gh-k-dense-ai-claude-scientific-skills-scientific-skills/skills/exploratory-data-analysis/references/chemistry_molecular_formats.md

Chemistry and Molecular File Formats Reference

This reference covers file formats commonly used in computational chemistry, cheminformatics, molecular modeling, and related fields.

Structure File Formats

.pdb - Protein Data Bank

Description: Standard format for 3D structures of biological macromolecules Typical Data: Atomic coordinates, residue information, secondary structure, crystal structure data Use Cases: Protein structure analysis, molecular visualization, docking studies Python Libraries:

• Biopython: Bio.PDB
• MDAnalysis: MDAnalysis.Universe('file.pdb')
• PyMOL: pymol.cmd.load('file.pdb')
• ProDy: prody.parsePDB('file.pdb') EDA Approach:
• Structure validation (bond lengths, angles, clashes)
• Secondary structure analysis
• B-factor distribution
• Missing residues/atoms detection
• Ramachandran plots for validation
• Surface area and volume calculations

.cif - Crystallographic Information File

Description: Structured data format for crystallographic information Typical Data: Unit cell parameters, atomic coordinates, symmetry operations, experimental data Use Cases: Crystal structure determination, structural biology, materials science Python Libraries:

• gemmi: gemmi.cif.read_file('file.cif')
• PyCifRW: CifFile.ReadCif('file.cif')
• Biopython: Bio.PDB.MMCIFParser() EDA Approach:
• Data completeness check
• Resolution and quality metrics
• Unit cell parameter analysis
• Symmetry group validation
• Atomic displacement parameters
• R-factors and validation metrics

.mol - MDL Molfile

Description: Chemical structure file format by MDL/Accelrys Typical Data: 2D/3D coordinates, atom types, bond orders, charges Use Cases: Chemical database storage, cheminformatics, drug design Python Libraries:

• RDKit: Chem.MolFromMolFile('file.mol')
• Open Babel: pybel.readfile('mol', 'file.mol')
• ChemoPy: For descriptor calculation EDA Approach:
• Molecular property calculation (MW, logP, TPSA)
• Functional group analysis
• Ring system detection
• Stereochemistry validation
• 2D/3D coordinate consistency
• Valence and charge validation

.mol2 - Tripos Mol2

Description: Complete 3D molecular structure format with atom typing Typical Data: Coordinates, SYBYL atom types, bond types, charges, substructures Use Cases: Molecular docking, QSAR studies, drug discovery Python Libraries:

• RDKit: Chem.MolFromMol2File('file.mol2')
• Open Babel: pybel.readfile('mol2', 'file.mol2')
• MDAnalysis: Can parse mol2 topology EDA Approach:
• Atom type distribution
• Partial charge analysis
• Bond type statistics
• Substructure identification
• Conformational analysis
• Energy minimization status check

.sdf - Structure Data File

Description: Multi-structure file format with associated data Typical Data: Multiple molecular structures with properties/annotations Use Cases: Chemical databases, virtual screening, compound libraries Python Libraries:

• RDKit: Chem.SDMolSupplier('file.sdf')
• Open Babel: pybel.readfile('sdf', 'file.sdf')
• PandasTools (RDKit): For DataFrame integration EDA Approach:
• Dataset size and diversity metrics
• Property distribution analysis (MW, logP, etc.)
• Structural diversity (Tanimoto similarity)
• Missing data assessment
• Outlier detection in properties
• Scaffold analysis

.xyz - XYZ Coordinates

Description: Simple Cartesian coordinate format Typical Data: Atom types and 3D coordinates Use Cases: Quantum chemistry, geometry optimization, molecular dynamics Python Libraries:

• ASE: ase.io.read('file.xyz')
• Open Babel: pybel.readfile('xyz', 'file.xyz')
• cclib: For parsing QM outputs with xyz EDA Approach:
• Geometry analysis (bond lengths, angles, dihedrals)
• Center of mass calculation
• Moment of inertia
• Molecular size metrics
• Coordinate validation
• Symmetry detection

.smi / .smiles - SMILES String

Description: Line notation for chemical structures Typical Data: Text representation of molecular structure Use Cases: Chemical databases, literature mining, data exchange Python Libraries:

• RDKit: Chem.MolFromSmiles(smiles)
• Open Babel: Can parse SMILES
• DeepChem: For ML on SMILES EDA Approach:
• SMILES syntax validation
• Descriptor calculation from SMILES
• Fingerprint generation
• Substructure searching
• Tautomer enumeration
• Stereoisomer handling

.pdbqt - AutoDock PDBQT

Description: Modified PDB format for AutoDock docking Typical Data: Coordinates, partial charges, atom types for docking Use Cases: Molecular docking, virtual screening Python Libraries:

• Meeko: For PDBQT preparation
• Open Babel: Can read PDBQT
• ProDy: Limited PDBQT support EDA Approach:
• Charge distribution analysis
• Rotatable bond identification
• Atom type validation
• Coordinate quality check
• Hydrogen placement validation
• Torsion definition analysis

.mae - Maestro Format

Description: Schrödinger's proprietary molecular structure format Typical Data: Structures, properties, annotations from Schrödinger suite Use Cases: Drug discovery, molecular modeling with Schrödinger tools Python Libraries:

• schrodinger.structure: Requires Schrödinger installation
• Custom parsers for basic reading EDA Approach:
• Property extraction and analysis
• Structure quality metrics
• Conformer analysis
• Docking score distributions
• Ligand efficiency metrics

.gro - GROMACS Coordinate File

Description: Molecular structure file for GROMACS MD simulations Typical Data: Atom positions, velocities, box vectors Use Cases: Molecular dynamics simulations, GROMACS workflows Python Libraries:

• MDAnalysis: Universe('file.gro')
• MDTraj: mdtraj.load_gro('file.gro')
• GromacsWrapper: For GROMACS integration EDA Approach:
• System composition analysis
• Box dimension validation
• Atom position distribution
• Velocity distribution (if present)
• Density calculation
• Solvation analysis

Computational Chemistry Output Formats

.log - Gaussian Log File

Description: Output from Gaussian quantum chemistry calculations Typical Data: Energies, geometries, frequencies, orbitals, populations Use Cases: QM calculations, geometry optimization, frequency analysis Python Libraries:

• cclib: cclib.io.ccread('file.log')
• GaussianRunPack: For Gaussian workflows
• Custom parsers with regex EDA Approach:
• Convergence analysis
• Energy profile extraction
• Vibrational frequency analysis
• Orbital energy levels
• Population analysis (Mulliken, NBO)
• Thermochemistry data extraction

.out - Quantum Chemistry Output

Description: Generic output file from various QM packages Typical Data: Calculation results, energies, properties Use Cases: QM calculations across different software Python Libraries:

• cclib: Universal parser for QM outputs
• ASE: Can read some output formats EDA Approach:
• Software-specific parsing
• Convergence criteria check
• Energy and gradient trends
• Basis set and method validation
• Computational cost analysis

.wfn / .wfx - Wavefunction Files

Description: Wavefunction data for quantum chemical analysis Typical Data: Molecular orbitals, basis sets, density matrices Use Cases: Electron density analysis, QTAIM analysis Python Libraries:

• Multiwfn: Interface via Python
• Horton: For wavefunction analysis
• Custom parsers for specific formats EDA Approach:
• Orbital population analysis
• Electron density distribution
• Critical point analysis (QTAIM)
• Molecular orbital visualization
• Bonding analysis

.fchk - Gaussian Formatted Checkpoint

Description: Formatted checkpoint file from Gaussian Typical Data: Complete wavefunction data, results, geometry Use Cases: Post-processing Gaussian calculations Python Libraries:

• cclib: Can parse fchk files
• GaussView Python API (if available)
• Custom parsers EDA Approach:
• Wavefunction quality assessment
• Property extraction
• Basis set information
• Gradient and Hessian analysis
• Natural orbital analysis

.cube - Gaussian Cube File

Description: Volumetric data on a 3D grid Typical Data: Electron density, molecular orbitals, ESP on grid Use Cases: Visualization of volumetric properties Python Libraries:

• cclib: cclib.io.ccread('file.cube')
• ase.io: ase.io.read('file.cube')
• pyquante: For cube file manipulation EDA Approach:
• Grid dimension and spacing analysis
• Value distribution statistics
• Isosurface value determination
• Integration over volume
• Comparison between different cubes

Molecular Dynamics Formats

.dcd - Binary Trajectory

Description: Binary trajectory format (CHARMM, NAMD) Typical Data: Time series of atomic coordinates Use Cases: MD trajectory analysis Python Libraries:

• MDAnalysis: Universe(topology, 'traj.dcd')
• MDTraj: mdtraj.load_dcd('traj.dcd', top='topology.pdb')
• PyTraj (Amber): Limited support EDA Approach:
• RMSD/RMSF analysis
• Trajectory length and frame count
• Coordinate range and drift
• Periodic boundary handling
• File integrity check
• Time step validation

.xtc - Compressed Trajectory

Description: GROMACS compressed trajectory format Typical Data: Compressed coordinates from MD simulations Use Cases: Space-efficient MD trajectory storage Python Libraries:

• MDAnalysis: Universe(topology, 'traj.xtc')
• MDTraj: mdtraj.load_xtc('traj.xtc', top='topology.pdb') EDA Approach:
• Compression ratio assessment
• Precision loss evaluation
• RMSD over time
• Structural stability metrics
• Sampling frequency analysis

.trr - GROMACS Trajectory

Description: Full precision GROMACS trajectory Typical Data: Coordinates, velocities, forces from MD Use Cases: High-precision MD analysis Python Libraries:

• MDAnalysis: Full support
• MDTraj: Can read trr files
• GromacsWrapper EDA Approach:
• Full system dynamics analysis
• Energy conservation check (with velocities)
• Force analysis
• Temperature and pressure validation
• System equilibration assessment

.nc / .netcdf - Amber NetCDF Trajectory

Description: Network Common Data Form trajectory Typical Data: MD coordinates, velocities, forces Use Cases: Amber MD simulations, large trajectory storage Python Libraries:

• MDAnalysis: NetCDF support
• PyTraj: Native Amber analysis
• netCDF4: Low-level access EDA Approach:
• Metadata extraction
• Trajectory statistics
• Time series analysis
• Replica exchange analysis
• Multi-dimensional data extraction

.top - GROMACS Topology

Description: Molecular topology for GROMACS Typical Data: Atom types, bonds, angles, force field parameters Use Cases: MD simulation setup and analysis Python Libraries:

• ParmEd: parmed.load_file('system.top')
• MDAnalysis: Can parse topology
• Custom parsers for specific fields EDA Approach:
• Force field parameter validation
• System composition
• Bond/angle/dihedral distribution
• Charge neutrality check
• Molecule type enumeration

.psf - Protein Structure File (CHARMM)

Description: Topology file for CHARMM/NAMD Typical Data: Atom connectivity, types, charges Use Cases: CHARMM/NAMD MD simulations Python Libraries:

• MDAnalysis: Native PSF support
• ParmEd: Can read PSF files EDA Approach:
• Topology validation
• Connectivity analysis
• Charge distribution
• Atom type statistics
• Segment analysis

.prmtop - Amber Parameter/Topology

Description: Amber topology and parameter file Typical Data: System topology, force field parameters Use Cases: Amber MD simulations Python Libraries:

• ParmEd: parmed.load_file('system.prmtop')
• PyTraj: Native Amber support EDA Approach:
• Force field completeness
• Parameter validation
• System size and composition
• Periodic box information
• Atom mask creation for analysis

.inpcrd / .rst7 - Amber Coordinates

Description: Amber coordinate/restart file Typical Data: Atomic coordinates, velocities, box info Use Cases: Starting coordinates for Amber MD Python Libraries:

• ParmEd: Works with prmtop
• PyTraj: Amber coordinate reading EDA Approach:
• Coordinate validity
• System initialization check
• Box vector validation
• Velocity distribution (if restart)
• Energy minimization status

Spectroscopy and Analytical Data

.jcamp / .jdx - JCAMP-DX

Description: Joint Committee on Atomic and Molecular Physical Data eXchange Typical Data: Spectroscopic data (IR, NMR, MS, UV-Vis) Use Cases: Spectroscopy data exchange and archiving Python Libraries:

• jcamp: jcamp.jcamp_reader('file.jdx')
• nmrglue: For NMR JCAMP files
• Custom parsers for specific subtypes EDA Approach:
• Peak detection and analysis
• Baseline correction assessment
• Signal-to-noise calculation
• Spectral range validation
• Integration analysis
• Comparison with reference spectra

.mzML - Mass Spectrometry Markup Language

Description: Standard XML format for mass spectrometry data Typical Data: MS/MS spectra, chromatograms, metadata Use Cases: Proteomics, metabolomics, mass spectrometry workflows Python Libraries:

• pymzml: pymzml.run.Reader('file.mzML')
• pyteomics: pyteomics.mzml.read('file.mzML')
• MSFileReader wrappers EDA Approach:
• Scan count and types
• MS level distribution
• Retention time range
• m/z range and resolution
• Peak intensity distribution
• Data completeness
• Quality control metrics

.mzXML - Mass Spectrometry XML

Description: Open XML format for MS data Typical Data: Mass spectra, retention times, peak lists Use Cases: Legacy MS data, metabolomics Python Libraries:

• pymzml: Can read mzXML
• pyteomics.mzxml
• lxml for direct XML parsing EDA Approach:
• Similar to mzML
• Version compatibility check
• Conversion quality assessment
• Peak picking validation

.raw - Vendor Raw Data

Description: Proprietary instrument data files (Thermo, Bruker, etc.) Typical Data: Raw instrument signals, unprocessed data Use Cases: Direct instrument data access Python Libraries:

• pymsfilereader: For Thermo RAW files
• ThermoRawFileParser: CLI wrapper
• Vendor-specific APIs (Thermo, Bruker Compass) EDA Approach:
• Instrument method extraction
• Raw signal quality
• Calibration status
• Scan function analysis
• Chromatographic quality metrics

.d - Agilent Data Directory

Description: Agilent's data folder structure Typical Data: LC-MS, GC-MS data and metadata Use Cases: Agilent instrument data processing Python Libraries:

• agilent-reader: Community tools
• Chemstation Python integration
• Custom directory parsing EDA Approach:
• Directory structure validation
• Method parameter extraction
• Signal file integrity
• Calibration curve analysis
• Sequence information extraction

.fid - NMR Free Induction Decay

Description: Raw NMR time-domain data Typical Data: Time-domain NMR signal Use Cases: NMR processing and analysis Python Libraries:

• nmrglue: nmrglue.bruker.read_fid('fid')
• nmrstarlib: For NMR-STAR files EDA Approach:
• Signal decay analysis
• Noise level assessment
• Acquisition parameter validation
• Apodization function selection
• Zero-filling optimization
• Phasing parameter estimation

.ft - NMR Frequency-Domain Data

Description: Processed NMR spectrum Typical Data: Frequency-domain NMR data Use Cases: NMR analysis and interpretation Python Libraries:

• nmrglue: Comprehensive NMR support
• pyNMR: For processing EDA Approach:
• Peak picking and integration
• Chemical shift calibration
• Multiplicity analysis
• Coupling constant extraction
• Spectral quality metrics
• Reference compound identification

.spc - Spectroscopy File

Description: Thermo Galactic spectroscopy format Typical Data: IR, Raman, UV-Vis spectra Use Cases: Spectroscopic data from various instruments Python Libraries:

• spc: spc.File('file.spc')
• Custom parsers for binary format EDA Approach:
• Spectral resolution
• Wavelength/wavenumber range
• Baseline characterization
• Peak identification
• Derivative spectra calculation

Chemical Database Formats

.inchi - International Chemical Identifier

Description: Text identifier for chemical substances Typical Data: Layered chemical structure representation Use Cases: Chemical database keys, structure searching Python Libraries:

• RDKit: Chem.MolFromInchi(inchi)
• Open Babel: InChI conversion EDA Approach:
• InChI validation
• Layer analysis
• Stereochemistry verification
• InChI key generation
• Structure round-trip validation

.cdx / .cdxml - ChemDraw Exchange

Description: ChemDraw drawing file format Typical Data: 2D chemical structures with annotations Use Cases: Chemical drawing, publication figures Python Libraries:

• RDKit: Can import some CDXML
• Open Babel: Limited support
• ChemDraw Python API (commercial) EDA Approach:
• Structure extraction
• Annotation preservation
• Style consistency
• 2D coordinate validation

.cml - Chemical Markup Language

Description: XML-based chemical structure format Typical Data: Chemical structures, reactions, properties Use Cases: Semantic chemical data representation Python Libraries:

• RDKit: CML support
• Open Babel: Good CML support
• lxml: For XML parsing EDA Approach:
• XML schema validation
• Namespace handling
• Property extraction
• Reaction scheme analysis
• Metadata completeness

.rxn - MDL Reaction File

Description: Chemical reaction structure file Typical Data: Reactants, products, reaction arrows Use Cases: Reaction databases, synthesis planning Python Libraries:

• RDKit: Chem.ReactionFromRxnFile('file.rxn')
• Open Babel: Reaction support EDA Approach:
• Reaction balancing validation
• Atom mapping analysis
• Reagent identification
• Stereochemistry changes
• Reaction classification

.rdf - Reaction Data File

Description: Multi-reaction file format Typical Data: Multiple reactions with data Use Cases: Reaction databases Python Libraries:

• RDKit: RDF reading capabilities
• Custom parsers EDA Approach:
• Reaction yield statistics
• Condition analysis
• Success rate patterns
• Reagent frequency analysis

Computational Output and Data

.hdf5 / .h5 - Hierarchical Data Format

Description: Container for scientific data arrays Typical Data: Large arrays, metadata, hierarchical organization Use Cases: Large dataset storage, computational results Python Libraries:

• h5py: h5py.File('file.h5', 'r')
• pytables: Advanced HDF5 interface
• pandas: Can read HDF5 EDA Approach:
• Dataset structure exploration
• Array shape and dtype analysis
• Metadata extraction
• Memory-efficient data sampling
• Chunk optimization analysis
• Compression ratio assessment

.pkl / .pickle - Python Pickle

Description: Serialized Python objects Typical Data: Any Python object (molecules, dataframes, models) Use Cases: Intermediate data storage, model persistence Python Libraries:

• pickle: Built-in serialization
• joblib: Enhanced pickling for large arrays
• dill: Extended pickle support EDA Approach:
• Object type inspection
• Size and complexity analysis
• Version compatibility check
• Security validation (trusted source)
• Deserialization testing

.npy / .npz - NumPy Arrays

Description: NumPy array binary format Typical Data: Numerical arrays (coordinates, features, matrices) Use Cases: Fast numerical data I/O Python Libraries:

• numpy: np.load('file.npy')
• Direct memory mapping for large files EDA Approach:
• Array shape and dimensions
• Data type and precision
• Statistical summary (mean, std, range)
• Missing value detection
• Outlier identification
• Memory footprint analysis

.mat - MATLAB Data File

Description: MATLAB workspace data Typical Data: Arrays, structures from MATLAB Use Cases: MATLAB-Python data exchange Python Libraries:

• scipy.io: scipy.io.loadmat('file.mat')
• h5py: For v7.3 MAT files EDA Approach:
• Variable extraction and types
• Array dimension analysis
• Structure field exploration
• MATLAB version compatibility
• Data type conversion validation

.csv - Comma-Separated Values

Description: Tabular data in text format Typical Data: Chemical properties, experimental data, descriptors Use Cases: Data exchange, analysis, machine learning Python Libraries:

• pandas: pd.read_csv('file.csv')
• csv: Built-in module
• polars: Fast CSV reading EDA Approach:
• Data types inference
• Missing value patterns
• Statistical summaries
• Correlation analysis
• Distribution visualization
• Outlier detection

.json - JavaScript Object Notation

Description: Structured text data format Typical Data: Chemical properties, metadata, API responses Use Cases: Data interchange, configuration, web APIs Python Libraries:

• json: Built-in JSON support
• pandas: pd.read_json()
• ujson: Faster JSON parsing EDA Approach:
• Schema validation
• Nesting depth analysis
• Key-value distribution
• Data type consistency
• Array length statistics

.parquet - Apache Parquet

Description: Columnar storage format Typical Data: Large tabular datasets efficiently Use Cases: Big data, efficient columnar analytics Python Libraries:

• pandas: pd.read_parquet('file.parquet')
• pyarrow: Direct parquet access
• fastparquet: Alternative implementation EDA Approach:
• Column statistics from metadata
• Partition analysis
• Compression efficiency
• Row group structure
• Fast sampling for large files
• Schema evolution tracking