Fix/docker-build: Migrate to Micromamba to resolve dependency errors

[rayhanmp]

Description

This PR fixes the Docker build failure caused by dimorphite_dl==1.3.2 being unavailable on PyPI.

To address this, the Dockerfile has been refactored to use Micromamba instead of a standard Python virtual environment.

Key Changes

• Dependency Management: Switched from venv to micromamba.
• Package Source: dimorphite_dl==1.3.2, rdkit, and openmm are now installed via conda-forge, where version 1.3.2 is still available.
• Path Updates: Updated the edit_moleculekit.py script path and LD_LIBRARY_PATH to point to the new Conda environment locations.

Reasoning

The build was failing with: ERROR: Could not find a version that satisfies the requirement dimorphite_dl==1.3.2. Since the PyPI release for this specific version appears to have been removed or deprecated, switching to Conda-forge allows us to keep the version pinned as required by the workflow without introducing breaking changes. Upgrading dimorphite_dl would create additional problems because the newer versions include API changes that require code modifications.

Verification

• Docker build completes successfully locally.
• Program completes a partial charge calculation for 1alf

Closes

This PR closes issue #6