pyphyschemtools

📚 Docs and Theory

  • Fundamental Units
    • Quick Start
      • Initialization
      • Smart Arithmetic
        • Basic operations
        • Arithmetic Rules
      • Discovering Supported Units of each class
      • CODATA Traceability & Metadata
      • Universal Prefix Support
      • Accessing Numerical Data
      • Batch Processing (Vectorization)
    • Energy
      • Mathematical relationships
      • Spectroscopic & Molar Conversions
      • Supported units
    • Pressure
      • Standard & Industrial Units
      • Supported Units
      • Common Conversions
    • Length
      • From Atomic to Macroscopic Scales
      • Supported Units
      • Common Conversions
    • Area
      • Surface and Interface Dimensions
      • Supported Units
      • Common Conversions
    • Volume
      • Three-Dimensional Capacity
      • Supported Units
      • Common Conversions
    • Mass
      • From Subatomic to Industrial Scales
      • Supported Units
      • Common Conversions
    • Molar Mass
      • The Stoichiometric Bridge
      • Supported Units
      • Common Conversions
    • Density
      • Mass per Volume Relationships
      • Supported Units
      • Common Conversions
    • Temperature
      • Absolute and Relative Scales
      • Supported Units
      • Common Conversions
    • API reference
      • Area
        • Area.to()
      • Density
        • Density.to()
      • Energy
        • Energy.to()
      • Length
        • Length.to()
      • Mass
        • Mass.to()
      • MolarMass
        • MolarMass.to()
      • PhysicalQuantity
        • PhysicalQuantity.parse()
        • PhysicalQuantity.show_available_prefixes()
        • PhysicalQuantity.show_available_units()
        • PhysicalQuantity.show_constants_metadata()
      • Pressure
        • Pressure.to()
      • Temperature
        • Temperature.show_available_units()
        • Temperature.to()
      • Volume
        • Volume.to()
  • Hydrogen and hydrogen-like atoms
    • Quick Start
    • Reduced-mass correction
    • Energy levels
    • Ionization energy
    • Spectral series
    • Energy-level diagrams
    • Line spectra
    • API reference
      • Ei_hydrogenic()
      • En_hydrogenic()
      • plot_energy_levels()
      • plot_line_spectrum()
      • rydberg_Z()
      • spectral_series()
  • Atomic Orbitals
    • Physical background
    • Quick start
    • Orbital naming convention
    • API reference
      • plot_electron_cloud()
      • plot_orbital_3D()
      • plot_polar()
      • plot_radial()
  • Periodic Table
    • Quick Start
    • Element properties
    • Isotopes
    • Mononuclidic elements
    • Interactive periodic table
    • API reference
      • PeriodicTable
        • PeriodicTable.afficher()
        • PeriodicTable.isotopes()
        • PeriodicTable.mononucleides()
        • PeriodicTable.prop()
      • TableauPeriodique
        • TableauPeriodique.afficher()
        • TableauPeriodique.exceptionsRadiogenic
        • TableauPeriodique.exceptionsRadiogeniques
        • TableauPeriodique.intervallesCIAAW
        • TableauPeriodique.isotopes()
        • TableauPeriodique.mononucleides()
        • TableauPeriodique.nomsFr
        • TableauPeriodique.patch_elements()
        • TableauPeriodique.prop()
        • TableauPeriodique.trad
  • Cheminformatics
    • 2D representation of organic and inorganic compounds
      • Principle
      • Molecular Descriptors Reference
        • Physico-chemical Properties (Lipinski & Veber Criteria)
        • Topological & Structural Indices
      • Practical examples
        • A. Basic use
        • B. Comprehensive Electronic View: Lewis structure
        • C. Fetching a SMILES from its PubChem CID
        • D. Mastering Complex Geometry
        • E. Calculation of descriptors
        • F. Store descriptors in a dataframe
        • G. Display the smiles of a dataframe on a grid, with legends
    • API reference
      • easy_rdkit
        • easy_rdkit.analyze_lewis()
        • easy_rdkit.analyze_stereochemistry()
        • easy_rdkit.descriptors
        • easy_rdkit.draw_consistent_svg()
        • easy_rdkit.fetch_pubchem_data()
        • easy_rdkit.from_cid()
        • easy_rdkit.from_name()
        • easy_rdkit.get_isomers()
        • easy_rdkit.plot_grid_from_df()
        • easy_rdkit.show_descriptors()
        • easy_rdkit.show_isomers()
        • easy_rdkit.show_mol()
        • easy_rdkit.to_dict()
  • Structural Chemistry - Chemistry in 3 dimensions
    • Overview
    • Supported input sources
    • Quick start
    • Headless mode
    • Cavity and bounding-sphere analysis
    • Symmetry analysis
    • API reference
      • molView
        • molView.data
        • molView.v
        • molView.analyze_symmetry()
        • molView.show_bounding_sphere()
        • molView.show_cage_cavity()
        • molView.view_grid()
      • XYZData
        • XYZData.get_bounding_sphere()
        • XYZData.get_cage_volume()
        • XYZData.get_cavity_dimensions()
        • XYZData.get_center_of_geometry()
        • XYZData.get_center_of_mass()
  • Hückel Molecular Orbital method
    • Theory
      • σ/π separability
      • The two Hückel parameters
      • Secular matrix and the benzene example
      • Pi population and bond orders
      • Delocalization and conjugation energies
      • From the toy model to HMO
    • API reference
      • huckel.py
        • Overview
      • HMO
        • HMO.atomization_energy()
        • HMO.bond_order()
        • HMO.conjugation_energy()
        • HMO.density_matrix()
        • HMO.electron_density
        • HMO.free_valence
        • HMO.huckel_matrix()
        • HMO.mo_table()
        • HMO.pi_charge
        • HMO.plot_all_mo()
        • HMO.plot_energy_diagram()
        • HMO.plot_mo_list()
        • HMO.plot_mo_on_graph()
        • HMO.plot_pi_population()
        • HMO.properties()
        • HMO.save_results()
        • HMO.show()
        • HMO.summary()
        • HMO.total_pi_energy()
        • HMO.used_parameters()
      • hmo_properties_table()
      • parameter_table()
      • save_data()
      • save_fig()
  • Molecular Symmetry
    • Two ways of using the module
    • 1. Principle
      • 1.1 Symmetry operations as matrices
      • 1.2 Atom tracking
      • 1.3 Reduction
    • 2. Symmetry operations
    • 3. Character tables
    • 4. The MolSym class
      • 4.1 Building a MolSym molecule
      • 4.2 Point group and orientation
      • 4.3 Arguments
      • 4.4 Main methods
    • 5. Representations and their reduction
      • 5.1 Principle
      • 5.2 Atomic orbitals
      • 5.3 Simple molecular orbitals
      • 5.4 Vibrations
    • 6. Visualization
    • 7. Conventions
    • 8. Limitations
    • API reference
      • Cn()
      • MolSym
        • MolSym.group
        • MolSym.symbols
        • MolSym.atom_labels
        • MolSym.coords
        • MolSym.coords_input
        • MolSym.labels
        • MolSym.order
        • MolSym.activity()
        • MolSym.apply()
        • MolSym.bonds()
        • MolSym.character_table()
        • MolSym.equivalent_atoms()
        • MolSym.fixed_atoms()
        • MolSym.flowchart()
        • MolSym.from_molView()
        • MolSym.gamma_3N()
        • MolSym.gamma_atoms()
        • MolSym.gamma_bonds()
        • MolSym.gamma_orbitals()
        • MolSym.gamma_vib()
        • MolSym.is_symmetry()
        • MolSym.matrices()
        • MolSym.orbital_symmetries()
        • MolSym.orbital_symmetry()
        • MolSym.orientation()
        • MolSym.reduce()
        • MolSym.representation_matrix()
        • MolSym.show()
        • MolSym.show_elements()
        • MolSym.show_operation()
        • MolSym.symmetry_elements()
        • MolSym.track()
      • Sn()
      • available_groups()
      • character_table()
      • identify()
      • identity()
      • inv()
      • inversion()
      • ir_raman_activity()
      • point_group_flowchart()
      • reduce_representation()
      • show_matrix()
      • sigma()
  • Chemical Kinetics
    • Kinetic Order of Reaction Determination, KORD
      • 1. Principle
        • 1.1 Experimental Measurements (\(G_\mathrm{EXP}\))
        • 1.2 Theoretical Model (\(G_\mathrm{THEO}\))
        • 1.3 Optimization (RMSD)
        • 1.4 Input
      • 2. Theoretical Model
        • 2.1 Reactant Expression \(a(t)\)
        • 2.2 Product Expression \(B(t)\)
        • 2.3 Global Expression \(G_\mathrm{THEO}(t)\)
    • API reference
      • KORD
        • KORD.G0_theo()
        • KORD.G1_theo()
        • KORD.G2_theo()
        • KORD.concentrations()
        • KORD.fit()
        • KORD.get_best_order()
        • KORD.halflife()
        • KORD.load_from_excel()
        • KORD.plot_all_fits()
        • KORD.simulate_plot()
      • kbasic
        • kbasic.fit()
        • kbasic.plot()
        • kbasic.read()
  • Nanochemistry
    • API reference
      • get_coordination_numbers()
      • view_coordination()
  • Organic Chemsitry
    • API reference
      • FunctionalGroupExplorer
        • FunctionalGroupExplorer.T()
        • FunctionalGroupExplorer.afficher_quiz_nom()
        • FunctionalGroupExplorer.afficher_quiz_struct()
        • FunctionalGroupExplorer.check_nom()
        • FunctionalGroupExplorer.check_struct()
        • FunctionalGroupExplorer.detecter_delimiteur()
        • FunctionalGroupExplorer.fuzzy_match()
        • FunctionalGroupExplorer.get_lives_html()
        • FunctionalGroupExplorer.get_match_svg()
        • FunctionalGroupExplorer.mol_to_svg()
        • FunctionalGroupExplorer.next_nom()
        • FunctionalGroupExplorer.next_struct()
        • FunctionalGroupExplorer.on_lang_change()
        • FunctionalGroupExplorer.on_survival_change()
        • FunctionalGroupExplorer.run_3d()
        • FunctionalGroupExplorer.run_iupac()
        • FunctionalGroupExplorer.setup_ui()
        • FunctionalGroupExplorer.show_3d_mol()
        • FunctionalGroupExplorer.start_timer_thread()
        • FunctionalGroupExplorer.timeout_struct()
        • FunctionalGroupExplorer.update_combobox_options()
        • FunctionalGroupExplorer.update_explorer()
        • FunctionalGroupExplorer.update_labels()
  • Spectroscopy
    • QuantitativeAnalysis Class Documentation
      • Initialization & Data Ingestion
      • Method Fitting & Diagnostics
      • Advanced Visualization
      • Sample Quantification
      • Summary of Methods
    • Simulation of VUV spectra by TDDFT calculations (SpectrumSimulator)
      • Principle
        • Pre-requisite: the Jablonski energy diagram
        • Vertical transitions
      • From Quantum Chemistry to UV-Vis Spectra
        • The Nature of TDDFT Results
        • Basic equations
      • Practical examples
        • A. Data Input Format
        • B. Basic TD-DFT Simulation
        • C. Comparative Absorbance Analysis
    • API reference
  • Miscellaneous tools
    • Branded QR Code Generation
    • API reference
      • QRCodeGenerator
        • QRCodeGenerator.generate()
  • Thermochemistry tools
    • API reference
      • aiThermo
        • aiThermo.ListOfStableSurfaceCompositions()
        • aiThermo.plot_palette()
        • aiThermo.plot_surface()
  • Core utilities
    • API reference
      • centerTitle()
      • centertxt()
      • crop_images()
      • get_qc_examples()
      • save_data()
      • save_fig()
      • smart_trim()
  • Machine Learning tools
    • API reference
      • categorizeY_2ohe()
      • y2c()
  • Survey tools
    • API reference
      • SurveyApp
        • SurveyApp.analyze_text_columns()
        • SurveyApp.build_admin_dashboard()
        • SurveyApp.build_participant_form()
        • SurveyApp.enable_slider_css()
        • SurveyApp.get_or_create_user_id()
        • SurveyApp.list_drafts()
        • SurveyApp.load_all_responses()
        • SurveyApp.load_draft()
        • SurveyApp.load_questions()
        • SurveyApp.plot_spider_multi()
        • SurveyApp.print_questions_summary()
        • SurveyApp.run()
        • SurveyApp.save_draft()
        • SurveyApp.semantic_analysis()
        • SurveyApp.submit_form()
        • SurveyApp.summarize_by_block()
  • Sympy utilities
    • API reference
      • PrintLatexStyleSymPyEquation()
      • e2Lists()
  • Tools4AS
    • API reference
      • ApplySecondeChance()
      • BoiteAMoustachesByMentionEtParcours()
      • BoiteAMoustachesByMentionEtParcoursHue()
      • ComparaisonMoyennesDMCC()
      • CreationDfADMAJGH()
      • Histogrammes()
      • MentionAuModule()
      • RenameDfHeader()
      • ReplaceABSByNan()
      • ReplaceNanBy0()
      • ReplaceNanBy0OLD()
      • StackedBarPop()
      • StackedBarPopPO()
      • StatsRéussiteParMentionOuParcours()
      • StatsRéussiteParMentionOuParcoursWithAb()
      • checkNoID_DuplicateID()
      • concat2ApoG()
      • css_styling()
      • dropColumnsByIndex()
      • kdePlotByMentionEtParcours()
      • mentionD()
      • parcours()
      • plotTauxADMasBars()
      • read_excel()
      • verifNotes()
  • Visual identity tools
    • API reference
      • chrono_show()
      • chrono_start()
      • chrono_stop()
      • color
        • color.BLUE
        • color.BOLD
        • color.CYAN
        • color.DARKCYAN
        • color.GREEN
        • color.OFF
        • color.PURPLE
        • color.RED
        • color.UNDERLINE
        • color.YELLOW
      • css_styling()
      • display_md()
      • end()
      • hdelay()
      • hdelay_ms()
      • init()
  • Visual identity tools (English)
    • API reference
      • apply_css_style()
      • bg
        • bg.DARKRED
        • bg.DARKREDB
        • bg.LIGHTBLUE
        • bg.LIGHTBLUEB
        • bg.LIGHTGREEN
        • bg.LIGHTGREENB
        • bg.LIGHTRED
        • bg.LIGHTREDB
        • bg.LIGHTYELLOW
        • bg.LIGHTYELLOWB
        • bg.OFF
      • chrono_show()
      • chrono_start()
      • chrono_stop()
      • color
        • color.BLUE
        • color.BOLD
        • color.CYAN
        • color.DARKCYAN
        • color.GREEN
        • color.OFF
        • color.PURPLE
        • color.RED
        • color.UNDERLINE
        • color.YELLOW
      • display_md()
      • end()
      • fg
        • fg.BLACK
        • fg.BLUE
        • fg.CYAN
        • fg.DARKCYAN
        • fg.DARKGRAY
        • fg.GREEN
        • fg.LIGHTGRAY
        • fg.OFF
        • fg.PURPLE
        • fg.RED
        • fg.WHITE
        • fg.YELLOW
      • hdelay()
      • hdelay_ms()
      • hl
        • hl.BLINK
        • hl.BOLD
        • hl.ITALIC
        • hl.OFF
        • hl.UNDERL
        • hl.blink
        • hl.bold
        • hl.italic
        • hl.underl
      • init()

🐍 Python Environment Management

  • Python environmennt management
    • Key Features
    • Usage
    • Configuration: Setting up PIP_MGMT_FOLDER
      • 🐧 Linux & 🍎 macOS (Zsh/Bash)
      • 🪟 Windows (PowerShell / CMD)

🚀 Interactive Examples

  • Examples (Google Colab)

⚛️ Quantum Chemistry Corner

  • Quantum Chemistry Corner
    • 🚀 Brief introduction, dependencies and examples
    • ⚛️ Tools for VASP
      • 📖 Citation
      • ✅ VASPcv (bash & python)
      • ✅ cpVASP (bash)
      • ✅ RestartVASP (bash)
      • ✅ cleanVASPf (bash & python)
      • ✅ ManipCell (fortran binary)
      • ✅ sel4vibVASP (fortran binary)
      • ✅ vibVASP (fortran binary)
      • ✅ ThermoWithVASP (fortran binary)
      • ✅ selectLOBSTER (fortran binary)
      • ✅ hVASP (bash)
    • ⚛️ Tools for Gaussian
      • ✅ GParser (bash)
      • ✅ cpG (bash)
      • ✅ GScan_Analyzis (python)
    • 🤝 How to contribute?
      • 📋 Technical Requirements
      • 📖 Documentation Requirements
      • 🚀 Integration Procedure
      • 💡 Why the “Wrapper” approach?

🛠️ API Reference (Technical)

  • pyphyschemtools
    • pyphyschemtools package
      • save_data()
      • save_fig()
      • Subpackages
        • pyphyschemtools.quantumChem_corner package
        • pyphyschemtools.utils package
      • Submodules
      • pyphyschemtools.AO module
      • pyphyschemtools.Chem3D module
      • pyphyschemtools.ML module
      • pyphyschemtools.PeriodicTable module
      • pyphyschemtools.aithermo module
      • pyphyschemtools.cheminformatics module
      • pyphyschemtools.core module
      • pyphyschemtools.huckel module
        • huckel.py
      • pyphyschemtools.hydrogen module
      • pyphyschemtools.kinetics module
      • pyphyschemtools.misc module
      • pyphyschemtools.nano module
      • pyphyschemtools.orgachem module
      • pyphyschemtools.spectro module
      • pyphyschemtools.symmetry module
      • pyphyschemtools.survey module
      • pyphyschemtools.sympyUtilities module
      • pyphyschemtools.tools4AS module
      • pyphyschemtools.units module
      • pyphyschemtools.visualID module
      • pyphyschemtools.visualID_Eng module
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