Meeko
Interface for AutoDock, molecule parameterization
File Explorer
Download Latest Version (.zip)- pypi-build.yml
- pytest_ci.yml
- pull_request_template.md
- annotated_HIE_AMP.png
- docking_workflow.png
- embedded_CRO.png
- highlighted_AMP.png
- lg-importance.png
- pdbqt-example.png
- raccoon.png
- starting_CRO.png
- xgb-shap.png
- cli_rec_prep.rst
- colab_examples.rst
- conf.py
- export_cli_options.rst
- export_usage.rst
- flex_rec_pdbqt.rst
- index.rst
- installation.rst
- lig_cli_options.rst
- lig_overview.rst
- lig_prep_advanced.rst
- lig_prep_basic.rst
- pdbqt_spec.rst
- py_build_temp.rst
- py_rec_prep.rst
- rec_cli_options.rst
- rec_overview.rst
- tutorial1.rst
- tutorial2.rst
- tutorial3.rst
- tutorial4a.rst
- tutorial4b.rst
- tutorial_anchored.rst
- tutorials.rst
- make.bat
- Makefile
- README.md
- requirements.txt
- 5fnt.pdb
- test_5fnt_A382_asn_flex.pdbqt
- test_5fnt_A382_asn_rigid.pdbqt
- test_5fnt_A530_gln_flex.pdbqt
- test_5fnt_A530_gln_rigid.pdbqt
- test_5fnt_A555_ser_flex.pdbqt
- test_5fnt_A555_ser_rigid.pdbqt
- test_5fnt_A602_ser_flex.pdbqt
- test_5fnt_A602_ser_rigid.pdbqt
- 1iep_protein.pdb
- 2hzn_protein.pdb
- mols.smi
- xray-imatinib.pdb
- boron-silicon-atom_par.dat
- imatinib.sdf
- imatinib_protomer-1.pdbqt
- imatinib_protomer-2.pdbqt
- mols.sdf
- rec_1iep.box.pdb
- rec_1iep.box.txt
- rec_1iep.gpf
- rec_1iep.pdbqt
- rec_2hzn.box.pdb
- rec_2hzn.box.txt
- rec_2hzn.json
- rec_2hzn_flex.pdbqt
- rec_2hzn_rigid.gpf
- rec_2hzn_rigid.pdbqt
- __init__.py
- fingerprint_interactions.py
- interactions.py
- __init__.py
- mk_export.py
- mk_prepare_ligand.py
- mk_prepare_receptor.py
- scofu1.json
- ad4_desolv_param.json
- ad4_desolv_volume.json
- ad4_hb.json
- ad4_types.json
- ad4_vdw.json
- example_offatom_charge.json
- gb_mbondi.json
- metal_vdw.toml
- vina_params.json
- NAKB_templates.json
- residue_chem_templates.json
- template_charges.json
- compute_water_map.py
- water_builder.py
- water_map_builder.py
- __init__.py
- autodock4_atom_types_elements.py
- covalent_radius_table.py
- geomutils.py
- jsonutils.py
- pdbutils.py
- prodyutils.py
- rdkitutils.py
- utils.py
- van_der_waals_radius_table.py
- __init__.py
- AD_to_STD_ATOMTYPES.json
- atomtyper.py
- bondtyper.py
- chemtempgen.py
- covalentbuilder.py
- espalomatyper.py
- export_flexres.py
- flexibility.py
- gridbox.py
- hydrate.py
- macrocycle.py
- molecule_pdbqt.py
- molsetup.py
- openff_xml_parser.py
- polymer.py
- preparation.py
- rdkit_mol_create.py
- reactive.py
- receptor_pdbqt.py
- writer.py
- has_alkene.mol
- non_sequential_atom_ordering_01.mol
- non_sequential_atom_ordering_02.mol
- single-triple-single-bond.mol
- lorlatinib.mol
- macrocycle2.sdf
- macrocycle3.sdf
- macrocycle4.sdf
- macrocycle5.sdf
- non_sequential_atom_ordering_03.mol
- non_sequential_atom_ordering_04.mol
- non_sequential_atom_ordering_05.mol
- open-ring-3D-graph-intact_small.mol
- tetrahedron1.sdf
- tetrahedron2.sdf
- vancomycin.sdf
- 3zlq_lig_a.sdf
- 3zlq_lig_b.sdf
- 2xo1_rec.pdb
- 1FAS_dry.pqr
- 1igy_B_82-83_has-icode.pdb
- AHHY-v0.6.1.json
- AHHY.pdb
- AHHY_reference_fewer_templates.json
- disulfide_bridge_in_adjacent_residues.pdb
- has-altloc.pdb
- has-lyn.pdb
- has-lys-resname-lyn.pdb
- has-lys.pdb
- just-one-ALA-missing-CB.pdb
- just-one-ALA.pdb
- just-three-residues.pdb
- just-three-residues_vina_flexres.pdbqt
- just-three-residues_vina_flexres_idxmap.pdbqt
- just_a_disulfide_bridge.pdb
- loop_with_disulfide.pdb
- nglu.pdb
- non-sequential-res.pdb
- NPHE_SER.pdb
- 22-flexres.pdbqt
- adgpu-result-ethanol.dlg
- arg_gln_asn_phe_badphe.pdbqt
- arg_his.pdbqt
- chiral_deutorated_D_gly.sdf
- chiral_deutorated_L_gly.sdf
- macrocycle-water-asn-phe.pdbqt
- small-01_four-deuterium.sdf
- small-01_one-deuterium.sdf
- small-01_three-deuterium.sdf
- small-01_two-deuterium.sdf
- small-01_zero-deuterium.sdf
- small-02_five-deuterium.sdf
- small-02_one-deuterium-A.sdf
- small-02_one-deuterium-B.sdf
- small-02_one-deuterium-C.sdf
- small-02_two-deuterium-A.sdf
- small-02_two-deuterium-B.sdf
- small-02_two-deuterium-C.sdf
- small-02_two-deuterium-D.sdf
- small-02_zero-deuterium.sdf
- small-03_one-deuterium-A.sdf
- small-03_one-deuterium-B.sdf
- small-03_three-deuterium.sdf
- small-03_two-deuterium.sdf
- small-03_zero-deuterium.sdf
- small-04.sdf
- vina-result-ethanol.pdbqt
- adamantane-stretched.sdf
- adamantane.sdf
- adamantanish-5-5-6.sdf
- break-equiv-2.sdf
- break-equiv-a.sdf
- break-equiv-b.sdf
- break-equiv-small.sdf
- break-equiv.sdf
- cubane.sdf
- oxabicyclo-2-2-2-octane.sdf
- tricycle-5-6-7.sdf
- tricycle-6-5-5.sdf
- tricycle-6-5-6.sdf
- tricycle-6-5-6_B.sdf
- tricycle-6-7-7.sdf
- chemtempgen_test.py
- cyclopentane_rigid_test.py
- flexibility_test.py
- flexres_export_test.py
- json_serialization_test.py
- macrocycle_test.py
- merge_custom_types_test.py
- molsetup_test.py
- parameterization_test.py
- polymer_creation_test.py
- rdkitmol_from_docking_test.py
- ring_detection_test.py
- skip_bad_mols_test.py
- test-oids.py
- precalculate_charges.py
- .gitignore
- .readthedocs.yaml
- LICENSE
- MANIFEST.in
- README.md
- requirements.txt
- setup.py
# Installation Guide
1. Get the code
git clone https://github.com/forlilab/Meeko
Downloads the entire project code from GitHub to your computer.
cd Meeko
Moves into the project folder you just downloaded.
2. Official Install Script
Easy RecommendedPrerequisites
- Python 3 Python is required to use pip.
pip install meeko
Installs the package published on PyPI directly β no need to clone the source.
pip install git+https://github.com/forlilab/meeko
Installs the package published on PyPI directly β no need to clone the source.
After installing, open a new terminal and run the program's version command (e.g. --version) to confirm it worked.
Pulled directly from this repo's README.
3. Python
EasyPrerequisites
pip install meeko
Installs the package published on PyPI directly β no need to clone the source.
pip install git+https://github.com/forlilab/meeko
Installs the package published on PyPI directly β no need to clone the source.
If it runs without errors and prints output in the terminal, it worked.
Pulled directly from this repo's README.
// repository documentation
Was this content helpful?
(0 ratings)
