t1t2ne 0.0.2.dev0__tar.gz

t1t2ne-0.0.2.dev0/LICENSE.txt

@@ -0,0 +1,68 @@
+		      GNU GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+                            Preamble
+
+  The GNU General Public License is a free, copyleft license for
+software and other kinds of works.
+
+[...]
+
+                        (Full standard GPL v3 text omitted for brevity.
+                         Download the complete version from:
+                         https://www.gnu.org/licenses/gpl-3.0.txt )
+
+                    PROGRAM-SPECIFIC INFORMATION
+
+Program name: t1t2ne
+Author: Enrico Ravera, Francesco Bruno, and Letizia Fiorucci
+Version: 0.0.2
+Year: 2026
+
+This program is distributed under the terms of the GNU General Public
+License version 3 or (at your option) any later version.
+
+===============================================================================
+                      *** IMPORTANT – LIABILITY DISCLAIMER ***
+===============================================================================
+
+This software (t1t2ne) calculates technical parameters for the acquisition
+of Nuclear Magnetic Resonance (NMR) experiments.
+
+The use of certain parameters suggested or generated by this program may,
+under some conditions, cause:
+
+- physical damage to the NMR spectrometer
+- overheating of probes or amplifiers
+- destruction of expensive electronic components
+- data loss or interruption of long acquisitions
+
+The author and all contributors DISCLAIM ANY AND ALL LIABILITY
+for any direct or indirect damage, economic or material, arising from
+the use (correct or incorrect) of parameters generated by this software.
+
+NO AUTOMATIC HARDWARE SAFETY CHECK is implemented in this software.
+The warnings present in the program are for informational purposes only
+and do not replace critical and responsible evaluation by the user.
+
+The end user is solely responsible for the safety of the hardware and
+for the scientific correctness of the parameters used.
+
+By using this program, you expressly accept these terms and acknowledge
+that you are aware of the associated risks.
+
+===============================================================================
+
+The program is provided "AS IS", WITHOUT ANY WARRANTY OF ANY KIND,
+express or implied, including but not limited to the implied warranties
+of merchantability or fitness for a particular purpose. See the GNU GPL v3
+for full details.
+
+For the complete text of the license, refer to:
+https://www.gnu.org/licenses/gpl-3.0.txt
+
+End of license.

t1t2ne-0.0.2.dev0/PKG-INFO

@@ -0,0 +1,25 @@
+Metadata-Version: 2.4
+Name: t1t2ne
+Version: 0.0.2.dev0
+Project-URL: Homepage, https://github.com/enricoravera/t1ttune
+Project-URL: Repository, https://github.com/enricoravera/t1ttune.git
+Project-URL: Documentation, https://t1ttune.readthedocs.io
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE.txt
+Requires-Dist: klassez>=0.1.0
+Requires-Dist: numpy
+Requires-Dist: scipy
+Requires-Dist: lmfit
+Requires-Dist: numdifftools
+Requires-Dist: seaborn
+Requires-Dist: nmrglue
+Requires-Dist: matplotlib>=3.8
+Requires-Dist: csaps
+Dynamic: license-file
+
+# **T1-T2-ne**
+
+This software computes the optimal delays for protein dynamics experiments.
+
+Full documentation is available at [https://t1ttune.readthedocs.io/en/latest/](https://t1ttune.readthedocs.io/en/latest/).

t1t2ne-0.0.2.dev0/README.md

@@ -0,0 +1,5 @@
+# **T1-T2-ne**
+
+This software computes the optimal delays for protein dynamics experiments.
+
+Full documentation is available at [https://t1ttune.readthedocs.io/en/latest/](https://t1ttune.readthedocs.io/en/latest/).

t1t2ne-0.0.2.dev0/pyproject.toml

@@ -0,0 +1,40 @@
+[build-system]
+requires = ["setuptools>=68", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "t1t2ne"
+version = "0.0.2.dev0"
+description = ""
+requires-python = ">=3.10"
+dependencies = [
+    'klassez>=0.1.0',
+    'numpy',
+    'scipy',
+    'lmfit',
+    'numdifftools',
+    'seaborn',
+    'nmrglue',
+    'matplotlib>=3.8',
+    'csaps',
+]
+
+[project.urls]
+Homepage = 'https://github.com/enricoravera/t1ttune'
+Repository = 'https://github.com/enricoravera/t1ttune.git'
+Documentation = 'https://t1ttune.readthedocs.io'
+
+[tool.setuptools.packages.find]
+where = ['.']
+include = ['t1t2ne*']
+
+[tool.setuptools.package-data]
+t1ttune = ['*.txt', '*.md', '*.yaml']
+
+[project.readme]
+file = "README.md"
+content-type = "text/markdown"
+
+[project.scripts]
+t1ttune = "t1t2ne.cli:main"
+

t1t2ne-0.0.2.dev0/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+

t1t2ne-0.0.2.dev0/t1t2ne/__init__.py

@@ -0,0 +1,17 @@
+#! /usr/bin/env python3
+
+"""
+T1Ttune package for computing the optimal parameters for protein dynamics NMR experiments.
+
+The package includes modules for computing:
+
+    * Relaxation rates (R1, R2, NOE) based on a spectral density function and the provided correlation times and order parameters.
+    * The optimal set of relaxation delays for each experiment (module `t1ttune_makelists`).
+    * The optimal number of scans for each experiment (module `t1ttune_ns`).
+    * The optimal list for setting up a TRACT experiment (module `t1ttune_setuptract`).
+    * The correlation times or order parameters from a TRACT experiment (module `t1ttune_tract`).
+            
+"""
+
+__version__ = "0.0.2.dev1"
+__author__ = "Enrico Ravera, Francesco Bruno, Letizia Fiorucci"

t1t2ne-0.0.2.dev0/t1t2ne/cli.py

@@ -0,0 +1,51 @@
+#! /usr/bin/env python3 
+
+import argparse
+import sys
+
+from .scripts.__init__ import registry
+
+
+def main():
+    # Top-level parser — mostra i sottocomandi disponibili nell'help
+    parser = argparse.ArgumentParser(
+        prog="t1ttune",
+        description="Main program. Select a subcommand to start.",
+        formatter_class=argparse.RawDescriptionHelpFormatter,
+        epilog=_build_commands_epilog(),
+    )
+
+    subparsers = parser.add_subparsers(
+        dest="command",
+        metavar="<command>",
+    )
+
+    # Registra dinamicamente ogni sottocomando trovato nel registry
+    for name, cmd in registry.items():
+        sub = subparsers.add_parser(
+            name,
+            help=cmd.SHORT_HELP,           # mostrato in: M --help
+            description=cmd.DESCRIPTION,   # mostrato in: M T1 --help
+            formatter_class=argparse.RawDescriptionHelpFormatter,
+        )
+        cmd.add_arguments(sub)             # ogni comando aggiunge i propri argomenti
+
+    # Se invocato senza sottocomando → mostra help
+    if len(sys.argv) == 1:
+        parser.print_help()
+        sys.exit(0)
+
+    args = parser.parse_args()
+    registry[args.command].run(args)
+
+
+def _build_commands_epilog() -> str:
+    """Costruisce la sezione descrittiva dei comandi per l'help globale."""
+    if not registry:
+        return ""
+    lines = ["Available commands:"]
+    for name, cmd in registry.items():
+        lines.append(f"  {name:<12} {cmd.SHORT_HELP}")
+    lines.append("")
+    lines.append("Use 't1ttune <command> --help' for details on each command.")
+    return "\n".join(lines)

t1t2ne-0.0.2.dev0/t1t2ne/scripts/__init__.py

@@ -0,0 +1,3 @@
+#! /usr/bin/env python3
+
+from .create_registry import registry

t1t2ne-0.0.2.dev0/t1t2ne/scripts/base.py

@@ -0,0 +1,25 @@
+#! /usr/bin/env python3
+
+import argparse
+from abc import ABC, abstractmethod
+
+
+class BaseCommand(ABC):
+    # Testo breve mostrato nell'elenco di `M --help`
+    SHORT_HELP: str = "(nessuna descrizione)"
+
+    # Testo esteso mostrato in `M <comando> --help`
+    DESCRIPTION: str = ""
+
+    @staticmethod
+    @abstractmethod
+    def add_arguments(parser: argparse.ArgumentParser) -> None:
+        """Aggiunge gli argomenti specifici di questo comando al parser."""
+        ...
+
+    @staticmethod
+    @abstractmethod
+    def run(args: argparse.Namespace) -> None:
+        """Esegue la logica del comando."""
+        ...
+

t1t2ne-0.0.2.dev0/t1t2ne/scripts/create_registry.py

@@ -0,0 +1,26 @@
+#! /usr/bin/env python3
+
+"""
+Registry dei sottocomandi.
+
+"""
+
+from t1t2ne.scripts.t1t2ne_configure import ConfigureCmd
+from t1t2ne.scripts.t1t2ne_makelists import MakeListsCmd
+from t1t2ne.scripts.t1t2ne_setuptract import SetupTractCmd
+from t1t2ne.scripts.t1t2ne_tract import TractCmd
+from t1t2ne.scripts.t1t2ne_ns import NSCmd
+from t1t2ne.scripts.t1t2ne_interactive import InteractiveCmd
+from t1t2ne.scripts.t1t2ne_solventpre import SPREListsCmd
+
+registry = {
+    "makelists": MakeListsCmd,
+    "solventpre": SPREListsCmd,
+    #"shuttle": ShuttleCmd,
+    "setuptract": SetupTractCmd,    
+    "configure": ConfigureCmd,
+    "ns": NSCmd,    
+    "tract": TractCmd,
+    "interactive": InteractiveCmd,
+}
+