01 - Parse and inspect one calculation¶

This notebook follows the same water_mp2.out example as the quick start. It introduces the batch -> file -> frame access pattern and shows which results are available in the source. Download the example from the documentation and save it as water_mp2.out before running the notebook.

In [1]:

from pathlib import Path

from molop import AutoParser, molopconfig

molopconfig.quiet()
sample_candidates = (
    Path("docs/assets/examples/water_mp2.out"),
    Path("../../assets/examples/water_mp2.out"),
    Path("water_mp2.out"),
)
sample_path = next((path for path in sample_candidates if path.is_file()), None)
if sample_path is None:
    raise FileNotFoundError("Place water_mp2.out beside the notebook or use the bundled example.")

batch = AutoParser(sample_path, n_jobs=1)
parsed_file = batch[0]
frame = parsed_file[-1]

print("files:", len(batch))
print("frames:", len(parsed_file))
print("format:", parsed_file.detected_format_id)
print("atoms and coordinates:", len(frame.atoms), frame.coords.shape)
print("energy (hartree):", frame.energies.total_energy.m_as("hartree"))

from pathlib import Path from molop import AutoParser, molopconfig molopconfig.quiet() sample_candidates = ( Path("docs/assets/examples/water_mp2.out"), Path("../../assets/examples/water_mp2.out"), Path("water_mp2.out"), ) sample_path = next((path for path in sample_candidates if path.is_file()), None) if sample_path is None: raise FileNotFoundError("Place water_mp2.out beside the notebook or use the bundled example.") batch = AutoParser(sample_path, n_jobs=1) parsed_file = batch[0] frame = parsed_file[-1] print("files:", len(batch)) print("frames:", len(parsed_file)) print("format:", parsed_file.detected_format_id) print("atoms and coordinates:", len(frame.atoms), frame.coords.shape) print("energy (hartree):", frame.energies.total_energy.m_as("hartree"))

files: 1
frames: 1
format: orcaout
atoms and coordinates: 3 (3, 3)
energy (hartree): -74.999374598107

The parser identifies the source as ORCA output and exposes one final frame in this example.

In [2]:

import pandas as pd
from IPython.display import display

summary = batch.to_summary_df(
    frame=-1,
    brief=False,
    flatten_columns=True,
)
with pd.option_context("display.max_columns", None, "display.max_rows", None, "display.width", 240):
    display(summary)

import pandas as pd from IPython.display import display summary = batch.to_summary_df( frame=-1, brief=False, flatten_columns=True, ) with pd.option_context("display.max_columns", None, "display.max_rows", None, "display.width", 240): display(summary)

	DiskStorage.FilePath	DiskStorage.FileFormat	General.Charge	General.Multiplicity	General.CanonicalSMILES	General.NumAtoms	General.FrameID	Calc Parameter.Software	Calc Parameter.Version	Calc Parameter.Method	Calc Parameter.BasisSet	Calc Parameter.Functional	Calc Parameter.Keywords	Environment.SolventModel	Environment.Solvent	Status.IsError	Status.IsNormal	Status.IsTS	Status.IsOptimized	Energy.electronic_energy.hartree	Energy.reference_energy.hartree	Energy.mp2_energy.hartree	Energy.total_energy.hartree
0	/home/runner/work/MolOP/MolOP/docs/assets/exam...	.out	0	1	O	3	0	ORCA	6.0.1	MP2	sto-3g		MP2 sto-3g	None	None	False	True	False	False	-74.999375	-74.963574	-74.999375	-74.999375

Scientific result containers are optional. Check a container before using its fields.

In [3]:

if frame.energies and frame.energies.total_energy is not None:
    print(frame.energies.total_energy.m_as("eV"))

print("vibrations available:", frame.vibrations is not None)

if frame.energies and frame.energies.total_energy is not None: print(frame.energies.total_energy.m_as("eV")) print("vibrations available:", frame.vibrations is not None)

-2040.8369503966658
vibrations available: False

Accessing rdmol provides a molecular graph and records the topology reconstruction status.

In [4]:

mol = frame.rdmol
print("bonds:", mol.GetNumBonds())
print("topology status:", frame.topology_reconstruction_status)

mol = frame.rdmol print("bonds:", mol.GetNumBonds()) print("topology status:", frame.topology_reconstruction_status)

bonds: 2
topology status: succeeded