pygromos.files.blocks.html#module-pygromos.files.blocks">Module contents</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="pygromos.files.coord.html">pygromos.files.coord package</a><ul>
<li class="toctree-l4"><a class="reference internal" href="pygromos.files.coord.html#submodules">Submodules</a></li>
<li class="toctree-l4"><a class="reference internal" href="pygromos.files.coord.html#module-pygromos.files.coord.cnf">pygromos.files.coord.cnf module</a></li>
<li class="toctree-l4"><a class="reference internal" href="pygromos.files.coord.html#module-pygromos.files.coord.posres">pygromos.files.coord.posres module</a></li>
<li class="toctree-l4"><a class="reference internal" href="pygromos.files.coord.html#module-pygromos.files.coord.refpos">pygromos.files.coord.refpos module</a></li>
<li class="toctree-l4"><a class="reference internal" href="pygromos.files.coord.html#module-pygromos.files.coord">Module contents</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="pygromos.files.forcefield.html">pygromos.files.forcefield package</a><ul>
<li class="toctree-l4"><a class="reference internal" href="pygromos.files.forcefield.html#subpackages">Subpackages</a></li>
<li class="toctree-l4"><a class="reference internal" href="pygromos.files.forcefield.html#module-pygromos.files.forcefield">Module contents</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="pygromos.files.gromos_system.html">pygromos.files.gromos_system package</a><ul>
<li class="toctree-l4"><a class="reference internal" href="pygromos.files.gromos_system.html#submodules">Submodules</a></li>
<li class="toctree-l4"><a class="reference internal" href="pygromos.files.gromos_system.html#module-pygromos.files.gromos_system.gromos_system">pygromos.files.gromos_system.gromos_system module</a></li>
<li class="toctree-l4"><a class="reference internal" href="pygromos.files.gromos_system.html#module-pygromos.files.gromos_system">Module contents</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="pygromos.files.otherfiles.html">pygromos.files.otherfiles package</a><ul>
<li class="toctree-l4"><a class="reference internal" href="pygromos.files.otherfiles.html#submodules">Submodules</a></li>
<li class="toctree-l4"><a class="reference internal" href="pygromos.files.otherfiles.html#module-pygromos.files.otherfiles.new_repdat">pygromos.files.otherfiles.new_repdat module</a></li>
<li class="toctree-l4"><a class="reference internal" href="pygromos.files.otherfiles.html#module-pygromos.files.otherfiles.noe_output">pygromos.files.otherfiles.noe_output module</a></li>
<li class="toctree-l4"><a class="reference internal" href="pygromos.files.otherfiles.html#module-pygromos.files.otherfiles.repdat">pygromos.files.otherfiles.repdat module</a></li>
<li class="toctree-l4"><a class="reference internal" href="pygromos.files.otherfiles.html#module-pygromos.files.otherfiles.residue_library">pygromos.files.otherfiles.residue_library module</a></li>
<li class="toctree-l4"><a class="reference internal" href="pygromos.files.otherfiles.html#module-pygromos.files.otherfiles">Module contents</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="pygromos.files.qmmm.html">pygromos.files.qmmm package</a><ul>
<li class="toctree-l4"><a class="reference internal" href="pygromos.files.qmmm.html#submodules">Submodules</a></li>
<li class="toctree-l4"><a class="reference internal" href="pygromos.files.qmmm.html#module-pygromos.files.qmmm.qmmm">pygromos.files.qmmm.qmmm module</a></li>
<li class="toctree-l4"><a class="reference internal" href="pygromos.files.qmmm.html#module-pygromos.files.qmmm">Module contents</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="pygromos.files.simulation_parameters.html">pygromos.files.simulation_parameters package</a><ul>
<li class="toctree-l4"><a class="reference internal" href="pygromos.files.simulation_parameters.html#submodules">Submodules</a></li>
<li class="toctree-l4"><a class="reference internal" href="pygromos.files.simulation_parameters.html#module-pygromos.files.simulation_parameters.imd">pygromos.files.simulation_parameters.imd module</a></li>
<li class="toctree-l4"><a class="reference internal" href="pygromos.files.simulation_parameters.html#module-pygromos.files.simulation_parameters">Module contents</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="pygromos.files.topology.html">pygromos.files.topology package</a><ul>
<li class="toctree-l4"><a class="reference internal" href="pygromos.files.topology.html#submodules">Submodules</a></li>
<li class="toctree-l4"><a class="reference internal" href="pygromos.files.topology.html#module-pygromos.files.topology.disres">pygromos.files.topology.disres module</a></li>
<li class="toctree-l4"><a class="reference internal" href="pygromos.files.topology.html#module-pygromos.files.topology.ifp">pygromos.files.topology.ifp module</a></li>
<li class="toctree-l4"><a class="reference internal" href="pygromos.files.topology.html#module-pygromos.files.topology.mtb">pygromos.files.topology.mtb module</a></li>
<li class="toctree-l4"><a class="reference internal" href="pygromos.files.topology.html#module-pygromos.files.topology.ptp">pygromos.files.topology.ptp module</a></li>
<li class="toctree-l4"><a class="reference internal" href="pygromos.files.topology.html#module-pygromos.files.topology.top">pygromos.files.topology.top module</a></li>
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</li>
<li class="toctree-l3"><a class="reference internal" href="pygromos.files.trajectory.html">pygromos.files.trajectory package</a><ul>
<li class="toctree-l4"><a class="reference internal" href="pygromos.files.trajectory.html#subpackages">Subpackages</a></li>
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<li class="toctree-l4"><a class="reference internal" href="pygromos.files.trajectory.html#module-pygromos.files.trajectory.trc">pygromos.files.trajectory.trc module</a></li>
<li class="toctree-l4"><a class="reference internal" href="pygromos.files.trajectory.html#module-pygromos.files.trajectory.tre">pygromos.files.trajectory.tre module</a></li>
<li class="toctree-l4"><a class="reference internal" href="pygromos.files.trajectory.html#module-pygromos.files.trajectory.trg">pygromos.files.trajectory.trg module</a></li>
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<li class="toctree-l1"><a class="reference internal" href="pygromos.gromos.html">pygromos.gromos package</a><ul>
<li class="toctree-l2"><a class="reference internal" href="pygromos.gromos.html#subpackages">Subpackages</a><ul>
<li class="toctree-l3"><a class="reference internal" href="pygromos.gromos.pyGromosPP.html">pygromos.gromos.pyGromosPP package</a><ul>
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<li class="toctree-l4"><a class="reference internal" href="pygromos.gromos.pyGromosPP.html#module-pygromos.gromos.pyGromosPP.ran_box">pygromos.gromos.pyGromosPP.ran_box module</a></li>
<li class="toctree-l4"><a class="reference internal" href="pygromos.gromos.pyGromosPP.html#module-pygromos.gromos.pyGromosPP">Module contents</a></li>
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<li class="toctree-l2"><a class="reference internal" href="pygromos.gromos.html#module-pygromos.gromos.compile_gromos">pygromos.gromos.compile_gromos module</a></li>
<li class="toctree-l2"><a class="reference internal" href="pygromos.gromos.html#module-pygromos.gromos.gromosBashSyntaxParser">pygromos.gromos.gromosBashSyntaxParser module</a></li>
<li class="toctree-l2"><a class="reference internal" href="pygromos.gromos.html#module-pygromos.gromos.gromosPP">pygromos.gromos.gromosPP module</a></li>
<li class="toctree-l2"><a class="reference internal" href="pygromos.gromos.html#module-pygromos.gromos.gromosXX">pygromos.gromos.gromosXX module</a></li>
<li class="toctree-l2"><a class="reference internal" href="pygromos.gromos.html#module-pygromos.gromos">Module contents</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="pygromos.simulations.html">pygromos.simulations package</a><ul>
<li class="toctree-l2"><a class="reference internal" href="pygromos.simulations.html#subpackages">Subpackages</a><ul>
<li class="toctree-l3"><a class="reference internal" href="pygromos.simulations.approaches.html">pygromos.simulations.approaches package</a><ul>
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<li class="toctree-l4"><a class="reference internal" href="pygromos.simulations.approaches.html#module-pygromos.simulations.approaches">Module contents</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="pygromos.simulations.hpc_queuing.html">pygromos.simulations.hpc_queuing package</a><ul>
<li class="toctree-l4"><a class="reference internal" href="pygromos.simulations.hpc_queuing.html#subpackages">Subpackages</a></li>
<li class="toctree-l4"><a class="reference internal" href="pygromos.simulations.hpc_queuing.html#module-pygromos.simulations.hpc_queuing">Module contents</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="pygromos.simulations.modules.html">pygromos.simulations.modules package</a><ul>
<li class="toctree-l4"><a class="reference internal" href="pygromos.simulations.modules.html#submodules">Submodules</a></li>
<li class="toctree-l4"><a class="reference internal" href="pygromos.simulations.modules.html#module-pygromos.simulations.modules.general_analysis_modules">pygromos.simulations.modules.general_analysis_modules module</a></li>
<li class="toctree-l4"><a class="reference internal" href="pygromos.simulations.modules.html#module-pygromos.simulations.modules.general_simulation_modules">pygromos.simulations.modules.general_simulation_modules module</a></li>
<li class="toctree-l4"><a class="reference internal" href="pygromos.simulations.modules.html#module-pygromos.simulations.modules.preset_simulation_modules">pygromos.simulations.modules.preset_simulation_modules module</a></li>
<li class="toctree-l4"><a class="reference internal" href="pygromos.simulations.modules.html#module-pygromos.simulations.modules.ti_modules">pygromos.simulations.modules.ti_modules module</a></li>
<li class="toctree-l4"><a class="reference internal" href="pygromos.simulations.modules.html#module-pygromos.simulations.modules">Module contents</a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="pygromos.simulations.html#module-pygromos.simulations">Module contents</a></li>
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<li class="toctree-l1"><a class="reference internal" href="pygromos.tests.html">pygromos.tests package</a><ul>
<li class="toctree-l2"><a class="reference internal" href="pygromos.tests.html#subpackages">Subpackages</a><ul>
<li class="toctree-l3"><a class="reference internal" href="pygromos.tests.in_testfiles.html">pygromos.tests.in_testfiles package</a><ul>
<li class="toctree-l4"><a class="reference internal" href="pygromos.tests.in_testfiles.html#module-pygromos.tests.in_testfiles">Module contents</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="pygromos.tests.out_testresults.html">pygromos.tests.out_testresults package</a><ul>
<li class="toctree-l4"><a class="reference internal" href="pygromos.tests.out_testresults.html#module-pygromos.tests.out_testresults">Module contents</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="pygromos.tests.test_analysis.html">pygromos.tests.test_analysis package</a><ul>
<li class="toctree-l4"><a class="reference internal" href="pygromos.tests.test_analysis.html#submodules">Submodules</a></li>
<li class="toctree-l4"><a class="reference internal" href="pygromos.tests.test_analysis.html#module-pygromos.tests.test_analysis.test_error_estimate">pygromos.tests.test_analysis.test_error_estimate module</a></li>
<li class="toctree-l4"><a class="reference internal" href="pygromos.tests.test_analysis.html#module-pygromos.tests.test_analysis.test_freeEnergy">pygromos.tests.test_analysis.test_freeEnergy module</a></li>
<li class="toctree-l4"><a class="reference internal" href="pygromos.tests.test_analysis.html#module-pygromos.tests.test_analysis">Module contents</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="pygromos.tests.test_approaches.html">pygromos.tests.test_approaches package</a><ul>
<li class="toctree-l4"><a class="reference internal" href="pygromos.tests.test_approaches.html#submodules">Submodules</a></li>
<li class="toctree-l4"><a class="reference internal" href="pygromos.tests.test_approaches.html#module-pygromos.tests.test_approaches.test_solvation_free_ernergy">pygromos.tests.test_approaches.test_solvation_free_ernergy module</a></li>
<li class="toctree-l4"><a class="reference internal" href="pygromos.tests.test_approaches.html#module-pygromos.tests.test_approaches">Module contents</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="pygromos.tests.test_files.html">pygromos.tests.test_files package</a><ul>
<li class="toctree-l4"><a class="reference internal" href="pygromos.tests.test_files.html#submodules">Submodules</a></li>
<li class="toctree-l4"><a class="reference internal" href="pygromos.tests.test_files.html#module-pygromos.tests.test_files.general_file_functions">pygromos.tests.test_files.general_file_functions module</a></li>
<li class="toctree-l4"><a class="reference internal" href="pygromos.tests.test_files.html#module-pygromos.tests.test_files.test_cnf_funcs">pygromos.tests.test_files.test_cnf_funcs module</a></li>
<li class="toctree-l4"><a class="reference internal" href="pygromos.tests.test_files.html#module-pygromos.tests.test_files.test_disres">pygromos.tests.test_files.test_disres module</a></li>
<li class="toctree-l4"><a class="reference internal" href="pygromos.tests.test_files.html#module-pygromos.tests.test_files.test_disres_file">pygromos.tests.test_files.test_disres_file module</a></li>
<li class="toctree-l4"><a class="reference internal" href="pygromos.tests.test_files.html#module-pygromos.tests.test_files.test_gromosSystem">pygromos.tests.test_files.test_gromosSystem module</a></li>
<li class="toctree-l4"><a class="reference internal" href="pygromos.tests.test_files.html#module-pygromos.tests.test_files.test_gromosSystem_forcefields">pygromos.tests.test_files.test_gromosSystem_forcefields module</a></li>
<li class="toctree-l4"><a class="reference internal" href="pygromos.tests.test_files.html#module-pygromos.tests.test_files.test_imd">pygromos.tests.test_files.test_imd module</a></li>
<li class="toctree-l4"><a class="reference internal" href="pygromos.tests.test_files.html#module-pygromos.tests.test_files.test_imd_block">pygromos.tests.test_files.test_imd_block module</a></li>
<li class="toctree-l4"><a class="reference internal" href="pygromos.tests.test_files.html#module-pygromos.tests.test_files.test_mtb">pygromos.tests.test_files.test_mtb module</a></li>
<li class="toctree-l4"><a class="reference internal" href="pygromos.tests.test_files.html#module-pygromos.tests.test_files.test_ptp">pygromos.tests.test_files.test_ptp module</a></li>
<li class="toctree-l4"><a class="reference internal" href="pygromos.tests.test_files.html#module-pygromos.tests.test_files.test_qmmm">pygromos.tests.test_files.test_qmmm module</a></li>
<li class="toctree-l4"><a class="reference internal" href="pygromos.tests.test_files.html#module-pygromos.tests.test_files.test_repdat">pygromos.tests.test_files.test_repdat module</a></li>
<li class="toctree-l4"><a class="reference internal" href="pygromos.tests.test_files.html#module-pygromos.tests.test_files.test_resnlib">pygromos.tests.test_files.test_resnlib module</a></li>
<li class="toctree-l4"><a class="reference internal" href="pygromos.tests.test_files.html#module-pygromos.tests.test_files.test_top">pygromos.tests.test_files.test_top module</a></li>
<li class="toctree-l4"><a class="reference internal" href="pygromos.tests.test_files.html#module-pygromos.tests.test_files.test_trajectory">pygromos.tests.test_files.test_trajectory module</a></li>
<li class="toctree-l4"><a class="reference internal" href="pygromos.tests.test_files.html#module-pygromos.tests.test_files">Module contents</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="pygromos.tests.test_simulation_blocks.html">pygromos.tests.test_simulation_blocks package</a><ul>
<li class="toctree-l4"><a class="reference internal" href="pygromos.tests.test_simulation_blocks.html#submodules">Submodules</a></li>
<li class="toctree-l4"><a class="reference internal" href="pygromos.tests.test_simulation_blocks.html#module-pygromos.tests.test_simulation_blocks.test_simulation_runner_blocks">pygromos.tests.test_simulation_blocks.test_simulation_runner_blocks module</a></li>
<li class="toctree-l4"><a class="reference internal" href="pygromos.tests.test_simulation_blocks.html#module-pygromos.tests.test_simulation_blocks">Module contents</a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="pygromos.tests.test_submission.html">pygromos.tests.test_submission package</a><ul>
<li class="toctree-l4"><a class="reference internal" href="pygromos.tests.test_submission.html#submodules">Submodules</a></li>
<li class="toctree-l4"><a class="reference internal" href="pygromos.tests.test_submission.html#module-pygromos.tests.test_submission.test_hpc_queuing_submission_job">pygromos.tests.test_submission.test_hpc_queuing_submission_job module</a></li>
<li class="toctree-l4"><a class="reference internal" href="pygromos.tests.test_submission.html#module-pygromos.tests.test_submission.test_hpc_queuing_submission_scheduling">pygromos.tests.test_submission.test_hpc_queuing_submission_scheduling module</a></li>
<li class="toctree-l4"><a class="reference internal" href="pygromos.tests.test_submission.html#module-pygromos.tests.test_submission.test_hpc_queuing_submission_systems">pygromos.tests.test_submission.test_hpc_queuing_submission_systems module</a></li>
<li class="toctree-l4"><a class="reference internal" href="pygromos.tests.test_submission.html#module-pygromos.tests.test_submission">Module contents</a></li>
</ul>
</li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="pygromos.tests.html#submodules">Submodules</a></li>
<li class="toctree-l2"><a class="reference internal" href="pygromos.tests.html#module-pygromos.tests.test_pygromos">pygromos.tests.test_pygromos module</a></li>
<li class="toctree-l2"><a class="reference internal" href="pygromos.tests.html#module-pygromos.tests">Module contents</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="pygromos.utils.html">pygromos.utils package</a><ul>
<li class="toctree-l2"><a class="reference internal" href="pygromos.utils.html#submodules">Submodules</a></li>
<li class="toctree-l2"><a class="reference internal" href="pygromos.utils.html#module-pygromos.utils.amino_acids">pygromos.utils.amino_acids module</a></li>
<li class="toctree-l2"><a class="reference internal" href="pygromos.utils.html#module-pygromos.utils.bash">pygromos.utils.bash module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="pygromos.utils.html#description">Description</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="pygromos.utils.html#module-pygromos.utils.compiledProgram">pygromos.utils.compiledProgram module</a></li>
<li class="toctree-l2"><a class="reference internal" href="pygromos.utils.html#module-pygromos.utils.pdb">pygromos.utils.pdb module</a></li>
<li class="toctree-l2"><a class="reference internal" href="pygromos.utils.html#module-pygromos.utils.typing">pygromos.utils.typing module</a></li>
<li class="toctree-l2"><a class="reference internal" href="pygromos.utils.html#module-pygromos.utils.utils">pygromos.utils.utils module</a></li>
<li class="toctree-l2"><a class="reference internal" href="pygromos.utils.html#module-pygromos.utils">Module contents</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="pygromos.visualization.html">pygromos.visualization package</a><ul>
<li class="toctree-l2"><a class="reference internal" href="pygromos.visualization.html#submodules">Submodules</a></li>
<li class="toctree-l2"><a class="reference internal" href="pygromos.visualization.html#module-pygromos.visualization.coordinates_visualization">pygromos.visualization.coordinates_visualization module</a></li>
<li class="toctree-l2"><a class="reference internal" href="pygromos.visualization.html#module-pygromos.visualization">Module contents</a></li>
</ul>
</li>
</ul>
</div>
</section>
<section id="submodules">
<h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this headline">¶</a></h2>
</section>
<section id="module-pygromos.pygromos">
<span id="pygromos-pygromos-module"></span><h2>pygromos.pygromos module<a class="headerlink" href="#module-pygromos.pygromos" title="Permalink to this headline">¶</a></h2>
<p>pygromos.py
The aim of the module is to bring GROMOS to the Python3 World!</p>
<p>Handles the primary functions</p>
</section>
<section id="module-pygromos">
<span id="module-contents"></span><h2>Module contents<a class="headerlink" href="#module-pygromos" title="Permalink to this headline">¶</a></h2>
<p>PyGromos
The aim of the module is to bring GROMOS to the Python3 World!</p>
</section>
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