Function addHydrogens has a Cognitive Complexity of 186 (exceeds 5 allowed). Consider refactoring.

Open

    def addHydrogens(self, forcefield=None, pH=None, variants=None, platform=None):
        """Add missing hydrogens to the model.

        This function automatically changes compatible residues into their constant-pH variant if no variant is specified.:

• Read up
  Read up

File modeller.py has 329 lines of code (exceeds 250 allowed). Consider refactoring.

Open

# coding=utf-8
"""Pre-configured OpenMM Modeller object for use with the default protons forcefield. Modified from original source code by Peter Eastman."""

from .topology import Topology
from simtk.openmm.app import modeller

Consider simplifying this complex logical expression.

Open

                if residue.name in Modeller._residueHydrogens:
                    # Add hydrogens.  First select which variant to use.

                    spec = Modeller._residueHydrogens[residue.name]
                    variant = variants[residue.index]

Avoid deeply nested control flow statements.

Open

                        if residue.name == "ASP":
                            variant = "AS4"
                    if variant is not None and variant not in spec.variants:

Avoid deeply nested control flow statements.

Open

                        if residue.name == "GLU":
                            variant = "GL4"
                        if residue.name == "ASP":

Avoid deeply nested control flow statements.

Open

                        if (
                            removeExtraHydrogens
                            and parent.element == elem.hydrogen
                            and not any(parent.name == h.name for h in hydrogens)
                        ):

Avoid deeply nested control flow statements.

Open

                        if residue.name == "CYS":
                            # If this is part of a disulfide, use CYX.

                            sulfur = [
                                atom

Avoid deeply nested control flow statements.

Open

                        if residue.name == "HIS":
                            variant = "HIP"
                        if residue.name == "GLU":

Avoid deeply nested control flow statements.

Open

                        if (
                            atom.element == elem.oxygen
                            and len(bondedTo[index]) == 2
                            and elem.hydrogen in (a.element for a in bondedTo[index])
                        ):

Avoid deeply nested control flow statements.

Open

                        if parent in parents:
                            # Match expected hydrogens with existing ones and find which ones need to be added.

                            existing = [
                                atom