docs(cli): Add complete configuration file template for SCREAM++ CLI

Author: TKanX

docs/cli/config.template.toml

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+# =============================================================================
+# SCREAM++ Complete Configuration File Template
+# =============================================================================
+#
+# This file contains ALL available settings for a `scream place` run.
+# - To use a setting, uncomment it and modify its value.
+# - Settings that are commented out will use the application's default value,
+#   which is shown in the comment for reference.
+# - For detailed explanations, please refer to the full user manual.
+
+# -----------------------------------------------------------------------------
+# [forcefield] - Energy function and forcefield parameters
+# -----------------------------------------------------------------------------
+[forcefield]
+
+# s-factor for the flat-bottom potential. This is a critical parameter for accuracy.
+# Its optimal value is dependent on the diversity of the chosen rotamer library.
+# Default: 1.1 (optimized for rmsd-1.0 libraries)
+s-factor = 1.1
+
+# Path or logical name for the main forcefield parameter file.
+# Logical names: 'exp-6@0.4', 'lj-12-6@0.4', etc.
+# Default: "exp-6@0.4"
+# forcefield-path = "exp-6@0.4"
+
+# Path or logical name for the flat-bottom delta parameter file.
+# The diversity (e.g., "rmsd-1.0") should match the rotamer library.
+# Default: "rmsd-1.0"
+# delta-params-path = "rmsd-1.0"
+
+# [Optional] Rules for applying custom weights to energy components between
+# different types of atoms (Atom Roles: Backbone, Sidechain, Ligand, Water, Other).
+# By default, all interactions have a weight of 1.0.
+# [[forcefield.energy-weights.rules]]
+# groups = ["Backbone", "Sidechain"]
+# weights = { vdw = 1.0, coulomb = 1.0, hbond = 1.0 }
+
+# -----------------------------------------------------------------------------
+# [sampling] - Side-chain conformation sampling
+# -----------------------------------------------------------------------------
+[sampling]
+
+# Path or logical name for the rotamer library.
+# The diversity (e.g., "rmsd-1.0") should match `delta-params-path`.
+# Logical names: 'charmm@rmsd-1.0', 'amber@rmsd-1.0', etc.
+# Default: "charmm@rmsd-1.0"
+# rotamer-library = "charmm@rmsd-1.0"
+
+# -----------------------------------------------------------------------------
+# [optimization] - Algorithm control
+# -----------------------------------------------------------------------------
+[optimization]
+
+# The number of lowest-energy, unique solutions to generate and save.
+# Default: 1
+num-solutions = 1
+
+# Maximum number of iterations for the main clash resolution algorithm.
+# Default: 100
+# max-iterations = 100
+
+# Whether to include the input structure's original side-chain conformation as
+# a candidate solution during the optimization.
+# Default: true
+# include-input-conformation = true
+
+# Number of refinement iterations (singlet optimization) to run after the
+# main loop converges. Set to 0 to disable.
+# Default: 2
+# final-refinement-iterations = 2
+
+# [optimization.convergence]
+# --- Convergence Criteria ---
+# The algorithm is considered converged if the best energy improves by less than
+# this threshold over a 'patience' number of iterations.
+# Default: 0.01 (kcal/mol)
+# energy-threshold = 0.01
+
+# The number of consecutive iterations with insufficient energy improvement
+# before the optimization loop terminates.
+# Default: 5
+# patience-iterations = 5
+
+# [optimization.simulated-annealing]
+# --- [Optional] Simulated Annealing ---
+# To enable, uncomment this entire section. This can help the algorithm escape
+# local energy minima but will increase runtime.
+# initial-temperature = 5.0
+# final-temperature = 0.1
+# cooling-rate = 0.9
+# steps-per-temperature = 100
+
+# -----------------------------------------------------------------------------
+# [residues-to-optimize] - Defines which residues to modify
+# -----------------------------------------------------------------------------
+[residues-to-optimize]
+
+# Choose ONE of the following types: "all", "list", or "ligand-binding-site".
+
+# TYPE 1: Optimize all residues.
+# This is the default if the section is omitted.
+type = "all"
+
+# TYPE 2: Optimize a specific list of residues.
+# `include` specifies which residues to target. If `include` is empty, it defaults to all residues.
+# `exclude` specifies which residues to ignore, even if they are in the `include` selection.
+# type = "list"
+# include = [
+#   { chain-id = 'A', residue-number = 25 },
+#   { chain-id = 'A', residue-number = 101 },
+# ]
+# exclude = []
+
+# TYPE 3: Optimize residues within a certain radius of a ligand.
+# The radius is measured from any heavy atom of the ligand to any heavy atom of a protein residue.
+# type = "ligand-binding-site"
+# radius-angstroms = 5.0
+# [residues-to-optimize.ligand-residue]
+# chain-id = 'X'
+# residue-number = 999
+
+# -----------------------------------------------------------------------------
+# Global Settings
+# -----------------------------------------------------------------------------
+
+# Path or logical name for the residue topology registry.
+# In most cases, the default is sufficient.
+# Default: "default"
+# topology-registry-path = "default"