Analysis API¶

Trajectory analysis and visualization tools.

TrajAnalysis¶

Main class for MD trajectory analysis.

from prism import TrajAnalysis

analyzer = TrajAnalysis(
    topology="system.gro",
    trajectory="md.xtc",
    ligand_resname="LIG"
)

Parameters¶

topology (str): Topology file (.gro, .pdb, .tpr)
trajectory (str): Trajectory file (.xtc, .dcd, .trr)
ligand_resname (str): Ligand residue name (default: "LIG")

Methods¶

analyze_all()¶

Run complete analysis suite.

analyzer.analyze_all(output_dir="analysis_results")

Generates: - RMSD plots - RMSF per-residue - Contact maps - H-bond analysis - Interactive HTML

calc_rmsd()¶

Calculate RMSD.

rmsd = analyzer.calc_rmsd(
    selection="protein",
    reference_frame=0
)

Returns: numpy array of RMSD values (Å)

calc_rmsf()¶

Calculate RMSF.

rmsf = analyzer.calc_rmsf(selection="protein")

Returns: numpy array of RMSF values (Å)

calc_contacts()¶

Calculate protein-ligand contacts.

contacts = analyzer.calc_contacts(
    cutoff=3.5,  # Å
    scheme='closest-heavy'
)

Returns: Contact frequency array

calc_hbonds()¶

Calculate hydrogen bonds.

hbonds = analyzer.calc_hbonds(
    distance_cutoff=3.5,  # Å
    angle_cutoff=120  # degrees
)

Returns: H-bond data

calc_sasa()¶

Calculate solvent accessible surface area.

sasa = analyzer.calc_sasa(selection="resname LIG")

Returns: SASA values (nm²)

Visualization¶

visualize_trajectory()¶

Generate interactive HTML visualization.

import prism

html_file = prism.visualize_trajectory(
    trajectory="md.xtc",
    topology="system.gro",
    ligand="ligand.sdf",
    output="contacts.html"
)

Parameters: - trajectory (str): Trajectory file - topology (str): Topology file - ligand (str): Ligand structure file - output (str): Output HTML file

Returns: Path to HTML file

HTMLGenerator¶

Advanced visualization control.

from prism.analysis.visualization import HTMLGenerator

generator = HTMLGenerator(
    "trajectory.xtc",
    "topology.gro",
    "ligand.sdf"
)

generator.analyze()
generator.generate("output.html")

Trajectory Processing¶

process_trajectory()¶

Fix PBC artifacts and center system.

import prism

processed = prism.process_trajectory(
    input_trajectory="raw.dcd",
    output_trajectory="processed.xtc",
    topology_file="system.tpr",
    center_selection="Protein",
    pbc_method="mol"
)

batch_process_trajectories()¶

Process multiple trajectories.

trajectories = ["traj1.dcd", "traj2.dcd", "traj3.dcd"]

processed = prism.batch_process_trajectories(
    input_trajectories=trajectories,
    output_dir="processed",
    topology_file="system.tpr"
)

Examples¶

Basic Analysis¶

from prism import TrajAnalysis

analyzer = TrajAnalysis("system.gro", "md.xtc")

# RMSD
rmsd_protein = analyzer.calc_rmsd(selection="protein")
rmsd_ligand = analyzer.calc_rmsd(selection="resname LIG")

# Contacts
contacts = analyzer.calc_contacts()
print(f"Average contacts: {contacts.mean()}")

Complete Workflow¶

import prism

# Analyze trajectory
analyzer = prism.analyze_trajectory(
    "system.gro",
    "md.xtc",
    ligand_resname="LIG",
    output_dir="analysis"
)

# Generate visualization
prism.visualize_trajectory(
    "md.xtc",
    "system.gro",
    "ligand.sdf",
    output="interactive_contacts.html"
)