mutadock 2.2.0__py3-none-any.whl

mutadock/__init__.py

@@ -0,0 +1,30 @@
+################################################################################
+#                           PROJECT INFORMATION                                #
+#                              Name: MUTADOCK                                  #
+#                           Author: Naisarg Patel                              #
+#                                                                              #
+#       Copyright (C) 2026 Naisarg Patel (https://github.com/naisarg14)        #
+#                                                                              #
+#          Project: https://github.com/naisarg14/mutadock                      #
+#                                                                              #
+#   This program is free software; you can redistribute it and/or modify it    #
+#  under the terms of the GNU General Public License version 3 as published    #
+#  by the Free Software Foundation.                                            #
+#                                                                              #
+#  This program is distributed in the hope that it will be useful, but         #
+#  WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY  #
+#  or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License    #
+#  for more details.                                                           #
+################################################################################
+
+"""MUTADOCK — mutation studies and receptor-ligand docking.
+
+Top-level package exposing two subpackages:
+
+* :mod:`mutadock.mutation` — amino-acid substitution analysis (mutation CSVs,
+  ddG calculations, mutant PDB generation via PyRosetta).
+* :mod:`mutadock.docking` — AutoDock Vina integration for receptor/ligand
+  preparation and batch docking workflows.
+"""
+
+__version__ = "2.2.0"

mutadock/data/BLOSUM62

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+#  Matrix made by matblas from blosum62.iij
+#  * column uses minimum score
+#  BLOSUM Clustered Scoring Matrix in 1/2 Bit Units
+#  Blocks Database = /data/blocks_5.0/blocks.dat
+#  Cluster Percentage: >= 62
+#  Entropy =   0.6979, Expected =  -0.5209
+   A  R  N  D  C  Q  E  G  H  I  L  K  M  F  P  S  T  W  Y  V  B  Z  X  *
+A  4 -1 -2 -2  0 -1 -1  0 -2 -1 -1 -1 -1 -2 -1  1  0 -3 -2  0 -2 -1  0 -4
+R -1  5  0 -2 -3  1  0 -2  0 -3 -2  2 -1 -3 -2 -1 -1 -3 -2 -3 -1  0 -1 -4
+N -2  0  6  1 -3  0  0  0  1 -3 -3  0 -2 -3 -2  1  0 -4 -2 -3  3  0 -1 -4
+D -2 -2  1  6 -3  0  2 -1 -1 -3 -4 -1 -3 -3 -1  0 -1 -4 -3 -3  4  1 -1 -4
+C  0 -3 -3 -3  9 -3 -4 -3 -3 -1 -1 -3 -1 -2 -3 -1 -1 -2 -2 -1 -3 -3 -2 -4
+Q -1  1  0  0 -3  5  2 -2  0 -3 -2  1  0 -3 -1  0 -1 -2 -1 -2  0  3 -1 -4
+E -1  0  0  2 -4  2  5 -2  0 -3 -3  1 -2 -3 -1  0 -1 -3 -2 -2  1  4 -1 -4
+G  0 -2  0 -1 -3 -2 -2  6 -2 -4 -4 -2 -3 -3 -2  0 -2 -2 -3 -3 -1 -2 -1 -4
+H -2  0  1 -1 -3  0  0 -2  8 -3 -3 -1 -2 -1 -2 -1 -2 -2  2 -3  0  0 -1 -4
+I -1 -3 -3 -3 -1 -3 -3 -4 -3  4  2 -3  1  0 -3 -2 -1 -3 -1  3 -3 -3 -1 -4
+L -1 -2 -3 -4 -1 -2 -3 -4 -3  2  4 -2  2  0 -3 -2 -1 -2 -1  1 -4 -3 -1 -4
+K -1  2  0 -1 -3  1  1 -2 -1 -3 -2  5 -1 -3 -1  0 -1 -3 -2 -2  0  1 -1 -4
+M -1 -1 -2 -3 -1  0 -2 -3 -2  1  2 -1  5  0 -2 -1 -1 -1 -1  1 -3 -1 -1 -4
+F -2 -3 -3 -3 -2 -3 -3 -3 -1  0  0 -3  0  6 -4 -2 -2  1  3 -1 -3 -3 -1 -4
+P -1 -2 -2 -1 -3 -1 -1 -2 -2 -3 -3 -1 -2 -4  7 -1 -1 -4 -3 -2 -2 -1 -2 -4
+S  1 -1  1  0 -1  0  0  0 -1 -2 -2  0 -1 -2 -1  4  1 -3 -2 -2  0  0  0 -4
+T  0 -1  0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1  1  5 -2 -2  0 -1 -1  0 -4
+W -3 -3 -4 -4 -2 -2 -3 -2 -2 -3 -2 -3 -1  1 -4 -3 -2 11  2 -3 -4 -3 -2 -4
+Y -2 -2 -2 -3 -2 -1 -2 -3  2 -1 -1 -2 -1  3 -3 -2 -2  2  7 -1 -3 -2 -1 -4
+V  0 -3 -3 -3 -1 -2 -2 -3 -3  3  1 -2  1 -1 -2 -2  0 -3 -1  4 -3 -2 -1 -4
+B -2 -1  3  4 -3  0  1 -1  0 -3 -4  0 -3 -3 -2  0 -1 -4 -3 -3  4  1 -1 -4
+Z -1  0  0  1 -3  3  4 -2  0 -3 -3  1 -1 -3 -1  0 -1 -3 -2 -2  1  4 -1 -4
+X  0 -1 -1 -1 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -2  0  0 -2 -1 -1 -1 -1 -1 -4
+* -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4  1

mutadock/data/PAM250

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+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 250 substitution matrix, scale = ln(2)/3 = 0.231049
+#
+# Expected score = -0.844, Entropy = 0.354 bits
+#
+# Lowest score = -8, Highest score = 17
+#
+   A  R  N  D  C  Q  E  G  H  I  L  K  M  F  P  S  T  W  Y  V  B  Z  X  *
+A  2 -2  0  0 -2  0  0  1 -1 -1 -2 -1 -1 -3  1  1  1 -6 -3  0  0  0  0 -8
+R -2  6  0 -1 -4  1 -1 -3  2 -2 -3  3  0 -4  0  0 -1  2 -4 -2 -1  0 -1 -8
+N  0  0  2  2 -4  1  1  0  2 -2 -3  1 -2 -3  0  1  0 -4 -2 -2  2  1  0 -8
+D  0 -1  2  4 -5  2  3  1  1 -2 -4  0 -3 -6 -1  0  0 -7 -4 -2  3  3 -1 -8
+C -2 -4 -4 -5 12 -5 -5 -3 -3 -2 -6 -5 -5 -4 -3  0 -2 -8  0 -2 -4 -5 -3 -8
+Q  0  1  1  2 -5  4  2 -1  3 -2 -2  1 -1 -5  0 -1 -1 -5 -4 -2  1  3 -1 -8
+E  0 -1  1  3 -5  2  4  0  1 -2 -3  0 -2 -5 -1  0  0 -7 -4 -2  3  3 -1 -8
+G  1 -3  0  1 -3 -1  0  5 -2 -3 -4 -2 -3 -5  0  1  0 -7 -5 -1  0  0 -1 -8
+H -1  2  2  1 -3  3  1 -2  6 -2 -2  0 -2 -2  0 -1 -1 -3  0 -2  1  2 -1 -8
+I -1 -2 -2 -2 -2 -2 -2 -3 -2  5  2 -2  2  1 -2 -1  0 -5 -1  4 -2 -2 -1 -8
+L -2 -3 -3 -4 -6 -2 -3 -4 -2  2  6 -3  4  2 -3 -3 -2 -2 -1  2 -3 -3 -1 -8
+K -1  3  1  0 -5  1  0 -2  0 -2 -3  5  0 -5 -1  0  0 -3 -4 -2  1  0 -1 -8
+M -1  0 -2 -3 -5 -1 -2 -3 -2  2  4  0  6  0 -2 -2 -1 -4 -2  2 -2 -2 -1 -8
+F -3 -4 -3 -6 -4 -5 -5 -5 -2  1  2 -5  0  9 -5 -3 -3  0  7 -1 -4 -5 -2 -8
+P  1  0  0 -1 -3  0 -1  0  0 -2 -3 -1 -2 -5  6  1  0 -6 -5 -1 -1  0 -1 -8
+S  1  0  1  0  0 -1  0  1 -1 -1 -3  0 -2 -3  1  2  1 -2 -3 -1  0  0  0 -8
+T  1 -1  0  0 -2 -1  0  0 -1  0 -2  0 -1 -3  0  1  3 -5 -3  0  0 -1  0 -8
+W -6  2 -4 -7 -8 -5 -7 -7 -3 -5 -2 -3 -4  0 -6 -2 -5 17  0 -6 -5 -6 -4 -8
+Y -3 -4 -2 -4  0 -4 -4 -5  0 -1 -1 -4 -2  7 -5 -3 -3  0 10 -2 -3 -4 -2 -8
+V  0 -2 -2 -2 -2 -2 -2 -1 -2  4  2 -2  2 -1 -1 -1  0 -6 -2  4 -2 -2 -1 -8
+B  0 -1  2  3 -4  1  3  0  1 -2 -3  1 -2 -4 -1  0  0 -5 -3 -2  3  2 -1 -8
+Z  0  0  1  3 -5  3  3  0  2 -2 -3  0 -2 -5  0  0 -1 -6 -4 -2  2  3 -1 -8
+X  0 -1  0 -1 -3 -1 -1 -1 -1 -1 -1 -1 -1 -2 -1  0  0 -4 -2 -1 -1 -1 -1 -8
+* -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8  1

mutadock/docking/__init__.py

@@ -0,0 +1,57 @@
+################################################################################
+#                           PROJECT INFORMATION                                #
+#                              Name: MUTADOCK                                  #
+#                           Author: Naisarg Patel                              #
+#                                                                              #
+#       Copyright (C) 2026 Naisarg Patel (https://github.com/naisarg14)        #
+#                                                                              #
+#          Project: https://github.com/naisarg14/mutadock                      #
+#                                                                              #
+#   This program is free software; you can redistribute it and/or modify it    #
+#  under the terms of the GNU General Public License version 3 as published    #
+#  by the Free Software Foundation.                                            #
+#                                                                              #
+#  This program is distributed in the hope that it will be useful, but         #
+#  WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY  #
+#  or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License    #
+#  for more details.                                                           #
+################################################################################
+
+"""Docking package — AutoDock Vina integration for MUTADOCK.
+
+Provides helpers for receptor/ligand preparation, docking execution,
+result parsing, and batch docking workflows via the :mod:`np_docking` entry
+point.  Custom exceptions are exported from :mod:`exceptions`.
+"""
+
+import logging
+
+# Configure logging
+logging.basicConfig(
+    level=logging.INFO, format="%(asctime)s - %(name)s - %(levelname)s - %(message)s"
+)
+logger = logging.getLogger(__name__)
+
+if __name__ == "__main__":
+    logger.info(
+        """
+################################################################################
+#                           PROJECT INFORMATION                                #
+#                              Name: MUTADOCK                                  #
+#                           Author: Naisarg Patel                              #
+#                                                                              #
+#       Copyright (C) 2026 Naisarg Patel (https://github.com/naisarg14)        #
+#                                                                              #
+#          Project: https://github.com/naisarg14/mutadock                      #
+#                                                                              #
+#   This program is free software; you can redistribute it and/or modify it    #
+#  under the terms of the GNU General Public License version 3 as published    #
+#  by the Free Software Foundation.                                            #
+#                                                                              #
+#  This program is distributed in the hope that it will be useful, but         #
+#  WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY  #
+#  or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License    #
+#  for more details.                                                           #
+################################################################################
+"""
+    )

mutadock/docking/exceptions.py

@@ -0,0 +1,22 @@
+class DockingError(Exception):
+    """Base exception for the docking package."""
+
+
+class PDBFileError(DockingError):
+    """Raised when a PDB file cannot be read or parsed."""
+
+
+class ConfigError(DockingError):
+    """Raised when a Vina config file cannot be read or parsed."""
+
+
+class LigandPreparationError(DockingError):
+    """Raised when ligand PDBQT preparation fails."""
+
+
+class ReceptorPreparationError(DockingError):
+    """Raised when receptor PDBQT preparation fails."""
+
+
+class DockingRunError(DockingError):
+    """Raised when an AutoDock Vina run fails."""