The System class represents the topology of a molecular system, containing atom-level information such as names, residue names, masses, and coordinates.
Loading Systems from_pdb System.from_pdb(path: str ) -> System
Load a molecular system from a PDB file.
A System object containing the topology and initial coordinates
from warp_md import System # Load protein structure system = System.from_pdb( "protein.pdb" ) print ( f "Loaded { system.n_atoms() } atoms" )
PDB files use Angstrom units. Coordinates are automatically stored in the appropriate format.
from_gro System.from_gro(path: str ) -> System
Load a molecular system from a GROMACS GRO file.
A System object containing the topology and initial coordinates
from warp_md import System # Load GROMACS structure system = System.from_gro( "conf.gro" )
GRO files use nanometers. Coordinates are automatically converted to Angstroms internally.
from_pdbqt System.from_pdbqt(path: str ) -> System
Load a molecular system from a PDBQT file (AutoDock format).
A System object containing the topology
from warp_md import System # Load docking structure system = System.from_pdbqt( "ligand.pdbqt" )
Selection Methods select system.select(expr: str ) -> Selection
Create a selection of atoms using a selection expression.
Selection expression using the warp-md selection language
A Selection object containing the matched atom indices
Basic Selection
Complex Selection
# Select backbone atoms backbone = system.select( "backbone" ) # Select by residue name water = system.select( "resname SOL" ) # Select by atom name ca_atoms = system.select( "name CA" )
Selections are cached internally for performance. Repeated calls with the same expression return instantly.
Supported Keywords:
name - Atom name (e.g., “CA”, “N”, “O”)resname - Residue name (e.g., “ALA”, “SOL”)resid - Residue ID or range (e.g., “1”, “10:20”)chain - Chain identifier (e.g., “A”, “B”)protein - All protein residuesbackbone - Protein backbone atoms (N, CA, C, O, OXT)
Operators:
and - Logical ANDor - Logical ORnot - Logical NOT() - Grouping
select_indices system.select_indices(indices: list[ int ]) -> Selection
Create a selection from an explicit list of atom indices.
List of zero-based atom indices
A Selection object containing the specified indices
# Select specific atoms by index indices = [ 0 , 5 , 10 , 15 ] custom_sel = system.select_indices(indices)
n_atoms Get the total number of atoms in the system.
count = system.n_atoms() print ( f "System contains { count } atoms" )
atom_table system.atom_table() -> dict
Get detailed information about all atoms as a dictionary.
Dictionary containing atom properties:
name: List of atom names (str)resname: List of residue names (str)resid: List of residue IDs (int)chain_id: List of chain IDs (int)mass: List of atomic masses (float) atoms = system.atom_table() # Access atom properties for i in range ( 10 ): print ( f "Atom { i } : { atoms[ 'name' ][i] } { atoms[ 'resname' ][i] } { atoms[ 'resid' ][i] } " ) # Get all CA atom indices ca_indices = [i for i, name in enumerate (atoms[ 'name' ]) if name == 'CA' ]
positions0 system.positions0() -> np.ndarray | None
Get the initial/reference coordinates from the topology file.
Array of shape (n_atoms, 3) containing xyz coordinates in Angstroms, or None if not available
coords = system.positions0() if coords is not None : print ( f "Initial coords shape: { coords.shape } " ) print ( f "First atom position: { coords[ 0 ] } " )
Not all file formats include coordinates. PDBQT files may return None.
Usage Example from warp_md import System, Trajectory, RgPlan # Load system system = System.from_pdb( "protein.pdb" ) print ( f "Loaded { system.n_atoms() } atoms" ) # Inspect atom information atoms = system.atom_table() print ( f "First residue: { atoms[ 'resname' ][ 0 ] } { atoms[ 'resid' ][ 0 ] } " ) # Create selections backbone = system.select( "backbone" ) ca_atoms = system.select( "name CA" ) chain_a = system.select( "chain A" ) # Use selections in analysis traj = Trajectory.open_xtc( "trajectory.xtc" , system) plan = RgPlan(ca_atoms, mass_weighted = True ) rg = plan.run(traj, system, device = "auto" ) print ( f "Computed Rg for { len (rg) } frames" )