├── .github └── workflows │ └── documentation.yml ├── .idea ├── .gitignore ├── .name ├── inspectionProfiles │ └── profiles_settings.xml ├── metallicious.iml ├── misc.xml ├── modules.xml └── vcs.xml ├── .readthedocs.yaml ├── LICENSE.md ├── MANIFEST.in ├── README.md ├── doc ├── Makefile ├── _build │ ├── doctrees │ │ ├── environment.pickle │ │ └── index.doctree │ └── html │ │ ├── .buildinfo │ │ ├── _sources │ │ └── index.rst.txt │ │ ├── _static │ │ ├── alabaster.css │ │ ├── basic.css │ │ ├── custom.css │ │ ├── doctools.js │ │ ├── documentation_options.js │ │ ├── file.png │ │ ├── language_data.js │ │ ├── minus.png │ │ ├── plus.png │ │ ├── pygments.css │ │ ├── searchtools.js │ │ └── sphinx_highlight.js │ │ ├── genindex.html │ │ ├── index.html │ │ ├── objects.inv │ │ ├── search.html │ │ └── searchindex.js ├── conf.py ├── index.rst └── make.bat ├── docs ├── Makefile ├── make.bat ├── requirements.txt └── source │ ├── _static │ └── custom.css │ ├── api.rst │ ├── conf.py │ ├── custom.css │ ├── examples.rst │ ├── icon.ico │ ├── images │ ├── benzoquinone_complex.png │ ├── docs_templates.png │ ├── favicon.png │ ├── gallium.png │ ├── lewis.png │ ├── periodic_table.png │ ├── summary.png │ └── truncation.png │ ├── index.rst │ ├── installation.rst │ ├── logo.png │ ├── logo_rect.png │ ├── logo_square.png │ ├── tutorials.rst │ └── usage.rst ├── images ├── logo.png └── summary.png ├── metallicious.egg-info ├── PKG-INFO ├── SOURCES.txt ├── dependency_links.txt └── top_level.txt ├── metallicious ├── __init__.py ├── __main__.py ├── __pycache__ │ └── __init__.cpython-311.pyc ├── antechamber_interface.py ├── asserts.py ├── charges.py ├── copy_topology_params.py ├── data.py ├── examples │ ├── __init__.py │ ├── example1_quick_start │ │ ├── example1.py │ │ ├── ru_pd.pdb │ │ └── ru_pd.top │ ├── example2_no_topology │ │ ├── example2.py │ │ └── ru_pd.xyz │ ├── example3_only_linker_topology │ │ ├── example3.py │ │ ├── linker.top │ │ └── ru_pd.xyz │ ├── example4_template_parametrization │ │ ├── cage.pdb │ │ ├── example4.py │ │ └── topol.top │ ├── example5_truncation_scheme │ │ ├── cage.pdb │ │ ├── example5.py │ │ ├── out.pdb │ │ ├── out.top │ │ ├── temp.pdb │ │ ├── temp │ │ │ ├── out.pdb │ │ │ ├── out.pse │ │ │ ├── temp.pdb │ │ │ └── temp.top │ │ └── topol.top │ ├── example6_mof │ │ ├── Co_mof.pdb │ │ └── example6.py │ ├── tutorial5 │ │ ├── final.zip │ │ └── tutorial.zip │ └── tutorial6 │ │ └── start.xyz ├── extract_metal_site.py ├── improper_torsion.py ├── initial_site.py ├── library │ ├── .Pd1.top.swn │ ├── Co_2_merz-opc_0.pdb │ ├── Co_2_merz-opc_0.top │ ├── Co_2_merz-opc_1.pdb │ ├── Co_2_merz-opc_1.top │ ├── Co_2_merz-opc_2.pdb │ ├── Co_2_merz-opc_2.top │ ├── Co_2_merz-opc_3.pdb │ ├── Co_2_merz-opc_3.top │ ├── Co_2_merz-opc_4.pdb │ ├── Co_2_merz-opc_4.top │ ├── Co_2_uff_0.pdb │ ├── Co_2_uff_0.top │ ├── Co_2_uff_1.pdb │ ├── Co_2_uff_1.top │ ├── Co_2_uff_2.pdb │ ├── Co_2_uff_2.top │ ├── Co_2_uff_3.pdb │ ├── Co_2_uff_3.top │ ├── Co_2_uff_4.pdb │ ├── Co_2_uff_4.top │ ├── Co_2_zhang-opc_0.pdb │ ├── Co_2_zhang-opc_0.top │ ├── Co_2_zhang-opc_1.pdb │ ├── Co_2_zhang-opc_1.top │ ├── Co_2_zhang-opc_2.pdb │ ├── Co_2_zhang-opc_2.top │ ├── Co_2_zhang-opc_3.pdb │ ├── Co_2_zhang-opc_3.top │ ├── Co_2_zhang-opc_4.pdb │ ├── Co_2_zhang-opc_4.top │ ├── Fe_2_merz-opc_0.pdb │ ├── Fe_2_merz-opc_0.top │ ├── Fe_2_merz-opc_3.pdb │ ├── Fe_2_merz-opc_3.top │ ├── Fe_2_uff_0.pdb │ ├── Fe_2_uff_0.top │ ├── Fe_2_zhang-opc_0.pdb │ ├── Fe_2_zhang-opc_0.top │ ├── Fe_2_zhang-opc_1.pdb │ ├── Fe_2_zhang-opc_1.top │ ├── Fe_3_merz-opc_0.pdb │ ├── Fe_3_merz-opc_0.top │ ├── Ga_3_uff_0.pdb │ ├── Ga_3_uff_0.top │ ├── Pd_2_merz-opc3_0.pdb │ ├── Pd_2_merz-opc3_0.top │ ├── Pd_2_merz-opc_0.pdb │ ├── Pd_2_merz-opc_0.top │ ├── Pd_2_merz-opc_1.pdb │ ├── Pd_2_merz-opc_1.top │ ├── Pd_2_merz-opc_2.pdb │ ├── Pd_2_merz-opc_2.top │ ├── Pd_2_merz-opc_3.pdb │ ├── Pd_2_merz-opc_3.top │ ├── Pd_2_merz-opc_4.pdb │ ├── Pd_2_merz-opc_4.top │ ├── Pd_2_merz-spce_0.pdb │ ├── Pd_2_merz-spce_0.top │ ├── Pd_2_merz-tip3p-fb_0.pdb │ ├── Pd_2_merz-tip3p-fb_0.top │ ├── Pd_2_merz-tip3p_0.pdb │ ├── Pd_2_merz-tip3p_0.top │ ├── Pd_2_merz-tip4-ew_0.pdb │ ├── Pd_2_merz-tip4-ew_0.top │ ├── Pd_2_merz-tip4p-fb_0.pdb │ ├── Pd_2_merz-tip4p-fb_0.top │ ├── Pd_2_uff_0.pdb │ ├── Pd_2_uff_0.top │ ├── Pd_2_uff_1.pdb │ ├── Pd_2_uff_1.top │ ├── Pd_2_uff_2.pdb │ ├── Pd_2_uff_2.top │ ├── Ru_2_uff_0.pdb │ ├── Ru_2_uff_0.top │ ├── Zn_2_merz-opc_0.pdb │ ├── Zn_2_merz-opc_0.top │ ├── Zn_2_merz-opc_1.pdb │ ├── Zn_2_merz-opc_1.top │ ├── Zn_2_merz-opc_2.pdb │ ├── Zn_2_merz-opc_2.top │ ├── Zn_2_uff_0.pdb │ ├── Zn_2_uff_0.top │ ├── Zn_2_uff_1.pdb │ ├── Zn_2_uff_1.top │ ├── Zn_2_uff_2.pdb │ ├── Zn_2_uff_2.top │ ├── Zn_2_uff_3.pdb │ ├── Zn_2_uff_3.top │ ├── Zn_2_zhang-opc_0.pdb │ ├── Zn_2_zhang-opc_0.top │ ├── Zn_2_zhang-opc_1.pdb │ ├── Zn_2_zhang-opc_1.top │ ├── Zn_2_zhang-opc_2.pdb │ ├── Zn_2_zhang-opc_2.top │ └── metallicious.egg-info │ │ ├── PKG-INFO │ │ ├── SOURCES.txt │ │ ├── dependency_links.txt │ │ ├── entry_points.txt │ │ ├── requires.txt │ │ └── top_level.txt ├── load_fingerprint.py ├── log.py ├── mapping.py ├── mod_seminario.py ├── parametrize_new_sites.py ├── patcher.py ├── prepare_initial_topology.py ├── seminario.py ├── tests │ ├── __init__.py │ ├── example3_mof │ │ ├── Ag_tet.pdb │ │ ├── __init__.py │ │ ├── example3.py │ │ ├── linker_topol.top │ │ ├── out.pdb │ │ ├── out.top │ │ └── temp.pdb │ ├── example5_extract │ │ ├── Co8L16.xyz │ │ ├── Co8L16_fp0 │ │ │ ├── ligand_0.pdb │ │ │ ├── ligand_0.xyz │ │ │ ├── site.pdb │ │ │ └── site.xyz │ │ ├── Co8L16_fp1 │ │ │ ├── ligand_0.pdb │ │ │ ├── ligand_0.xyz │ │ │ ├── site.pdb │ │ │ └── site.xyz │ │ ├── Co8L16_fp2 │ │ │ ├── ligand_0.pdb │ │ │ ├── ligand_0.xyz │ │ │ ├── site.pdb │ │ │ └── site.xyz │ │ ├── Co8L16_fp3 │ │ │ ├── ligand_0.pdb │ │ │ ├── ligand_0.xyz │ │ │ ├── site.pdb │ │ │ └── site.xyz │ │ ├── Fe4L6_2_fp0 │ │ │ ├── ligand_0.pdb │ │ │ ├── ligand_0.xyz │ │ │ ├── site.pdb │ │ │ └── site.xyz │ │ ├── Fe4L6_2_fp1 │ │ │ ├── ligand_0.pdb │ │ │ ├── ligand_0.xyz │ │ │ ├── site.pdb │ │ │ └── site.xyz │ │ ├── Fe4L6_fp0 │ │ │ ├── ligand_0.pdb │ │ │ ├── ligand_0.xyz │ │ │ ├── site.pdb │ │ │ └── site.xyz │ │ ├── Fe4L6_fp1 │ │ │ ├── ligand_0.pdb │ │ │ ├── ligand_0.xyz │ │ │ ├── site.pdb │ │ │ └── site.xyz │ │ ├── Ga4L6_fp0 │ │ │ ├── ligand_0.pdb │ │ │ ├── ligand_0.xyz │ │ │ ├── site.pdb │ │ │ └── site.xyz │ │ ├── INFO.dat │ │ ├── Pd2L4_sphere_engineer.xyz │ │ ├── Pd4L6.xyz │ │ ├── Pd4L6_fp0 │ │ │ ├── ligand_0.pdb │ │ │ ├── ligand_0.xyz │ │ │ ├── ligand_1.pdb │ │ │ ├── ligand_1.xyz │ │ │ ├── site.pdb │ │ │ └── site.xyz │ │ ├── ZAYDAH.mol2 │ │ ├── __init__.py │ │ ├── aaa.pdb │ │ ├── cage.pdb │ │ ├── example5.py │ │ ├── knot_3n.pdb │ │ ├── knot_3n_fp0 │ │ │ ├── ligand_0.pdb │ │ │ ├── ligand_0.xyz │ │ │ ├── site.pdb │ │ │ └── site.xyz │ │ ├── knot_4.mol2 │ │ ├── knot_4n.pdb │ │ ├── knot_4n_fp0 │ │ │ ├── ligand_0.pdb │ │ │ ├── ligand_0.xyz │ │ │ ├── site.pdb │ │ │ └── site.xyz │ │ ├── pd2l4_tall.gro │ │ ├── pd2l4_tall.pdb │ │ ├── pd2l4_tall.xyz │ │ ├── pd2l4_tall_fp10 │ │ │ ├── ligand_0.pdb │ │ │ ├── ligand_0.xyz │ │ │ ├── site.pdb │ │ │ └── site.xyz │ │ ├── pd2l4_tall_fp20 │ │ │ ├── ligand_0.pdb │ │ │ ├── ligand_0.xyz │ │ │ ├── site.pdb │ │ │ └── site.xyz │ │ ├── pd2l4_tall_fp30 │ │ │ ├── ligand_0.pdb │ │ │ ├── ligand_0.xyz │ │ │ ├── site.pdb │ │ │ └── site.xyz │ │ ├── ru_fp0 │ │ │ ├── ligand_0.pdb │ │ │ ├── ligand_0.xyz │ │ │ ├── site.pdb │ │ │ └── site.xyz │ │ ├── ru_pd.xyz │ │ ├── temp.pdb │ │ ├── temp1.pdb │ │ ├── temp1.xyz │ │ ├── temp2.pdb │ │ ├── temp2.xyz │ │ ├── topol0.top │ │ ├── topol1.top │ │ ├── topol2.top │ │ └── topol3.top │ ├── example6_extract_pbc │ │ ├── Co_tet.pdb │ │ ├── INFO.dat │ │ ├── Zn_tet.pdb │ │ ├── __init__.py │ │ ├── cage.pdb │ │ ├── example6.py │ │ ├── ligand0_0.pdb │ │ ├── ligand0_0.xyz │ │ ├── out0.pdb │ │ ├── out0.xyz │ │ ├── site_Co0 │ │ │ └── ligand_0.xyz │ │ ├── site_Zn0 │ │ │ ├── ligand_0.itp │ │ │ ├── ligand_0.pdb │ │ │ ├── ligand_0.xyz │ │ │ ├── site.pdb │ │ │ ├── site.xyz │ │ │ └── topol.top │ │ ├── temp.pdb │ │ ├── temp1.pdb │ │ ├── temp1.xyz │ │ ├── temp2.pdb │ │ ├── temp2.xyz │ │ ├── temp_temp.pdb │ │ ├── temp_temp0.pdb │ │ ├── temp_temp2.pdb │ │ └── temp_temp2.xyz │ ├── extract_metal_site │ │ ├── INFO.dat │ │ ├── __init__.py │ │ └── test_extract.py │ ├── fingerprint │ │ ├── __init__.py │ │ ├── cage.xyz │ │ ├── cage2.xyz │ │ ├── cage3.xyz │ │ └── test_fingerprint.py │ └── parametrize_new_site │ │ ├── Co8L16.pdb │ │ ├── Co8L16.top │ │ ├── Co8L16.xyz │ │ ├── Fe5L5.pdb │ │ ├── Fe5L5.top │ │ ├── Pd2L4.pdb │ │ ├── Pd2L4.top │ │ ├── Pd6L4.pdb │ │ ├── Pd6L4.top │ │ ├── Pd6Ru8L28.pdb │ │ ├── Pd6Ru8L28.top │ │ └── test_supramolecular.py └── utils.py ├── pyproject.toml ├── requirements.txt └── setup.py /.github/workflows/documentation.yml: -------------------------------------------------------------------------------- 1 | name: documentation 2 | 3 | on: [push, pull_request, workflow_dispatch] 4 | 5 | permissions: 6 | contents: write 7 | 8 | jobs: 9 | docs: 10 | runs-on: ubuntu-latest 11 | steps: 12 | - uses: actions/checkout@v3 13 | - uses: actions/setup-python@v3 14 | - name: Install dependencies 15 | run: | 16 | pip install sphinx sphinx_rtd_theme myst_parser 17 | - name: Sphinx build 18 | run: | 19 | sphinx-build doc _build 20 | - name: Deploy to GitHub Pages 21 | uses: peaceiris/actions-gh-pages@v3 22 | if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' }} 23 | with: 24 | publish_branch: gh-pages 25 | github_token: ${{ secrets.GITHUB_TOKEN }} 26 | publish_dir: _build/ 27 | force_orphan: true 28 | -------------------------------------------------------------------------------- /.idea/.gitignore: -------------------------------------------------------------------------------- 1 | # Default ignored files 2 | /workspace.xml 3 | -------------------------------------------------------------------------------- /.idea/.name: -------------------------------------------------------------------------------- 1 | metallicious -------------------------------------------------------------------------------- /.idea/inspectionProfiles/profiles_settings.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 6 | -------------------------------------------------------------------------------- /.idea/metallicious.iml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 11 | -------------------------------------------------------------------------------- /.idea/misc.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | -------------------------------------------------------------------------------- /.idea/modules.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | -------------------------------------------------------------------------------- /.idea/vcs.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | -------------------------------------------------------------------------------- /.readthedocs.yaml: -------------------------------------------------------------------------------- 1 | version: "2" 2 | 3 | build: 4 | os: "ubuntu-22.04" 5 | tools: 6 | python: "3.10" 7 | 8 | python: 9 | install: 10 | - requirements: docs/requirements.txt 11 | 12 | sphinx: 13 | configuration: docs/source/conf.py 14 | -------------------------------------------------------------------------------- /LICENSE.md: -------------------------------------------------------------------------------- 1 | The MIT License (MIT) 2 | 3 | Copyright (c) 2024 4 | 5 | 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: 6 | 7 | The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. 8 | 9 | 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. 10 | -------------------------------------------------------------------------------- /MANIFEST.in: -------------------------------------------------------------------------------- 1 | # MANIFEST.in 2 | 3 | include metallicious/library/* -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 |

2 | 3 |

4 | 5 | # Metallicious 6 | 7 | Metallicious (a playful combination of "metal" and "delicious") is an automated tool for creating force fields for 8 | metal-containing systems with a covalent model of the metal. By utilizing a library of templates, metallicious identifies 9 | the template that matches the metal site in the structure. It copies the bonded parameters from the template and performs 10 | charge redistribution to account for charge transfer. In cases where no suitable template is found, metallicious 11 | automatically performs parameterization. 12 | 13 | 14 | 15 | Metallicious works with minimal user input, relying heavily on educated guesses, which may not always yield the expected 16 | results. Therefore, it is recommended to use the tool with caution. 17 | 18 | 19 | 20 | ## Installation: 21 | ``` 22 | conda install rdkit autode psiresp mdanalysis networkx qcelemental==0.25.1 ambertools --channel conda-forge 23 | pip install metallicious 24 | ``` 25 | ## Quick start 26 | Parametrization of structure with coordinates saved as `supramolecular_cage.xyz` (*.xyz, *.pdb, *gro, etc. formats 27 | supported by MDAnalysis) with (nonbonded) force-field parameters `supramolecular_cage.top` (*top, *prmtop, etc. supported by ParmEd), 28 | which consists of two metals Pd2+ and Ru2+ and organic linkers, the input file might look like this: 29 | 30 | ``` 31 | from metallicious import supramolecular_structure 32 | cage = supramolecular_structure('supramolecular_cage.xyz', 33 | metal_charges={'Ru': 2, 'Pd':2 }, 34 | topol='supramolecular_cage.top', 35 | vdw_type='uff') 36 | cage.parametrize(out_coord='out.pdb', out_topol='out.top') 37 | ``` 38 | The `supramolecular_structure` function takes a coordination file, topology file , dictionary of metal ions along with 39 | their charge (and in case template parametrization is needed multiplicity) and type of Lennard-Jones library as an input. 40 | 41 | See [examples/](https://github.com/tkpiskorz/metallicious/tree/main/metallicious/examples) for more examples and 42 | [metallicious.readthedocs.io](https://metallicious.readthedocs.io/en/latest/) for additional documentation. 43 | 44 | ## Command line 45 | It is also possible to use the metallicious just form command line. For example: 46 | ``` 47 | metallicious -f supramolecular_cage.xyz -vdw_type merz-tip3p -metal_and_charges Pd 2 Ru 2 -prepare_topol 48 | ``` 49 | For details, see: 50 | ``` 51 | metallicious -h 52 | ``` 53 | -------------------------------------------------------------------------------- /doc/Makefile: -------------------------------------------------------------------------------- 1 | # Minimal makefile for Sphinx documentation 2 | # 3 | 4 | # You can set these variables from the command line, and also 5 | # from the environment for the first two. 6 | SPHINXOPTS ?= 7 | SPHINXBUILD ?= sphinx-build 8 | SOURCEDIR = . 9 | BUILDDIR = _build 10 | 11 | # Put it first so that "make" without argument is like "make help". 12 | help: 13 | @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) 14 | 15 | .PHONY: help Makefile 16 | 17 | # Catch-all target: route all unknown targets to Sphinx using the new 18 | # "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). 19 | %: Makefile 20 | @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) 21 | -------------------------------------------------------------------------------- /doc/_build/doctrees/environment.pickle: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/duartegroup/metallicious/3254b283fe22af19bc477ca36b96533d8fd463a4/doc/_build/doctrees/environment.pickle -------------------------------------------------------------------------------- /doc/_build/doctrees/index.doctree: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/duartegroup/metallicious/3254b283fe22af19bc477ca36b96533d8fd463a4/doc/_build/doctrees/index.doctree -------------------------------------------------------------------------------- /doc/_build/html/.buildinfo: -------------------------------------------------------------------------------- 1 | # Sphinx build info version 1 2 | # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. 3 | config: d739328f85113f7b9f5d862e41934ec8 4 | tags: 645f666f9bcd5a90fca523b33c5a78b7 5 | -------------------------------------------------------------------------------- /doc/_build/html/_sources/index.rst.txt: -------------------------------------------------------------------------------- 1 | .. metallicious documentation master file, created by 2 | sphinx-quickstart on Wed May 1 08:14:39 2024. 3 | You can adapt this file completely to your liking, but it should at least 4 | contain the root `toctree` directive. 5 | 6 | Welcome to metallicious's documentation! 7 | ======================================== 8 | 9 | .. toctree:: 10 | :maxdepth: 2 11 | :caption: Contents: 12 | 13 | 14 | 15 | Indices and tables 16 | ================== 17 | 18 | * :ref:`genindex` 19 | * :ref:`modindex` 20 | * :ref:`search` 21 | -------------------------------------------------------------------------------- /doc/_build/html/_static/custom.css: -------------------------------------------------------------------------------- 1 | /* This file intentionally left blank. */ 2 | -------------------------------------------------------------------------------- /doc/_build/html/_static/documentation_options.js: -------------------------------------------------------------------------------- 1 | const DOCUMENTATION_OPTIONS = { 2 | VERSION: '', 3 | LANGUAGE: 'en', 4 | COLLAPSE_INDEX: false, 5 | BUILDER: 'html', 6 | FILE_SUFFIX: '.html', 7 | LINK_SUFFIX: '.html', 8 | HAS_SOURCE: true, 9 | SOURCELINK_SUFFIX: '.txt', 10 | NAVIGATION_WITH_KEYS: false, 11 | SHOW_SEARCH_SUMMARY: true, 12 | ENABLE_SEARCH_SHORTCUTS: true, 13 | }; -------------------------------------------------------------------------------- /doc/_build/html/_static/file.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/duartegroup/metallicious/3254b283fe22af19bc477ca36b96533d8fd463a4/doc/_build/html/_static/file.png -------------------------------------------------------------------------------- /doc/_build/html/_static/minus.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/duartegroup/metallicious/3254b283fe22af19bc477ca36b96533d8fd463a4/doc/_build/html/_static/minus.png -------------------------------------------------------------------------------- /doc/_build/html/_static/plus.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/duartegroup/metallicious/3254b283fe22af19bc477ca36b96533d8fd463a4/doc/_build/html/_static/plus.png -------------------------------------------------------------------------------- /doc/_build/html/genindex.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | Index — metallicious documentation 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 |
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Index

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87 | ©2024, TK Piskorz. 88 | 89 | | 90 | Powered by Sphinx 7.3.7 91 | & Alabaster 0.7.16 92 | 93 |
94 | 95 | 96 | 97 | 98 | 99 | -------------------------------------------------------------------------------- /doc/_build/html/index.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | Welcome to metallicious’s documentation! — metallicious documentation 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 |
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Indices and tables

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105 | 106 | 107 | 108 | 109 | 110 | -------------------------------------------------------------------------------- /doc/_build/html/objects.inv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/duartegroup/metallicious/3254b283fe22af19bc477ca36b96533d8fd463a4/doc/_build/html/objects.inv -------------------------------------------------------------------------------- /doc/_build/html/search.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | Search — metallicious documentation 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 |
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104 | ©2024, TK Piskorz. 105 | 106 | | 107 | Powered by Sphinx 7.3.7 108 | & Alabaster 0.7.16 109 | 110 |
111 | 112 | 113 | 114 | 115 | 116 | -------------------------------------------------------------------------------- /doc/_build/html/searchindex.js: -------------------------------------------------------------------------------- 1 | Search.setIndex({"alltitles": {"Indices and tables": [[0, "indices-and-tables"]], "Welcome to metallicious\u2019s documentation!": [[0, "welcome-to-metallicious-s-documentation"]]}, "docnames": ["index"], "envversion": {"sphinx": 61, "sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2}, "filenames": ["index.rst"], "indexentries": {}, "objects": {}, "objnames": {}, "objtypes": {}, "terms": {"index": 0, "modul": 0, "page": 0, "search": 0}, "titles": ["Welcome to metallicious\u2019s documentation!"], "titleterms": {"": 0, "document": 0, "indic": 0, "metallici": 0, "tabl": 0, "welcom": 0}}) -------------------------------------------------------------------------------- /doc/conf.py: -------------------------------------------------------------------------------- 1 | # Configuration file for the Sphinx documentation builder. 2 | # 3 | # For the full list of built-in configuration values, see the documentation: 4 | # https://www.sphinx-doc.org/en/master/usage/configuration.html 5 | 6 | # -- Project information ----------------------------------------------------- 7 | # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information 8 | 9 | project = 'metallicious' 10 | copyright = '2024, TK Piskorz' 11 | author = 'TK Piskorz' 12 | 13 | # -- General configuration --------------------------------------------------- 14 | # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration 15 | 16 | extensions = [] 17 | 18 | templates_path = ['_templates'] 19 | exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store'] 20 | 21 | 22 | 23 | # -- Options for HTML output ------------------------------------------------- 24 | # https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output 25 | 26 | html_theme = 'alabaster' 27 | html_static_path = ['_static'] 28 | -------------------------------------------------------------------------------- /doc/index.rst: -------------------------------------------------------------------------------- 1 | .. metallicious documentation master file, created by 2 | sphinx-quickstart on Wed May 1 08:14:39 2024. 3 | You can adapt this file completely to your liking, but it should at least 4 | contain the root `toctree` directive. 5 | 6 | Welcome to metallicious's documentation! 7 | ======================================== 8 | 9 | .. toctree:: 10 | :maxdepth: 2 11 | :caption: Contents: 12 | 13 | 14 | 15 | Indices and tables 16 | ================== 17 | 18 | * :ref:`genindex` 19 | * :ref:`modindex` 20 | * :ref:`search` 21 | -------------------------------------------------------------------------------- /doc/make.bat: -------------------------------------------------------------------------------- 1 | @ECHO OFF 2 | 3 | pushd %~dp0 4 | 5 | REM Command file for Sphinx documentation 6 | 7 | if "%SPHINXBUILD%" == "" ( 8 | set SPHINXBUILD=sphinx-build 9 | ) 10 | set SOURCEDIR=. 11 | set BUILDDIR=_build 12 | 13 | %SPHINXBUILD% >NUL 2>NUL 14 | if errorlevel 9009 ( 15 | echo. 16 | echo.The 'sphinx-build' command was not found. Make sure you have Sphinx 17 | echo.installed, then set the SPHINXBUILD environment variable to point 18 | echo.to the full path of the 'sphinx-build' executable. Alternatively you 19 | echo.may add the Sphinx directory to PATH. 20 | echo. 21 | echo.If you don't have Sphinx installed, grab it from 22 | echo.https://www.sphinx-doc.org/ 23 | exit /b 1 24 | ) 25 | 26 | if "%1" == "" goto help 27 | 28 | %SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% 29 | goto end 30 | 31 | :help 32 | %SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% 33 | 34 | :end 35 | popd 36 | -------------------------------------------------------------------------------- /docs/Makefile: -------------------------------------------------------------------------------- 1 | # Minimal makefile for Sphinx documentation 2 | # 3 | 4 | # You can set these variables from the command line, and also 5 | # from the environment for the first two. 6 | SPHINXOPTS ?= 7 | SPHINXBUILD ?= sphinx-build 8 | SOURCEDIR = source 9 | BUILDDIR = build 10 | 11 | # Put it first so that "make" without argument is like "make help". 12 | help: 13 | @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) 14 | 15 | .PHONY: help Makefile 16 | 17 | # Catch-all target: route all unknown targets to Sphinx using the new 18 | # "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). 19 | %: Makefile 20 | @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) 21 | -------------------------------------------------------------------------------- /docs/make.bat: -------------------------------------------------------------------------------- 1 | @ECHO OFF 2 | 3 | pushd %~dp0 4 | 5 | REM Command file for Sphinx documentation 6 | 7 | if "%SPHINXBUILD%" == "" ( 8 | set SPHINXBUILD=sphinx-build 9 | ) 10 | set SOURCEDIR=source 11 | set BUILDDIR=build 12 | 13 | if "%1" == "" goto help 14 | 15 | %SPHINXBUILD% >NUL 2>NUL 16 | if errorlevel 9009 ( 17 | echo. 18 | echo.The 'sphinx-build' command was not found. Make sure you have Sphinx 19 | echo.installed, then set the SPHINXBUILD environment variable to point 20 | echo.to the full path of the 'sphinx-build' executable. Alternatively you 21 | echo.may add the Sphinx directory to PATH. 22 | echo. 23 | echo.If you don't have Sphinx installed, grab it from 24 | echo.http://sphinx-doc.org/ 25 | exit /b 1 26 | ) 27 | 28 | %SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% 29 | goto end 30 | 31 | :help 32 | %SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% 33 | 34 | :end 35 | popd 36 | -------------------------------------------------------------------------------- /docs/requirements.txt: -------------------------------------------------------------------------------- 1 | sphinx==7.1.2 2 | sphinx-rtd-theme==1.3.0rc1 3 | -------------------------------------------------------------------------------- /docs/source/_static/custom.css: -------------------------------------------------------------------------------- 1 | /* override table width restrictions */ 2 | .wy-table-responsive table td, .wy-table-responsive table th { 3 | white-space: normal; 4 | } 5 | 6 | .wy-table-responsive { 7 | margin-bottom: 24px; 8 | max-width: 100%; 9 | overflow: visible; 10 | } -------------------------------------------------------------------------------- /docs/source/api.rst: -------------------------------------------------------------------------------- 1 | API 2 | === 3 | 4 | .. autosummary:: 5 | :toctree: generated 6 | 7 | lumache 8 | -------------------------------------------------------------------------------- /docs/source/conf.py: -------------------------------------------------------------------------------- 1 | # Configuration file for the Sphinx documentation builder. 2 | 3 | # -- Project information 4 | 5 | project = 'metallicious' 6 | copyright = '2024, Piskorz' 7 | author = 'tkpiskorz' 8 | 9 | release = '0.1' 10 | version = '0.1.0' 11 | 12 | # -- General configuration 13 | 14 | extensions = [ 15 | 'sphinx.ext.duration', 16 | 'sphinx.ext.doctest', 17 | 'sphinx.ext.autodoc', 18 | 'sphinx.ext.autosummary', 19 | 'sphinx.ext.intersphinx', 20 | ] 21 | 22 | intersphinx_mapping = { 23 | 'python': ('https://docs.python.org/3/', None), 24 | 'sphinx': ('https://www.sphinx-doc.org/en/master/', None), 25 | } 26 | intersphinx_disabled_domains = ['std'] 27 | 28 | templates_path = ['_templates'] 29 | 30 | # -- Options for HTML output 31 | 32 | html_theme = 'sphinx_rtd_theme' 33 | html_static_path = ['_static'] 34 | 35 | html_css_files = [ 36 | 'custom.css', 37 | ] 38 | 39 | html_logo = "logo_rect.png" 40 | html_theme_options = {'logo_only': False} 41 | 42 | html_favicon = 'icon.ico' 43 | 44 | # -- Options for EPUB output 45 | epub_show_urls = 'footnote' 46 | -------------------------------------------------------------------------------- /docs/source/custom.css: -------------------------------------------------------------------------------- 1 | /* override table width restrictions */ 2 | .wy-table-responsive table td, .wy-table-responsive table th { 3 | white-space: normal; 4 | } 5 | 6 | .wy-table-responsive { 7 | margin-bottom: 24px; 8 | max-width: 100%; 9 | overflow: visible; 10 | } -------------------------------------------------------------------------------- /docs/source/icon.ico: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/duartegroup/metallicious/3254b283fe22af19bc477ca36b96533d8fd463a4/docs/source/icon.ico -------------------------------------------------------------------------------- /docs/source/images/benzoquinone_complex.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/duartegroup/metallicious/3254b283fe22af19bc477ca36b96533d8fd463a4/docs/source/images/benzoquinone_complex.png -------------------------------------------------------------------------------- /docs/source/images/docs_templates.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/duartegroup/metallicious/3254b283fe22af19bc477ca36b96533d8fd463a4/docs/source/images/docs_templates.png -------------------------------------------------------------------------------- /docs/source/images/favicon.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/duartegroup/metallicious/3254b283fe22af19bc477ca36b96533d8fd463a4/docs/source/images/favicon.png -------------------------------------------------------------------------------- /docs/source/images/gallium.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/duartegroup/metallicious/3254b283fe22af19bc477ca36b96533d8fd463a4/docs/source/images/gallium.png -------------------------------------------------------------------------------- /docs/source/images/lewis.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/duartegroup/metallicious/3254b283fe22af19bc477ca36b96533d8fd463a4/docs/source/images/lewis.png -------------------------------------------------------------------------------- /docs/source/images/periodic_table.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/duartegroup/metallicious/3254b283fe22af19bc477ca36b96533d8fd463a4/docs/source/images/periodic_table.png -------------------------------------------------------------------------------- /docs/source/images/summary.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/duartegroup/metallicious/3254b283fe22af19bc477ca36b96533d8fd463a4/docs/source/images/summary.png -------------------------------------------------------------------------------- /docs/source/images/truncation.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/duartegroup/metallicious/3254b283fe22af19bc477ca36b96533d8fd463a4/docs/source/images/truncation.png -------------------------------------------------------------------------------- /docs/source/index.rst: -------------------------------------------------------------------------------- 1 | Welcome to metallicious's documentation! 2 | =================================== 3 | 4 | *metallicious* is an automated tool for creating force fields for metal-containing systems with a covalent model of the 5 | metal. By utilizing a library of templates, *metallicious* identifies the template that matches the metal site in the 6 | structure. It copies the bonded parameters from the template and performs charge redistribution to account for charge transfer. 7 | In cases where no suitable template is found, *metallicious* automatically performs parameterization. 8 | 9 | .. image:: images/summary.png 10 | :align: center 11 | :width: 400 12 | :alt: Figure of summary of metallicious protocol 13 | 14 | | 15 | 16 | **Limitations**: The code currently supports organometallic structures with metals separated by at least 2 non-metal atoms. Metal clusters are not supported. Additionally, metals of the same type must have the same charge and multiplicity. 17 | 18 | .. note:: 19 | 20 | This project is under active development. 21 | 22 | Contents 23 | -------- 24 | 25 | .. toctree:: 26 | 27 | installation 28 | usage 29 | examples 30 | tutorials 31 | -------------------------------------------------------------------------------- /docs/source/installation.rst: -------------------------------------------------------------------------------- 1 | Installation 2 | ===== 3 | .. _installation: 4 | 5 | 6 | The easiest way to install *metallicious* is to use `Anaconda `_, as *metallicious* depends on external packages. 7 | Create a new conda environment: 8 | 9 | .. code-block:: bash 10 | 11 | conda create --name metallicious 12 | conda activate metallicious 13 | 14 | Install dependencies and the *metallicious*: 15 | 16 | .. code-block:: bash 17 | 18 | conda install rdkit parmed autode psiresp mdanalysis networkx qcelemental==0.25.1 ambertools --channel conda-forge 19 | pip install metallicious 20 | 21 | Alternatively, if you do not need to parametrize templates, install core dependencies + antechamber : 22 | 23 | .. code-block:: bash 24 | 25 | conda install rdkit parmed mdanalysis networkx ambertools --channel conda-forge 26 | pip install metallicious 27 | 28 | 29 | Dependencies 30 | ---------------- 31 | 32 | The core dependencies of *metallicious*: 33 | 34 | * `rdkit `_ 35 | * `networkx `_ 36 | * `MDAnalysis `_ 37 | * `ParmEd `_ 38 | 39 | (**Optional**) the parametrization of templates requires: 40 | 41 | * `autode `_ 42 | * `ORCA `_ 43 | * `psiRESP `_ 44 | 45 | (**Optional**) simple force-field parametrization with General Amber Force-field (GAFF) requires: 46 | 47 | * `ambertools `_ 48 | -------------------------------------------------------------------------------- /docs/source/logo.png: -------------------------------------------------------------------------------- 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-------------------------------------------------------------------------------- 1 | 2 | -------------------------------------------------------------------------------- /metallicious.egg-info/top_level.txt: -------------------------------------------------------------------------------- 1 | metallicious 2 | -------------------------------------------------------------------------------- /metallicious/__init__.py: -------------------------------------------------------------------------------- 1 | #__all__ = ['metallicious'] 2 | 3 | from metallicious.parametrize_new_sites import supramolecular_structure -------------------------------------------------------------------------------- /metallicious/__pycache__/__init__.cpython-311.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/duartegroup/metallicious/3254b283fe22af19bc477ca36b96533d8fd463a4/metallicious/__pycache__/__init__.cpython-311.pyc -------------------------------------------------------------------------------- /metallicious/asserts.py: -------------------------------------------------------------------------------- 1 | import parmed as pmd 2 | import MDAnalysis 3 | 4 | 5 | def compare_topology_and_coords(topol_filename, coord_filename): 6 | ''' 7 | Asserts that force-fields parameters have the same number of atoms as coorindation file 8 | 9 | :param topol_filename: 10 | :param coord_filename: 11 | :return: 12 | ''' 13 | syst = MDAnalysis.Universe(coord_filename) 14 | topol = pmd.load_file(topol_filename) 15 | 16 | assert len(syst.atoms) == len(topol.atoms) 17 | 18 | def check_if_orca_available(): 19 | ''' 20 | Checks if autode and ORCA are available 21 | 22 | :return: 23 | ''' 24 | 25 | try: 26 | import autode as ade 27 | except: 28 | raise ImportError("No autode found") 29 | 30 | method = ade.methods.ORCA() 31 | 32 | if method.is_available is False: 33 | raise NameError("For parametrization of templates, QM software ORCA is required") 34 | 35 | 36 | def check_if_psriresp_available(): 37 | ''' 38 | Checks if psiresp module is available 39 | :return: (bool) 40 | ''' 41 | try: 42 | import psiresp 43 | except: 44 | raise ImportError("No psiresp found") 45 | 46 | def check_if_parametrization_modules_available(): 47 | check_if_orca_available() 48 | check_if_psriresp_available() -------------------------------------------------------------------------------- /metallicious/examples/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/duartegroup/metallicious/3254b283fe22af19bc477ca36b96533d8fd463a4/metallicious/examples/__init__.py -------------------------------------------------------------------------------- /metallicious/examples/example1_quick_start/example1.py: -------------------------------------------------------------------------------- 1 | ''' 2 | Parametrization of the cage, using non-bonded topology of the whole cage 3 | 4 | Equivalent bash command: 5 | metallicious -f ru_pd.pdb -p ru_pd.top -vdw_type uff -metal_and_charges Pd 2 Ru 2 6 | ''' 7 | 8 | from metallicious import supramolecular_structure 9 | cage = supramolecular_structure('ru_pd.pdb', metal_charges={'Ru': 2, 'Pd':2 }, topol='ru_pd.top', LJ_type='uff') 10 | cage.parametrize(out_coord='out.pdb', out_topol='out.top') 11 | -------------------------------------------------------------------------------- /metallicious/examples/example2_no_topology/example2.py: -------------------------------------------------------------------------------- 1 | ''' 2 | Parametrization of the homoleptic cage using antechamber interface 3 | 4 | Equivalent command line prompt: 5 | metallicious -f ru_pd.xyz -vdw_type uff -metal_and_charges Pd 2 Ru 2 -prepare_topol 6 | ''' 7 | 8 | from metallicious import supramolecular_structure 9 | cage = supramolecular_structure('ru_pd.xyz', metal_charges={'Ru': 2, 'Pd':2 }, LJ_type='uff') 10 | cage.prepare_initial_topology() 11 | cage.parametrize(out_coord='out.pdb', out_topol='out.top') 12 | 13 | -------------------------------------------------------------------------------- /metallicious/examples/example3_only_linker_topology/example3.py: -------------------------------------------------------------------------------- 1 | ''' 2 | Parametrization of the homoleptic cage using only topology of the linker 3 | 4 | Equivalent command line prompt: 5 | metallicious -f ru_pd.xyz -vdw_type uff -metal_and_charges Pd 2 Ru 2 -prepare_topol -linker_topol linker.top 6 | ''' 7 | 8 | from metallicious import supramolecular_structure 9 | cage = supramolecular_structure('ru_pd.xyz', metal_charges={'Ru': 2, 'Pd':2 }, LJ_type='uff') 10 | cage.prepare_initial_topology(homoleptic_ligand_topol='linker.top') 11 | cage.parametrize(out_coord='out.pdb', out_topol='out.top') -------------------------------------------------------------------------------- /metallicious/examples/example4_template_parametrization/example4.py: -------------------------------------------------------------------------------- 1 | ''' 2 | Parametrization cage using trunction scheme 3 | 4 | Equivalent command line prompt: 5 | metallicious -f cage.pdb -p topol.top -vdw_type merz-opc -metal_and_charges Pd 2 -truncate dihedral 6 | ''' 7 | 8 | from metallicious import supramolecular_structure 9 | # This will not work becasue there is no exact template for this site: 10 | # cage = supramolecular_structure('cage.pdb', topol='topol.top', metal_charges={'Pd':2 }, vdw_type='merz-opc') 11 | 12 | cage = supramolecular_structure('cage.pdb', topol='topol.top', metal_charges_mult={'Pd': (2,1)}, LJ_type='merz-opc') 13 | cage.parametrize(out_coord='out.pdb', out_topol='out.top') 14 | 15 | -------------------------------------------------------------------------------- /metallicious/examples/example5_truncation_scheme/example5.py: -------------------------------------------------------------------------------- 1 | ''' 2 | Parametrization cage using trunction scheme 3 | 4 | Equivalent command line prompt: 5 | metallicious -f cage.pdb -p topol.top -vdw_type merz-opc -metal_and_charges Pd 2 -truncate dihedral 6 | ''' 7 | 8 | from metallicious import supramolecular_structure 9 | # This will not work becasue there is no exact template for this site: 10 | # cage = supramolecular_structure('cage.pdb', topol='topol.top', metal_charges={'Pd':2 }, vdw_type='merz-opc') 11 | 12 | cage = supramolecular_structure('cage.pdb', topol='topol.top', metal_charges={'Pd':2 }, LJ_type='merz-opc', truncation_scheme='dihedral') 13 | cage.parametrize(out_coord='out.pdb', out_topol='out.top') 14 | 15 | -------------------------------------------------------------------------------- /metallicious/examples/example5_truncation_scheme/temp.pdb: -------------------------------------------------------------------------------- 1 | HEADER 2 | TITLE MDANALYSIS FRAME 0: Created by PDBWriter 3 | REMARK 285 UNITARY VALUES FOR THE UNIT CELL AUTOMATICALLY SET 4 | REMARK 285 BY MDANALYSIS PDBWRITER BECAUSE UNIT CELL INFORMATION 5 | REMARK 285 WAS MISSING. 6 | REMARK 285 PROTEIN DATA BANK CONVENTIONS REQUIRE THAT 7 | REMARK 285 CRYST1 RECORD IS INCLUDED, BUT THE VALUES ON 8 | REMARK 285 THIS RECORD ARE MEANINGLESS. 9 | CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 10 | REMARK 285 UNITARY VALUES FOR THE UNIT CELL AUTOMATICALLY SET 11 | REMARK 285 BY MDANALYSIS PDBWRITER BECAUSE UNIT CELL INFORMATION 12 | REMARK 285 WAS MISSING. 13 | REMARK 285 PROTEIN DATA BANK CONVENTIONS REQUIRE THAT 14 | REMARK 285 CRYST1 RECORD IS INCLUDED, BUT THE VALUES ON 15 | REMARK 285 THIS RECORD ARE MEANINGLESS. 16 | ATOM 1 Pd UNK X 1 -1.988 12.232 11.571 1.00 0.00 SYSTPD 17 | ATOM 2 C UNK X 1 -5.282 14.855 10.774 1.00 0.00 SYST C 18 | ATOM 3 C UNK X 1 -6.202 12.844 11.756 1.00 0.00 SYST C 19 | ATOM 4 C UNK X 1 -4.915 12.333 11.856 1.00 0.00 SYST C 20 | ATOM 5 N UNK X 1 -3.853 13.034 11.431 1.00 0.00 SYST N 21 | ATOM 6 C UNK X 1 -4.029 14.259 10.904 1.00 0.00 SYST C 22 | ATOM 7 H UNK X 1 -4.723 11.348 12.285 1.00 0.00 SYST H 23 | ATOM 8 H UNK X 1 -3.129 14.781 10.569 1.00 0.00 SYST H 24 | ATOM 9 C UNK X 1 -2.747 12.943 15.724 1.00 0.00 SYST C 25 | ATOM 10 C UNK X 1 -2.260 10.584 15.496 1.00 0.00 SYST C 26 | ATOM 11 C UNK X 1 -2.089 10.775 14.132 1.00 0.00 SYST C 27 | ATOM 12 N UNK X 1 -2.243 11.986 13.574 1.00 0.00 SYST N 28 | ATOM 13 C UNK X 1 -2.565 13.039 14.345 1.00 0.00 SYST C 29 | ATOM 14 H UNK X 1 -1.821 9.950 13.468 1.00 0.00 SYST H 30 | ATOM 15 H UNK X 1 -2.685 13.999 13.837 1.00 0.00 SYST H 31 | ATOM 16 C UNK X 1 -0.505 13.410 7.729 1.00 0.00 SYST C 32 | ATOM 17 C UNK X 1 -2.481 12.068 7.342 1.00 0.00 SYST C 33 | ATOM 18 C UNK X 1 -2.618 11.918 8.715 1.00 0.00 SYST C 34 | ATOM 19 N UNK X 1 -1.744 12.475 9.567 1.00 0.00 SYST N 35 | ATOM 20 C UNK X 1 -0.715 13.197 9.091 1.00 0.00 SYST C 36 | ATOM 21 H UNK X 1 -3.442 11.346 9.148 1.00 0.00 SYST H 37 | ATOM 22 H UNK X 1 -0.030 13.619 9.830 1.00 0.00 SYST H 38 | ATOM 23 C UNK X 1 2.057 11.403 12.711 1.00 0.00 SYST C 39 | ATOM 24 C UNK X 1 1.450 9.768 11.034 1.00 0.00 SYST C 40 | ATOM 25 C UNK X 1 0.195 10.356 10.948 1.00 0.00 SYST C 41 | ATOM 26 N UNK X 1 -0.131 11.413 11.708 1.00 0.00 SYST N 42 | ATOM 27 C UNK X 1 0.771 11.922 12.566 1.00 0.00 SYST C 43 | ATOM 28 H UNK X 1 -0.566 9.981 10.261 1.00 0.00 SYST H 44 | ATOM 29 H UNK X 1 0.449 12.777 13.164 1.00 0.00 SYST H 45 | END 46 | -------------------------------------------------------------------------------- /metallicious/examples/example5_truncation_scheme/temp/out.pse: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/duartegroup/metallicious/3254b283fe22af19bc477ca36b96533d8fd463a4/metallicious/examples/example5_truncation_scheme/temp/out.pse -------------------------------------------------------------------------------- /metallicious/examples/example6_mof/example6.py: -------------------------------------------------------------------------------- 1 | ''' 2 | Parametrization of the cage, using non-bonded topology of the whole cage 3 | 4 | Equivalent bash command: 5 | metallicious -f protein.gro -p protein.top -vdw_type merz-opc -metal_and_charges Zn 2 6 | ''' 7 | 8 | from metallicious import supramolecular_structure 9 | cage = supramolecular_structure('Co_mof.pdb', metal_charges={'Co':2}, LJ_type='merz-opc') 10 | cage.prepare_initial_topology() 11 | cage.parametrize(out_coord='out.pdb', out_topol='out.top') 12 | -------------------------------------------------------------------------------- /metallicious/examples/tutorial5/final.zip: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/duartegroup/metallicious/3254b283fe22af19bc477ca36b96533d8fd463a4/metallicious/examples/tutorial5/final.zip -------------------------------------------------------------------------------- /metallicious/examples/tutorial5/tutorial.zip: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/duartegroup/metallicious/3254b283fe22af19bc477ca36b96533d8fd463a4/metallicious/examples/tutorial5/tutorial.zip -------------------------------------------------------------------------------- /metallicious/initial_site.py: -------------------------------------------------------------------------------- 1 | import parmed as pmd 2 | import os 3 | 4 | # try: 5 | from metallicious.data import name2mass 6 | from metallicious.data import name_to_atomic_number 7 | from metallicious.data import vdw_data 8 | from metallicious.antechamber_interface import antechamber 9 | # except: 10 | # from data import name2mass 11 | # from data import name_to_atomic_number 12 | # from data import vdw_data 13 | # from antechamber_interface import antechamber 14 | 15 | 16 | def create_metal_topol(metal_name, metal_charge, vdw_data_name): 17 | ''' 18 | Creates force-field parameters of the metal, reading from library of available L-J parameters 19 | 20 | :param metal_name: (string) name of the metal 21 | :param metal_charge: (int) charge of the metal 22 | :param vdw_data_name: (string) name of the library from which take the L-J parameters 23 | :return: (parmed.topologyobject) topology 24 | ''' 25 | data = vdw_data[vdw_data_name] 26 | 27 | if f"{metal_name.title():}{metal_charge:}" in data: 28 | name = f"{metal_name.title():}{metal_charge:}" 29 | elif metal_name in data: 30 | name = metal_name 31 | else: 32 | raise Exception(f"Metal {metal_name.title():}{metal_charge:} not in the library") 33 | 34 | if name in data: 35 | eps = data[name][0] 36 | radius = data[name][1] 37 | 38 | mass = name2mass[metal_name] 39 | atomic_number = name_to_atomic_number[metal_name] 40 | 41 | new_atom = pmd.topologyobjects.Atom(atomic_number=atomic_number, type=metal_name, name=metal_name, 42 | rmin=radius, epsilon=eps, mass=mass, charge=metal_charge, number=0) 43 | 44 | struct = pmd.structure.Structure() 45 | struct.add_atom(new_atom, metal_name, metal_name) 46 | 47 | # I don't know how to convert struct to GromacsTopol, easiest is to save and load it ... 48 | struct.save(f"{name:s}.top", overwrite=True) 49 | metal_topol = pmd.load_file(f"{name:s}.top") 50 | metal_topol.defaults.fudgeLJ = 0.5 51 | metal_topol.defaults.fudgeQQ = 0.833333 52 | 53 | os.remove(f"{name:s}.top") 54 | 55 | 56 | ''' I have several attemps how to make it without file but did not manage to figure out: 57 | metal_topol = pmd.gromacs.GromacsTopologyFile() 58 | metal_topol.add_atom(new_atom, metal_name, metal_name) 59 | #atomtype = pmd.topologyobjects.AtomType("Pd", None, 106) 60 | 61 | residue = pmd.topologyobjects.Residue(metal_name, number=0) 62 | residue.add_atom(new_atom) 63 | residue_list = pmd.topologyobjects.ResidueList() 64 | residue_list.append(residue) 65 | metal_topol.residues = residue_list 66 | ''' 67 | 68 | return metal_topol 69 | 70 | 71 | -------------------------------------------------------------------------------- /metallicious/library/.Pd1.top.swn: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/duartegroup/metallicious/3254b283fe22af19bc477ca36b96533d8fd463a4/metallicious/library/.Pd1.top.swn -------------------------------------------------------------------------------- /metallicious/library/Ga_3_uff_0.pdb: -------------------------------------------------------------------------------- 1 | TITLE MDANALYSIS FRAME 0: Created by PDBWriter 2 | CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 3 | REMARK 285 UNITARY VALUES FOR THE UNIT CELL AUTOMATICALLY SET 4 | REMARK 285 BY MDANALYSIS PDBWRITER BECAUSE UNIT CELL INFORMATION 5 | REMARK 285 WAS MISSING. 6 | REMARK 285 PROTEIN DATA BANK CONVENTIONS REQUIRE THAT 7 | REMARK 285 CRYST1 RECORD IS INCLUDED, BUT THE VALUES ON 8 | REMARK 285 THIS RECORD ARE MEANINGLESS. 9 | ATOM 1 Ga UNK X 1 -20.461 -28.199 -18.305 1.00 0.00 SYSTGA 10 | ATOM 2 C UNK X 1 -23.084 -25.353 -15.420 1.00 0.00 SYST C 11 | ATOM 3 C UNK X 1 -21.976 -26.254 -14.961 1.00 0.00 SYST C 12 | ATOM 4 C UNK X 1 -21.315 -27.017 -15.942 1.00 0.00 SYST C 13 | ATOM 5 O UNK X 1 -21.621 -26.976 -17.203 1.00 0.00 SYST O 14 | ATOM 6 C UNK X 1 -20.234 -27.904 -15.553 1.00 0.00 SYST C 15 | ATOM 7 O UNK X 1 -19.664 -28.577 -16.503 1.00 0.00 SYST O 16 | ATOM 8 C UNK X 1 -19.883 -27.970 -14.194 1.00 0.00 SYST C 17 | ATOM 9 C UNK X 1 -20.558 -27.200 -13.223 1.00 0.00 SYST C 18 | ATOM 10 C UNK X 1 -21.591 -26.351 -13.604 1.00 0.00 SYST C 19 | ATOM 11 H UNK X 1 -19.065 -28.643 -13.913 1.00 0.00 SYST H 20 | ATOM 12 H UNK X 1 -20.263 -27.272 -12.167 1.00 0.00 SYST H 21 | ATOM 13 H UNK X 1 -22.122 -25.746 -12.854 1.00 0.00 SYST H 22 | ATOM 14 C UNK X 1 -23.249 -27.637 -22.201 1.00 0.00 SYST C 23 | ATOM 15 C UNK X 1 -23.373 -28.758 -21.212 1.00 0.00 SYST C 24 | ATOM 16 C UNK X 1 -22.474 -28.764 -20.129 1.00 0.00 SYST C 25 | ATOM 17 O UNK X 1 -21.565 -27.855 -19.954 1.00 0.00 SYST O 26 | ATOM 18 C UNK X 1 -22.540 -29.832 -19.148 1.00 0.00 SYST C 27 | ATOM 19 O UNK X 1 -21.680 -29.786 -18.180 1.00 0.00 SYST O 28 | ATOM 20 C UNK X 1 -23.519 -30.827 -19.312 1.00 0.00 SYST C 29 | ATOM 21 C UNK X 1 -24.415 -30.803 -20.401 1.00 0.00 SYST C 30 | ATOM 22 C UNK X 1 -24.342 -29.780 -21.341 1.00 0.00 SYST C 31 | ATOM 23 H UNK X 1 -23.560 -31.627 -18.563 1.00 0.00 SYST H 32 | ATOM 24 H UNK X 1 -25.171 -31.594 -20.505 1.00 0.00 SYST H 33 | ATOM 25 H UNK X 1 -25.035 -29.755 -22.194 1.00 0.00 SYST H 34 | ATOM 26 C UNK X 1 -17.252 -24.799 -19.506 1.00 0.00 SYST C 35 | ATOM 27 C UNK X 1 -17.109 -26.261 -19.809 1.00 0.00 SYST C 36 | ATOM 28 C UNK X 1 -18.147 -27.114 -19.388 1.00 0.00 SYST C 37 | ATOM 29 O UNK X 1 -19.202 -26.695 -18.759 1.00 0.00 SYST O 38 | ATOM 30 C UNK X 1 -18.058 -28.538 -19.654 1.00 0.00 SYST C 39 | ATOM 31 O UNK X 1 -19.045 -29.269 -19.239 1.00 0.00 SYST O 40 | ATOM 32 C UNK X 1 -16.926 -29.019 -20.334 1.00 0.00 SYST C 41 | ATOM 33 C UNK X 1 -15.896 -28.151 -20.750 1.00 0.00 SYST C 42 | ATOM 34 C UNK X 1 -15.986 -26.788 -20.490 1.00 0.00 SYST C 43 | ATOM 35 H UNK X 1 -16.872 -30.097 -20.530 1.00 0.00 SYST H 44 | ATOM 36 H UNK X 1 -15.021 -28.554 -21.279 1.00 0.00 SYST H 45 | ATOM 37 H UNK X 1 -15.187 -26.104 -20.810 1.00 0.00 SYST H 46 | END 47 | -------------------------------------------------------------------------------- /metallicious/library/Zn_2_merz-opc_1.pdb: -------------------------------------------------------------------------------- 1 | TITLE MDANALYSIS FRAME 0: Created by PDBWriter 2 | CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 3 | REMARK 285 UNITARY VALUES FOR THE UNIT CELL AUTOMATICALLY SET 4 | REMARK 285 BY MDANALYSIS PDBWRITER BECAUSE UNIT CELL INFORMATION 5 | REMARK 285 WAS MISSING. 6 | REMARK 285 PROTEIN DATA BANK CONVENTIONS REQUIRE THAT 7 | REMARK 285 CRYST1 RECORD IS INCLUDED, BUT THE VALUES ON 8 | REMARK 285 THIS RECORD ARE MEANINGLESS. 9 | ATOM 1 Zn UNK X 1 36.791 36.717 30.007 1.00 0.00 SYSTZN 10 | ATOM 2 N UNK X 1 40.131 33.746 26.565 1.00 0.00 SYST N 11 | ATOM 3 C UNK X 1 39.444 35.031 26.606 1.00 0.00 SYST C 12 | ATOM 4 H UNK X 1 38.743 35.057 25.751 1.00 0.00 SYST H 13 | ATOM 5 C UNK X 1 38.616 35.215 27.881 1.00 0.00 SYST C 14 | ATOM 6 H UNK X 1 39.307 35.249 28.744 1.00 0.00 SYST H 15 | ATOM 7 H UNK X 1 37.980 34.323 28.021 1.00 0.00 SYST H 16 | ATOM 8 S UNK X 1 37.570 36.714 27.846 1.00 0.00 SYST S 17 | ATOM 9 C UNK X 1 40.457 36.147 26.420 1.00 0.00 SYST C 18 | ATOM 10 N UNK X 1 39.955 37.553 30.199 1.00 0.00 SYST N 19 | ATOM 11 C UNK X 1 39.812 38.878 30.795 1.00 0.00 SYST C 20 | ATOM 12 H UNK X 1 40.392 39.637 30.224 1.00 0.00 SYST H 21 | ATOM 13 C UNK X 1 38.359 39.355 30.714 1.00 0.00 SYST C 22 | ATOM 14 H UNK X 1 38.072 39.432 29.653 1.00 0.00 SYST H 23 | ATOM 15 H UNK X 1 38.307 40.371 31.137 1.00 0.00 SYST H 24 | ATOM 16 S UNK X 1 37.149 38.318 31.609 1.00 0.00 SYST S 25 | ATOM 17 C UNK X 1 40.340 38.861 32.220 1.00 0.00 SYST C 26 | ATOM 18 C UNK X 1 37.679 31.548 32.388 1.00 0.00 SYST C 27 | ATOM 19 C UNK X 1 37.739 32.939 31.872 1.00 0.00 SYST C 28 | ATOM 20 N UNK X 1 38.833 33.763 32.040 1.00 0.00 SYST N 29 | ATOM 21 H UNK X 1 39.689 33.519 32.520 1.00 0.00 SYST H 30 | ATOM 22 C UNK X 1 38.576 34.959 31.467 1.00 0.00 SYST C 31 | ATOM 23 H UNK X 1 39.259 35.819 31.393 1.00 0.00 SYST H 32 | ATOM 24 N UNK X 1 37.371 34.941 30.935 1.00 0.00 SYST N 33 | ATOM 25 C UNK X 1 36.837 33.703 31.173 1.00 0.00 SYST C 34 | ATOM 26 H UNK X 1 35.838 33.431 30.838 1.00 0.00 SYST H 35 | ATOM 27 C UNK X 1 31.302 35.828 28.682 1.00 0.00 SYST C 36 | ATOM 28 C UNK X 1 32.579 36.267 29.298 1.00 0.00 SYST C 37 | ATOM 29 N UNK X 1 32.655 37.237 30.276 1.00 0.00 SYST N 38 | ATOM 30 H UNK X 1 31.873 37.748 30.665 1.00 0.00 SYST H 39 | ATOM 31 C UNK X 1 33.950 37.415 30.614 1.00 0.00 SYST C 40 | ATOM 32 H UNK X 1 34.333 38.143 31.332 1.00 0.00 SYST H 41 | ATOM 33 N UNK X 1 34.708 36.604 29.910 1.00 0.00 SYST N 42 | ATOM 34 C UNK X 1 33.882 35.889 29.084 1.00 0.00 SYST C 43 | ATOM 35 H UNK X 1 34.278 35.175 28.366 1.00 0.00 SYST H 44 | END 45 | -------------------------------------------------------------------------------- /metallicious/library/Zn_2_uff_1.pdb: -------------------------------------------------------------------------------- 1 | TITLE MDANALYSIS FRAME 0: Created by PDBWriter 2 | CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 3 | REMARK 285 UNITARY VALUES FOR THE UNIT CELL AUTOMATICALLY SET 4 | REMARK 285 BY MDANALYSIS PDBWRITER BECAUSE UNIT CELL INFORMATION 5 | REMARK 285 WAS MISSING. 6 | REMARK 285 PROTEIN DATA BANK CONVENTIONS REQUIRE THAT 7 | REMARK 285 CRYST1 RECORD IS INCLUDED, BUT THE VALUES ON 8 | REMARK 285 THIS RECORD ARE MEANINGLESS. 9 | ATOM 1 Zn UNK X 1 45.184 10.579 -27.412 1.00 0.00 SYSTZN 10 | ATOM 2 N UNK X 1 44.841 7.282 -22.821 1.00 0.00 SYST N 11 | ATOM 3 C UNK X 1 44.827 7.143 -24.285 1.00 0.00 SYST C 12 | ATOM 4 H UNK X 1 43.961 6.505 -24.545 1.00 0.00 SYST H 13 | ATOM 5 C UNK X 1 44.640 8.484 -24.997 1.00 0.00 SYST C 14 | ATOM 6 H UNK X 1 43.766 8.990 -24.541 1.00 0.00 SYST H 15 | ATOM 7 H UNK X 1 45.520 9.130 -24.804 1.00 0.00 SYST H 16 | ATOM 8 S UNK X 1 44.421 8.342 -26.796 1.00 0.00 SYST S 17 | ATOM 9 C UNK X 1 46.092 6.431 -24.731 1.00 0.00 SYST C 18 | ATOM 10 N UNK X 1 47.842 8.317 -27.663 1.00 0.00 SYST N 19 | ATOM 11 C UNK X 1 48.840 9.224 -27.132 1.00 0.00 SYST C 20 | ATOM 12 H UNK X 1 49.719 9.182 -27.813 1.00 0.00 SYST H 21 | ATOM 13 C UNK X 1 48.420 10.706 -27.088 1.00 0.00 SYST C 22 | ATOM 14 H UNK X 1 49.288 11.311 -26.761 1.00 0.00 SYST H 23 | ATOM 15 H UNK X 1 48.178 11.023 -28.116 1.00 0.00 SYST H 24 | ATOM 16 S UNK X 1 47.014 11.099 -25.991 1.00 0.00 SYST S 25 | ATOM 17 C UNK X 1 49.298 8.738 -25.764 1.00 0.00 SYST C 26 | ATOM 18 N UNK X 1 41.466 9.515 -28.078 1.00 0.00 SYST N 27 | ATOM 19 C UNK X 1 40.947 10.456 -27.101 1.00 0.00 SYST C 28 | ATOM 20 H UNK X 1 40.279 9.950 -26.360 1.00 0.00 SYST H 29 | ATOM 21 C UNK X 1 42.087 11.043 -26.260 1.00 0.00 SYST C 30 | ATOM 22 H UNK X 1 41.633 11.660 -25.463 1.00 0.00 SYST H 31 | ATOM 23 H UNK X 1 42.597 10.197 -25.771 1.00 0.00 SYST H 32 | ATOM 24 S UNK X 1 43.318 12.046 -27.150 1.00 0.00 SYST S 33 | ATOM 25 C UNK X 1 40.123 11.533 -27.796 1.00 0.00 SYST C 34 | ATOM 26 N UNK X 1 43.205 11.781 -30.636 1.00 0.00 SYST N 35 | ATOM 27 C UNK X 1 43.561 10.502 -31.225 1.00 0.00 SYST C 36 | ATOM 28 H UNK X 1 44.145 10.712 -32.146 1.00 0.00 SYST H 37 | ATOM 29 C UNK X 1 44.438 9.619 -30.324 1.00 0.00 SYST C 38 | ATOM 30 H UNK X 1 43.821 9.271 -29.480 1.00 0.00 SYST H 39 | ATOM 31 H UNK X 1 44.757 8.720 -30.884 1.00 0.00 SYST H 40 | ATOM 32 S UNK X 1 45.915 10.480 -29.679 1.00 0.00 SYST S 41 | ATOM 33 C UNK X 1 42.289 9.755 -31.612 1.00 0.00 SYST C 42 | END 43 | -------------------------------------------------------------------------------- /metallicious/library/Zn_2_uff_2.pdb: -------------------------------------------------------------------------------- 1 | TITLE MDANALYSIS FRAME 0: Created by PDBWriter 2 | CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 3 | REMARK 285 UNITARY VALUES FOR THE UNIT CELL AUTOMATICALLY SET 4 | REMARK 285 BY MDANALYSIS PDBWRITER BECAUSE UNIT CELL INFORMATION 5 | REMARK 285 WAS MISSING. 6 | REMARK 285 PROTEIN DATA BANK CONVENTIONS REQUIRE THAT 7 | REMARK 285 CRYST1 RECORD IS INCLUDED, BUT THE VALUES ON 8 | REMARK 285 THIS RECORD ARE MEANINGLESS. 9 | ATOM 1 Zn UNK X 1 36.791 36.717 30.007 1.00 0.00 SYSTZN 10 | ATOM 2 N UNK X 1 40.131 33.746 26.565 1.00 0.00 SYST N 11 | ATOM 3 C UNK X 1 39.444 35.031 26.606 1.00 0.00 SYST C 12 | ATOM 4 H UNK X 1 38.743 35.057 25.751 1.00 0.00 SYST H 13 | ATOM 5 C UNK X 1 38.616 35.215 27.881 1.00 0.00 SYST C 14 | ATOM 6 H UNK X 1 39.307 35.249 28.744 1.00 0.00 SYST H 15 | ATOM 7 H UNK X 1 37.980 34.323 28.021 1.00 0.00 SYST H 16 | ATOM 8 S UNK X 1 37.570 36.714 27.846 1.00 0.00 SYST S 17 | ATOM 9 C UNK X 1 40.457 36.147 26.420 1.00 0.00 SYST C 18 | ATOM 10 N UNK X 1 39.955 37.553 30.199 1.00 0.00 SYST N 19 | ATOM 11 C UNK X 1 39.812 38.878 30.795 1.00 0.00 SYST C 20 | ATOM 12 H UNK X 1 40.392 39.637 30.224 1.00 0.00 SYST H 21 | ATOM 13 C UNK X 1 38.359 39.355 30.714 1.00 0.00 SYST C 22 | ATOM 14 H UNK X 1 38.072 39.432 29.653 1.00 0.00 SYST H 23 | ATOM 15 H UNK X 1 38.307 40.371 31.137 1.00 0.00 SYST H 24 | ATOM 16 S UNK X 1 37.149 38.318 31.609 1.00 0.00 SYST S 25 | ATOM 17 C UNK X 1 40.340 38.861 32.220 1.00 0.00 SYST C 26 | ATOM 18 C UNK X 1 37.679 31.548 32.388 1.00 0.00 SYST C 27 | ATOM 19 C UNK X 1 37.739 32.939 31.872 1.00 0.00 SYST C 28 | ATOM 20 N UNK X 1 38.833 33.763 32.040 1.00 0.00 SYST N 29 | ATOM 21 H UNK X 1 39.689 33.519 32.520 1.00 0.00 SYST H 30 | ATOM 22 C UNK X 1 38.576 34.959 31.467 1.00 0.00 SYST C 31 | ATOM 23 H UNK X 1 39.259 35.819 31.393 1.00 0.00 SYST H 32 | ATOM 24 N UNK X 1 37.371 34.941 30.935 1.00 0.00 SYST N 33 | ATOM 25 C UNK X 1 36.837 33.703 31.173 1.00 0.00 SYST C 34 | ATOM 26 H UNK X 1 35.838 33.431 30.838 1.00 0.00 SYST H 35 | ATOM 27 C UNK X 1 31.302 35.828 28.682 1.00 0.00 SYST C 36 | ATOM 28 C UNK X 1 32.579 36.267 29.298 1.00 0.00 SYST C 37 | ATOM 29 N UNK X 1 32.655 37.237 30.276 1.00 0.00 SYST N 38 | ATOM 30 H UNK X 1 31.873 37.748 30.665 1.00 0.00 SYST H 39 | ATOM 31 C UNK X 1 33.950 37.415 30.614 1.00 0.00 SYST C 40 | ATOM 32 H UNK X 1 34.333 38.143 31.332 1.00 0.00 SYST H 41 | ATOM 33 N UNK X 1 34.708 36.604 29.910 1.00 0.00 SYST N 42 | ATOM 34 C UNK X 1 33.882 35.889 29.084 1.00 0.00 SYST C 43 | ATOM 35 H UNK X 1 34.278 35.175 28.366 1.00 0.00 SYST H 44 | END 45 | -------------------------------------------------------------------------------- /metallicious/library/Zn_2_zhang-opc_1.pdb: -------------------------------------------------------------------------------- 1 | TITLE MDANALYSIS FRAME 0: Created by PDBWriter 2 | CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 3 | REMARK 285 UNITARY VALUES FOR THE UNIT CELL AUTOMATICALLY SET 4 | REMARK 285 BY MDANALYSIS PDBWRITER BECAUSE UNIT CELL INFORMATION 5 | REMARK 285 WAS MISSING. 6 | REMARK 285 PROTEIN DATA BANK CONVENTIONS REQUIRE THAT 7 | REMARK 285 CRYST1 RECORD IS INCLUDED, BUT THE VALUES ON 8 | REMARK 285 THIS RECORD ARE MEANINGLESS. 9 | ATOM 1 Zn UNK X 1 36.791 36.717 30.007 1.00 0.00 SYSTZN 10 | ATOM 2 N UNK X 1 40.131 33.746 26.565 1.00 0.00 SYST N 11 | ATOM 3 C UNK X 1 39.444 35.031 26.606 1.00 0.00 SYST C 12 | ATOM 4 H UNK X 1 38.743 35.057 25.751 1.00 0.00 SYST H 13 | ATOM 5 C UNK X 1 38.616 35.215 27.881 1.00 0.00 SYST C 14 | ATOM 6 H UNK X 1 39.307 35.249 28.744 1.00 0.00 SYST H 15 | ATOM 7 H UNK X 1 37.980 34.323 28.021 1.00 0.00 SYST H 16 | ATOM 8 S UNK X 1 37.570 36.714 27.846 1.00 0.00 SYST S 17 | ATOM 9 C UNK X 1 40.457 36.147 26.420 1.00 0.00 SYST C 18 | ATOM 10 N UNK X 1 39.955 37.553 30.199 1.00 0.00 SYST N 19 | ATOM 11 C UNK X 1 39.812 38.878 30.795 1.00 0.00 SYST C 20 | ATOM 12 H UNK X 1 40.392 39.637 30.224 1.00 0.00 SYST H 21 | ATOM 13 C UNK X 1 38.359 39.355 30.714 1.00 0.00 SYST C 22 | ATOM 14 H UNK X 1 38.072 39.432 29.653 1.00 0.00 SYST H 23 | ATOM 15 H UNK X 1 38.307 40.371 31.137 1.00 0.00 SYST H 24 | ATOM 16 S UNK X 1 37.149 38.318 31.609 1.00 0.00 SYST S 25 | ATOM 17 C UNK X 1 40.340 38.861 32.220 1.00 0.00 SYST C 26 | ATOM 18 C UNK X 1 37.679 31.548 32.388 1.00 0.00 SYST C 27 | ATOM 19 C UNK X 1 37.739 32.939 31.872 1.00 0.00 SYST C 28 | ATOM 20 N UNK X 1 38.833 33.763 32.040 1.00 0.00 SYST N 29 | ATOM 21 H UNK X 1 39.689 33.519 32.520 1.00 0.00 SYST H 30 | ATOM 22 C UNK X 1 38.576 34.959 31.467 1.00 0.00 SYST C 31 | ATOM 23 H UNK X 1 39.259 35.819 31.393 1.00 0.00 SYST H 32 | ATOM 24 N UNK X 1 37.371 34.941 30.935 1.00 0.00 SYST N 33 | ATOM 25 C UNK X 1 36.837 33.703 31.173 1.00 0.00 SYST C 34 | ATOM 26 H UNK X 1 35.838 33.431 30.838 1.00 0.00 SYST H 35 | ATOM 27 C UNK X 1 31.302 35.828 28.682 1.00 0.00 SYST C 36 | ATOM 28 C UNK X 1 32.579 36.267 29.298 1.00 0.00 SYST C 37 | ATOM 29 N UNK X 1 32.655 37.237 30.276 1.00 0.00 SYST N 38 | ATOM 30 H UNK X 1 31.873 37.748 30.665 1.00 0.00 SYST H 39 | ATOM 31 C UNK X 1 33.950 37.415 30.614 1.00 0.00 SYST C 40 | ATOM 32 H UNK X 1 34.333 38.143 31.332 1.00 0.00 SYST H 41 | ATOM 33 N UNK X 1 34.708 36.604 29.910 1.00 0.00 SYST N 42 | ATOM 34 C UNK X 1 33.882 35.889 29.084 1.00 0.00 SYST C 43 | ATOM 35 H UNK X 1 34.278 35.175 28.366 1.00 0.00 SYST H 44 | END 45 | -------------------------------------------------------------------------------- /metallicious/library/metallicious.egg-info/PKG-INFO: -------------------------------------------------------------------------------- 1 | Metadata-Version: 2.1 2 | Name: metallicious 3 | Version: 0.2.12 4 | -------------------------------------------------------------------------------- /metallicious/library/metallicious.egg-info/SOURCES.txt: -------------------------------------------------------------------------------- 1 | README.md 2 | pyproject.toml 3 | setup.py 4 | metallicious/library/metallicious.egg-info/PKG-INFO 5 | metallicious/library/metallicious.egg-info/SOURCES.txt 6 | metallicious/library/metallicious.egg-info/dependency_links.txt 7 | metallicious/library/metallicious.egg-info/entry_points.txt 8 | metallicious/library/metallicious.egg-info/requires.txt 9 | metallicious/library/metallicious.egg-info/top_level.txt -------------------------------------------------------------------------------- /metallicious/library/metallicious.egg-info/dependency_links.txt: -------------------------------------------------------------------------------- 1 | 2 | -------------------------------------------------------------------------------- /metallicious/library/metallicious.egg-info/entry_points.txt: -------------------------------------------------------------------------------- 1 | [console_scripts] 2 | metallicious = metallicious.__main__:main 3 | -------------------------------------------------------------------------------- /metallicious/library/metallicious.egg-info/requires.txt: -------------------------------------------------------------------------------- 1 | numpy 2 | MDAnalysis 3 | rdkit 4 | parmed 5 | networkx 6 | psiresp 7 | -------------------------------------------------------------------------------- /metallicious/library/metallicious.egg-info/top_level.txt: -------------------------------------------------------------------------------- 1 | 2 | -------------------------------------------------------------------------------- /metallicious/log.py: -------------------------------------------------------------------------------- 1 | """ 2 | Set up logging with the standard python logging module. Set the log level with 3 | $METALLICIOUS_LOG_LEVEL = {'', INFO, WARNING, DEBUG} 4 | 5 | i.e. export METALLICIOUS_LOG_LEVEL=DEBUG 6 | 7 | """ 8 | import logging 9 | import os 10 | 11 | 12 | def get_log_level(): 13 | try: 14 | log_level_str = os.environ['METALLICIOUS_LOG_LEVEL'] 15 | except KeyError: 16 | log_level_str = '' 17 | if log_level_str == 'DEBUG': 18 | return logging.DEBUG 19 | if log_level_str == 'WARNING': 20 | return logging.WARNING 21 | if log_level_str == 'INFO': 22 | return logging.INFO 23 | return logging.ERROR 24 | 25 | 26 | logging.basicConfig(level=get_log_level(), 27 | format='%(name)-12s: %(levelname)-8s %(message)s') 28 | logger = logging.getLogger(__name__) 29 | logger.info(f"Logger works") 30 | logger.warning(f"Logger warning works") 31 | 32 | # Try and use colourful logs... 33 | try: 34 | import coloredlogs 35 | coloredlogs.install(level=get_log_level(), logger=logger) 36 | except ImportError: 37 | pass 38 | -------------------------------------------------------------------------------- /metallicious/tests/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/duartegroup/metallicious/3254b283fe22af19bc477ca36b96533d8fd463a4/metallicious/tests/__init__.py -------------------------------------------------------------------------------- /metallicious/tests/example3_mof/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/duartegroup/metallicious/3254b283fe22af19bc477ca36b96533d8fd463a4/metallicious/tests/example3_mof/__init__.py -------------------------------------------------------------------------------- /metallicious/tests/example3_mof/example3.py: -------------------------------------------------------------------------------- 1 | import sys 2 | sys.path.insert(0, '/home/fd05/fd/chem1540/github/cgbind2pmd/') 3 | 4 | 5 | try: 6 | from metallicious.patcher import patcher 7 | except: 8 | from cgbind2pmd.main import cgbind2pmd 9 | 10 | f='Ag_tet.pdb' 11 | linker_topol='linker_topol.top' 12 | metal='Ag' 13 | metal_charge=1 14 | fingerprint='Ag1' 15 | fingerprint_style='trunc' 16 | 17 | cgbind2gmx = patcher() 18 | cgbind2gmx.name_of_binding_side = fingerprint 19 | cgbind2gmx.fingerprint_style = fingerprint_style 20 | 21 | cgbind2gmx.from_coords(f, linker_topol, metal, int(metal_charge)) 22 | cgbind2gmx.save(output_coords="out.pdb", output_topol="out.top") 23 | -------------------------------------------------------------------------------- /metallicious/tests/example5_extract/Co8L16_fp0/ligand_0.pdb: -------------------------------------------------------------------------------- 1 | TITLE MDANALYSIS FRAME 0: Created by PDBWriter 2 | CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 3 | REMARK 285 UNITARY VALUES FOR THE UNIT CELL AUTOMATICALLY SET 4 | REMARK 285 BY MDANALYSIS PDBWRITER BECAUSE UNIT CELL INFORMATION 5 | REMARK 285 WAS MISSING. 6 | REMARK 285 PROTEIN DATA BANK CONVENTIONS REQUIRE THAT 7 | REMARK 285 CRYST1 RECORD IS INCLUDED, BUT THE VALUES ON 8 | REMARK 285 THIS RECORD ARE MEANINGLESS. 9 | ATOM 1 N UNK X 1 6.528 29.262 1.718 1.00 0.00 N 10 | ATOM 2 C UNK X 1 6.743 30.558 2.084 1.00 0.00 C 11 | ATOM 3 C UNK X 1 6.277 31.601 1.318 1.00 0.00 C 12 | ATOM 4 H UNK X 1 6.442 32.501 1.571 1.00 0.00 H 13 | ATOM 5 C UNK X 1 5.564 31.323 0.188 1.00 0.00 C 14 | ATOM 6 H UNK X 1 5.236 32.034 -0.349 1.00 0.00 H 15 | ATOM 7 C UNK X 1 5.316 30.034 -0.181 1.00 0.00 C 16 | ATOM 8 H UNK X 1 4.805 29.836 -0.958 1.00 0.00 H 17 | ATOM 9 C UNK X 1 5.833 29.023 0.609 1.00 0.00 C 18 | ATOM 10 H UNK X 1 5.685 28.123 0.346 1.00 0.00 H 19 | ATOM 11 N UNK X 1 8.459 30.090 5.136 1.00 0.00 N 20 | ATOM 12 N UNK X 1 7.920 29.640 3.976 1.00 0.00 N 21 | ATOM 13 C UNK X 1 8.384 31.435 5.178 1.00 0.00 C 22 | ATOM 14 H UNK X 1 8.707 31.988 5.880 1.00 0.00 H 23 | ATOM 15 C UNK X 1 7.762 31.870 4.045 1.00 0.00 C 24 | ATOM 16 H UNK X 1 7.572 32.767 3.792 1.00 0.00 H 25 | ATOM 17 C UNK X 1 7.474 30.725 3.343 1.00 0.00 C 26 | ATOM 18 C UNK X 1 9.163 29.215 6.046 1.00 0.00 C 27 | ATOM 19 H UNK X 1 8.703 28.338 6.082 1.00 0.00 H 28 | ATOM 20 H UNK X 1 9.146 29.604 6.955 1.00 0.00 H 29 | ATOM 21 C UNK X 1 10.604 29.011 5.612 1.00 0.00 C 30 | ATOM 22 H UNK X 1 11.262 29.064 6.490 1.00 0.00 H 31 | ATOM 23 H UNK X 1 10.707 28.027 5.137 1.00 0.00 H 32 | ATOM 24 H UNK X 1 10.885 29.794 4.896 1.00 0.00 H 33 | END 34 | -------------------------------------------------------------------------------- /metallicious/tests/example5_extract/Co8L16_fp0/ligand_0.xyz: -------------------------------------------------------------------------------- 1 | 24 2 | frame 0 | Written by MDAnalysis XYZWriter (release 2.4.2) 3 | N 6.52800 29.26200 1.71800 4 | C 6.74300 30.55800 2.08400 5 | C 6.27700 31.60100 1.31800 6 | H 6.44200 32.50100 1.57100 7 | C 5.56400 31.32300 0.18800 8 | H 5.23600 32.03400 -0.34900 9 | C 5.31600 30.03400 -0.18100 10 | H 4.80500 29.83600 -0.95800 11 | C 5.83300 29.02300 0.60900 12 | H 5.68500 28.12300 0.34600 13 | N 8.45900 30.09000 5.13600 14 | N 7.92000 29.64000 3.97600 15 | C 8.38400 31.43500 5.17800 16 | H 8.70700 31.98800 5.88000 17 | C 7.76200 31.87000 4.04500 18 | H 7.57200 32.76700 3.79200 19 | C 7.47400 30.72500 3.34300 20 | C 9.16300 29.21500 6.04600 21 | H 8.70300 28.33800 6.08200 22 | H 9.14600 29.60400 6.95500 23 | C 10.60400 29.01100 5.61200 24 | H 11.26174 29.06444 6.48964 25 | H 10.70721 28.02657 5.13671 26 | H 10.88496 29.79450 4.89586 27 | 28 | -------------------------------------------------------------------------------- /metallicious/tests/example5_extract/Co8L16_fp0/site.xyz: -------------------------------------------------------------------------------- 1 | 73 2 | Frame 0 | Written By Mdanalysis Xyzwriter (Release 2.4.2) 3 | Co 7.30600 27.79100 3.06800 4 | N 6.52800 29.26200 1.71800 5 | C 6.74300 30.55800 2.08400 6 | C 6.27700 31.60100 1.31800 7 | H 6.44200 32.50100 1.57100 8 | C 5.56400 31.32300 0.18800 9 | H 5.23600 32.03400 -0.34900 10 | C 5.31600 30.03400 -0.18100 11 | H 4.80500 29.83600 -0.95800 12 | C 5.83300 29.02300 0.60900 13 | H 5.68500 28.12300 0.34600 14 | N 8.45900 30.09000 5.13600 15 | N 7.92000 29.64000 3.97600 16 | C 8.38400 31.43500 5.17800 17 | H 8.70700 31.98800 5.88000 18 | C 7.76200 31.87000 4.04500 19 | H 7.57200 32.76700 3.79200 20 | C 7.47400 30.72500 3.34300 21 | C 9.16300 29.21500 6.04600 22 | H 8.70300 28.33800 6.08200 23 | H 9.14600 29.60400 6.95500 24 | C 10.60400 29.01100 5.61200 25 | H 11.26174 29.06444 6.48964 26 | H 10.70721 28.02657 5.13671 27 | H 10.88496 29.79450 4.89586 28 | N 8.26900 26.39500 4.35800 29 | C 9.52700 26.05200 4.00500 30 | C 10.25800 25.14700 4.78800 31 | H 11.14300 24.91500 4.53500 32 | C 9.71000 24.60000 5.89300 33 | H 10.20700 24.00400 6.44400 34 | C 8.36400 24.94900 6.20500 35 | H 7.93100 24.55900 6.95500 36 | C 7.72400 25.82900 5.43600 37 | H 6.83600 26.06100 5.66800 38 | N 9.90900 27.74100 0.95300 39 | N 9.20000 27.40700 2.05500 40 | C 11.14300 27.17800 1.01600 41 | H 11.82100 27.26400 0.35600 42 | C 11.25400 26.47600 2.17200 43 | H 12.00800 25.98900 2.48100 44 | C 10.02300 26.61900 2.80500 45 | C 9.43300 28.65000 -0.05500 46 | H 8.46200 28.50400 -0.18100 47 | H 9.88100 28.44100 -0.91000 48 | C 9.66900 30.12000 0.27800 49 | H 10.72917 30.27536 0.51809 50 | H 9.39484 30.73959 -0.58607 51 | H 9.05288 30.40310 1.14166 52 | N 5.43600 27.90700 4.23100 53 | C 4.53200 27.00900 3.89000 54 | C 3.21900 26.98600 4.49000 55 | H 2.56500 26.34100 4.24000 56 | C 2.95600 27.94600 5.44200 57 | H 2.10200 27.97400 5.85200 58 | C 3.90300 28.85400 5.80500 59 | H 3.73600 29.48700 6.49200 60 | C 5.13900 28.82200 5.13400 61 | H 5.78400 29.48700 5.34300 62 | N 6.13400 25.25800 1.31400 63 | N 6.06800 26.23000 2.25100 64 | C 5.03000 24.49100 1.33100 65 | H 4.84600 23.76000 0.75600 66 | C 4.21900 24.96100 2.34100 67 | H 3.38100 24.60800 2.62200 68 | C 4.88300 26.05800 2.86100 69 | C 7.26700 25.19300 0.40500 70 | H 6.95300 24.86000 -0.47200 71 | H 7.62300 26.10700 0.27000 72 | C 8.37600 24.31000 0.88300 73 | H 8.84660 24.75954 1.76741 74 | H 7.97123 23.32360 1.14538 75 | H 9.12418 24.19874 0.08707 76 | 77 | -------------------------------------------------------------------------------- /metallicious/tests/example5_extract/Co8L16_fp1/ligand_0.pdb: -------------------------------------------------------------------------------- 1 | TITLE MDANALYSIS FRAME 0: Created by PDBWriter 2 | CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 3 | REMARK 285 UNITARY VALUES FOR THE UNIT CELL AUTOMATICALLY SET 4 | REMARK 285 BY MDANALYSIS PDBWRITER BECAUSE UNIT CELL INFORMATION 5 | REMARK 285 WAS MISSING. 6 | REMARK 285 PROTEIN DATA BANK CONVENTIONS REQUIRE THAT 7 | REMARK 285 CRYST1 RECORD IS INCLUDED, BUT THE VALUES ON 8 | REMARK 285 THIS RECORD ARE MEANINGLESS. 9 | ATOM 1 N UNK X 1 17.845 27.407 10.293 1.00 0.00 N 10 | ATOM 2 C UNK X 1 17.856 26.104 9.983 1.00 0.00 C 11 | ATOM 3 C UNK X 1 18.577 25.153 10.695 1.00 0.00 C 12 | ATOM 4 H UNK X 1 18.587 24.242 10.428 1.00 0.00 H 13 | ATOM 5 C UNK X 1 19.270 25.579 11.794 1.00 0.00 C 14 | ATOM 6 H UNK X 1 19.767 24.955 12.311 1.00 0.00 H 15 | ATOM 7 C UNK X 1 19.252 26.877 12.136 1.00 0.00 C 16 | ATOM 8 H UNK X 1 19.738 27.164 12.899 1.00 0.00 H 17 | ATOM 9 C UNK X 1 18.539 27.814 11.400 1.00 0.00 C 18 | ATOM 10 H UNK X 1 18.528 28.728 11.664 1.00 0.00 H 19 | ATOM 11 N UNK X 1 15.849 26.132 7.107 1.00 0.00 N 20 | ATOM 12 N UNK X 1 16.458 26.717 8.119 1.00 0.00 N 21 | ATOM 13 C UNK X 1 17.079 25.748 8.809 1.00 0.00 C 22 | ATOM 14 C UNK X 1 16.861 24.517 8.180 1.00 0.00 C 23 | ATOM 15 H UNK X 1 17.186 23.671 8.457 1.00 0.00 H 24 | ATOM 16 C UNK X 1 16.087 24.769 7.091 1.00 0.00 C 25 | ATOM 17 H UNK X 1 15.771 24.141 6.455 1.00 0.00 H 26 | ATOM 18 C UNK X 1 15.033 26.846 6.175 1.00 0.00 C 27 | ATOM 19 H UNK X 1 15.059 26.376 5.305 1.00 0.00 H 28 | ATOM 20 H UNK X 1 15.418 27.748 6.041 1.00 0.00 H 29 | ATOM 21 C UNK X 1 13.599 26.983 6.618 1.00 0.00 C 30 | ATOM 22 H UNK X 1 12.958 27.143 5.741 1.00 0.00 H 31 | ATOM 23 H UNK X 1 13.287 26.067 7.137 1.00 0.00 H 32 | ATOM 24 H UNK X 1 13.507 27.839 7.300 1.00 0.00 H 33 | END 34 | -------------------------------------------------------------------------------- /metallicious/tests/example5_extract/Co8L16_fp1/ligand_0.xyz: -------------------------------------------------------------------------------- 1 | 24 2 | frame 0 | Written by MDAnalysis XYZWriter (release 2.4.2) 3 | N 17.84500 27.40700 10.29300 4 | C 17.85600 26.10400 9.98300 5 | C 18.57700 25.15300 10.69500 6 | H 18.58700 24.24200 10.42800 7 | C 19.27000 25.57900 11.79400 8 | H 19.76700 24.95500 12.31100 9 | C 19.25200 26.87700 12.13600 10 | H 19.73800 27.16400 12.89900 11 | C 18.53900 27.81400 11.40000 12 | H 18.52800 28.72800 11.66400 13 | N 15.84900 26.13200 7.10700 14 | N 16.45800 26.71700 8.11900 15 | C 17.07900 25.74800 8.80900 16 | C 16.86100 24.51700 8.18000 17 | H 17.18600 23.67100 8.45700 18 | C 16.08700 24.76900 7.09100 19 | H 15.77100 24.14100 6.45500 20 | C 15.03300 26.84600 6.17500 21 | H 15.05900 26.37600 5.30500 22 | H 15.41800 27.74800 6.04100 23 | C 13.59900 26.98300 6.61800 24 | H 12.95847 27.14310 5.74060 25 | H 13.28702 26.06680 7.13658 26 | H 13.50668 27.83891 7.29958 27 | 28 | -------------------------------------------------------------------------------- /metallicious/tests/example5_extract/Co8L16_fp1/site.xyz: -------------------------------------------------------------------------------- 1 | 73 2 | Frame 0 | Written By Mdanalysis Xyzwriter (Release 2.4.2) 3 | Co 16.54000 28.64700 9.10400 4 | N 17.84500 27.40700 10.29300 5 | C 17.85600 26.10400 9.98300 6 | C 18.57700 25.15300 10.69500 7 | H 18.58700 24.24200 10.42800 8 | C 19.27000 25.57900 11.79400 9 | H 19.76700 24.95500 12.31100 10 | C 19.25200 26.87700 12.13600 11 | H 19.73800 27.16400 12.89900 12 | C 18.53900 27.81400 11.40000 13 | H 18.52800 28.72800 11.66400 14 | N 15.84900 26.13200 7.10700 15 | N 16.45800 26.71700 8.11900 16 | C 17.07900 25.74800 8.80900 17 | C 16.86100 24.51700 8.18000 18 | H 17.18600 23.67100 8.45700 19 | C 16.08700 24.76900 7.09100 20 | H 15.77100 24.14100 6.45500 21 | C 15.03300 26.84600 6.17500 22 | H 15.05900 26.37600 5.30500 23 | H 15.41800 27.74800 6.04100 24 | C 13.59900 26.98300 6.61800 25 | H 12.95847 27.14310 5.74060 26 | H 13.28702 26.06680 7.13658 27 | H 13.50668 27.83891 7.29958 28 | N 16.96100 30.39800 10.29300 29 | C 18.08400 31.06000 9.98300 30 | C 18.54800 32.16000 10.69500 31 | H 19.33100 32.62400 10.42800 32 | C 17.83100 32.54600 11.79400 33 | H 18.12400 33.28800 12.31100 34 | C 16.71700 31.88200 12.13600 35 | H 16.22500 32.16000 12.89900 36 | C 16.26200 30.79600 11.40000 37 | H 15.47600 30.32900 11.66400 38 | N 19.06300 29.30700 7.10700 39 | N 18.25200 29.54200 8.11900 40 | C 18.78100 30.56400 8.80900 41 | C 19.95700 30.99100 8.18000 42 | H 20.52600 31.69600 8.45700 43 | C 20.12500 30.19400 7.09100 44 | H 20.82700 30.23500 6.45500 45 | C 18.85400 28.24400 6.17500 46 | H 19.24700 28.50100 5.30500 47 | H 17.87900 28.12600 6.04100 48 | C 19.45200 26.93300 6.61800 49 | H 20.40175 27.12037 7.13628 50 | H 18.75690 26.42550 7.29987 51 | H 19.63295 26.29819 5.74054 52 | N 14.81300 28.13800 10.29300 53 | C 13.67800 28.77900 9.98300 54 | C 12.49400 28.63000 10.69500 55 | H 11.70000 29.07700 10.42800 56 | C 12.51700 27.81700 11.79400 57 | H 11.72800 27.69900 12.31100 58 | C 13.65000 27.18400 12.13600 59 | H 13.65500 26.61900 12.89900 60 | C 14.81800 27.33300 11.40000 61 | H 15.61500 26.88600 11.66400 62 | N 14.70600 30.50300 7.10700 63 | N 14.90900 29.68300 8.11900 64 | C 13.75900 29.63000 8.80900 65 | C 12.80200 30.43500 8.18000 66 | H 11.90700 30.57600 8.45700 67 | C 13.40700 30.97900 7.09100 68 | H 13.02200 31.56700 6.45500 69 | C 15.73300 30.85300 6.17500 70 | H 15.31200 31.06500 5.30500 71 | H 16.32100 30.06800 6.04100 72 | C 16.56900 32.02700 6.61800 73 | H 17.35654 31.67920 7.29958 74 | H 17.02775 32.50150 5.74047 75 | H 15.93156 32.75528 7.13658 76 | 77 | -------------------------------------------------------------------------------- /metallicious/tests/example5_extract/Co8L16_fp2/ligand_0.pdb: -------------------------------------------------------------------------------- 1 | TITLE MDANALYSIS FRAME 0: Created by PDBWriter 2 | CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 3 | REMARK 285 UNITARY VALUES FOR THE UNIT CELL AUTOMATICALLY SET 4 | REMARK 285 BY MDANALYSIS PDBWRITER BECAUSE UNIT CELL INFORMATION 5 | REMARK 285 WAS MISSING. 6 | REMARK 285 PROTEIN DATA BANK CONVENTIONS REQUIRE THAT 7 | REMARK 285 CRYST1 RECORD IS INCLUDED, BUT THE VALUES ON 8 | REMARK 285 THIS RECORD ARE MEANINGLESS. 9 | ATOM 1 N UNK X 1 27.643 29.388 -4.231 1.00 0.00 N 10 | ATOM 2 C UNK X 1 28.547 30.286 -3.890 1.00 0.00 C 11 | ATOM 3 C UNK X 1 29.861 30.309 -4.490 1.00 0.00 C 12 | ATOM 4 H UNK X 1 30.514 30.954 -4.240 1.00 0.00 H 13 | ATOM 5 C UNK X 1 30.124 29.349 -5.442 1.00 0.00 C 14 | ATOM 6 H UNK X 1 30.977 29.321 -5.852 1.00 0.00 H 15 | ATOM 7 C UNK X 1 29.176 28.441 -5.805 1.00 0.00 C 16 | ATOM 8 H UNK X 1 29.343 27.808 -6.492 1.00 0.00 H 17 | ATOM 9 C UNK X 1 27.940 28.473 -5.134 1.00 0.00 C 18 | ATOM 10 H UNK X 1 27.295 27.808 -5.343 1.00 0.00 H 19 | ATOM 11 N UNK X 1 26.945 32.036 -1.314 1.00 0.00 N 20 | ATOM 12 N UNK X 1 27.012 31.065 -2.251 1.00 0.00 N 21 | ATOM 13 C UNK X 1 28.197 31.237 -2.861 1.00 0.00 C 22 | ATOM 14 C UNK X 1 28.860 32.334 -2.341 1.00 0.00 C 23 | ATOM 15 H UNK X 1 29.699 32.687 -2.622 1.00 0.00 H 24 | ATOM 16 C UNK X 1 28.050 32.804 -1.331 1.00 0.00 C 25 | ATOM 17 H UNK X 1 28.233 33.535 -0.756 1.00 0.00 H 26 | ATOM 18 C UNK X 1 25.812 32.102 -0.405 1.00 0.00 C 27 | ATOM 19 H UNK X 1 26.126 32.435 0.472 1.00 0.00 H 28 | ATOM 20 H UNK X 1 25.456 31.188 -0.270 1.00 0.00 H 29 | ATOM 21 C UNK X 1 24.704 32.985 -0.883 1.00 0.00 C 30 | ATOM 22 H UNK X 1 25.037 33.544 -1.767 1.00 0.00 H 31 | ATOM 23 H UNK X 1 23.833 32.370 -1.146 1.00 0.00 H 32 | ATOM 24 H UNK X 1 24.428 33.689 -0.087 1.00 0.00 H 33 | END 34 | -------------------------------------------------------------------------------- /metallicious/tests/example5_extract/Co8L16_fp2/ligand_0.xyz: -------------------------------------------------------------------------------- 1 | 24 2 | frame 0 | Written by MDAnalysis XYZWriter (release 2.4.2) 3 | N 27.64300 29.38800 -4.23100 4 | C 28.54700 30.28600 -3.89000 5 | C 29.86100 30.30900 -4.49000 6 | H 30.51400 30.95400 -4.24000 7 | C 30.12400 29.34900 -5.44200 8 | H 30.97700 29.32100 -5.85200 9 | C 29.17600 28.44100 -5.80500 10 | H 29.34300 27.80800 -6.49200 11 | C 27.94000 28.47300 -5.13400 12 | H 27.29500 27.80800 -5.34300 13 | N 26.94500 32.03600 -1.31400 14 | N 27.01200 31.06500 -2.25100 15 | C 28.19700 31.23700 -2.86100 16 | C 28.86000 32.33400 -2.34100 17 | H 29.69900 32.68700 -2.62200 18 | C 28.05000 32.80400 -1.33100 19 | H 28.23300 33.53500 -0.75600 20 | C 25.81200 32.10200 -0.40500 21 | H 26.12600 32.43500 0.47200 22 | H 25.45600 31.18800 -0.27000 23 | C 24.70400 32.98500 -0.88300 24 | H 25.03722 33.54447 -1.76714 25 | H 23.83328 32.36986 -1.14590 26 | H 24.42783 33.68912 -0.08701 27 | 28 | -------------------------------------------------------------------------------- /metallicious/tests/example5_extract/Co8L16_fp2/site.xyz: -------------------------------------------------------------------------------- 1 | 73 2 | Frame 0 | Written By Mdanalysis Xyzwriter (Release 2.4.2) 3 | Co 25.77300 29.50400 -3.06800 4 | N 27.64300 29.38800 -4.23100 5 | C 28.54700 30.28600 -3.89000 6 | C 29.86100 30.30900 -4.49000 7 | H 30.51400 30.95400 -4.24000 8 | C 30.12400 29.34900 -5.44200 9 | H 30.97700 29.32100 -5.85200 10 | C 29.17600 28.44100 -5.80500 11 | H 29.34300 27.80800 -6.49200 12 | C 27.94000 28.47300 -5.13400 13 | H 27.29500 27.80800 -5.34300 14 | N 26.94500 32.03600 -1.31400 15 | N 27.01200 31.06500 -2.25100 16 | C 28.19700 31.23700 -2.86100 17 | C 28.86000 32.33400 -2.34100 18 | H 29.69900 32.68700 -2.62200 19 | C 28.05000 32.80400 -1.33100 20 | H 28.23300 33.53500 -0.75600 21 | C 25.81200 32.10200 -0.40500 22 | H 26.12600 32.43500 0.47200 23 | H 25.45600 31.18800 -0.27000 24 | C 24.70400 32.98500 -0.88300 25 | H 25.03722 33.54447 -1.76714 26 | H 23.83328 32.36986 -1.14590 27 | H 24.42783 33.68912 -0.08701 28 | N 26.55200 28.03300 -1.71800 29 | C 26.33600 26.73700 -2.08400 30 | C 26.80200 25.69400 -1.31800 31 | H 26.63700 24.79400 -1.57100 32 | C 27.51500 25.97200 -0.18800 33 | H 27.84300 25.26100 0.34900 34 | C 27.76400 27.26100 0.18100 35 | H 28.27400 27.45900 0.95800 36 | C 27.24600 28.27200 -0.60900 37 | H 27.39500 29.17200 -0.34600 38 | N 24.62000 27.20500 -5.13600 39 | N 25.15900 27.65500 -3.97600 40 | C 25.60500 26.57100 -3.34300 41 | C 25.31700 25.42500 -4.04500 42 | H 25.50700 24.52800 -3.79200 43 | C 24.69500 25.86000 -5.17800 44 | H 24.37300 25.30700 -5.88000 45 | C 23.91600 28.08000 -6.04600 46 | H 24.37600 28.95700 -6.08200 47 | H 23.93300 27.69100 -6.95500 48 | C 22.47600 28.28400 -5.61200 49 | H 21.85882 28.51810 -6.48951 50 | H 22.10356 27.36689 -5.13677 51 | H 22.42379 29.11461 -4.89575 52 | N 24.81000 30.90000 -4.35800 53 | C 23.55200 31.24300 -4.00500 54 | C 22.82100 32.14800 -4.78800 55 | H 21.93700 32.38000 -4.53500 56 | C 23.36900 32.69500 -5.89300 57 | H 22.87300 33.29100 -6.44400 58 | C 24.71500 32.34600 -6.20500 59 | H 25.14900 32.73600 -6.95500 60 | C 25.35500 31.46600 -5.43600 61 | H 26.24300 31.23400 -5.66800 62 | N 23.17000 29.55400 -0.95300 63 | N 23.88000 29.88800 -2.05500 64 | C 23.05600 30.67600 -2.80500 65 | C 21.82600 30.81900 -2.17200 66 | H 21.07200 31.30600 -2.48100 67 | C 21.93700 30.11700 -1.01600 68 | H 21.25800 30.03100 -0.35600 69 | C 23.64700 28.64500 0.05500 70 | H 24.61800 28.79100 0.18100 71 | H 23.19800 28.85400 0.91000 72 | C 23.41000 27.17500 -0.27800 73 | H 24.36786 26.69510 -0.51868 74 | H 22.95591 26.67255 0.58629 75 | H 22.73568 27.09940 -1.14127 76 | 77 | -------------------------------------------------------------------------------- /metallicious/tests/example5_extract/Co8L16_fp3/ligand_0.pdb: -------------------------------------------------------------------------------- 1 | TITLE MDANALYSIS FRAME 0: Created by PDBWriter 2 | CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 3 | REMARK 285 UNITARY VALUES FOR THE UNIT CELL AUTOMATICALLY SET 4 | REMARK 285 BY MDANALYSIS PDBWRITER BECAUSE UNIT CELL INFORMATION 5 | REMARK 285 WAS MISSING. 6 | REMARK 285 PROTEIN DATA BANK CONVENTIONS REQUIRE THAT 7 | REMARK 285 CRYST1 RECORD IS INCLUDED, BUT THE VALUES ON 8 | REMARK 285 THIS RECORD ARE MEANINGLESS. 9 | ATOM 1 N UNK X 1 15.235 29.888 -10.293 1.00 0.00 N 10 | ATOM 2 C UNK X 1 15.223 31.191 -9.983 1.00 0.00 C 11 | ATOM 3 C UNK X 1 14.502 32.143 -10.695 1.00 0.00 C 12 | ATOM 4 H UNK X 1 14.492 33.054 -10.428 1.00 0.00 H 13 | ATOM 5 C UNK X 1 13.809 31.716 -11.794 1.00 0.00 C 14 | ATOM 6 H UNK X 1 13.313 32.340 -12.311 1.00 0.00 H 15 | ATOM 7 C UNK X 1 13.827 30.418 -12.136 1.00 0.00 C 16 | ATOM 8 H UNK X 1 13.341 30.132 -12.899 1.00 0.00 H 17 | ATOM 9 C UNK X 1 14.540 29.481 -11.400 1.00 0.00 C 18 | ATOM 10 H UNK X 1 14.552 28.567 -11.664 1.00 0.00 H 19 | ATOM 11 N UNK X 1 17.230 31.163 -7.107 1.00 0.00 N 20 | ATOM 12 N UNK X 1 16.621 30.578 -8.119 1.00 0.00 N 21 | ATOM 13 C UNK X 1 16.000 31.547 -8.809 1.00 0.00 C 22 | ATOM 14 C UNK X 1 16.219 32.778 -8.180 1.00 0.00 C 23 | ATOM 15 H UNK X 1 15.893 33.624 -8.457 1.00 0.00 H 24 | ATOM 16 C UNK X 1 16.993 32.526 -7.091 1.00 0.00 C 25 | ATOM 17 H UNK X 1 17.309 33.154 -6.455 1.00 0.00 H 26 | ATOM 18 C UNK X 1 18.046 30.449 -6.175 1.00 0.00 C 27 | ATOM 19 H UNK X 1 18.020 30.919 -5.305 1.00 0.00 H 28 | ATOM 20 H UNK X 1 17.661 29.547 -6.041 1.00 0.00 H 29 | ATOM 21 C UNK X 1 19.481 30.312 -6.618 1.00 0.00 C 30 | ATOM 22 H UNK X 1 20.140 30.348 -5.740 1.00 0.00 H 31 | ATOM 23 H UNK X 1 19.614 29.353 -7.137 1.00 0.00 H 32 | ATOM 24 H UNK X 1 19.734 31.135 -7.299 1.00 0.00 H 33 | END 34 | -------------------------------------------------------------------------------- /metallicious/tests/example5_extract/Co8L16_fp3/ligand_0.xyz: -------------------------------------------------------------------------------- 1 | 24 2 | frame 0 | Written by MDAnalysis XYZWriter (release 2.4.2) 3 | N 15.23500 29.88800 -10.29300 4 | C 15.22300 31.19100 -9.98300 5 | C 14.50200 32.14300 -10.69500 6 | H 14.49200 33.05400 -10.42800 7 | C 13.80900 31.71600 -11.79400 8 | H 13.31300 32.34000 -12.31100 9 | C 13.82700 30.41800 -12.13600 10 | H 13.34100 30.13200 -12.89900 11 | C 14.54000 29.48100 -11.40000 12 | H 14.55200 28.56700 -11.66400 13 | N 17.23000 31.16300 -7.10700 14 | N 16.62100 30.57800 -8.11900 15 | C 16.00000 31.54700 -8.80900 16 | C 16.21900 32.77800 -8.18000 17 | H 15.89300 33.62400 -8.45700 18 | C 16.99300 32.52600 -7.09100 19 | H 17.30900 33.15400 -6.45500 20 | C 18.04600 30.44900 -6.17500 21 | H 18.02000 30.91900 -5.30500 22 | H 17.66100 29.54700 -6.04100 23 | C 19.48100 30.31200 -6.61800 24 | H 20.14008 30.34791 -5.74047 25 | H 19.61400 29.35334 -7.13660 26 | H 19.73381 31.13500 -7.29949 27 | 28 | -------------------------------------------------------------------------------- /metallicious/tests/example5_extract/Co8L16_fp3/site.xyz: -------------------------------------------------------------------------------- 1 | 73 2 | Frame 0 | Written By Mdanalysis Xyzwriter (Release 2.4.2) 3 | Co 16.54000 28.64700 -9.10400 4 | N 15.23500 29.88800 -10.29300 5 | C 15.22300 31.19100 -9.98300 6 | C 14.50200 32.14300 -10.69500 7 | H 14.49200 33.05400 -10.42800 8 | C 13.80900 31.71600 -11.79400 9 | H 13.31300 32.34000 -12.31100 10 | C 13.82700 30.41800 -12.13600 11 | H 13.34100 30.13200 -12.89900 12 | C 14.54000 29.48100 -11.40000 13 | H 14.55200 28.56700 -11.66400 14 | N 17.23000 31.16300 -7.10700 15 | N 16.62100 30.57800 -8.11900 16 | C 16.00000 31.54700 -8.80900 17 | C 16.21900 32.77800 -8.18000 18 | H 15.89300 33.62400 -8.45700 19 | C 16.99300 32.52600 -7.09100 20 | H 17.30900 33.15400 -6.45500 21 | C 18.04600 30.44900 -6.17500 22 | H 18.02000 30.91900 -5.30500 23 | H 17.66100 29.54700 -6.04100 24 | C 19.48100 30.31200 -6.61800 25 | H 20.14008 30.34791 -5.74047 26 | H 19.61400 29.35334 -7.13660 27 | H 19.73381 31.13500 -7.29949 28 | N 16.11800 26.89700 -10.29300 29 | C 14.99500 26.23500 -9.98300 30 | C 14.53200 25.13500 -10.69500 31 | H 13.74800 24.67100 -10.42800 32 | C 15.24800 24.74900 -11.79400 33 | H 14.95500 24.00700 -12.31100 34 | C 16.36300 25.41300 -12.13600 35 | H 16.85400 25.13500 -12.89900 36 | C 16.81700 26.49900 -11.40000 37 | H 17.60300 26.96600 -11.66400 38 | N 14.01600 27.98800 -7.10700 39 | N 14.82700 27.75300 -8.11900 40 | C 14.29900 26.73100 -8.80900 41 | C 13.12300 26.30400 -8.18000 42 | H 12.55400 25.59900 -8.45700 43 | C 12.95400 27.10100 -7.09100 44 | H 12.25300 27.06000 -6.45500 45 | C 14.22600 29.05100 -6.17500 46 | H 13.83200 28.79400 -5.30500 47 | H 15.20000 29.16900 -6.04100 48 | C 13.62800 30.36200 -6.61800 49 | H 14.39211 30.95641 -7.13622 50 | H 12.78914 30.16978 -7.29992 51 | H 13.26718 30.91476 -5.74055 52 | N 18.26600 29.15700 -10.29300 53 | C 19.40100 28.51600 -9.98300 54 | C 20.58500 28.66500 -10.69500 55 | H 21.37900 28.21800 -10.42800 56 | C 20.56200 29.47800 -11.79400 57 | H 21.35100 29.59600 -12.31100 58 | C 19.42900 30.11100 -12.13600 59 | H 19.42400 30.67600 -12.89900 60 | C 18.26100 29.96200 -11.40000 61 | H 17.46400 30.40900 -11.66400 62 | N 18.37300 26.79200 -7.10700 63 | N 18.17100 27.61200 -8.11900 64 | C 19.32000 27.66500 -8.80900 65 | C 20.27800 26.86000 -8.18000 66 | H 21.17200 26.71900 -8.45700 67 | C 19.67200 26.31600 -7.09100 68 | H 20.05800 25.72800 -6.45500 69 | C 17.34700 26.44200 -6.17500 70 | H 17.76700 26.23000 -5.30500 71 | H 16.75800 27.22700 -6.04100 72 | C 16.51000 25.26800 -6.61800 73 | H 17.09567 24.63742 -7.29997 74 | H 16.21181 24.67924 -5.74044 75 | H 15.61320 25.63266 -7.13610 76 | 77 | -------------------------------------------------------------------------------- /metallicious/tests/example5_extract/Fe4L6_2_fp0/ligand_0.pdb: -------------------------------------------------------------------------------- 1 | TITLE MDANALYSIS FRAME 0: Created by PDBWriter 2 | CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 3 | REMARK 285 UNITARY VALUES FOR THE UNIT CELL AUTOMATICALLY SET 4 | REMARK 285 BY MDANALYSIS PDBWRITER BECAUSE UNIT CELL INFORMATION 5 | REMARK 285 WAS MISSING. 6 | REMARK 285 PROTEIN DATA BANK CONVENTIONS REQUIRE THAT 7 | REMARK 285 CRYST1 RECORD IS INCLUDED, BUT THE VALUES ON 8 | REMARK 285 THIS RECORD ARE MEANINGLESS. 9 | ATOM 1 C UNK X 1 6.270 12.684 31.072 1.00 0.00 C 10 | ATOM 2 C UNK X 1 4.980 12.390 30.478 1.00 0.00 C 11 | ATOM 3 C UNK X 1 4.618 11.096 30.171 1.00 0.00 C 12 | ATOM 4 C UNK X 1 3.393 10.828 29.565 1.00 0.00 C 13 | ATOM 5 C UNK X 1 4.107 13.435 30.179 1.00 0.00 C 14 | ATOM 6 S UNK X 1 4.467 15.098 30.582 1.00 0.00 S 15 | ATOM 7 C UNK X 1 2.894 13.118 29.574 1.00 0.00 C 16 | ATOM 8 C UNK X 1 2.512 11.840 29.258 1.00 0.00 C 17 | ATOM 9 N UNK X 1 1.266 11.580 28.642 1.00 0.00 N 18 | ATOM 10 C UNK X 1 0.216 11.206 29.285 1.00 0.00 C 19 | ATOM 11 C UNK X 1 -1.063 10.938 28.662 1.00 0.00 C 20 | ATOM 12 C UNK X 1 -2.115 10.545 29.446 1.00 0.00 C 21 | ATOM 13 C UNK X 1 -3.328 10.288 28.870 1.00 0.00 C 22 | ATOM 14 C UNK X 1 -3.476 10.427 27.514 1.00 0.00 C 23 | ATOM 15 C UNK X 1 -2.414 10.824 26.719 1.00 0.00 C 24 | ATOM 16 N UNK X 1 -1.255 11.060 27.343 1.00 0.00 N 25 | ATOM 17 H UNK X 1 5.278 10.244 30.393 1.00 0.00 H 26 | ATOM 18 H UNK X 1 3.147 9.805 29.342 1.00 0.00 H 27 | ATOM 19 H UNK X 1 2.216 13.919 29.339 1.00 0.00 H 28 | ATOM 20 H UNK X 1 0.312 11.091 30.351 1.00 0.00 H 29 | ATOM 21 H UNK X 1 -1.983 10.437 30.537 1.00 0.00 H 30 | ATOM 22 H UNK X 1 -4.168 9.973 29.509 1.00 0.00 H 31 | ATOM 23 H UNK X 1 -4.454 10.216 27.078 1.00 0.00 H 32 | ATOM 24 H UNK X 1 -2.560 10.925 25.653 1.00 0.00 H 33 | ATOM 25 H UNK X 1 6.244 12.442 32.143 1.00 0.00 H 34 | ATOM 26 H UNK X 1 7.045 12.082 30.580 1.00 0.00 H 35 | ATOM 27 H UNK X 1 6.498 13.750 30.943 1.00 0.00 H 36 | ATOM 28 H UNK X 1 3.280 15.523 30.103 1.00 0.00 H 37 | END 38 | -------------------------------------------------------------------------------- /metallicious/tests/example5_extract/Fe4L6_2_fp0/ligand_0.xyz: -------------------------------------------------------------------------------- 1 | 28 2 | frame 0 | Written by MDAnalysis XYZWriter (release 2.4.2) 3 | C 6.27000 12.68400 31.07200 4 | C 4.98000 12.39000 30.47800 5 | C 4.61800 11.09600 30.17100 6 | C 3.39300 10.82800 29.56500 7 | C 4.10700 13.43500 30.17900 8 | S 4.46700 15.09800 30.58200 9 | C 2.89400 13.11800 29.57400 10 | C 2.51200 11.84000 29.25800 11 | N 1.26600 11.58000 28.64200 12 | C 0.21600 11.20600 29.28500 13 | C -1.06300 10.93800 28.66200 14 | C -2.11500 10.54500 29.44600 15 | C -3.32800 10.28800 28.87000 16 | C -3.47600 10.42700 27.51400 17 | C -2.41400 10.82400 26.71900 18 | N -1.25500 11.06000 27.34300 19 | H 5.27800 10.24400 30.39300 20 | H 3.14700 9.80500 29.34200 21 | H 2.21600 13.91900 29.33900 22 | H 0.31200 11.09100 30.35100 23 | H -1.98300 10.43700 30.53700 24 | H -4.16800 9.97300 29.50900 25 | H -4.45400 10.21600 27.07800 26 | H -2.56000 10.92500 25.65300 27 | H 6.24369 12.44208 32.14276 28 | H 7.04530 12.08211 30.57977 29 | H 6.49772 13.75041 30.94324 30 | H 3.27984 15.52321 30.10314 31 | 32 | -------------------------------------------------------------------------------- /metallicious/tests/example5_extract/Fe4L6_2_fp1/ligand_0.pdb: -------------------------------------------------------------------------------- 1 | TITLE MDANALYSIS FRAME 0: Created by PDBWriter 2 | CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 3 | REMARK 285 UNITARY VALUES FOR THE UNIT CELL AUTOMATICALLY SET 4 | REMARK 285 BY MDANALYSIS PDBWRITER BECAUSE UNIT CELL INFORMATION 5 | REMARK 285 WAS MISSING. 6 | REMARK 285 PROTEIN DATA BANK CONVENTIONS REQUIRE THAT 7 | REMARK 285 CRYST1 RECORD IS INCLUDED, BUT THE VALUES ON 8 | REMARK 285 THIS RECORD ARE MEANINGLESS. 9 | ATOM 1 S UNK X 1 5.184 6.516 29.008 1.00 0.00 S 10 | ATOM 2 C UNK X 1 4.174 7.843 29.535 1.00 0.00 C 11 | ATOM 3 C UNK X 1 3.381 8.548 28.625 1.00 0.00 C 12 | ATOM 4 C UNK X 1 2.596 9.624 28.980 1.00 0.00 C 13 | ATOM 5 N UNK X 1 1.809 10.305 28.008 1.00 0.00 N 14 | ATOM 6 C UNK X 1 0.884 9.676 27.368 1.00 0.00 C 15 | ATOM 7 C UNK X 1 0.049 10.346 26.354 1.00 0.00 C 16 | ATOM 8 C UNK X 1 -0.929 9.632 25.694 1.00 0.00 C 17 | ATOM 9 C UNK X 1 -1.732 10.247 24.731 1.00 0.00 C 18 | ATOM 10 C UNK X 1 -1.535 11.583 24.444 1.00 0.00 C 19 | ATOM 11 C UNK X 1 -0.547 12.253 25.130 1.00 0.00 C 20 | ATOM 12 N UNK X 1 0.215 11.629 26.059 1.00 0.00 N 21 | ATOM 13 C UNK X 1 2.605 10.010 30.302 1.00 0.00 C 22 | ATOM 14 C UNK X 1 3.379 9.330 31.222 1.00 0.00 C 23 | ATOM 15 C UNK X 1 4.160 8.253 30.851 1.00 0.00 C 24 | ATOM 16 C UNK X 1 4.942 7.512 31.823 1.00 0.00 C 25 | ATOM 17 H UNK X 1 3.379 8.240 27.589 1.00 0.00 H 26 | ATOM 18 H UNK X 1 0.720 8.631 27.582 1.00 0.00 H 27 | ATOM 19 H UNK X 1 -1.074 8.597 25.922 1.00 0.00 H 28 | ATOM 20 H UNK X 1 -2.493 9.678 24.221 1.00 0.00 H 29 | ATOM 21 H UNK X 1 -2.124 12.108 23.711 1.00 0.00 H 30 | ATOM 22 H UNK X 1 -0.382 13.299 24.917 1.00 0.00 H 31 | ATOM 23 H UNK X 1 2.017 10.833 30.624 1.00 0.00 H 32 | ATOM 24 H UNK X 1 3.339 9.688 32.250 1.00 0.00 H 33 | ATOM 25 H UNK X 1 6.176 7.352 28.640 1.00 0.00 H 34 | ATOM 26 H UNK X 1 5.264 8.188 32.626 1.00 0.00 H 35 | ATOM 27 H UNK X 1 4.329 6.705 32.247 1.00 0.00 H 36 | ATOM 28 H UNK X 1 5.824 7.081 31.331 1.00 0.00 H 37 | END 38 | -------------------------------------------------------------------------------- /metallicious/tests/example5_extract/Fe4L6_2_fp1/ligand_0.xyz: -------------------------------------------------------------------------------- 1 | 28 2 | frame 0 | Written by MDAnalysis XYZWriter (release 2.4.2) 3 | S 5.18384 6.51615 29.00792 4 | C 4.17403 7.84324 29.53506 5 | C 3.38135 8.54779 28.62460 6 | C 2.59607 9.62441 28.98041 7 | N 1.80858 10.30475 28.00764 8 | C 0.88397 9.67585 27.36798 9 | C 0.04869 10.34566 26.35385 10 | C -0.92901 9.63233 25.69408 11 | C -1.73170 10.24650 24.73097 12 | C -1.53527 11.58304 24.44405 13 | C -0.54729 12.25319 25.12994 14 | N 0.21537 11.62907 26.05937 15 | C 2.60509 10.00964 30.30190 16 | C 3.37899 9.32974 31.22188 17 | C 4.16038 8.25287 30.85082 18 | C 4.94200 7.51187 31.82262 19 | H 3.37852 8.24042 27.58855 20 | H 0.72041 8.63088 27.58171 21 | H -1.07424 8.59667 25.92238 22 | H -2.49262 9.67838 24.22132 23 | H -2.12438 12.10758 23.71086 24 | H -0.38194 13.29943 24.91665 25 | H 2.01732 10.83303 30.62401 26 | H 3.33921 9.68783 32.25030 27 | H 6.17644 7.35215 28.64009 28 | H 5.26399 8.18799 32.62569 29 | H 4.32932 6.70544 32.24683 30 | H 5.82435 7.08129 31.33097 31 | 32 | -------------------------------------------------------------------------------- /metallicious/tests/example5_extract/Fe4L6_fp0/ligand_0.pdb: -------------------------------------------------------------------------------- 1 | TITLE MDANALYSIS FRAME 0: Created by PDBWriter 2 | CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 3 | REMARK 285 UNITARY VALUES FOR THE UNIT CELL AUTOMATICALLY SET 4 | REMARK 285 BY MDANALYSIS PDBWRITER BECAUSE UNIT CELL INFORMATION 5 | REMARK 285 WAS MISSING. 6 | REMARK 285 PROTEIN DATA BANK CONVENTIONS REQUIRE THAT 7 | REMARK 285 CRYST1 RECORD IS INCLUDED, BUT THE VALUES ON 8 | REMARK 285 THIS RECORD ARE MEANINGLESS. 9 | ATOM 1 C UNK X 1 6.270 12.684 31.072 1.00 0.00 C 10 | ATOM 2 C UNK X 1 4.980 12.390 30.478 1.00 0.00 C 11 | ATOM 3 C UNK X 1 4.618 11.096 30.171 1.00 0.00 C 12 | ATOM 4 C UNK X 1 3.393 10.828 29.565 1.00 0.00 C 13 | ATOM 5 C UNK X 1 4.107 13.435 30.179 1.00 0.00 C 14 | ATOM 6 S UNK X 1 4.467 15.098 30.582 1.00 0.00 S 15 | ATOM 7 C UNK X 1 2.894 13.118 29.574 1.00 0.00 C 16 | ATOM 8 C UNK X 1 2.512 11.840 29.258 1.00 0.00 C 17 | ATOM 9 N UNK X 1 1.266 11.580 28.642 1.00 0.00 N 18 | ATOM 10 C UNK X 1 0.216 11.206 29.285 1.00 0.00 C 19 | ATOM 11 C UNK X 1 -1.063 10.938 28.662 1.00 0.00 C 20 | ATOM 12 C UNK X 1 -2.115 10.545 29.446 1.00 0.00 C 21 | ATOM 13 C UNK X 1 -3.328 10.288 28.870 1.00 0.00 C 22 | ATOM 14 C UNK X 1 -3.476 10.427 27.514 1.00 0.00 C 23 | ATOM 15 C UNK X 1 -2.414 10.824 26.719 1.00 0.00 C 24 | ATOM 16 N UNK X 1 -1.255 11.060 27.343 1.00 0.00 N 25 | ATOM 17 H UNK X 1 5.278 10.244 30.393 1.00 0.00 H 26 | ATOM 18 H UNK X 1 3.147 9.805 29.342 1.00 0.00 H 27 | ATOM 19 H UNK X 1 2.216 13.919 29.339 1.00 0.00 H 28 | ATOM 20 H UNK X 1 0.312 11.091 30.351 1.00 0.00 H 29 | ATOM 21 H UNK X 1 -1.983 10.437 30.537 1.00 0.00 H 30 | ATOM 22 H UNK X 1 -4.168 9.973 29.509 1.00 0.00 H 31 | ATOM 23 H UNK X 1 -4.454 10.216 27.078 1.00 0.00 H 32 | ATOM 24 H UNK X 1 -2.560 10.925 25.653 1.00 0.00 H 33 | ATOM 25 H UNK X 1 6.244 12.442 32.143 1.00 0.00 H 34 | ATOM 26 H UNK X 1 7.045 12.082 30.580 1.00 0.00 H 35 | ATOM 27 H UNK X 1 6.498 13.750 30.943 1.00 0.00 H 36 | ATOM 28 H UNK X 1 3.280 15.523 30.103 1.00 0.00 H 37 | END 38 | -------------------------------------------------------------------------------- /metallicious/tests/example5_extract/Fe4L6_fp0/ligand_0.xyz: -------------------------------------------------------------------------------- 1 | 28 2 | frame 0 | Written by MDAnalysis XYZWriter (release 2.4.2) 3 | C 6.27000 12.68400 31.07200 4 | C 4.98000 12.39000 30.47800 5 | C 4.61800 11.09600 30.17100 6 | C 3.39300 10.82800 29.56500 7 | C 4.10700 13.43500 30.17900 8 | S 4.46700 15.09800 30.58200 9 | C 2.89400 13.11800 29.57400 10 | C 2.51200 11.84000 29.25800 11 | N 1.26600 11.58000 28.64200 12 | C 0.21600 11.20600 29.28500 13 | C -1.06300 10.93800 28.66200 14 | C -2.11500 10.54500 29.44600 15 | C -3.32800 10.28800 28.87000 16 | C -3.47600 10.42700 27.51400 17 | C -2.41400 10.82400 26.71900 18 | N -1.25500 11.06000 27.34300 19 | H 5.27800 10.24400 30.39300 20 | H 3.14700 9.80500 29.34200 21 | H 2.21600 13.91900 29.33900 22 | H 0.31200 11.09100 30.35100 23 | H -1.98300 10.43700 30.53700 24 | H -4.16800 9.97300 29.50900 25 | H -4.45400 10.21600 27.07800 26 | H -2.56000 10.92500 25.65300 27 | H 6.24369 12.44208 32.14276 28 | H 7.04530 12.08211 30.57977 29 | H 6.49772 13.75041 30.94324 30 | H 3.27984 15.52321 30.10314 31 | 32 | -------------------------------------------------------------------------------- /metallicious/tests/example5_extract/Fe4L6_fp0/site.xyz: -------------------------------------------------------------------------------- 1 | 85 2 | Frame 0 | Written By Mdanalysis Xyzwriter (Release 2.4.2) 3 | Fe 0.60700 11.61200 26.62800 4 | C 6.27000 12.68400 31.07200 5 | C 4.98000 12.39000 30.47800 6 | C 4.61800 11.09600 30.17100 7 | C 3.39300 10.82800 29.56500 8 | C 4.10700 13.43500 30.17900 9 | S 4.46700 15.09800 30.58200 10 | C 2.89400 13.11800 29.57400 11 | C 2.51200 11.84000 29.25800 12 | N 1.26600 11.58000 28.64200 13 | C 0.21600 11.20600 29.28500 14 | C -1.06300 10.93800 28.66200 15 | C -2.11500 10.54500 29.44600 16 | C -3.32800 10.28800 28.87000 17 | C -3.47600 10.42700 27.51400 18 | C -2.41400 10.82400 26.71900 19 | N -1.25500 11.06000 27.34300 20 | H 5.27800 10.24400 30.39300 21 | H 3.14700 9.80500 29.34200 22 | H 2.21600 13.91900 29.33900 23 | H 0.31200 11.09100 30.35100 24 | H -1.98300 10.43700 30.53700 25 | H -4.16800 9.97300 29.50900 26 | H -4.45400 10.21600 27.07800 27 | H -2.56000 10.92500 25.65300 28 | H 6.24369 12.44208 32.14276 29 | H 6.49772 13.75041 30.94324 30 | H 7.04530 12.08211 30.57977 31 | H 3.27984 15.52321 30.10314 32 | C 7.21700 9.91200 23.62000 33 | C 6.04500 10.56300 24.17600 34 | C 6.03900 11.02800 25.47300 35 | C 4.89700 11.61700 26.01000 36 | C 4.89500 10.68700 23.39900 37 | S 4.83300 10.17000 21.72900 38 | C 3.77700 11.28100 23.97900 39 | C 3.74700 11.75100 25.26600 40 | N 2.58100 12.34600 25.80100 41 | C 2.39000 13.61700 25.85700 42 | C 1.19900 14.23400 26.40400 43 | C 1.10200 15.59900 26.41300 44 | C -0.01700 16.19400 26.92600 45 | C -1.02900 15.41600 27.42500 46 | C -0.93400 14.03400 27.41700 47 | N 0.18600 13.51400 26.90200 48 | H 6.92800 10.95100 26.11800 49 | H 4.93400 11.96700 27.02600 50 | H 2.88500 11.37900 23.38500 51 | H 3.17300 14.24600 25.47000 52 | H 1.92400 16.21600 26.00800 53 | H -0.08500 17.29300 26.92900 54 | H -1.91200 15.91300 27.82900 55 | H -1.74600 13.44500 27.81700 56 | H 8.05979 10.01888 24.31571 57 | H 7.47375 10.37843 22.65970 58 | H 7.00417 8.84616 23.46395 59 | H 5.94980 9.42604 21.86588 60 | C 3.61000 5.31700 29.06400 61 | C 2.96700 6.37000 28.30100 62 | C 3.60900 6.97000 27.23800 63 | C 2.99900 8.00600 26.53600 64 | C 1.69600 6.80800 28.66900 65 | S 0.79200 6.06800 29.97000 66 | C 1.12800 7.84700 27.93700 67 | C 1.74600 8.46000 26.87900 68 | N 1.11800 9.51100 26.17300 69 | C 0.47900 9.34900 25.06800 70 | C -0.16700 10.42100 24.34000 71 | C -0.82000 10.13200 23.17200 72 | C -1.43400 11.13500 22.47400 73 | C -1.38700 12.41900 22.95300 74 | C -0.72700 12.71400 24.13400 75 | N -0.14800 11.68900 24.76800 76 | H 4.61200 6.65000 26.91600 77 | H 3.53300 8.44700 25.71300 78 | H 0.14700 8.19100 28.21600 79 | H 0.43100 8.34800 24.67500 80 | H -0.85000 9.09400 22.79600 81 | H -1.95600 10.89200 21.53600 82 | H -1.88400 13.20200 22.37900 83 | H -0.70600 13.73400 24.48800 84 | H 4.37841 5.75390 29.71546 85 | H 4.07770 4.60008 28.37629 86 | H 2.86062 4.79996 29.67781 87 | H 0.40165 5.04429 29.18317 88 | 89 | -------------------------------------------------------------------------------- /metallicious/tests/example5_extract/Fe4L6_fp1/ligand_0.pdb: -------------------------------------------------------------------------------- 1 | TITLE MDANALYSIS FRAME 0: Created by PDBWriter 2 | CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 3 | REMARK 285 UNITARY VALUES FOR THE UNIT CELL AUTOMATICALLY SET 4 | REMARK 285 BY MDANALYSIS PDBWRITER BECAUSE UNIT CELL INFORMATION 5 | REMARK 285 WAS MISSING. 6 | REMARK 285 PROTEIN DATA BANK CONVENTIONS REQUIRE THAT 7 | REMARK 285 CRYST1 RECORD IS INCLUDED, BUT THE VALUES ON 8 | REMARK 285 THIS RECORD ARE MEANINGLESS. 9 | ATOM 1 S UNK X 1 5.184 6.516 29.008 1.00 0.00 S 10 | ATOM 2 C UNK X 1 4.174 7.843 29.535 1.00 0.00 C 11 | ATOM 3 C UNK X 1 3.381 8.548 28.625 1.00 0.00 C 12 | ATOM 4 C UNK X 1 2.596 9.624 28.980 1.00 0.00 C 13 | ATOM 5 N UNK X 1 1.809 10.305 28.008 1.00 0.00 N 14 | ATOM 6 C UNK X 1 0.884 9.676 27.368 1.00 0.00 C 15 | ATOM 7 C UNK X 1 0.049 10.346 26.354 1.00 0.00 C 16 | ATOM 8 C UNK X 1 -0.929 9.632 25.694 1.00 0.00 C 17 | ATOM 9 C UNK X 1 -1.732 10.247 24.731 1.00 0.00 C 18 | ATOM 10 C UNK X 1 -1.535 11.583 24.444 1.00 0.00 C 19 | ATOM 11 C UNK X 1 -0.547 12.253 25.130 1.00 0.00 C 20 | ATOM 12 N UNK X 1 0.215 11.629 26.059 1.00 0.00 N 21 | ATOM 13 C UNK X 1 2.605 10.010 30.302 1.00 0.00 C 22 | ATOM 14 C UNK X 1 3.379 9.330 31.222 1.00 0.00 C 23 | ATOM 15 C UNK X 1 4.160 8.253 30.851 1.00 0.00 C 24 | ATOM 16 C UNK X 1 4.942 7.512 31.823 1.00 0.00 C 25 | ATOM 17 H UNK X 1 3.379 8.240 27.589 1.00 0.00 H 26 | ATOM 18 H UNK X 1 0.720 8.631 27.582 1.00 0.00 H 27 | ATOM 19 H UNK X 1 -1.074 8.597 25.922 1.00 0.00 H 28 | ATOM 20 H UNK X 1 -2.493 9.678 24.221 1.00 0.00 H 29 | ATOM 21 H UNK X 1 -2.124 12.108 23.711 1.00 0.00 H 30 | ATOM 22 H UNK X 1 -0.382 13.299 24.917 1.00 0.00 H 31 | ATOM 23 H UNK X 1 2.017 10.833 30.624 1.00 0.00 H 32 | ATOM 24 H UNK X 1 3.339 9.688 32.250 1.00 0.00 H 33 | ATOM 25 H UNK X 1 6.176 7.352 28.640 1.00 0.00 H 34 | ATOM 26 H UNK X 1 5.264 8.188 32.626 1.00 0.00 H 35 | ATOM 27 H UNK X 1 4.329 6.705 32.247 1.00 0.00 H 36 | ATOM 28 H UNK X 1 5.824 7.081 31.331 1.00 0.00 H 37 | END 38 | -------------------------------------------------------------------------------- /metallicious/tests/example5_extract/Fe4L6_fp1/ligand_0.xyz: -------------------------------------------------------------------------------- 1 | 28 2 | frame 0 | Written by MDAnalysis XYZWriter (release 2.4.2) 3 | S 5.18384 6.51615 29.00792 4 | C 4.17403 7.84324 29.53506 5 | C 3.38135 8.54779 28.62460 6 | C 2.59607 9.62441 28.98041 7 | N 1.80858 10.30475 28.00764 8 | C 0.88397 9.67585 27.36798 9 | C 0.04869 10.34566 26.35385 10 | C -0.92901 9.63233 25.69408 11 | C -1.73170 10.24650 24.73097 12 | C -1.53527 11.58304 24.44405 13 | C -0.54729 12.25319 25.12994 14 | N 0.21537 11.62907 26.05937 15 | C 2.60509 10.00964 30.30190 16 | C 3.37899 9.32974 31.22188 17 | C 4.16038 8.25287 30.85082 18 | C 4.94200 7.51187 31.82262 19 | H 3.37852 8.24042 27.58855 20 | H 0.72041 8.63088 27.58171 21 | H -1.07424 8.59667 25.92238 22 | H -2.49262 9.67838 24.22132 23 | H -2.12438 12.10758 23.71086 24 | H -0.38194 13.29943 24.91665 25 | H 2.01732 10.83303 30.62401 26 | H 3.33921 9.68783 32.25030 27 | H 6.17644 7.35215 28.64009 28 | H 5.26399 8.18799 32.62569 29 | H 4.32932 6.70544 32.24683 30 | H 5.82435 7.08129 31.33097 31 | 32 | -------------------------------------------------------------------------------- /metallicious/tests/example5_extract/Fe4L6_fp1/site.xyz: -------------------------------------------------------------------------------- 1 | 85 2 | Frame 0 | Written By Mdanalysis Xyzwriter (Release 2.4.2) 3 | Fe 1.89270 12.20149 27.16462 4 | S 5.18384 6.51615 29.00792 5 | C 4.17403 7.84324 29.53506 6 | C 3.38135 8.54779 28.62460 7 | C 2.59607 9.62441 28.98041 8 | N 1.80858 10.30475 28.00764 9 | C 0.88397 9.67585 27.36798 10 | C 0.04869 10.34566 26.35385 11 | C -0.92901 9.63233 25.69408 12 | C -1.73170 10.24650 24.73097 13 | C -1.53527 11.58304 24.44405 14 | C -0.54729 12.25319 25.12994 15 | N 0.21537 11.62907 26.05937 16 | C 2.60509 10.00964 30.30190 17 | C 3.37899 9.32974 31.22188 18 | C 4.16038 8.25287 30.85082 19 | C 4.94200 7.51187 31.82262 20 | H 3.37852 8.24042 27.58855 21 | H 0.72041 8.63088 27.58171 22 | H -1.07424 8.59667 25.92238 23 | H -2.49262 9.67838 24.22132 24 | H -2.12438 12.10758 23.71086 25 | H -0.38194 13.29943 24.91665 26 | H 2.01732 10.83303 30.62401 27 | H 3.33921 9.68783 32.25030 28 | H 6.17644 7.35215 28.64009 29 | H 5.26399 8.18799 32.62569 30 | H 4.32932 6.70544 32.24683 31 | H 5.82435 7.08129 31.33097 32 | S 7.23766 8.89518 24.31348 33 | C 5.50754 9.02129 24.53463 34 | C 4.92154 10.22379 24.93823 35 | C 3.56845 10.36815 25.16271 36 | N 3.02659 11.62052 25.57259 37 | C 3.14346 12.65589 24.81643 38 | C 2.59602 13.96947 25.20631 39 | C 2.74568 15.04955 24.36319 40 | C 2.23533 16.30136 24.71287 41 | C 1.57656 16.44687 25.91729 42 | C 1.45342 15.33799 26.72472 43 | N 1.95962 14.13736 26.35774 44 | C 2.77038 9.26342 24.97572 45 | C 3.32429 8.06136 24.57613 46 | C 4.68122 7.93322 24.35512 47 | C 5.26040 6.68316 23.89635 48 | H 5.55241 11.08918 25.08402 49 | H 3.65600 12.55583 23.87122 50 | H 3.25725 14.92662 23.43105 51 | H 2.35856 17.13816 24.04514 52 | H 1.16437 17.38931 26.23737 53 | H 0.94039 15.43770 27.67072 54 | H 1.72297 9.32394 25.13592 55 | H 2.63534 7.22694 24.44703 56 | H 7.09631 8.53302 23.02185 57 | H 6.31650 6.63810 24.19361 58 | H 4.71740 5.84139 24.34606 59 | H 5.18529 6.62468 22.80246 60 | S 8.18563 11.03629 29.76146 61 | C 7.16525 11.95153 28.67626 62 | C 5.78258 12.01355 28.87237 63 | C 4.92925 12.69048 28.02634 64 | N 3.52672 12.71964 28.27733 65 | C 3.07316 13.24175 29.36358 66 | C 1.62932 13.29158 29.65874 67 | C 1.19133 13.85994 30.83428 68 | C -0.17192 13.91685 31.13418 69 | C -1.08046 13.39410 30.23480 70 | C -0.59341 12.83608 29.07344 71 | N 0.73436 12.79666 28.81235 72 | C 5.48253 13.33007 26.94085 73 | C 6.84681 13.28452 26.72414 74 | C 7.68913 12.60336 27.58157 75 | C 9.12565 12.58836 27.37882 76 | H 5.35275 11.50985 29.72635 77 | H 3.77312 13.65484 30.07467 78 | H 1.90204 14.26238 31.52575 79 | H -0.50186 14.36459 32.05674 80 | H -2.14209 13.41122 30.41440 81 | H -1.29287 12.42335 28.36157 82 | H 4.86586 13.86293 26.26123 83 | H 7.21791 13.81279 25.84674 84 | H 7.84247 9.86883 29.17945 85 | H 9.63291 12.59388 28.35268 86 | H 9.40759 11.68347 26.82445 87 | H 9.42370 13.47639 26.80591 88 | 89 | -------------------------------------------------------------------------------- /metallicious/tests/example5_extract/Ga4L6_fp0/ligand_0.pdb: -------------------------------------------------------------------------------- 1 | TITLE MDANALYSIS FRAME 0: Created by PDBWriter 2 | CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 3 | REMARK 285 UNITARY VALUES FOR THE UNIT CELL AUTOMATICALLY SET 4 | REMARK 285 BY MDANALYSIS PDBWRITER BECAUSE UNIT CELL INFORMATION 5 | REMARK 285 WAS MISSING. 6 | REMARK 285 PROTEIN DATA BANK CONVENTIONS REQUIRE THAT 7 | REMARK 285 CRYST1 RECORD IS INCLUDED, BUT THE VALUES ON 8 | REMARK 285 THIS RECORD ARE MEANINGLESS. 9 | ATOM 1 C UNK X 1 -23.016 -25.001 -14.910 1.00 0.00 C 10 | ATOM 2 C UNK X 1 -22.109 -26.133 -14.556 1.00 0.00 C 11 | ATOM 3 C UNK X 1 -21.371 -26.887 -15.497 1.00 0.00 C 12 | ATOM 4 O UNK X 1 -21.401 -26.705 -16.776 1.00 0.00 O 13 | ATOM 5 H UNK X 1 -22.512 -24.338 -15.625 1.00 0.00 H 14 | ATOM 6 H UNK X 1 -23.935 -25.397 -15.361 1.00 0.00 H 15 | ATOM 7 H UNK X 1 -23.267 -24.437 -14.002 1.00 0.00 H 16 | ATOM 8 C UNK X 1 -20.487 -27.949 -15.033 1.00 0.00 C 17 | ATOM 9 C UNK X 1 -21.970 -26.439 -13.208 1.00 0.00 C 18 | ATOM 10 C UNK X 1 -21.129 -27.461 -12.767 1.00 0.00 C 19 | ATOM 11 O UNK X 1 -19.825 -28.591 -15.928 1.00 0.00 O 20 | ATOM 12 H UNK X 1 -22.537 -25.849 -12.503 1.00 0.00 H 21 | ATOM 13 C UNK X 1 -20.392 -28.208 -13.658 1.00 0.00 C 22 | ATOM 14 H UNK X 1 -21.057 -27.665 -11.709 1.00 0.00 H 23 | ATOM 15 H UNK X 1 -19.738 -29.000 -13.328 1.00 0.00 H 24 | END 25 | -------------------------------------------------------------------------------- /metallicious/tests/example5_extract/Ga4L6_fp0/ligand_0.xyz: -------------------------------------------------------------------------------- 1 | 15 2 | frame 0 | Written by MDAnalysis XYZWriter (release 2.4.2) 3 | C -23.01589 -25.00122 -14.90954 4 | C -22.10869 -26.13282 -14.55626 5 | C -21.37144 -26.88711 -15.49687 6 | O -21.40051 -26.70480 -16.77630 7 | H -22.51233 -24.33802 -15.62531 8 | H -23.93532 -25.39654 -15.36124 9 | H -23.26736 -24.43668 -14.00195 10 | C -20.48699 -27.94869 -15.03267 11 | C -21.96979 -26.43854 -13.20828 12 | C -21.12899 -27.46148 -12.76678 13 | O -19.82491 -28.59116 -15.92837 14 | H -22.53710 -25.84939 -12.50312 15 | C -20.39185 -28.20818 -13.65775 16 | H -21.05696 -27.66471 -11.70945 17 | H -19.73774 -28.99993 -13.32764 18 | 19 | -------------------------------------------------------------------------------- /metallicious/tests/example5_extract/Ga4L6_fp0/site.xyz: -------------------------------------------------------------------------------- 1 | 46 2 | Frame 0 | Written By Mdanalysis Xyzwriter (Release 2.4.2) 3 | Ga -20.36318 -28.12122 -17.74401 4 | C -23.01589 -25.00122 -14.90954 5 | C -22.10869 -26.13282 -14.55626 6 | C -21.37144 -26.88711 -15.49687 7 | O -21.40051 -26.70480 -16.77630 8 | H -22.51233 -24.33802 -15.62531 9 | H -23.93532 -25.39654 -15.36124 10 | H -23.26736 -24.43668 -14.00195 11 | C -20.48699 -27.94869 -15.03267 12 | C -21.96979 -26.43854 -13.20828 13 | C -21.12899 -27.46148 -12.76678 14 | O -19.82491 -28.59116 -15.92837 15 | H -22.53710 -25.84939 -12.50312 16 | C -20.39185 -28.20818 -13.65775 17 | H -21.05696 -27.66471 -11.70945 18 | H -19.73774 -28.99993 -13.32764 19 | C -22.04717 -27.78544 -22.38170 20 | C -22.45115 -28.70144 -21.27743 21 | C -22.03099 -28.56158 -19.93572 22 | O -21.34189 -27.57842 -19.47308 23 | H -20.95640 -27.65949 -22.37235 24 | H -22.35796 -28.21305 -23.34411 25 | H -22.52953 -26.80896 -22.24218 26 | C -22.35070 -29.61061 -18.97309 27 | C -23.25612 -29.78221 -21.60717 28 | C -23.63003 -30.74346 -20.66384 29 | O -21.82224 -29.50281 -17.81284 30 | H -23.58529 -29.86331 -22.63257 31 | C -23.17754 -30.67671 -19.36799 32 | H -24.26431 -31.56138 -20.96937 33 | H -23.42505 -31.43359 -18.64015 34 | C -17.34900 -24.86982 -20.02477 35 | C -17.57833 -26.32547 -20.22360 36 | C -18.32323 -27.14267 -19.34500 37 | O -18.98299 -26.72091 -18.31896 38 | H -16.28574 -24.69185 -19.81611 39 | H -17.63966 -24.32606 -20.93334 40 | H -17.95224 -24.51658 -19.17801 41 | C -18.44540 -28.56418 -19.62925 42 | C -17.01198 -26.90633 -21.35095 43 | C -17.14063 -28.26745 -21.62570 44 | O -19.14252 -29.25829 -18.80217 45 | H -16.45738 -26.26206 -22.01677 46 | C -17.84957 -29.09303 -20.78382 47 | H -16.67537 -28.67502 -22.50981 48 | H -17.95519 -30.14882 -20.98047 49 | 50 | -------------------------------------------------------------------------------- /metallicious/tests/example5_extract/Pd4L6_fp0/ligand_0.pdb: -------------------------------------------------------------------------------- 1 | TITLE MDANALYSIS FRAME 0: Created by PDBWriter 2 | CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 3 | REMARK 285 UNITARY VALUES FOR THE UNIT CELL AUTOMATICALLY SET 4 | REMARK 285 BY MDANALYSIS PDBWRITER BECAUSE UNIT CELL INFORMATION 5 | REMARK 285 WAS MISSING. 6 | REMARK 285 PROTEIN DATA BANK CONVENTIONS REQUIRE THAT 7 | REMARK 285 CRYST1 RECORD IS INCLUDED, BUT THE VALUES ON 8 | REMARK 285 THIS RECORD ARE MEANINGLESS. 9 | ATOM 1 N UNK X 1 31.760 -0.849 3.416 1.00 0.00 N 10 | ATOM 2 C UNK X 1 30.917 -0.957 2.393 1.00 0.00 C 11 | ATOM 3 H UNK X 1 30.536 -0.166 2.034 1.00 0.00 H 12 | ATOM 4 C UNK X 1 30.575 -2.170 1.824 1.00 0.00 C 13 | ATOM 5 H UNK X 1 29.994 -2.209 1.074 1.00 0.00 H 14 | ATOM 6 C UNK X 1 31.095 -3.327 2.374 1.00 0.00 C 15 | ATOM 7 C UNK X 1 31.980 -3.223 3.440 1.00 0.00 C 16 | ATOM 8 H UNK X 1 32.376 -4.000 3.815 1.00 0.00 H 17 | ATOM 9 C UNK X 1 32.277 -1.977 3.944 1.00 0.00 C 18 | ATOM 10 H UNK X 1 32.865 -1.910 4.687 1.00 0.00 H 19 | ATOM 11 C UNK X 1 30.705 -4.672 1.873 1.00 0.00 C 20 | ATOM 12 H UNK X 1 31.591 -5.187 1.478 1.00 0.00 H 21 | ATOM 13 H UNK X 1 30.277 -5.259 2.696 1.00 0.00 H 22 | ATOM 14 H UNK X 1 29.959 -4.562 1.075 1.00 0.00 H 23 | END 24 | -------------------------------------------------------------------------------- /metallicious/tests/example5_extract/Pd4L6_fp0/ligand_0.xyz: -------------------------------------------------------------------------------- 1 | 14 2 | frame 0 | Written by MDAnalysis XYZWriter (release 2.4.2) 3 | N 31.75970 -0.84930 3.41570 4 | C 30.91720 -0.95660 2.39260 5 | H 30.53640 -0.16570 2.03390 6 | C 30.57480 -2.16960 1.82400 7 | H 29.99450 -2.20880 1.07400 8 | C 31.09540 -3.32670 2.37430 9 | C 31.98030 -3.22260 3.44020 10 | H 32.37610 -4.00000 3.81520 11 | C 32.27650 -1.97710 3.94360 12 | H 32.86460 -1.91000 4.68740 13 | C 30.70490 -4.67180 1.87290 14 | H 31.59069 -5.18659 1.47779 15 | H 30.27702 -5.25920 2.69603 16 | H 29.95877 -4.56246 1.07478 17 | 18 | -------------------------------------------------------------------------------- /metallicious/tests/example5_extract/Pd4L6_fp0/ligand_1.pdb: -------------------------------------------------------------------------------- 1 | TITLE MDANALYSIS FRAME 0: Created by PDBWriter 2 | CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 3 | REMARK 285 UNITARY VALUES FOR THE UNIT CELL AUTOMATICALLY SET 4 | REMARK 285 BY MDANALYSIS PDBWRITER BECAUSE UNIT CELL INFORMATION 5 | REMARK 285 WAS MISSING. 6 | REMARK 285 PROTEIN DATA BANK CONVENTIONS REQUIRE THAT 7 | REMARK 285 CRYST1 RECORD IS INCLUDED, BUT THE VALUES ON 8 | REMARK 285 THIS RECORD ARE MEANINGLESS. 9 | ATOM 1 N UNK X 1 32.608 2.696 5.260 1.00 0.00 N 10 | ATOM 2 N UNK X 1 33.723 1.373 3.065 1.00 0.00 N 11 | ATOM 3 C UNK X 1 32.792 2.565 6.673 1.00 0.00 C 12 | ATOM 4 H UNK X 1 33.528 1.940 6.850 1.00 0.00 H 13 | ATOM 5 H UNK X 1 31.969 2.222 7.078 1.00 0.00 H 14 | ATOM 6 H UNK X 1 33.006 3.441 7.056 1.00 0.00 H 15 | ATOM 7 C UNK X 1 31.662 3.714 4.983 1.00 0.00 C 16 | ATOM 8 H UNK X 1 31.457 3.720 4.025 1.00 0.00 H 17 | ATOM 9 H UNK X 1 32.029 4.582 5.244 1.00 0.00 H 18 | ATOM 10 H UNK X 1 30.840 3.542 5.492 1.00 0.00 H 19 | ATOM 11 C UNK X 1 33.952 3.043 4.814 1.00 0.00 C 20 | ATOM 12 H UNK X 1 34.078 4.019 4.920 1.00 0.00 H 21 | ATOM 13 H UNK X 1 34.608 2.591 5.401 1.00 0.00 H 22 | ATOM 14 C UNK X 1 34.232 2.698 3.481 1.00 0.00 C 23 | ATOM 15 H UNK X 1 35.213 2.714 3.351 1.00 0.00 H 24 | ATOM 16 H UNK X 1 33.840 3.388 2.888 1.00 0.00 H 25 | ATOM 17 C UNK X 1 33.275 1.502 1.657 1.00 0.00 C 26 | ATOM 18 H UNK X 1 34.027 1.803 1.100 1.00 0.00 H 27 | ATOM 19 H UNK X 1 32.549 2.159 1.604 1.00 0.00 H 28 | ATOM 20 H UNK X 1 32.956 0.632 1.335 1.00 0.00 H 29 | ATOM 21 C UNK X 1 34.771 0.347 3.147 1.00 0.00 C 30 | ATOM 22 H UNK X 1 34.427 -0.501 2.798 1.00 0.00 H 31 | ATOM 23 H UNK X 1 35.044 0.231 4.080 1.00 0.00 H 32 | ATOM 24 H UNK X 1 35.545 0.628 2.613 1.00 0.00 H 33 | END 34 | -------------------------------------------------------------------------------- /metallicious/tests/example5_extract/Pd4L6_fp0/ligand_1.xyz: -------------------------------------------------------------------------------- 1 | 24 2 | frame 0 | Written by MDAnalysis XYZWriter (release 2.4.2) 3 | N 32.60830 2.69590 5.26010 4 | N 33.72280 1.37350 3.06520 5 | C 32.79220 2.56500 6.67250 6 | H 33.52780 1.94040 6.84980 7 | H 31.96880 2.22210 7.07800 8 | H 33.00600 3.44130 7.05560 9 | C 31.66190 3.71400 4.98300 10 | H 31.45660 3.71970 4.02510 11 | H 32.02900 4.58190 5.24380 12 | H 30.84050 3.54210 5.49250 13 | C 33.95160 3.04340 4.81380 14 | H 34.07780 4.01890 4.91980 15 | H 34.60810 2.59100 5.40080 16 | C 34.23200 2.69800 3.48090 17 | H 35.21280 2.71370 3.35050 18 | H 33.83970 3.38770 2.88790 19 | C 33.27490 1.50220 1.65690 20 | H 34.02660 1.80270 1.10050 21 | H 32.54930 2.15880 1.60390 22 | H 32.95600 0.63250 1.33490 23 | C 34.77130 0.34680 3.14670 24 | H 34.42690 -0.50120 2.79820 25 | H 35.04370 0.23110 4.08010 26 | H 35.54540 0.62800 2.61270 27 | 28 | -------------------------------------------------------------------------------- /metallicious/tests/example5_extract/Pd4L6_fp0/site.xyz: -------------------------------------------------------------------------------- 1 | 53 2 | Frame 0 | Written By Mdanalysis Xyzwriter (Release 2.4.2) 3 | Pd 32.15210 0.92430 4.32220 4 | N 31.75970 -0.84930 3.41570 5 | C 32.27650 -1.97710 3.94360 6 | H 32.86460 -1.91000 4.68740 7 | C 31.98030 -3.22260 3.44020 8 | H 32.37610 -4.00000 3.81520 9 | C 31.09540 -3.32670 2.37430 10 | C 30.57480 -2.16960 1.82400 11 | H 29.99450 -2.20880 1.07400 12 | C 30.91720 -0.95660 2.39260 13 | H 30.53640 -0.16570 2.03390 14 | C 30.70490 -4.67180 1.87290 15 | H 31.59069 -5.18659 1.47779 16 | H 30.27702 -5.25920 2.69603 17 | H 29.95877 -4.56246 1.07478 18 | N 30.58500 0.49320 5.52710 19 | C 30.72150 -0.24010 6.61540 20 | H 31.59730 -0.49290 6.88040 21 | C 29.67180 -0.65800 7.38170 22 | H 29.82140 -1.16810 8.16840 23 | C 28.38360 -0.32600 6.99650 24 | C 28.20520 0.45480 5.86540 25 | H 27.33840 0.72100 5.58010 26 | C 29.34660 0.83640 5.16230 27 | H 29.23810 1.37040 4.38170 28 | C 27.18790 -0.82220 7.77100 29 | H 26.59642 -1.49729 7.13843 30 | H 27.52882 -1.36245 8.66406 31 | H 26.56811 0.03195 8.07424 32 | N 32.60830 2.69590 5.26010 33 | N 33.72280 1.37350 3.06520 34 | C 32.79220 2.56500 6.67250 35 | H 33.52780 1.94040 6.84980 36 | H 31.96880 2.22210 7.07800 37 | H 33.00600 3.44130 7.05560 38 | C 31.66190 3.71400 4.98300 39 | H 31.45660 3.71970 4.02510 40 | H 32.02900 4.58190 5.24380 41 | H 30.84050 3.54210 5.49250 42 | C 33.95160 3.04340 4.81380 43 | H 34.07780 4.01890 4.91980 44 | H 34.60810 2.59100 5.40080 45 | C 34.23200 2.69800 3.48090 46 | H 35.21280 2.71370 3.35050 47 | H 33.83970 3.38770 2.88790 48 | C 33.27490 1.50220 1.65690 49 | H 34.02660 1.80270 1.10050 50 | H 32.54930 2.15880 1.60390 51 | H 32.95600 0.63250 1.33490 52 | C 34.77130 0.34680 3.14670 53 | H 34.42690 -0.50120 2.79820 54 | H 35.04370 0.23110 4.08010 55 | H 35.54540 0.62800 2.61270 56 | 57 | -------------------------------------------------------------------------------- /metallicious/tests/example5_extract/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/duartegroup/metallicious/3254b283fe22af19bc477ca36b96533d8fd463a4/metallicious/tests/example5_extract/__init__.py -------------------------------------------------------------------------------- /metallicious/tests/example5_extract/example5.py: -------------------------------------------------------------------------------- 1 | from metallicious.extract_metal_site import extract_metal_structure 2 | 3 | f='pd2l4_tall.xyz' 4 | metal='Pd' 5 | extract_metal_structure(f, metal, "pd2l4_tall_fp1") 6 | 7 | f='pd2l4_tall.pdb' 8 | metal='Pd' 9 | extract_metal_structure(f, metal, "pd2l4_tall_fp2") 10 | 11 | f='pd2l4_tall.gro' 12 | metal='Pd' 13 | extract_metal_structure(f, metal, "pd2l4_tall_fp3") 14 | 15 | f='Fe4L6.pdb' 16 | metal='Fe' 17 | extract_metal_structure(f, metal, "Fe4L6_fp") 18 | 19 | f='Fe4L6_2.pdb' 20 | metal='Fe' 21 | extract_metal_structure(f, metal, "Fe4L6_2_fp") 22 | 23 | f='Ga4L6.xyz' 24 | metal='Ga' 25 | extract_metal_structure(f, metal, "Ga4L6_fp") 26 | 27 | f='Pd4L6.xyz' 28 | metal='Pd' 29 | extract_metal_structure(f, metal, "Pd4L6_fp") 30 | 31 | f='knot_4n.pdb' 32 | metal='Fe' 33 | extract_metal_structure(f, metal, "knot_4n_fp") 34 | 35 | f='knot_3n.pdb' 36 | metal='Zn' 37 | extract_metal_structure(f, metal, "knot_3n_fp") 38 | 39 | f='Co8L16.xyz' 40 | metal='Co' 41 | extract_metal_structure(f, metal, "Co8L16_fp") 42 | 43 | f='ru_pd.xyz' 44 | metal='Ru' 45 | extract_metal_structure(f, metal, "ru_fp") 46 | -------------------------------------------------------------------------------- /metallicious/tests/example5_extract/knot_3n_fp0/ligand_0.pdb: -------------------------------------------------------------------------------- 1 | TITLE MDANALYSIS FRAME 0: Created by PDBWriter 2 | CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 3 | REMARK 285 UNITARY VALUES FOR THE UNIT CELL AUTOMATICALLY SET 4 | REMARK 285 BY MDANALYSIS PDBWRITER BECAUSE UNIT CELL INFORMATION 5 | REMARK 285 WAS MISSING. 6 | REMARK 285 PROTEIN DATA BANK CONVENTIONS REQUIRE THAT 7 | REMARK 285 CRYST1 RECORD IS INCLUDED, BUT THE VALUES ON 8 | REMARK 285 THIS RECORD ARE MEANINGLESS. 9 | ATOM 1 N UNK X 1 -0.014 6.893 12.712 1.00 0.00 N 10 | ATOM 2 C UNK X 1 -1.125 7.404 13.259 1.00 0.00 C 11 | ATOM 3 C UNK X 1 1.084 7.647 12.734 1.00 0.00 C 12 | ATOM 4 O UNK X 1 1.616 14.210 19.834 1.00 0.00 O 13 | ATOM 5 C UNK X 1 1.952 13.909 18.554 1.00 0.00 C 14 | ATOM 6 H UNK X 1 0.672 14.022 19.863 1.00 0.00 H 15 | ATOM 7 N UNK X 1 -0.012 9.378 13.986 1.00 0.00 N 16 | ATOM 8 C UNK X 1 1.084 8.886 13.390 1.00 0.00 C 17 | ATOM 9 C UNK X 1 -1.126 8.656 13.876 1.00 0.00 C 18 | ATOM 10 N UNK X 1 2.295 10.733 14.262 1.00 0.00 N 19 | ATOM 11 C UNK X 1 2.315 9.696 13.530 1.00 0.00 C 20 | ATOM 12 C UNK X 1 3.530 11.521 14.414 1.00 0.00 C 21 | ATOM 13 N UNK X 1 1.631 12.769 16.450 1.00 0.00 N 22 | ATOM 14 C UNK X 1 1.253 13.040 17.724 1.00 0.00 C 23 | ATOM 15 C UNK X 1 2.745 13.364 15.977 1.00 0.00 C 24 | ATOM 16 C UNK X 1 -2.331 6.558 13.223 1.00 0.00 C 25 | ATOM 17 H UNK X 1 -1.923 8.995 14.217 1.00 0.00 H 26 | ATOM 18 H UNK X 1 -2.272 5.873 12.367 1.00 0.00 H 27 | ATOM 19 H UNK X 1 -2.399 5.977 14.152 1.00 0.00 H 28 | ATOM 20 H UNK X 1 -3.221 7.193 13.123 1.00 0.00 H 29 | ATOM 21 H UNK X 1 0.490 12.627 18.058 1.00 0.00 H 30 | ATOM 22 H UNK X 1 3.094 9.447 13.087 1.00 0.00 H 31 | ATOM 23 H UNK X 1 1.857 7.350 12.311 1.00 0.00 H 32 | ATOM 24 C UNK X 1 3.110 14.498 18.052 1.00 0.00 C 33 | ATOM 25 C UNK X 1 3.495 14.223 16.772 1.00 0.00 C 34 | ATOM 26 C UNK X 1 3.195 13.005 14.589 1.00 0.00 C 35 | ATOM 27 H UNK X 1 4.091 11.404 13.631 1.00 0.00 H 36 | ATOM 28 H UNK X 1 4.025 11.206 15.188 1.00 0.00 H 37 | ATOM 29 H UNK X 1 4.266 14.615 16.428 1.00 0.00 H 38 | ATOM 30 H UNK X 1 3.981 13.530 14.368 1.00 0.00 H 39 | ATOM 31 H UNK X 1 2.496 13.242 13.961 1.00 0.00 H 40 | ATOM 32 H UNK X 1 3.616 15.071 18.583 1.00 0.00 H 41 | END 42 | -------------------------------------------------------------------------------- /metallicious/tests/example5_extract/knot_3n_fp0/ligand_0.xyz: -------------------------------------------------------------------------------- 1 | 32 2 | frame 0 | Written by MDAnalysis XYZWriter (release 2.4.2) 3 | N -0.01400 6.89300 12.71200 4 | C -1.12500 7.40400 13.25900 5 | C 1.08400 7.64700 12.73400 6 | O 1.61600 14.21000 19.83400 7 | C 1.95200 13.90900 18.55400 8 | H 0.67225 14.02229 19.86261 9 | N -0.01200 9.37800 13.98600 10 | C 1.08400 8.88600 13.39000 11 | C -1.12600 8.65600 13.87600 12 | N 2.29500 10.73300 14.26200 13 | C 2.31500 9.69600 13.53000 14 | C 3.53000 11.52100 14.41400 15 | N 1.63100 12.76900 16.45000 16 | C 1.25300 13.04000 17.72400 17 | C 2.74500 13.36400 15.97700 18 | C -2.33100 6.55800 13.22300 19 | H -1.92300 8.99500 14.21700 20 | H -2.27225 5.87299 12.36682 21 | H -2.39852 5.97721 14.15240 22 | H -3.22092 7.19337 13.12294 23 | H 0.49000 12.62700 18.05800 24 | H 3.09400 9.44700 13.08700 25 | H 1.85700 7.35000 12.31100 26 | C 3.11000 14.49800 18.05200 27 | C 3.49500 14.22300 16.77200 28 | C 3.19500 13.00500 14.58900 29 | H 4.09100 11.40400 13.63100 30 | H 4.02500 11.20600 15.18800 31 | H 4.26600 14.61500 16.42800 32 | H 3.98100 13.53000 14.36800 33 | H 2.49600 13.24200 13.96100 34 | H 3.61600 15.07100 18.58300 35 | 36 | -------------------------------------------------------------------------------- /metallicious/tests/example5_extract/knot_3n_fp0/site.xyz: -------------------------------------------------------------------------------- 1 | 65 2 | Frame 0 | Written By Mdanalysis Xyzwriter (Release 2.4.2) 3 | Zn 0.58600 11.30900 15.29300 4 | N -0.01400 6.89300 12.71200 5 | C -1.12500 7.40400 13.25900 6 | C 1.08400 7.64700 12.73400 7 | O 1.61600 14.21000 19.83400 8 | C 1.95200 13.90900 18.55400 9 | H 0.67225 14.02229 19.86261 10 | N -0.01200 9.37800 13.98600 11 | C 1.08400 8.88600 13.39000 12 | C -1.12600 8.65600 13.87600 13 | N 2.29500 10.73300 14.26200 14 | C 2.31500 9.69600 13.53000 15 | C 3.53000 11.52100 14.41400 16 | N 1.63100 12.76900 16.45000 17 | C 1.25300 13.04000 17.72400 18 | C 2.74500 13.36400 15.97700 19 | C -2.33100 6.55800 13.22300 20 | H -1.92300 8.99500 14.21700 21 | H -2.27225 5.87299 12.36682 22 | H -2.39852 5.97721 14.15240 23 | H -3.22092 7.19337 13.12294 24 | H 0.49000 12.62700 18.05800 25 | H 3.09400 9.44700 13.08700 26 | H 1.85700 7.35000 12.31100 27 | C 3.11000 14.49800 18.05200 28 | C 3.49500 14.22300 16.77200 29 | C 3.19500 13.00500 14.58900 30 | H 4.09100 11.40400 13.63100 31 | H 4.02500 11.20600 15.18800 32 | H 4.26600 14.61500 16.42800 33 | H 3.98100 13.53000 14.36800 34 | H 2.49600 13.24200 13.96100 35 | H 3.61600 15.07100 18.58300 36 | N 1.34300 7.45000 18.65100 37 | C 2.41900 7.87300 17.98300 38 | C 0.23400 8.18600 18.50800 39 | O -0.67000 13.28000 10.34500 40 | C -0.94500 13.22000 11.65800 41 | H 0.17036 12.81555 10.27581 42 | N 1.27000 9.66800 16.94500 43 | C 0.19300 9.27300 17.64000 44 | C 2.39900 8.98700 17.15300 45 | N -1.08200 10.88800 16.46300 46 | C -1.06200 10.02200 17.37500 47 | C -2.33800 11.60700 16.19700 48 | N -0.52200 12.50500 13.91900 49 | C -0.19000 12.53900 12.61800 50 | C -1.62600 13.16200 14.32300 51 | C 3.63300 7.02900 18.13300 52 | H 3.18300 9.26300 16.73600 53 | H 4.19893 7.35525 19.01562 54 | H 3.33592 5.97914 18.25626 55 | H 4.26115 7.12901 17.23797 56 | H 0.57700 12.09100 12.34300 57 | H -1.82600 9.85300 17.87800 58 | H -0.52500 7.96400 18.99900 59 | C -2.06100 13.92000 12.09700 60 | C -2.39900 13.88400 13.42700 61 | C -2.04100 13.05000 15.76200 62 | H -2.88500 11.61400 16.99800 63 | H -2.83200 11.15100 15.49800 64 | H -3.14600 14.34800 13.72800 65 | H -2.83200 13.59100 15.90500 66 | H -1.33300 13.40700 16.32100 67 | H -2.57600 14.40800 11.49600 68 | 69 | -------------------------------------------------------------------------------- /metallicious/tests/example5_extract/knot_4n_fp0/ligand_0.pdb: -------------------------------------------------------------------------------- 1 | TITLE MDANALYSIS FRAME 0: Created by PDBWriter 2 | CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 3 | REMARK 285 UNITARY VALUES FOR THE UNIT CELL AUTOMATICALLY SET 4 | REMARK 285 BY MDANALYSIS PDBWRITER BECAUSE UNIT CELL INFORMATION 5 | REMARK 285 WAS MISSING. 6 | REMARK 285 PROTEIN DATA BANK CONVENTIONS REQUIRE THAT 7 | REMARK 285 CRYST1 RECORD IS INCLUDED, BUT THE VALUES ON 8 | REMARK 285 THIS RECORD ARE MEANINGLESS. 9 | ATOM 1 C UNK X 1 16.199 14.907 3.190 1.00 0.00 C 10 | ATOM 2 N UNK X 1 12.531 14.120 2.724 1.00 0.00 N 11 | ATOM 3 C UNK X 1 12.280 14.702 1.531 1.00 0.00 C 12 | ATOM 4 C UNK X 1 13.273 15.349 0.806 1.00 0.00 C 13 | ATOM 5 C UNK X 1 14.562 15.419 1.337 1.00 0.00 C 14 | ATOM 6 C UNK X 1 14.840 14.828 2.564 1.00 0.00 C 15 | ATOM 7 C UNK X 1 13.782 14.188 3.218 1.00 0.00 C 16 | ATOM 8 N UNK X 1 10.052 14.037 1.996 1.00 0.00 N 17 | ATOM 9 C UNK X 1 10.886 14.607 1.081 1.00 0.00 C 18 | ATOM 10 C UNK X 1 10.411 15.086 -0.135 1.00 0.00 C 19 | ATOM 11 C UNK X 1 9.073 14.979 -0.433 1.00 0.00 C 20 | ATOM 12 C UNK X 1 8.209 14.411 0.510 1.00 0.00 C 21 | ATOM 13 C UNK X 1 8.746 13.953 1.693 1.00 0.00 C 22 | ATOM 14 C UNK X 1 6.723 14.378 0.261 1.00 0.00 C 23 | ATOM 15 H UNK X 1 13.077 15.740 -0.039 1.00 0.00 H 24 | ATOM 16 H UNK X 1 15.248 15.869 0.861 1.00 0.00 H 25 | ATOM 17 H UNK X 1 13.953 13.779 4.058 1.00 0.00 H 26 | ATOM 18 H UNK X 1 11.009 15.483 -0.757 1.00 0.00 H 27 | ATOM 19 H UNK X 1 8.740 15.290 -1.267 1.00 0.00 H 28 | ATOM 20 H UNK X 1 8.161 13.555 2.328 1.00 0.00 H 29 | ATOM 21 H UNK X 1 16.103 14.841 4.282 1.00 0.00 H 30 | ATOM 22 H UNK X 1 16.818 14.077 2.826 1.00 0.00 H 31 | ATOM 23 H UNK X 1 16.671 15.861 2.921 1.00 0.00 H 32 | ATOM 24 H UNK X 1 6.533 14.351 -0.820 1.00 0.00 H 33 | ATOM 25 H UNK X 1 6.293 13.483 0.731 1.00 0.00 H 34 | ATOM 26 H UNK X 1 6.260 15.276 0.691 1.00 0.00 H 35 | END 36 | -------------------------------------------------------------------------------- /metallicious/tests/example5_extract/knot_4n_fp0/ligand_0.xyz: -------------------------------------------------------------------------------- 1 | 26 2 | frame 0 | Written by MDAnalysis XYZWriter (release 2.4.2) 3 | C 16.19900 14.90700 3.19000 4 | N 12.53100 14.12000 2.72400 5 | C 12.28000 14.70200 1.53100 6 | C 13.27300 15.34900 0.80600 7 | C 14.56200 15.41900 1.33700 8 | C 14.84000 14.82800 2.56400 9 | C 13.78200 14.18800 3.21800 10 | N 10.05200 14.03700 1.99600 11 | C 10.88600 14.60700 1.08100 12 | C 10.41100 15.08600 -0.13500 13 | C 9.07300 14.97900 -0.43300 14 | C 8.20900 14.41100 0.51000 15 | C 8.74600 13.95300 1.69300 16 | C 6.72300 14.37800 0.26100 17 | H 13.07700 15.74000 -0.03900 18 | H 15.24800 15.86900 0.86100 19 | H 13.95300 13.77900 4.05800 20 | H 11.00900 15.48300 -0.75700 21 | H 8.74000 15.29000 -1.26700 22 | H 8.16100 13.55500 2.32800 23 | H 16.10349 14.84127 4.28192 24 | H 16.81838 14.07654 2.82617 25 | H 16.67110 15.86108 2.92070 26 | H 6.53348 14.35080 -0.82024 27 | H 6.29301 13.48340 0.73053 28 | H 6.25979 15.27576 0.69127 29 | 30 | -------------------------------------------------------------------------------- /metallicious/tests/example5_extract/knot_4n_fp0/site.xyz: -------------------------------------------------------------------------------- 1 | 79 2 | Frame 0 | Written By Mdanalysis Xyzwriter (Release 2.4.2) 3 | Fe 10.93700 13.38700 3.64500 4 | C 16.19900 14.90700 3.19000 5 | N 12.53100 14.12000 2.72400 6 | C 12.28000 14.70200 1.53100 7 | C 13.27300 15.34900 0.80600 8 | C 14.56200 15.41900 1.33700 9 | C 14.84000 14.82800 2.56400 10 | C 13.78200 14.18800 3.21800 11 | N 10.05200 14.03700 1.99600 12 | C 10.88600 14.60700 1.08100 13 | C 10.41100 15.08600 -0.13500 14 | C 9.07300 14.97900 -0.43300 15 | C 8.20900 14.41100 0.51000 16 | C 8.74600 13.95300 1.69300 17 | C 6.72300 14.37800 0.26100 18 | H 13.07700 15.74000 -0.03900 19 | H 15.24800 15.86900 0.86100 20 | H 13.95300 13.77900 4.05800 21 | H 11.00900 15.48300 -0.75700 22 | H 8.74000 15.29000 -1.26700 23 | H 8.16100 13.55500 2.32800 24 | H 16.81838 14.07654 2.82617 25 | H 16.10349 14.84127 4.28192 26 | H 16.67110 15.86108 2.92070 27 | H 6.29301 13.48340 0.73053 28 | H 6.25979 15.27576 0.69127 29 | H 6.53348 14.35080 -0.82024 30 | C 6.19200 13.54100 6.35000 31 | N 9.25500 12.65400 4.38000 32 | C 8.99200 11.37600 4.02800 33 | C 7.83100 10.73500 4.41400 34 | C 6.89100 11.42300 5.17600 35 | C 7.15400 12.73800 5.53400 36 | C 8.34300 13.30100 5.12600 37 | N 11.06800 11.56900 2.88100 38 | C 10.03000 10.74400 3.19300 39 | C 9.98500 9.43700 2.76000 40 | C 11.02300 8.91700 2.01900 41 | C 12.10100 9.74200 1.69700 42 | C 12.07800 11.05400 2.14700 43 | C 13.25600 9.23000 0.88700 44 | H 7.67400 9.83200 4.16000 45 | H 6.08500 11.00100 5.44700 46 | H 8.53100 14.19600 5.38500 47 | H 9.23600 8.89100 2.97500 48 | H 11.00700 8.01000 1.73400 49 | H 12.81100 11.61900 1.92900 50 | H 6.04868 14.52480 5.88381 51 | H 5.22872 13.01647 6.40123 52 | H 6.59218 13.67140 7.36415 53 | H 13.06629 8.18810 0.59697 54 | H 13.37206 9.84565 -0.01475 55 | H 14.17476 9.28162 1.48613 56 | C 9.52100 18.66100 4.34700 57 | N 10.77100 15.10200 4.62100 58 | C 11.25000 15.08600 5.90100 59 | C 11.17400 16.19100 6.70100 60 | C 10.62900 17.36900 6.21900 61 | C 10.13900 17.40800 4.91900 62 | C 10.24500 16.25200 4.15700 63 | N 11.86800 12.86700 5.31300 64 | C 11.84600 13.81300 6.29900 65 | C 12.37500 13.55200 7.54900 66 | C 12.94500 12.32400 7.81700 67 | C 12.99900 11.37000 6.82600 68 | C 12.44500 11.68600 5.59200 69 | C 13.65300 10.04400 7.03600 70 | H 11.49900 16.15200 7.59400 71 | H 10.59000 18.14100 6.77100 72 | H 9.92900 16.27200 3.26200 73 | H 12.34400 14.21800 8.22400 74 | H 13.30100 12.13700 8.67800 75 | H 12.47300 11.02900 4.90800 76 | H 8.69558 18.38857 3.67609 77 | H 9.13737 19.28586 5.16433 78 | H 10.28056 19.21995 3.78452 79 | H 14.61751 10.18736 7.54088 80 | H 13.00549 9.41078 7.65683 81 | H 13.81691 9.55884 6.06471 82 | 83 | -------------------------------------------------------------------------------- /metallicious/tests/example5_extract/pd2l4_tall_fp10/ligand_0.pdb: -------------------------------------------------------------------------------- 1 | TITLE MDANALYSIS FRAME 0: Created by PDBWriter 2 | CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 3 | REMARK 285 UNITARY VALUES FOR THE UNIT CELL AUTOMATICALLY SET 4 | REMARK 285 BY MDANALYSIS PDBWRITER BECAUSE UNIT CELL INFORMATION 5 | REMARK 285 WAS MISSING. 6 | REMARK 285 PROTEIN DATA BANK CONVENTIONS REQUIRE THAT 7 | REMARK 285 CRYST1 RECORD IS INCLUDED, BUT THE VALUES ON 8 | REMARK 285 THIS RECORD ARE MEANINGLESS. 9 | ATOM 1 N UNK X 1 11.540 23.880 16.350 1.00 0.00 N 10 | ATOM 2 C UNK X 1 11.200 24.760 17.310 1.00 0.00 C 11 | ATOM 3 H UNK X 1 11.600 25.620 17.320 1.00 0.00 H 12 | ATOM 4 C UNK X 1 10.280 24.440 18.300 1.00 0.00 C 13 | ATOM 5 H UNK X 1 10.060 25.070 18.980 1.00 0.00 H 14 | ATOM 6 C UNK X 1 9.660 23.190 18.260 1.00 0.00 C 15 | ATOM 7 H UNK X 1 9.000 22.970 18.910 1.00 0.00 H 16 | ATOM 8 C UNK X 1 10.020 22.260 17.290 1.00 0.00 C 17 | ATOM 9 C UNK X 1 10.970 22.670 16.320 1.00 0.00 C 18 | ATOM 10 H UNK X 1 11.200 22.070 15.620 1.00 0.00 H 19 | ATOM 11 C UNK X 1 9.420 20.970 17.220 1.00 0.00 C 20 | ATOM 12 H UNK X 1 10.126 20.262 16.766 1.00 0.00 H 21 | ATOM 13 H UNK X 1 9.162 20.631 18.232 1.00 0.00 H 22 | ATOM 14 H UNK X 1 8.510 21.022 16.608 1.00 0.00 H 23 | END 24 | -------------------------------------------------------------------------------- /metallicious/tests/example5_extract/pd2l4_tall_fp10/ligand_0.xyz: -------------------------------------------------------------------------------- 1 | 14 2 | frame 0 | Written by MDAnalysis XYZWriter (release 2.4.2) 3 | N 11.54000 23.88000 16.35000 4 | C 11.20000 24.76000 17.31000 5 | H 11.60000 25.62000 17.32000 6 | C 10.28000 24.44000 18.30000 7 | H 10.06000 25.07000 18.98000 8 | C 9.66000 23.19000 18.26000 9 | H 9.00000 22.97000 18.91000 10 | C 10.02000 22.26000 17.29000 11 | C 10.97000 22.67000 16.32000 12 | H 11.20000 22.07000 15.62000 13 | C 9.42000 20.97000 17.22000 14 | H 10.12596 20.26203 16.76597 15 | H 9.16173 20.63108 18.23197 16 | H 8.50980 21.02243 16.60808 17 | 18 | -------------------------------------------------------------------------------- /metallicious/tests/example5_extract/pd2l4_tall_fp10/site.xyz: -------------------------------------------------------------------------------- 1 | 57 2 | Frame 0 | Written By Mdanalysis Xyzwriter (Release 2.4.2) 3 | Pd 12.86000 24.45000 14.93000 4 | N 11.54000 23.88000 16.35000 5 | C 11.20000 24.76000 17.31000 6 | H 11.60000 25.62000 17.32000 7 | C 10.28000 24.44000 18.30000 8 | H 10.06000 25.07000 18.98000 9 | C 9.66000 23.19000 18.26000 10 | H 9.00000 22.97000 18.91000 11 | C 10.02000 22.26000 17.29000 12 | C 10.97000 22.67000 16.32000 13 | H 11.20000 22.07000 15.62000 14 | C 9.42000 20.97000 17.22000 15 | H 10.12596 20.26203 16.76597 16 | H 9.16173 20.63108 18.23197 17 | H 8.50980 21.02243 16.60808 18 | N 11.30000 24.99000 13.76000 19 | C 10.65000 26.15000 13.98000 20 | H 10.93000 26.71000 14.70000 21 | C 9.58000 26.55000 13.20000 22 | H 9.13000 27.37000 13.37000 23 | C 9.16000 25.75000 12.17000 24 | H 8.42000 26.01000 11.63000 25 | C 9.82000 24.54000 11.91000 26 | C 10.89000 24.21000 12.73000 27 | H 11.35000 23.40000 12.56000 28 | C 9.44000 23.66000 10.86000 29 | H 8.93114 22.78375 11.28298 30 | H 8.76054 24.18170 10.17311 31 | H 10.33484 23.33487 10.31293 32 | N 14.39000 23.97000 16.16000 33 | C 15.08000 24.91000 16.81000 34 | H 14.83000 25.82000 16.70000 35 | C 16.13000 24.61000 17.64000 36 | H 16.61000 25.31000 18.08000 37 | C 16.50000 23.29000 17.84000 38 | H 17.22000 23.07000 18.41000 39 | C 15.78000 22.28000 17.17000 40 | C 14.72000 22.68000 16.35000 41 | H 14.21000 22.01000 15.91000 42 | C 16.06000 20.89000 17.36000 43 | H 17.12115 20.76130 17.61128 44 | H 15.44026 20.50035 18.17838 45 | H 15.83353 20.34142 16.43618 46 | N 14.19000 25.09000 13.55000 47 | C 14.63000 26.35000 13.58000 48 | H 14.26000 26.96000 14.21000 49 | C 15.62000 26.78000 12.73000 50 | H 15.92000 27.68000 12.77000 51 | C 16.18000 25.93000 11.81000 52 | H 16.85000 26.23000 11.21000 53 | C 15.72000 24.58000 11.79000 54 | C 14.71000 24.22000 12.66000 55 | H 14.38000 23.33000 12.64000 56 | C 16.28000 23.61000 10.89000 57 | H 17.36123 23.53032 11.06417 58 | H 15.80833 22.63388 11.06426 59 | H 16.09844 23.92451 9.85377 60 | 61 | -------------------------------------------------------------------------------- /metallicious/tests/example5_extract/pd2l4_tall_fp20/ligand_0.pdb: -------------------------------------------------------------------------------- 1 | TITLE MDANALYSIS FRAME 0: Created by PDBWriter 2 | CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 3 | REMARK 285 UNITARY VALUES FOR THE UNIT CELL AUTOMATICALLY SET 4 | REMARK 285 BY MDANALYSIS PDBWRITER BECAUSE UNIT CELL INFORMATION 5 | REMARK 285 WAS MISSING. 6 | REMARK 285 PROTEIN DATA BANK CONVENTIONS REQUIRE THAT 7 | REMARK 285 CRYST1 RECORD IS INCLUDED, BUT THE VALUES ON 8 | REMARK 285 THIS RECORD ARE MEANINGLESS. 9 | ATOM 1 N0 UNK X 1 11.540 23.880 16.350 1.00 0.00 N 10 | ATOM 2 C2 UNK X 1 11.200 24.760 17.310 1.00 0.00 C 11 | ATOM 3 H3 UNK X 1 11.600 25.620 17.320 1.00 0.00 H 12 | ATOM 4 C4 UNK X 1 10.280 24.440 18.300 1.00 0.00 C 13 | ATOM 5 H5 UNK X 1 10.060 25.070 18.980 1.00 0.00 H 14 | ATOM 6 C6 UNK X 1 9.660 23.190 18.260 1.00 0.00 C 15 | ATOM 7 H7 UNK X 1 9.000 22.970 18.910 1.00 0.00 H 16 | ATOM 8 C8 UNK X 1 10.020 22.260 17.290 1.00 0.00 C 17 | ATOM 9 C9 UNK X 1 10.970 22.670 16.320 1.00 0.00 C 18 | ATOM 10 H10 UNK X 1 11.200 22.070 15.620 1.00 0.00 H 19 | ATOM 11 C11 UNK X 1 9.420 20.970 17.220 1.00 0.00 C 20 | ATOM 12 H UNK X 1 10.126 20.262 16.766 1.00 0.00 H 21 | ATOM 13 H UNK X 1 9.162 20.631 18.232 1.00 0.00 H 22 | ATOM 14 H UNK X 1 8.510 21.022 16.608 1.00 0.00 H 23 | END 24 | -------------------------------------------------------------------------------- /metallicious/tests/example5_extract/pd2l4_tall_fp20/ligand_0.xyz: -------------------------------------------------------------------------------- 1 | 14 2 | frame 0 | Written by MDAnalysis XYZWriter (release 2.4.2) 3 | N 11.54000 23.88000 16.35000 4 | C 11.20000 24.76000 17.31000 5 | H 11.60000 25.62000 17.32000 6 | C 10.28000 24.44000 18.30000 7 | H 10.06000 25.07000 18.98000 8 | C 9.66000 23.19000 18.26000 9 | H 9.00000 22.97000 18.91000 10 | C 10.02000 22.26000 17.29000 11 | C 10.97000 22.67000 16.32000 12 | H 11.20000 22.07000 15.62000 13 | C 9.42000 20.97000 17.22000 14 | H 10.12596 20.26203 16.76597 15 | H 9.16173 20.63108 18.23197 16 | H 8.50980 21.02243 16.60808 17 | 18 | -------------------------------------------------------------------------------- /metallicious/tests/example5_extract/pd2l4_tall_fp20/site.xyz: -------------------------------------------------------------------------------- 1 | 57 2 | Frame 0 | Written By Mdanalysis Xyzwriter (Release 2.4.2) 3 | Pd 12.86000 24.45000 14.93000 4 | N 11.54000 23.88000 16.35000 5 | C 11.20000 24.76000 17.31000 6 | H 11.60000 25.62000 17.32000 7 | C 10.28000 24.44000 18.30000 8 | H 10.06000 25.07000 18.98000 9 | C 9.66000 23.19000 18.26000 10 | H 9.00000 22.97000 18.91000 11 | C 10.02000 22.26000 17.29000 12 | C 10.97000 22.67000 16.32000 13 | H 11.20000 22.07000 15.62000 14 | C 9.42000 20.97000 17.22000 15 | H 10.12596 20.26203 16.76597 16 | H 9.16173 20.63108 18.23197 17 | H 8.50980 21.02243 16.60808 18 | N 11.30000 24.99000 13.76000 19 | C 10.65000 26.15000 13.98000 20 | H 10.93000 26.71000 14.70000 21 | C 9.58000 26.55000 13.20000 22 | H 9.13000 27.37000 13.37000 23 | C 9.16000 25.75000 12.17000 24 | H 8.42000 26.01000 11.63000 25 | C 9.82000 24.54000 11.91000 26 | C 10.89000 24.21000 12.73000 27 | H 11.35000 23.40000 12.56000 28 | C 9.44000 23.66000 10.86000 29 | H 8.93114 22.78375 11.28298 30 | H 8.76054 24.18170 10.17311 31 | H 10.33484 23.33487 10.31293 32 | N 14.39000 23.97000 16.16000 33 | C 15.08000 24.91000 16.81000 34 | H 14.83000 25.82000 16.70000 35 | C 16.13000 24.61000 17.64000 36 | H 16.61000 25.31000 18.08000 37 | C 16.50000 23.29000 17.84000 38 | H 17.22000 23.07000 18.41000 39 | C 15.78000 22.28000 17.17000 40 | C 14.72000 22.68000 16.35000 41 | H 14.21000 22.01000 15.91000 42 | C 16.06000 20.89000 17.36000 43 | H 17.12115 20.76131 17.61128 44 | H 15.44026 20.50035 18.17838 45 | H 15.83353 20.34142 16.43618 46 | N 14.19000 25.09000 13.55000 47 | C 14.63000 26.35000 13.58000 48 | H 14.26000 26.96000 14.21000 49 | C 15.62000 26.78000 12.73000 50 | H 15.92000 27.68000 12.77000 51 | C 16.18000 25.93000 11.81000 52 | H 16.85000 26.23000 11.21000 53 | C 15.72000 24.58000 11.79000 54 | C 14.71000 24.22000 12.66000 55 | H 14.38000 23.33000 12.64000 56 | C 16.28000 23.61000 10.89000 57 | H 17.36123 23.53032 11.06417 58 | H 15.80833 22.63388 11.06426 59 | H 16.09844 23.92451 9.85377 60 | 61 | -------------------------------------------------------------------------------- /metallicious/tests/example5_extract/pd2l4_tall_fp30/ligand_0.pdb: -------------------------------------------------------------------------------- 1 | TITLE MDANALYSIS FRAME 0: Created by PDBWriter 2 | CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 3 | REMARK 285 UNITARY VALUES FOR THE UNIT CELL AUTOMATICALLY SET 4 | REMARK 285 BY MDANALYSIS PDBWRITER BECAUSE UNIT CELL INFORMATION 5 | REMARK 285 WAS MISSING. 6 | REMARK 285 PROTEIN DATA BANK CONVENTIONS REQUIRE THAT 7 | REMARK 285 CRYST1 RECORD IS INCLUDED, BUT THE VALUES ON 8 | REMARK 285 THIS RECORD ARE MEANINGLESS. 9 | ATOM 1 N0 UNK X 1 11.540 23.880 16.350 1.00 0.00 N 10 | ATOM 2 C2 UNK X 1 11.200 24.760 17.310 1.00 0.00 C 11 | ATOM 3 H3 UNK X 1 11.600 25.620 17.320 1.00 0.00 H 12 | ATOM 4 C4 UNK X 1 10.280 24.440 18.300 1.00 0.00 C 13 | ATOM 5 H5 UNK X 1 10.060 25.070 18.980 1.00 0.00 H 14 | ATOM 6 C6 UNK X 1 9.660 23.190 18.260 1.00 0.00 C 15 | ATOM 7 H7 UNK X 1 9.000 22.970 18.910 1.00 0.00 H 16 | ATOM 8 C8 UNK X 1 10.020 22.260 17.290 1.00 0.00 C 17 | ATOM 9 C9 UNK X 1 10.970 22.670 16.320 1.00 0.00 C 18 | ATOM 10 H10 UNK X 1 11.200 22.070 15.620 1.00 0.00 H 19 | ATOM 11 C11 UNK X 1 9.420 20.970 17.220 1.00 0.00 C 20 | ATOM 12 H UNK X 1 10.126 20.262 16.766 1.00 0.00 H 21 | ATOM 13 H UNK X 1 9.162 20.631 18.232 1.00 0.00 H 22 | ATOM 14 H UNK X 1 8.510 21.022 16.608 1.00 0.00 H 23 | END 24 | -------------------------------------------------------------------------------- /metallicious/tests/example5_extract/pd2l4_tall_fp30/ligand_0.xyz: -------------------------------------------------------------------------------- 1 | 14 2 | frame 0 | Written by MDAnalysis XYZWriter (release 2.4.2) 3 | N 11.54000 23.88000 16.35000 4 | C 11.20000 24.76000 17.31000 5 | H 11.60000 25.62000 17.32000 6 | C 10.28000 24.44000 18.30000 7 | H 10.06000 25.07000 18.98000 8 | C 9.66000 23.19000 18.26000 9 | H 9.00000 22.97000 18.91000 10 | C 10.02000 22.26000 17.29000 11 | C 10.97000 22.67000 16.32000 12 | H 11.20000 22.07000 15.62000 13 | C 9.42000 20.97000 17.22000 14 | H 10.12596 20.26203 16.76597 15 | H 9.16173 20.63109 18.23197 16 | H 8.50980 21.02242 16.60808 17 | 18 | -------------------------------------------------------------------------------- /metallicious/tests/example5_extract/pd2l4_tall_fp30/site.xyz: -------------------------------------------------------------------------------- 1 | 57 2 | Frame 0 | Written By Mdanalysis Xyzwriter (Release 2.4.2) 3 | Pd 12.86000 24.45000 14.93000 4 | N 11.54000 23.88000 16.35000 5 | C 11.20000 24.76000 17.31000 6 | H 11.60000 25.62000 17.32000 7 | C 10.28000 24.44000 18.30000 8 | H 10.06000 25.07000 18.98000 9 | C 9.66000 23.19000 18.26000 10 | H 9.00000 22.97000 18.91000 11 | C 10.02000 22.26000 17.29000 12 | C 10.97000 22.67000 16.32000 13 | H 11.20000 22.07000 15.62000 14 | C 9.42000 20.97000 17.22000 15 | H 10.12596 20.26203 16.76597 16 | H 9.16173 20.63109 18.23197 17 | H 8.50980 21.02242 16.60808 18 | N 11.30000 24.99000 13.76000 19 | C 10.65000 26.15000 13.98000 20 | H 10.93000 26.71000 14.70000 21 | C 9.58000 26.55000 13.20000 22 | H 9.13000 27.37000 13.37000 23 | C 9.16000 25.75000 12.17000 24 | H 8.42000 26.01000 11.63000 25 | C 9.82000 24.54000 11.91000 26 | C 10.89000 24.21000 12.73000 27 | H 11.35000 23.40000 12.56000 28 | C 9.44000 23.66000 10.86000 29 | H 8.93115 22.78375 11.28298 30 | H 8.76054 24.18170 10.17311 31 | H 10.33484 23.33487 10.31293 32 | N 14.39000 23.97000 16.16000 33 | C 15.08000 24.91000 16.81000 34 | H 14.83000 25.82000 16.70000 35 | C 16.13000 24.61000 17.64000 36 | H 16.61000 25.31000 18.08000 37 | C 16.50000 23.29000 17.84000 38 | H 17.22000 23.07000 18.41000 39 | C 15.78000 22.28000 17.17000 40 | C 14.72000 22.68000 16.35000 41 | H 14.21000 22.01000 15.91000 42 | C 16.06000 20.89000 17.36000 43 | H 17.12115 20.76131 17.61128 44 | H 15.44026 20.50035 18.17838 45 | H 15.83353 20.34143 16.43618 46 | N 14.19000 25.09000 13.55000 47 | C 14.63000 26.35000 13.58000 48 | H 14.26000 26.96000 14.21000 49 | C 15.62000 26.78000 12.73000 50 | H 15.92000 27.68000 12.77000 51 | C 16.18000 25.93000 11.81000 52 | H 16.85000 26.23000 11.21000 53 | C 15.72000 24.58000 11.79000 54 | C 14.71000 24.22000 12.66000 55 | H 14.38000 23.33000 12.64000 56 | C 16.28000 23.61000 10.89000 57 | H 17.36123 23.53032 11.06417 58 | H 15.80833 22.63388 11.06426 59 | H 16.09843 23.92451 9.85377 60 | 61 | -------------------------------------------------------------------------------- /metallicious/tests/example5_extract/ru_fp0/ligand_0.pdb: -------------------------------------------------------------------------------- 1 | TITLE MDANALYSIS FRAME 0: Created by PDBWriter 2 | CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 3 | REMARK 285 UNITARY VALUES FOR THE UNIT CELL AUTOMATICALLY SET 4 | REMARK 285 BY MDANALYSIS PDBWRITER BECAUSE UNIT CELL INFORMATION 5 | REMARK 285 WAS MISSING. 6 | REMARK 285 PROTEIN DATA BANK CONVENTIONS REQUIRE THAT 7 | REMARK 285 CRYST1 RECORD IS INCLUDED, BUT THE VALUES ON 8 | REMARK 285 THIS RECORD ARE MEANINGLESS. 9 | ATOM 1 C UNK X 1 -3.702 -0.531 -0.778 1.00 0.00 C 10 | ATOM 2 C UNK X 1 -3.179 0.760 -0.942 1.00 0.00 C 11 | ATOM 3 C UNK X 1 -1.838 1.014 -0.596 1.00 0.00 C 12 | ATOM 4 N UNK X 1 -1.038 -0.001 -0.139 1.00 0.00 N 13 | ATOM 5 C UNK X 1 -2.883 -1.523 -0.208 1.00 0.00 C 14 | ATOM 6 C UNK X 1 -1.544 -1.205 0.116 1.00 0.00 C 15 | ATOM 7 H UNK X 1 -1.442 2.006 -0.755 1.00 0.00 H 16 | ATOM 8 H UNK X 1 -4.736 -0.725 -1.052 1.00 0.00 H 17 | ATOM 9 H UNK X 1 -3.802 1.554 -1.346 1.00 0.00 H 18 | ATOM 10 C UNK X 1 -3.271 -2.829 0.084 1.00 0.00 C 19 | ATOM 11 C UNK X 1 -2.411 -3.702 0.716 1.00 0.00 C 20 | ATOM 12 C UNK X 1 -1.161 -3.354 1.170 1.00 0.00 C 21 | ATOM 13 C UNK X 1 -0.723 -2.080 0.841 1.00 0.00 C 22 | ATOM 14 N UNK X 1 0.502 -1.656 1.234 1.00 0.00 N 23 | ATOM 15 C UNK X 1 1.327 -2.444 1.975 1.00 0.00 C 24 | ATOM 16 C UNK X 1 -0.338 -4.199 1.922 1.00 0.00 C 25 | ATOM 17 C UNK X 1 0.908 -3.731 2.348 1.00 0.00 C 26 | ATOM 18 H UNK X 1 2.309 -2.093 2.249 1.00 0.00 H 27 | ATOM 19 H UNK X 1 -0.655 -5.197 2.197 1.00 0.00 H 28 | ATOM 20 H UNK X 1 1.546 -4.373 2.939 1.00 0.00 H 29 | ATOM 21 N UNK X 1 -4.432 -3.455 -0.170 1.00 0.00 N 30 | ATOM 22 C UNK X 1 -4.177 -4.714 0.273 1.00 0.00 C 31 | ATOM 23 N UNK X 1 -2.973 -4.887 0.808 1.00 0.00 N 32 | ATOM 24 C UNK X 1 -5.024 -5.836 0.143 1.00 0.00 C 33 | ATOM 25 H UNK X 1 -2.579 -5.773 1.191 1.00 0.00 H 34 | ATOM 26 H UNK X 1 -4.549 -6.579 -0.511 1.00 0.00 H 35 | ATOM 27 H UNK X 1 -5.199 -6.278 1.132 1.00 0.00 H 36 | ATOM 28 H UNK X 1 -5.982 -5.523 -0.293 1.00 0.00 H 37 | END 38 | -------------------------------------------------------------------------------- /metallicious/tests/example5_extract/ru_fp0/ligand_0.xyz: -------------------------------------------------------------------------------- 1 | 28 2 | frame 0 | Written by MDAnalysis XYZWriter (release 2.4.2) 3 | C -3.70227 -0.53150 -0.77828 4 | C -3.17878 0.75966 -0.94175 5 | C -1.83792 1.01391 -0.59627 6 | N -1.03764 -0.00123 -0.13883 7 | C -2.88281 -1.52278 -0.20797 8 | C -1.54426 -1.20537 0.11588 9 | H -1.44175 2.00572 -0.75467 10 | H -4.73598 -0.72506 -1.05201 11 | H -3.80185 1.55360 -1.34583 12 | C -3.27125 -2.82948 0.08421 13 | C -2.41141 -3.70226 0.71619 14 | C -1.16083 -3.35439 1.16997 15 | C -0.72309 -2.07982 0.84141 16 | N 0.50170 -1.65586 1.23398 17 | C 1.32728 -2.44431 1.97513 18 | C -0.33755 -4.19851 1.92230 19 | C 0.90760 -3.73054 2.34811 20 | H 2.30938 -2.09255 2.24881 21 | H -0.65534 -5.19731 2.19749 22 | H 1.54554 -4.37311 2.93896 23 | N -4.43162 -3.45547 -0.17033 24 | C -4.17744 -4.71378 0.27259 25 | N -2.97261 -4.88671 0.80818 26 | C -5.02366 -5.83590 0.14290 27 | H -2.57876 -5.77268 1.19118 28 | H -4.54874 -6.57892 -0.51140 29 | H -5.19892 -6.27844 1.13240 30 | H -5.98168 -5.52337 -0.29321 31 | 32 | -------------------------------------------------------------------------------- /metallicious/tests/example5_extract/ru_fp0/site.xyz: -------------------------------------------------------------------------------- 1 | 85 2 | Frame 0 | Written By Mdanalysis Xyzwriter (Release 2.4.2) 3 | Ru 1.05128 0.15893 0.30694 4 | C -3.70227 -0.53150 -0.77828 5 | C -3.17878 0.75966 -0.94175 6 | C -1.83792 1.01391 -0.59627 7 | N -1.03764 -0.00123 -0.13883 8 | C -2.88281 -1.52278 -0.20797 9 | C -1.54426 -1.20537 0.11588 10 | H -1.44175 2.00572 -0.75467 11 | H -4.73598 -0.72506 -1.05201 12 | H -3.80185 1.55360 -1.34583 13 | C -3.27125 -2.82948 0.08421 14 | C -2.41141 -3.70226 0.71619 15 | C -1.16083 -3.35439 1.16997 16 | C -0.72309 -2.07982 0.84141 17 | N 0.50170 -1.65586 1.23398 18 | C 1.32728 -2.44431 1.97513 19 | C -0.33755 -4.19851 1.92230 20 | C 0.90760 -3.73054 2.34811 21 | H 2.30938 -2.09255 2.24881 22 | H -0.65534 -5.19731 2.19749 23 | H 1.54554 -4.37311 2.93896 24 | N -4.43162 -3.45547 -0.17033 25 | C -4.17744 -4.71378 0.27259 26 | N -2.97261 -4.88671 0.80818 27 | C -5.02366 -5.83590 0.14290 28 | H -2.57876 -5.77268 1.19118 29 | H -4.54874 -6.57892 -0.51140 30 | H -5.19892 -6.27844 1.13240 31 | H -5.98168 -5.52337 -0.29321 32 | C 5.85959 0.58626 1.18945 33 | C 4.99225 1.54588 1.74226 34 | C 3.61504 1.47779 1.47947 35 | N 3.11235 0.43272 0.76536 36 | C 5.33884 -0.42088 0.35358 37 | C 3.93031 -0.47711 0.17126 38 | H 2.94850 2.21543 1.90889 39 | H 6.92430 0.66650 1.38200 40 | H 5.38382 2.34382 2.36689 41 | C 6.12876 -1.36110 -0.35563 42 | C 5.57288 -2.27251 -1.22039 43 | C 4.16715 -2.35768 -1.39308 44 | C 3.34756 -1.41612 -0.70710 45 | N 1.98021 -1.43820 -0.81897 46 | C 1.36509 -2.44654 -1.50343 47 | C 3.53653 -3.32563 -2.18141 48 | C 2.13483 -3.38268 -2.21692 49 | H 0.28779 -2.49777 -1.56392 50 | H 4.11390 -4.05868 -2.73176 51 | H 1.64636 -4.15094 -2.80320 52 | N 7.47105 -1.52536 -0.34531 53 | C 7.72420 -2.52676 -1.24978 54 | N 6.57023 -2.99677 -1.79783 55 | C 9.13874 -3.05494 -1.50169 56 | H 6.47760 -3.77100 -2.48883 57 | H 9.75322 -2.89785 -0.60533 58 | H 9.09339 -4.12782 -1.73088 59 | H 9.58430 -2.51802 -2.34955 60 | C 1.62428 3.80061 -2.77257 61 | C 1.87323 2.50101 -3.22151 62 | C 1.75669 1.44529 -2.31866 63 | N 1.40928 1.69679 -1.02736 64 | C 1.24618 4.00343 -1.43088 65 | C 1.14644 2.91954 -0.56829 66 | H 1.90571 0.42752 -2.65254 67 | H 1.67130 4.61988 -3.48050 68 | H 2.11829 2.30755 -4.25941 69 | C 0.84760 5.21366 -0.92500 70 | C 0.34155 5.38659 0.34337 71 | C 0.16855 4.28951 1.20791 72 | C 0.61408 3.03828 0.72330 73 | N 0.33175 1.88297 1.37065 74 | C -0.44930 1.88898 2.48922 75 | C -0.52521 4.32889 2.42559 76 | C -0.84799 3.11597 3.06128 77 | H -0.71691 0.95709 2.97015 78 | H -0.89084 5.26293 2.83936 79 | H -1.43171 3.12670 3.97578 80 | N 0.75585 6.33058 -1.61817 81 | C 0.18655 7.19467 -0.76324 82 | N -0.04407 6.66926 0.47199 83 | C -0.16414 8.52002 -1.24499 84 | H -0.50334 7.12182 1.29403 85 | H 0.73746 9.02507 -1.61618 86 | H -0.89562 8.43182 -2.05913 87 | H -0.59925 9.10469 -0.42371 88 | 89 | -------------------------------------------------------------------------------- /metallicious/tests/example5_extract/temp.pdb: -------------------------------------------------------------------------------- 1 | TITLE MDANALYSIS FRAME 0: Created by PDBWriter 2 | CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 3 | REMARK 285 UNITARY VALUES FOR THE UNIT CELL AUTOMATICALLY SET 4 | REMARK 285 BY MDANALYSIS PDBWRITER BECAUSE UNIT CELL INFORMATION 5 | REMARK 285 WAS MISSING. 6 | REMARK 285 PROTEIN DATA BANK CONVENTIONS REQUIRE THAT 7 | REMARK 285 CRYST1 RECORD IS INCLUDED, BUT THE VALUES ON 8 | REMARK 285 THIS RECORD ARE MEANINGLESS. 9 | ATOM 1 C UNK X 1 -3.702 -0.531 -0.778 1.00 0.00 C 10 | ATOM 2 C UNK X 1 -3.179 0.760 -0.942 1.00 0.00 C 11 | ATOM 3 C UNK X 1 -1.838 1.014 -0.596 1.00 0.00 C 12 | ATOM 4 N UNK X 1 -1.038 -0.001 -0.139 1.00 0.00 N 13 | ATOM 5 C UNK X 1 -2.883 -1.523 -0.208 1.00 0.00 C 14 | ATOM 6 C UNK X 1 -1.544 -1.205 0.116 1.00 0.00 C 15 | ATOM 7 H UNK X 1 -1.442 2.006 -0.755 1.00 0.00 H 16 | ATOM 8 H UNK X 1 -4.736 -0.725 -1.052 1.00 0.00 H 17 | ATOM 9 H UNK X 1 -3.802 1.554 -1.346 1.00 0.00 H 18 | ATOM 10 C UNK X 1 -3.271 -2.829 0.084 1.00 0.00 C 19 | ATOM 11 C UNK X 1 -2.411 -3.702 0.716 1.00 0.00 C 20 | ATOM 12 C UNK X 1 -1.161 -3.354 1.170 1.00 0.00 C 21 | ATOM 13 C UNK X 1 -0.723 -2.080 0.841 1.00 0.00 C 22 | ATOM 14 N UNK X 1 0.502 -1.656 1.234 1.00 0.00 N 23 | ATOM 15 C UNK X 1 1.327 -2.444 1.975 1.00 0.00 C 24 | ATOM 16 C UNK X 1 -0.338 -4.199 1.922 1.00 0.00 C 25 | ATOM 17 C UNK X 1 0.908 -3.731 2.348 1.00 0.00 C 26 | ATOM 18 H UNK X 1 2.309 -2.093 2.249 1.00 0.00 H 27 | ATOM 19 H UNK X 1 -0.655 -5.197 2.197 1.00 0.00 H 28 | ATOM 20 H UNK X 1 1.546 -4.373 2.939 1.00 0.00 H 29 | ATOM 21 N UNK X 1 -4.432 -3.455 -0.170 1.00 0.00 N 30 | ATOM 22 C UNK X 1 -4.177 -4.714 0.273 1.00 0.00 C 31 | ATOM 23 N UNK X 1 -2.973 -4.887 0.808 1.00 0.00 N 32 | ATOM 24 C UNK X 1 -5.024 -5.836 0.143 1.00 0.00 C 33 | ATOM 25 H UNK X 1 -2.579 -5.773 1.191 1.00 0.00 H 34 | ATOM 26 H UNK X 1 -4.549 -6.579 -0.511 1.00 0.00 H 35 | ATOM 27 H UNK X 1 -5.199 -6.278 1.132 1.00 0.00 H 36 | ATOM 28 H UNK X 1 -5.982 -5.523 -0.293 1.00 0.00 H 37 | END 38 | -------------------------------------------------------------------------------- /metallicious/tests/example5_extract/temp1.pdb: -------------------------------------------------------------------------------- 1 | TITLE MDANALYSIS FRAME 0: Created by PDBWriter 2 | CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 3 | REMARK 285 UNITARY VALUES FOR THE UNIT CELL AUTOMATICALLY SET 4 | REMARK 285 BY MDANALYSIS PDBWRITER BECAUSE UNIT CELL INFORMATION 5 | REMARK 285 WAS MISSING. 6 | REMARK 285 PROTEIN DATA BANK CONVENTIONS REQUIRE THAT 7 | REMARK 285 CRYST1 RECORD IS INCLUDED, BUT THE VALUES ON 8 | REMARK 285 THIS RECORD ARE MEANINGLESS. 9 | ATOM 1 C UNK X 1 -0.164 8.520 -1.245 1.00 0.00 C 10 | ATOM 2 C UNK X 1 1.146 2.920 -0.568 1.00 0.00 C 11 | ATOM 3 C UNK X 1 0.848 5.214 -0.925 1.00 0.00 C 12 | ATOM 4 C UNK X 1 1.246 4.003 -1.431 1.00 0.00 C 13 | ATOM 5 C UNK X 1 -0.848 3.116 3.061 1.00 0.00 C 14 | ATOM 6 C UNK X 1 -0.449 1.889 2.489 1.00 0.00 C 15 | ATOM 7 C UNK X 1 0.342 5.387 0.343 1.00 0.00 C 16 | ATOM 8 C UNK X 1 0.614 3.038 0.723 1.00 0.00 C 17 | ATOM 9 C UNK X 1 0.169 4.290 1.208 1.00 0.00 C 18 | ATOM 10 C UNK X 1 0.187 7.195 -0.763 1.00 0.00 C 19 | ATOM 11 C UNK X 1 1.873 2.501 -3.222 1.00 0.00 C 20 | ATOM 12 C UNK X 1 1.757 1.445 -2.319 1.00 0.00 C 21 | ATOM 13 C UNK X 1 1.624 3.801 -2.773 1.00 0.00 C 22 | ATOM 14 C UNK X 1 -0.525 4.329 2.426 1.00 0.00 C 23 | ATOM 15 N UNK X 1 0.332 1.883 1.371 1.00 0.00 N 24 | ATOM 16 N UNK X 1 1.409 1.697 -1.027 1.00 0.00 N 25 | ATOM 17 N UNK X 1 -0.044 6.669 0.472 1.00 0.00 N 26 | ATOM 18 N UNK X 1 0.756 6.331 -1.618 1.00 0.00 N 27 | ATOM 19 H UNK X 1 1.671 4.620 -3.480 1.00 0.00 H 28 | ATOM 20 H UNK X 1 1.906 0.428 -2.653 1.00 0.00 H 29 | ATOM 21 H UNK X 1 -0.503 7.122 1.294 1.00 0.00 H 30 | ATOM 22 H UNK X 1 -1.432 3.127 3.976 1.00 0.00 H 31 | ATOM 23 H UNK X 1 -0.717 0.957 2.970 1.00 0.00 H 32 | ATOM 24 H UNK X 1 2.118 2.308 -4.259 1.00 0.00 H 33 | ATOM 25 H UNK X 1 -0.891 5.263 2.839 1.00 0.00 H 34 | ATOM 26 H UNK X 1 0.737 9.025 -1.616 1.00 0.00 H 35 | ATOM 27 H UNK X 1 -0.896 8.432 -2.059 1.00 0.00 H 36 | ATOM 28 H UNK X 1 -0.599 9.105 -0.424 1.00 0.00 H 37 | END 38 | -------------------------------------------------------------------------------- /metallicious/tests/example5_extract/temp1.xyz: -------------------------------------------------------------------------------- 1 | 28 2 | frame 0 | Written by MDAnalysis XYZWriter (release 2.4.2) 3 | C -0.16414 8.52002 -1.24499 4 | C 1.14644 2.91954 -0.56829 5 | C 0.84760 5.21366 -0.92500 6 | C 1.24618 4.00343 -1.43088 7 | C -0.84799 3.11597 3.06128 8 | C -0.44930 1.88898 2.48922 9 | C 0.34155 5.38659 0.34337 10 | C 0.61408 3.03828 0.72330 11 | C 0.16855 4.28951 1.20791 12 | C 0.18655 7.19467 -0.76324 13 | C 1.87323 2.50101 -3.22151 14 | C 1.75669 1.44529 -2.31866 15 | C 1.62428 3.80061 -2.77257 16 | C -0.52521 4.32889 2.42559 17 | N 0.33175 1.88297 1.37065 18 | N 1.40928 1.69679 -1.02736 19 | N -0.04407 6.66926 0.47199 20 | N 0.75585 6.33058 -1.61817 21 | H 1.67130 4.61988 -3.48050 22 | H 1.90571 0.42752 -2.65254 23 | H -0.50334 7.12182 1.29403 24 | H -1.43171 3.12670 3.97578 25 | H -0.71691 0.95709 2.97015 26 | H 2.11829 2.30755 -4.25941 27 | H -0.89084 5.26293 2.83936 28 | H 0.73746 9.02507 -1.61618 29 | H -0.89562 8.43182 -2.05913 30 | H -0.59925 9.10469 -0.42371 31 | 32 | -------------------------------------------------------------------------------- /metallicious/tests/example5_extract/temp2.pdb: -------------------------------------------------------------------------------- 1 | TITLE MDANALYSIS FRAME 0: Created by PDBWriter 2 | CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 3 | REMARK 285 UNITARY VALUES FOR THE UNIT CELL AUTOMATICALLY SET 4 | REMARK 285 BY MDANALYSIS PDBWRITER BECAUSE UNIT CELL INFORMATION 5 | REMARK 285 WAS MISSING. 6 | REMARK 285 PROTEIN DATA BANK CONVENTIONS REQUIRE THAT 7 | REMARK 285 CRYST1 RECORD IS INCLUDED, BUT THE VALUES ON 8 | REMARK 285 THIS RECORD ARE MEANINGLESS. 9 | ATOM 1 C UNK X 1 -3.702 -0.531 -0.778 1.00 0.00 C 10 | ATOM 2 C UNK X 1 -3.179 0.760 -0.942 1.00 0.00 C 11 | ATOM 3 C UNK X 1 -1.838 1.014 -0.596 1.00 0.00 C 12 | ATOM 4 N UNK X 1 -1.038 -0.001 -0.139 1.00 0.00 N 13 | ATOM 5 C UNK X 1 -2.883 -1.523 -0.208 1.00 0.00 C 14 | ATOM 6 C UNK X 1 -1.544 -1.205 0.116 1.00 0.00 C 15 | ATOM 7 H UNK X 1 -1.442 2.006 -0.755 1.00 0.00 H 16 | ATOM 8 H UNK X 1 -4.736 -0.725 -1.052 1.00 0.00 H 17 | ATOM 9 H UNK X 1 -3.802 1.554 -1.346 1.00 0.00 H 18 | ATOM 10 C UNK X 1 -3.271 -2.829 0.084 1.00 0.00 C 19 | ATOM 11 C UNK X 1 -2.411 -3.702 0.716 1.00 0.00 C 20 | ATOM 12 C UNK X 1 -1.161 -3.354 1.170 1.00 0.00 C 21 | ATOM 13 C UNK X 1 -0.723 -2.080 0.841 1.00 0.00 C 22 | ATOM 14 N UNK X 1 0.502 -1.656 1.234 1.00 0.00 N 23 | ATOM 15 C UNK X 1 1.327 -2.444 1.975 1.00 0.00 C 24 | ATOM 16 C UNK X 1 -0.338 -4.199 1.922 1.00 0.00 C 25 | ATOM 17 C UNK X 1 0.908 -3.731 2.348 1.00 0.00 C 26 | ATOM 18 H UNK X 1 2.309 -2.093 2.249 1.00 0.00 H 27 | ATOM 19 H UNK X 1 -0.655 -5.197 2.197 1.00 0.00 H 28 | ATOM 20 H UNK X 1 1.546 -4.373 2.939 1.00 0.00 H 29 | ATOM 21 N UNK X 1 -4.432 -3.455 -0.170 1.00 0.00 N 30 | ATOM 22 C UNK X 1 -4.177 -4.714 0.273 1.00 0.00 C 31 | ATOM 23 N UNK X 1 -2.973 -4.887 0.808 1.00 0.00 N 32 | ATOM 24 C UNK X 1 -5.024 -5.836 0.143 1.00 0.00 C 33 | ATOM 25 H UNK X 1 -2.579 -5.773 1.191 1.00 0.00 H 34 | ATOM 26 H UNK X 1 -4.549 -6.579 -0.511 1.00 0.00 H 35 | ATOM 27 H UNK X 1 -5.199 -6.278 1.132 1.00 0.00 H 36 | ATOM 28 H UNK X 1 -5.982 -5.523 -0.293 1.00 0.00 H 37 | END 38 | -------------------------------------------------------------------------------- /metallicious/tests/example5_extract/temp2.xyz: -------------------------------------------------------------------------------- 1 | 28 2 | frame 0 | Written by MDAnalysis XYZWriter (release 2.4.2) 3 | C -3.70227 -0.53150 -0.77828 4 | C -3.17878 0.75966 -0.94175 5 | C -1.83792 1.01391 -0.59627 6 | N -1.03764 -0.00123 -0.13883 7 | C -2.88281 -1.52278 -0.20797 8 | C -1.54426 -1.20537 0.11588 9 | H -1.44175 2.00572 -0.75467 10 | H -4.73598 -0.72506 -1.05201 11 | H -3.80185 1.55360 -1.34583 12 | C -3.27125 -2.82948 0.08421 13 | C -2.41141 -3.70226 0.71619 14 | C -1.16083 -3.35439 1.16997 15 | C -0.72309 -2.07982 0.84141 16 | N 0.50170 -1.65586 1.23398 17 | C 1.32728 -2.44431 1.97513 18 | C -0.33755 -4.19851 1.92230 19 | C 0.90760 -3.73054 2.34811 20 | H 2.30938 -2.09255 2.24881 21 | H -0.65534 -5.19731 2.19749 22 | H 1.54554 -4.37311 2.93896 23 | N -4.43162 -3.45547 -0.17033 24 | C -4.17744 -4.71378 0.27259 25 | N -2.97261 -4.88671 0.80818 26 | C -5.02366 -5.83590 0.14290 27 | H -2.57876 -5.77268 1.19118 28 | H -4.54874 -6.57892 -0.51140 29 | H -5.19892 -6.27844 1.13240 30 | H -5.98168 -5.52337 -0.29321 31 | 32 | -------------------------------------------------------------------------------- /metallicious/tests/example6_extract_pbc/INFO.dat: -------------------------------------------------------------------------------- 1 | ligand_pattern:0,0,0,0 2 | link_atoms: 3 | extra_atoms: 4 | starting_index:0,1,12,23,34,45 5 | charge_pattern:-1,-1,-1,-1 6 | -------------------------------------------------------------------------------- /metallicious/tests/example6_extract_pbc/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/duartegroup/metallicious/3254b283fe22af19bc477ca36b96533d8fd463a4/metallicious/tests/example6_extract_pbc/__init__.py -------------------------------------------------------------------------------- /metallicious/tests/example6_extract_pbc/example6.py: -------------------------------------------------------------------------------- 1 | '''import sys 2 | sys.path.insert(0, '/home/fd05/fd/chem1540/github/metallicious/') 3 | 4 | 5 | try: 6 | from main import metallicious 7 | from extract_metal_site import extract_metal_structure 8 | except: 9 | from metallicious.main import metallicious 10 | from metallicious.extract_metal_site import extract_metal_structure 11 | 12 | f='Zn_tet.pdb' 13 | metal='Zn' 14 | extract_metal_structure(f, metal, "out") 15 | 16 | ''' 17 | 18 | from metallicious.parametrize_new_sites import supramolecular_structure 19 | 20 | 21 | import os 22 | 23 | cage = supramolecular_structure('noncovalent_complex.pdb', {'Co': (2, 1)}, topol='noncovalent_complex.pdb', LJ_type='merz-opc') 24 | 25 | cage.extract_unique_metal_sites() 26 | 27 | site = cage.unique_sites[0] 28 | os.chdir(site.directory) 29 | print("---------------------------------------------------------------------------") 30 | site.create_initial_topol() 31 | 32 | 33 | 34 | #site = cage.sites[0] 35 | #os.chdir(site.filename) 36 | ##site.create_initial_topol() 37 | #site.seminario() 38 | 39 | #site.partial_charge() 40 | #site.cut_extra_atoms_and_save() 41 | 42 | print("") 43 | -------------------------------------------------------------------------------- /metallicious/tests/example6_extract_pbc/ligand0_0.pdb: -------------------------------------------------------------------------------- 1 | TITLE MDANALYSIS FRAME 0: Created by PDBWriter 2 | CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 3 | REMARK 285 UNITARY VALUES FOR THE UNIT CELL AUTOMATICALLY SET 4 | REMARK 285 BY MDANALYSIS PDBWRITER BECAUSE UNIT CELL INFORMATION 5 | REMARK 285 WAS MISSING. 6 | REMARK 285 PROTEIN DATA BANK CONVENTIONS REQUIRE THAT 7 | REMARK 285 CRYST1 RECORD IS INCLUDED, BUT THE VALUES ON 8 | REMARK 285 THIS RECORD ARE MEANINGLESS. 9 | HETATM 1 H UNL X 1 4.759 9.561 5.047 1.00 0.00 SYST H 10 | HETATM 2 C UNL X 1 4.104 10.218 4.985 1.00 0.00 SYST C 11 | HETATM 3 N UNL X 1 2.995 10.151 4.201 1.00 0.00 SYST N 12 | HETATM 4 H UNL X 1 0.916 12.795 3.808 1.00 0.00 SYST H 13 | ATOM 5 H UNK X 4 0.982 11.251 2.771 1.00 0.00 SYST H 14 | ATOM 6 H UNK X 5 0.193 11.207 4.456 1.00 0.00 SYST H 15 | HETATM 7 H UNL X 1 4.760 11.660 6.259 1.00 0.00 SYST H 16 | HETATM 8 C UNL X 1 4.104 11.385 5.659 1.00 0.00 SYST C 17 | HETATM 9 N UNL X 1 2.996 12.098 5.325 1.00 0.00 SYST N 18 | HETATM 10 C UNL X 1 2.355 11.309 4.443 1.00 0.00 SYST C 19 | HETATM 11 C UNL X 1 1.033 11.661 3.833 1.00 0.00 SYST C 20 | CONECT 1 2 21 | CONECT 2 1 3 8 22 | CONECT 3 2 10 23 | CONECT 7 8 24 | CONECT 8 2 7 9 25 | CONECT 9 8 10 26 | CONECT 10 3 9 11 27 | CONECT 11 4 5 6 10 28 | CONECT 4 11 29 | CONECT 5 11 30 | CONECT 6 11 31 | END 32 | -------------------------------------------------------------------------------- /metallicious/tests/example6_extract_pbc/ligand0_0.xyz: -------------------------------------------------------------------------------- 1 | 11 2 | frame 0 | Written by MDAnalysis XYZWriter (release 2.4.2) 3 | H 4.75900 9.56100 5.04700 4 | C 4.10400 10.21800 4.98500 5 | N 2.99500 10.15100 4.20100 6 | H 0.91596 12.79548 3.80800 7 | H 0.98200 11.25100 2.77100 8 | H 0.19300 11.20700 4.45600 9 | H 4.75996 11.66048 6.25900 10 | C 4.10396 11.38548 5.65900 11 | N 2.99596 12.09848 5.32500 12 | C 2.35496 11.30948 4.44300 13 | C 1.03296 11.66148 3.83300 14 | 15 | -------------------------------------------------------------------------------- /metallicious/tests/example6_extract_pbc/out0.xyz: -------------------------------------------------------------------------------- 1 | 45 2 | Frame 0 | Written By Mdanalysis Xyzwriter (Release 2.4.2) 3 | Zn 2.45300 8.67200 3.00400 4 | H 4.75900 9.56100 5.04700 5 | C 4.10400 10.21800 4.98500 6 | N 2.99500 10.15100 4.20100 7 | H 0.91596 12.79548 3.80800 8 | H 0.98200 11.25100 2.77100 9 | H 0.19300 11.20700 4.45600 10 | H 4.75996 11.66048 6.25900 11 | C 4.10396 11.38548 5.65900 12 | N 2.99596 12.09848 5.32500 13 | C 2.35496 11.30948 4.44300 14 | C 1.03296 11.66148 3.83300 15 | H -0.40300 8.17100 1.63400 16 | C -0.44400 8.00600 2.54900 17 | N 0.59700 8.12100 3.41500 18 | H 0.83800 6.79000 6.36400 19 | H 0.35600 8.57200 6.60500 20 | H 1.91300 8.14600 5.67800 21 | H -2.38300 7.47100 2.84700 22 | C -1.54500 7.61700 3.22300 23 | N -1.23900 7.47200 4.54000 24 | C 0.06700 7.79100 4.60700 25 | C 0.84000 7.82700 5.89000 26 | H -1.97300 4.35000 10.80300 27 | C -2.11400 3.60500 11.34200 28 | N -2.35400 2.34500 10.89100 29 | H -3.33004 -0.15461 12.92801 30 | H -1.70604 -0.39961 12.05202 31 | H -3.26900 -0.16400 11.06800 32 | H -1.97304 4.35139 13.22801 33 | C -2.11404 3.60639 12.69001 34 | N -2.35304 2.34539 13.14102 35 | C -2.48804 1.61839 12.01602 36 | C -2.71104 0.13639 12.01602 37 | H 4.50200 4.26700 4.12300 38 | C 4.46100 5.14100 3.80800 39 | N 5.50300 5.83400 3.27600 40 | H 5.40200 9.13500 2.69400 41 | H 5.56500 8.08100 1.16800 42 | H 6.85700 7.99000 2.50400 43 | H 2.52200 5.66700 4.12300 44 | C 3.36000 5.92000 3.80800 45 | N 3.66600 7.13300 3.27600 46 | C 4.97200 7.03200 2.96600 47 | C 5.74500 8.12500 2.29300 48 | 49 | -------------------------------------------------------------------------------- /metallicious/tests/example6_extract_pbc/site_Co0/ligand_0.xyz: -------------------------------------------------------------------------------- 1 | 11 2 | frame 0 | Written by MDAnalysis XYZWriter (release 2.4.2) 3 | H 9.88700 -4.36700 5.10900 4 | H 9.88700 -2.24100 6.33600 5 | C 9.02900 -3.62900 4.97100 6 | C 9.02900 -2.49000 5.62800 7 | C 7.24700 -2.56200 4.43700 8 | C 5.91700 -2.22500 3.85400 9 | N 7.88000 -3.69900 4.17400 10 | N 7.88100 -1.76500 5.29100 11 | H 5.43600 -3.17000 3.43400 12 | H 6.05000 -1.46200 3.01800 13 | H 5.24700 -1.78600 4.66500 14 | 15 | -------------------------------------------------------------------------------- /metallicious/tests/example6_extract_pbc/site_Zn0/ligand_0.pdb: -------------------------------------------------------------------------------- 1 | TITLE MDANALYSIS FRAME 0: Created by PDBWriter 2 | CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 3 | REMARK 285 UNITARY VALUES FOR THE UNIT CELL AUTOMATICALLY SET 4 | REMARK 285 BY MDANALYSIS PDBWRITER BECAUSE UNIT CELL INFORMATION 5 | REMARK 285 WAS MISSING. 6 | REMARK 285 PROTEIN DATA BANK CONVENTIONS REQUIRE THAT 7 | REMARK 285 CRYST1 RECORD IS INCLUDED, BUT THE VALUES ON 8 | REMARK 285 THIS RECORD ARE MEANINGLESS. 9 | HETATM 1 H UNL X 1 4.759 9.561 5.047 1.00 0.00 SYST H 10 | HETATM 2 C UNL X 1 4.104 10.218 4.985 1.00 0.00 SYST C 11 | HETATM 3 N UNL X 1 2.995 10.151 4.201 1.00 0.00 SYST N 12 | HETATM 4 H UNL X 1 0.916 12.795 3.808 1.00 0.00 SYST H 13 | ATOM 5 H UNK X 4 0.982 11.251 2.771 1.00 0.00 SYST H 14 | ATOM 6 H UNK X 5 0.193 11.207 4.456 1.00 0.00 SYST H 15 | HETATM 7 H UNL X 1 4.760 11.660 6.259 1.00 0.00 SYST H 16 | HETATM 8 C UNL X 1 4.104 11.385 5.659 1.00 0.00 SYST C 17 | HETATM 9 N UNL X 1 2.996 12.098 5.325 1.00 0.00 SYST N 18 | HETATM 10 C UNL X 1 2.355 11.309 4.443 1.00 0.00 SYST C 19 | HETATM 11 C UNL X 1 1.033 11.661 3.833 1.00 0.00 SYST C 20 | CONECT 1 2 21 | CONECT 2 1 3 8 22 | CONECT 3 2 10 23 | CONECT 4 11 24 | CONECT 5 11 25 | CONECT 6 11 26 | CONECT 7 8 27 | CONECT 8 2 7 9 28 | CONECT 9 8 10 29 | CONECT 10 3 9 11 30 | CONECT 11 4 5 6 10 31 | END 32 | -------------------------------------------------------------------------------- /metallicious/tests/example6_extract_pbc/site_Zn0/ligand_0.xyz: -------------------------------------------------------------------------------- 1 | 11 2 | frame 0 | Written by MDAnalysis XYZWriter (release 2.4.2) 3 | H 4.75900 9.56100 5.04700 4 | C 4.10400 10.21800 4.98500 5 | N 2.99500 10.15100 4.20100 6 | H 0.91596 12.79548 3.80800 7 | H 0.98200 11.25100 2.77100 8 | H 0.19300 11.20700 4.45600 9 | H 4.75996 11.66048 6.25900 10 | C 4.10396 11.38548 5.65900 11 | N 2.99596 12.09848 5.32500 12 | C 2.35496 11.30948 4.44300 13 | C 1.03296 11.66148 3.83300 14 | 15 | -------------------------------------------------------------------------------- /metallicious/tests/example6_extract_pbc/site_Zn0/site.xyz: -------------------------------------------------------------------------------- 1 | 45 2 | Frame 0 | Written By Mdanalysis Xyzwriter (Release 2.4.2) 3 | Zn 2.45300 8.67200 3.00400 4 | H 4.75900 9.56100 5.04700 5 | C 4.10400 10.21800 4.98500 6 | N 2.99500 10.15100 4.20100 7 | H 0.91596 12.79548 3.80800 8 | H 0.98200 11.25100 2.77100 9 | H 0.19300 11.20700 4.45600 10 | H 4.75996 11.66048 6.25900 11 | C 4.10396 11.38548 5.65900 12 | N 2.99596 12.09848 5.32500 13 | C 2.35496 11.30948 4.44300 14 | C 1.03296 11.66148 3.83300 15 | H -0.40300 8.17100 1.63400 16 | C -0.44400 8.00600 2.54900 17 | N 0.59700 8.12100 3.41500 18 | H 0.83800 6.79000 6.36400 19 | H 0.35600 8.57200 6.60500 20 | H 1.91300 8.14600 5.67800 21 | H -2.38300 7.47100 2.84700 22 | C -1.54500 7.61700 3.22300 23 | N -1.23900 7.47200 4.54000 24 | C 0.06700 7.79100 4.60700 25 | C 0.84000 7.82700 5.89000 26 | H 2.93204 11.28661 -1.21301 27 | C 2.79104 10.54161 -0.67401 28 | N 2.55104 9.28161 -1.12502 29 | H 1.57500 6.78200 0.91200 30 | H 3.19900 6.53700 0.03600 31 | H 1.63604 6.77261 -0.94802 32 | H 2.93200 11.28800 1.21200 33 | C 2.79100 10.54300 0.67400 34 | N 2.55200 9.28200 1.12500 35 | C 2.41700 8.55500 0.00000 36 | C 2.19400 7.07300 0.00000 37 | H 4.50200 4.26700 4.12300 38 | C 4.46100 5.14100 3.80800 39 | N 5.50300 5.83400 3.27600 40 | H 5.40200 9.13500 2.69400 41 | H 5.56500 8.08100 1.16800 42 | H 6.85700 7.99000 2.50400 43 | H 2.52200 5.66700 4.12300 44 | C 3.36000 5.92000 3.80800 45 | N 3.66600 7.13300 3.27600 46 | C 4.97200 7.03200 2.96600 47 | C 5.74500 8.12500 2.29300 48 | 49 | -------------------------------------------------------------------------------- /metallicious/tests/example6_extract_pbc/temp1.pdb: -------------------------------------------------------------------------------- 1 | TITLE MDANALYSIS FRAME 0: Created by PDBWriter 2 | CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 3 | REMARK 285 UNITARY VALUES FOR THE UNIT CELL AUTOMATICALLY SET 4 | REMARK 285 BY MDANALYSIS PDBWRITER BECAUSE UNIT CELL INFORMATION 5 | REMARK 285 WAS MISSING. 6 | REMARK 285 PROTEIN DATA BANK CONVENTIONS REQUIRE THAT 7 | REMARK 285 CRYST1 RECORD IS INCLUDED, BUT THE VALUES ON 8 | REMARK 285 THIS RECORD ARE MEANINGLESS. 9 | HETATM 1 H UNL X 1 7.830 2.224 1.398 1.00 0.00 SYST H 10 | HETATM 2 H UNL X 1 7.830 0.099 2.625 1.00 0.00 SYST H 11 | HETATM 3 H UNL X 1 7.528 4.451 5.768 1.00 0.00 SYST H 12 | HETATM 4 H UNL X 1 7.676 2.854 6.712 1.00 0.00 SYST H 13 | HETATM 5 C UNL X 1 7.655 2.216 2.524 1.00 0.00 SYST C 14 | HETATM 6 H UNL X 1 6.008 3.438 6.127 1.00 0.00 SYST H 15 | HETATM 7 C UNL X 1 7.655 1.078 3.181 1.00 0.00 SYST C 16 | HETATM 8 C UNL X 1 7.310 2.653 4.595 1.00 0.00 SYST C 17 | HETATM 9 C UNL X 1 7.119 3.393 5.876 1.00 0.00 SYST C 18 | HETATM 10 N UNL X 1 7.421 3.264 3.421 1.00 0.00 SYST N 19 | HETATM 11 N UNL X 1 7.421 1.331 4.538 1.00 0.00 SYST N 20 | CONECT 1 5 21 | CONECT 2 7 22 | CONECT 5 1 7 10 23 | CONECT 7 2 5 11 24 | CONECT 8 9 10 11 25 | CONECT 9 3 4 6 8 26 | CONECT 10 5 8 27 | CONECT 11 7 8 28 | CONECT 3 9 29 | CONECT 4 9 30 | CONECT 6 9 31 | END 32 | -------------------------------------------------------------------------------- /metallicious/tests/example6_extract_pbc/temp1.xyz: -------------------------------------------------------------------------------- 1 | 11 2 | frame 0 | Written by MDAnalysis XYZWriter (release 2.4.2) 3 | H 7.83000 2.22400 1.39800 4 | H 7.83000 0.09900 2.62500 5 | H 7.52800 4.45100 5.76800 6 | H 7.67600 2.85400 6.71200 7 | C 7.65500 2.21600 2.52400 8 | H 6.00800 3.43800 6.12700 9 | C 7.65500 1.07800 3.18100 10 | C 7.31000 2.65300 4.59500 11 | C 7.11900 3.39300 5.87600 12 | N 7.42100 3.26400 3.42100 13 | N 7.42100 1.33100 4.53800 14 | 15 | -------------------------------------------------------------------------------- /metallicious/tests/example6_extract_pbc/temp2.pdb: -------------------------------------------------------------------------------- 1 | TITLE MDANALYSIS FRAME 0: Created by PDBWriter 2 | CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 3 | REMARK 285 UNITARY VALUES FOR THE UNIT CELL AUTOMATICALLY SET 4 | REMARK 285 BY MDANALYSIS PDBWRITER BECAUSE UNIT CELL INFORMATION 5 | REMARK 285 WAS MISSING. 6 | REMARK 285 PROTEIN DATA BANK CONVENTIONS REQUIRE THAT 7 | REMARK 285 CRYST1 RECORD IS INCLUDED, BUT THE VALUES ON 8 | REMARK 285 THIS RECORD ARE MEANINGLESS. 9 | HETATM 1 N UNL X 1 3.677 -0.726 7.817 1.00 0.00 SYST N 10 | HETATM 2 H UNL X 1 4.383 1.651 5.656 1.00 0.00 SYST H 11 | HETATM 3 H UNL X 1 5.224 -3.067 7.836 1.00 0.00 SYST H 12 | HETATM 4 H UNL X 1 5.729 -1.998 9.274 1.00 0.00 SYST H 13 | HETATM 5 H UNL X 1 6.792 -2.068 7.748 1.00 0.00 SYST H 14 | HETATM 6 H UNL X 1 2.379 0.943 6.883 1.00 0.00 SYST H 15 | HETATM 7 C UNL X 1 4.434 0.760 6.364 1.00 0.00 SYST C 16 | HETATM 8 C UNL X 1 3.360 0.380 7.021 1.00 0.00 SYST C 17 | HETATM 9 C UNL X 1 4.960 -0.944 7.555 1.00 0.00 SYST C 18 | HETATM 10 C UNL X 1 5.721 -2.087 8.138 1.00 0.00 SYST C 19 | HETATM 11 N UNL X 1 5.500 -0.082 6.701 1.00 0.00 SYST N 20 | CONECT 2 7 21 | CONECT 6 8 22 | CONECT 7 2 8 11 23 | CONECT 8 1 6 7 24 | CONECT 9 1 10 11 25 | CONECT 10 3 4 5 9 26 | CONECT 11 7 9 27 | CONECT 1 8 9 28 | CONECT 5 10 29 | CONECT 3 10 30 | CONECT 4 10 31 | END 32 | -------------------------------------------------------------------------------- /metallicious/tests/example6_extract_pbc/temp2.xyz: -------------------------------------------------------------------------------- 1 | 11 2 | frame 0 | Written by MDAnalysis XYZWriter (release 2.4.2) 3 | N 3.67700 -0.72600 7.81700 4 | H 4.38300 1.65100 5.65600 5 | H 5.22400 -3.06700 7.83600 6 | H 5.72900 -1.99800 9.27400 7 | H 6.79200 -2.06800 7.74800 8 | H 2.37900 0.94300 6.88300 9 | C 4.43400 0.76000 6.36400 10 | C 3.36000 0.38000 7.02100 11 | C 4.96000 -0.94400 7.55500 12 | C 5.72100 -2.08700 8.13800 13 | N 5.50000 -0.08200 6.70100 14 | 15 | -------------------------------------------------------------------------------- /metallicious/tests/example6_extract_pbc/temp_temp2.xyz: -------------------------------------------------------------------------------- 1 | 45 2 | frame 0 | Written by MDAnalysis XYZWriter (release 2.4.2) 3 | Zn 2.45300 8.67200 3.00400 4 | H 4.75900 9.56100 5.04700 5 | C 4.10400 10.21800 4.98500 6 | N 2.99500 10.15100 4.20100 7 | H -0.40300 8.17100 1.63400 8 | C -0.44400 8.00600 2.54900 9 | N 0.59700 8.12100 3.41500 10 | H 2.93204 11.28661 -1.21301 11 | C 2.79104 10.54161 -0.67401 12 | N 2.55104 9.28161 -1.12502 13 | H 4.50200 4.26700 4.12300 14 | C 4.46100 5.14100 3.80800 15 | N 5.50300 5.83400 3.27600 16 | H 2.52200 5.66700 4.12300 17 | C 3.36000 5.92000 3.80800 18 | N 3.66600 7.13300 3.27600 19 | H 2.93200 11.28800 1.21200 20 | C 2.79100 10.54300 0.67400 21 | N 2.55200 9.28200 1.12500 22 | H 4.75996 11.66048 6.25900 23 | C 4.10396 11.38548 5.65900 24 | N 2.99596 12.09848 5.32500 25 | H -2.38300 7.47100 2.84700 26 | C -1.54500 7.61700 3.22300 27 | N -1.23900 7.47200 4.54000 28 | C 2.35496 11.30948 4.44300 29 | C 1.03296 11.66148 3.83300 30 | C 0.06700 7.79100 4.60700 31 | C 0.84000 7.82700 5.89000 32 | C 2.41700 8.55500 0.00000 33 | C 2.19400 7.07300 0.00000 34 | C 4.97200 7.03200 2.96600 35 | C 5.74500 8.12500 2.29300 36 | H 0.91596 12.79548 3.80800 37 | H 0.83800 6.79000 6.36400 38 | H 0.35600 8.57200 6.60500 39 | H 1.91300 8.14600 5.67800 40 | H 1.57500 6.78200 0.91200 41 | H 3.19900 6.53700 0.03600 42 | H 5.40200 9.13500 2.69400 43 | H 5.56500 8.08100 1.16800 44 | H 6.85700 7.99000 2.50400 45 | H 0.98200 11.25100 2.77100 46 | H 0.19300 11.20700 4.45600 47 | H 1.63604 6.77261 -0.94802 48 | 49 | -------------------------------------------------------------------------------- /metallicious/tests/extract_metal_site/INFO.dat: -------------------------------------------------------------------------------- 1 | ligand_pattern:0,0,0,0 2 | link_atoms:1,29,57,85 3 | extra_atoms:28,26,27,56,54,55,84,82,83,112,110,111 4 | starting_index:0,1,29,57,85,113 5 | ligand_pattern:0,0,0,0 6 | link_atoms:1,33,65,97 7 | extra_atoms:30,31,32,62,63,64,94,95,96,126,127,128 8 | starting_index:0,1,33,65,97,129 9 | ligand_pattern:0,0,0,0 10 | link_atoms:1,33,65,97 11 | extra_atoms:30,31,32,62,63,64,94,95,96,126,127,128 12 | starting_index:0,1,33,65,97,129 13 | ligand_pattern:0,0,0,0 14 | link_atoms:11,31,51,71 15 | extra_atoms:18,19,20,38,39,40,58,59,60,78,79,80 16 | starting_index:0,1,21,41,61,81 17 | ligand_pattern:0,0,0,0 18 | link_atoms:3,7,24,20,41,37,54,58 19 | extra_atoms:12,13,14,16,17,15,32,33,29,30,31,34,49,50,51,46,47,48,67,68,66,63,64,65 20 | starting_index:0,1,18,35,52,69 21 | -------------------------------------------------------------------------------- /metallicious/tests/extract_metal_site/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/duartegroup/metallicious/3254b283fe22af19bc477ca36b96533d8fd463a4/metallicious/tests/extract_metal_site/__init__.py -------------------------------------------------------------------------------- /metallicious/tests/fingerprint/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/duartegroup/metallicious/3254b283fe22af19bc477ca36b96533d8fd463a4/metallicious/tests/fingerprint/__init__.py -------------------------------------------------------------------------------- /metallicious/tests/parametrize_new_site/test_supramolecular.py: -------------------------------------------------------------------------------- 1 | # Parametrize cages which should be there 2 | from metallicious import supramolecular_structure 3 | import parmed as pmd 4 | 5 | def are_bonds_the_same(bond1, bond2): 6 | if bond1.type == bond2.type and bond1.atom1.idx == bond2.atom1.idx and bond1.atom2.idx == bond2.atom2.idx: 7 | return True 8 | else: 9 | return False 10 | def compare_bonds(topol1, topol2): 11 | count = 0 12 | for bond1 in topol1.bonds: 13 | for bond2 in topol2.bonds: 14 | if are_bonds_the_same(bond1, bond2): 15 | count +=1 16 | return count 17 | 18 | def test_patcher(): 19 | cage = supramolecular_structure('Co8L16.pdb', {'Co': (2,4)}, topol='Co8L16.top', LJ_type='merz-opc') 20 | cage.parametrize(out_coord='out_Co8L16.pdb', out_topol='out_Co8L16.top') 21 | topol = pmd.load_file('out_Co8L16.top') 22 | topol_old = pmd.load_file('Co8L16.top') 23 | assert len(topol.bonds) - len(topol_old.bonds) == 8*6 24 | 25 | cage = supramolecular_structure('Fe5L5.pdb', {'Fe': (2,1)}, topol='Fe5L5.top', LJ_type='merz-opc') 26 | cage.parametrize(out_coord='out_Fe5L5.pdb', out_topol='out_Fe5L5.top') 27 | topol = pmd.load_file('out_Fe5L5.top') 28 | topol_old = pmd.load_file('Fe5L5.top') 29 | assert len(topol.bonds) - len(topol_old.bonds) == 5*6 30 | 31 | cage = supramolecular_structure('Pd2L4.pdb', metal_charges={'Pd': 2}, topol='Pd2L4.top', LJ_type='merz-opc') 32 | cage.parametrize(out_coord='out_Pd2L4.pdb', out_topol='out_Pd2L4.top') 33 | topol = pmd.load_file('out_Pd2L4.top') 34 | topol_old = pmd.load_file('Pd2L4.top') 35 | assert len(topol.bonds) - len(topol_old.bonds) == 2*4 36 | 37 | cage = supramolecular_structure('Pd6Ru8L28.pdb', metal_charges={'Pd': 2, 'Ru': 2}, topol='Pd6Ru8L28.top', LJ_type='uff') 38 | cage.parametrize(out_coord='out_Pd6Ru8L28.pdb', out_topol='out_Pd6Ru8L28.top') 39 | topol = pmd.load_file('out_Pd6Ru8L28.top') 40 | topol_old = pmd.load_file('Pd6Ru8L28.top') 41 | assert len(topol.bonds) - len(topol_old.bonds) == 6*4 + 8*6 42 | 43 | cage = supramolecular_structure('Pd6L4.pdb', metal_charges={'Pd': 2}, topol='Pd6L4.top', LJ_type='merz-opc') 44 | cage.parametrize(out_coord='out_Pd6L4.pdb', out_topol='out_Pd6L4.top') 45 | topol = pmd.load_file('out_Pd6L4.top') 46 | topol_old = pmd.load_file('Pd6L4.top') 47 | assert len(topol.bonds) - len(topol_old.bonds) == 6*4 48 | 49 | 50 | def test_truncation_scheme(): 51 | cage = supramolecular_structure('Pd2L4.pdb', metal_charges={'Pd': 2}, topol='Pd2L4.top', 52 | LJ_type='merz-opc', truncation_scheme='dih') 53 | cage.parametrize(out_coord='out_Pd2L4.pdb', out_topol='out_Pd2L4.top') 54 | topol = pmd.load_file('out_Pd2L4.top') 55 | topol_old = pmd.load_file('Pd2L4.top') 56 | assert len(topol.bonds) - compare_bonds(topol, topol_old) == 7*4*2 57 | 58 | cage = supramolecular_structure('Pd2L4.pdb', metal_charges={'Pd': 2}, topol='Pd2L4.top', 59 | LJ_type='merz-opc', truncation_scheme='ang') 60 | cage.parametrize(out_coord='out_Pd2L4.pdb', out_topol='out_Pd2L4.top') 61 | topol = pmd.load_file('out_Pd2L4.top') 62 | topol_old = pmd.load_file('Pd2L4.top') 63 | assert len(topol.bonds) - compare_bonds(topol, topol_old) == 3*4*2 64 | 65 | cage = supramolecular_structure('Pd2L4.pdb', metal_charges={'Pd': 2}, topol='Pd2L4.top', 66 | LJ_type='merz-opc', truncation_scheme='bond') 67 | cage.parametrize(out_coord='out_Pd2L4.pdb', out_topol='out_Pd2L4.top') 68 | topol = pmd.load_file('out_Pd2L4.top') 69 | topol_old = pmd.load_file('Pd2L4.top') 70 | assert len(topol.bonds) - compare_bonds(topol, topol_old) == 1*4*2 71 | -------------------------------------------------------------------------------- /metallicious/utils.py: -------------------------------------------------------------------------------- 1 | 2 | import os 3 | import re 4 | 5 | import MDAnalysis 6 | import rdkit 7 | import numpy as np 8 | 9 | def new_directory(directory): 10 | ''' 11 | Creates new directory 12 | :param directory: (str) name of new directory 13 | :return: 14 | ''' 15 | if not os.path.isdir(directory): 16 | os.mkdir(directory) 17 | return True 18 | else: 19 | return False 20 | 21 | 22 | def strip_numbers_from_atom_name(atom_name): 23 | ''' 24 | Strips the numbers from the string (e.g., C4 -> C) 25 | :param atom_name: (str) atom name with possible number 26 | :return: (str) 27 | ''' 28 | return re.match("([a-zA-Z]+)", atom_name).group(0) 29 | 30 | def strip_numbers_from_atom_names(atom_names): 31 | ''' 32 | Strips numbers from the list of strings, useful for atom names from PDB 33 | 34 | :param atom_names: (list(str)) 35 | :return: (list(str)) 36 | ''' 37 | return np.array([strip_numbers_from_atom_name(atom_name) for atom_name in atom_names]) 38 | 39 | def guess_aromaticities(syst): 40 | ''' 41 | Find aromaticity using MDAnalysis, but skip DUMMY atoms as they break the code. 42 | :param syst: (MDAnalysis.Universe.atoms) input structure 43 | :return: (list(bool)) list of aromaticy of all atoms 44 | ''' 45 | aromaticity = [False] * len(syst) 46 | not_dummy = [idx for idx, name in enumerate(syst.elements) if name != 'DUMMY'] 47 | 48 | #aromaticity_from_mdanalysis = MDAnalysis.topology.guessers.guess_aromaticities(syst[not_dummy], force=True) 49 | mol = syst[not_dummy].convert_to("RDKIT", force=True) 50 | aromaticity_from_mdanalysis = np.array([atom.GetIsAromatic() for atom in mol.GetAtoms()]) 51 | 52 | for idx, _ in enumerate(not_dummy): 53 | aromaticity[not_dummy[idx]] = aromaticity_from_mdanalysis[idx] 54 | return aromaticity 55 | 56 | def guess_chirality(syst): 57 | ''' 58 | Returns chirality of the atoms using rdkit 59 | 60 | :param syst: (MDAnalysis.Universe.atoms) input structure 61 | :return: (list(str)) list of chirality of all atoms 62 | ''' 63 | chirality = [rdkit.Chem.rdchem.ChiralType.CHI_UNSPECIFIED] * len(syst) 64 | not_dummy = [idx for idx, name in enumerate(syst.elements) if name != 'DUMMY'] 65 | mol1 = syst[not_dummy].convert_to("RDKIT", force=True) 66 | 67 | for idx, atom in enumerate(mol1.GetAtoms()): 68 | chirality[not_dummy[idx]] = atom.GetChiralTag() 69 | 70 | return chirality 71 | -------------------------------------------------------------------------------- /pyproject.toml: -------------------------------------------------------------------------------- 1 | [build-system] 2 | requires = ["setuptools", "setuptools-scm"] 3 | build-backend = "setuptools.build_meta" 4 | 5 | [project] 6 | name = "metallicious" 7 | version = "0.2.34" 8 | 9 | dependencies = [ 10 | "numpy", 11 | "MDAnalysis", 12 | "rdkit", 13 | "parmed", 14 | "networkx"] 15 | 16 | [project.scripts] 17 | metallicious = "metallicious.__main__:main" 18 | 19 | [tool.setuptools.packages.find] 20 | include = ["metallicious"] 21 | 22 | -------------------------------------------------------------------------------- /requirements.txt: -------------------------------------------------------------------------------- 1 | mdanalysis>=2.4.2 2 | parmed>=3.4.4 3 | numpy>=1.22.4 4 | rdkit>=2022.09.1 5 | networkx>=3.0 6 | scipy>=1.7.3 7 | setuptools>=67.7.2 -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- 1 | from setuptools import setup 2 | 3 | setup() --------------------------------------------------------------------------------