Skip to content

PSVS Parser Module

parse_psvs_summary(text)

Parse the text summary from a PSVS validation report to extract key metrics.

Extracts
  • Verify3D score
  • PROCHECK G-factors (phi/psi and all-atom)
  • MolProbity Clashscore

Parameters:

Name Type Description Default
text str

The content of the PSVS summary file.

 required

Returns:

Type Description
dict

A dictionary of extracted metrics.
Source code in torsiontuner/psvs_parser.py 
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
def parse_psvs_summary(text: str) -> dict:
    """
    Parse the text summary from a PSVS validation report to extract key metrics.

    Extracts:
        - Verify3D score
        - PROCHECK G-factors (phi/psi and all-atom)
        - MolProbity Clashscore

    Args:
        text: The content of the PSVS summary file.

    Returns:
        A dictionary of extracted metrics.
    """
    results = {}

    # Regex patterns for PSVS 1.5 standard output
    patterns = {
        "verify3d": r"Verify3D\s*\(expected\s*>\s*-?[\d\.]+\):\s*(-?[\d\.]+)",
        "procheck_phi_psi": (
            r"PROCHECK\s*G-factor\s*\(phi/psi\)\s*\(expected\s*>\s*-?[\d\.]+\):\s*(-?[\d\.]+)"
        ),
        "procheck_all": (
            r"PROCHECK\s*G-factor\s*\(all-atom\)\s*\(expected\s*>\s*-?[\d\.]+\):\s*(-?[\d\.]+)"
        ),
        "clashscore": (r"MolProbity\s*clashscore\s*\(expected\s*<\s*-?[\d\.]+\):\s*(-?[\d\.]+)"),
    }

    for key, pattern in patterns.items():
        match = re.search(pattern, text)
        if match:
            results[key] = float(match.group(1))

    return results