mimicpy 0.2.0__py3-none-any.whl → 0.3.0__py3-none-any.whl

mimicpy/utils/elements.py

@@ -1,6 +1,6 @@
 #
 #    MiMiCPy: Python Based Tools for MiMiC
-#    Copyright (C) 2020-2021 Bharath Raghavan,
+#    Copyright (C) 2020-2023 Bharath Raghavan,
 #                            Florian Schackert
 #
 #    This file is part of MiMiCPy.

mimicpy/utils/errors.py

@@ -1,6 +1,6 @@
 #
 #    MiMiCPy: Python Based Tools for MiMiC
-#    Copyright (C) 2020-2021 Bharath Raghavan,
+#    Copyright (C) 2020-2023 Bharath Raghavan,
 #                            Florian Schackert
 #
 #    This file is part of MiMiCPy.

mimicpy/utils/file_handler.py

@@ -1,6 +1,6 @@
 #
 #    MiMiCPy: Python Based Tools for MiMiC
-#    Copyright (C) 2020-2021 Bharath Raghavan,
+#    Copyright (C) 2020-2023 Bharath Raghavan,
 #                            Florian Schackert
 #
 #    This file is part of MiMiCPy.

mimicpy/utils/strings.py

@@ -1,6 +1,6 @@
 #
 #    MiMiCPy: Python Based Tools for MiMiC
-#    Copyright (C) 2020-2021 Bharath Raghavan,
+#    Copyright (C) 2020-2023 Bharath Raghavan,
 #                            Florian Schackert
 #
 #    This file is part of MiMiCPy.

mimicpy-0.3.0.dist-info/METADATA

@@ -0,0 +1,156 @@
+Metadata-Version: 2.4
+Name: mimicpy
+Version: 0.3.0
+Summary: Companion library to the MiMiC framework for input preparation.
+Home-page: https://gitlab.com/mimic-project/mimicpy
+Author: Bharath Raghavan, Florian K. Schackert, Sachin Shivakumar
+Author-email: b.raghavan@fz-juelich.de
+License: GNU Lesser General Public License v3 or later (LGPLv3+)
+Project-URL: Issues, https://gitlab.com/mimic-project/mimicpy/issues
+Project-URL: User Support, https://gitlab.com/mimic-project/user-support
+Project-URL: Documentation, https://mimic-project.org/
+Platform: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: GNU Lesser General Public License v3 or later (LGPLv3+)
+Classifier: Operating System :: OS Independent
+Classifier: Topic :: Scientific/Engineering :: Physics
+Requires-Python: >=3.5,<3.12
+Description-Content-Type: text/markdown
+License-File: COPYING
+License-File: COPYING.LESSER
+Requires-Dist: numpy>=1.12.0
+Requires-Dist: pandas>=0.24.0
+Requires-Dist: h5py>=3.0.0
+Requires-Dist: mdanalysis>=2.0
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: license
+Dynamic: license-file
+Dynamic: platform
+Dynamic: project-url
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
+
+# MiMiCPy
+MiMiCPy is the companion library to the MiMiC framework for streamline preparation of input files. It includes a suite of command line tools and plugins for PyMOL/VMD. Visit the [MiMiC homepage](https://mimic-project.org/) for more details and documentation.
+
+## Requirements
+
+### Python
+- Python >= 3.5, < 3.12 (Python 3.11 and below)
+
+### Core Dependencies
+- pandas >= 0.24.0
+- numpy >= 1.12.0
+
+### Force Matching Module
+The force matching module requires additional dependencies:
+- h5py >= 3.0.0
+- MDAnalysis >= 2.0
+- GROMACS (must be installed and accessible in the system PATH)
+
+### Optional
+- PyMOL (for PrepQM plugin) - tested with version 2.3.4
+- VMD (for PrepQM plugin) - tested with version 1.9.4a38
+
+## Installation
+To install, run the following command:
+
+```
+pip install mimicpy
+```
+
+The PrepQM plugins for PyMOL and/or VMD can be optionally installed by running:
+
+```
+mimicpy_plugin_installer -pymoldir /path/to/plugin/ -vmddir /path/to/plugin/
+```
+
+The path to the plugin is usually either the path to the PyMOL/VMD installation, or the user home directory.
+
+## Demo
+A demo of atom selection for the QM region, and generation of the MiMiC-based CPMD input file using MiMiCPy is shown below.
+```console
+user@system:~$ mimicpy prepqm -top acetone.top -coords acetone.gro
+
+
+ 	                ***** MiMiCPy *****
+
+ 	 For more information type mimicpy [subcommand] --help
+
+=====> Running prepqm <=====
+
+
+**Reading topology**
+
+Cannot find path to Gromacs installation.
+Read atoms from acetone.itp.
+No atoms found in acetone.top.
+
+Some atom types had no atom numbers information.
+They were guessed as follows:
+
++---------------------+
+| Atom Type | Element |
++---------------------+
+|     c     |    C    |
++---------------------+
+|     c3    |    C    |
++---------------------+
+|     o     |    O    |
++---------------------+
+|     hc    |    H    |
++---------------------+
+
+**Reading coordinates**  |Done
+
+Please enter selection below. For more information type 'help'
+> add resname is ACT
+> q
+Using default values for maxstep and timestep
+Wrote Gromacs index file to index.ndx
+Wrote new CPMD input script to cpmd.inp
+
+=====> Done <=====
+
+```
+
+## Force Matching
+
+The force matching module in MiMiCPy automates the parameterization of molecular mechanics (MM) force field parameters by fitting to reference QM/MM data. It optimizes both non-bonded interactions (atomic charges via DRESP) and bonded interactions (bonds, angles, dihedrals) to reproduce QM forces and electrostatic properties.
+
+### Required Input Files
+
+The force matching workflow requires the following input files:
+
+- `-top`: GROMACS topology file (`.top`)
+- `-sele`: QM region selection file (`.txt` or `.dat`) - specifies which atoms are in the QM region
+- `-fmdata`: Force matching data file (`.json` or `.h5`) - contains QM/MM reference data (forces, charges, electrostatic potentials/fields)
+- `-fi`: Force matching input file (`.dat`) - configuration file with optimization parameters
+- `-trr`: GROMACS trajectory file (`.trr`) - trajectory from QM/MM simulation
+- `-ndx`: GROMACS index file (`.ndx`) - atom index groups
+- `-coords`: Coordinate file (`.gro`) - initial structure
+- `-mdp`: GROMACS MDP file (`.mdp`, optional) - MD parameters for force recalculation
+
+### Basic Usage
+
+The basic force matching command is:
+
+```console
+mimicpy fm -top system.top -sele qm_selection.txt -fmdata fm_data.json -fi fm_input.inp -trr trajectory.trr -ndx index.ndx -coords system.gro -mdp run.mdp
+```
+
+### Common Options
+
+- `-dresp`: Run only DRESP charge optimization (skip bonded parameter optimization)
+- `-opt_ff`: Run only force field parameter optimization (skip DRESP, uses existing charges)
+- `-grid_search`: Perform grid search over DRESP weight parameters (wv, we, wh)
+- `-ff`: Path to force field data directory (optional)
+- `-gmx`: GROMACS executable name (default: `gmx`)
+- `-n_processes`: Number of processes for parallel force computation
+

mimicpy-0.3.0.dist-info/RECORD

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{mimicpy-0.2.0.dist-info → mimicpy-0.3.0.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.38.4)
+Generator: setuptools (80.10.2)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

mimicpy-0.3.0.dist-info/entry_points.txt

@@ -0,0 +1,4 @@
+[console_scripts]
+mimicpy = mimicpy.__main__:main
+mimicpy_plugin_installer = mimicpy.plugins.__main_installer__:main
+mimicpy_vmd = mimicpy.plugins.__main_vmd__:main

mimicpy-0.2.0.dist-info/METADATA

@@ -1,86 +0,0 @@
-Metadata-Version: 2.1
-Name: mimicpy
-Version: 0.2.0
-Summary: Companion library to the MiMiC framework for input preparation.
-Home-page: https://gitlab.com/MiMiC-projects/mimicpy
-Author: Bharath Raghavan, Florian K. Schackert
-Author-email: b.raghavan@fz-juelich.de
-License: GNU Lesser General Public License v3 or later (LGPLv3+)
-Project-URL: Issues, https://gitlab.com/MiMiC-projects/mimicpy/issues
-Project-URL: User Support, https://gitlab.com/MiMiC-projects/user-support
-Project-URL: Documentation, https://mimic-project.org/
-Platform: OS Independent
-Classifier: Programming Language :: Python :: 3
-Classifier: License :: OSI Approved :: GNU Lesser General Public License v3 or later (LGPLv3+)
-Classifier: Operating System :: OS Independent
-Requires-Python: >=3.5
-Description-Content-Type: text/markdown
-License-File: COPYING
-License-File: COPYING.LESSER
-Requires-Dist: numpy (>=1.12.0)
-Requires-Dist: pandas (>=0.24.0)
-
-# MiMiCPy
-MiMiCPy is the companion library to the MiMiC framework. It comes with a set of command lines tools to prepare input files. Additionally, plugins for PyMOL and VMD are also provided. Visit the [MiMiC homepage](https://mimic-project.org/) for more details.
-
-## Installation
-To install, run the following command:
-
-```
-pip install mimicpy
-```
-
-To install with PyMOL and/or VMD support, pass the plugin path to ```PYMOLDIR``` or ```VMDDIR```. This path is usually either the path to PyMOL/VMD installation folder, or the user home directory. For example,
-```
-PYMOLDIR="/home/user/" VMDDIR="/home/user/" pip install mimicpy
-```
-
-## Portability Issues
-MiMiCPy requires Python >= 3.5, pandas >= 0.24.0 and numpy >= 1.12.0. The plugins have been tested with PyMOL version 2.3.4 and VMD version 1.9.4a38, although other versions are expected to work. If any incompatibilities are found, please post an issue on [here](https://gitlab.com/MiMiC-projects/user-support).
-
-## Demo
-A demo of atom selection for the QM region, and generation of the MiMiC-based CPMD input file using MiMiCPy is shown below.
-```console
-user@system:~$ mimicpy prepqm -top acetone.top -coords acetone.gro
-
-
- 	                ***** MiMiCPy *****
-
- 	 For more information type mimicpy [subcommand] --help
-
-=====> Running prepqm <=====
-
-
-**Reading topology**
-
-Cannot find path to Gromacs installation.
-Read atoms from acetone.itp.
-No atoms found in acetone.top.
-
-Some atom types had no atom numbers information.
-They were guessed as follows:
-
-+---------------------+
-| Atom Type | Element |
-+---------------------+
-|     c     |    C    |
-+---------------------+
-|     c3    |    C    |
-+---------------------+
-|     o     |    O    |
-+---------------------+
-|     hc    |    H    |
-+---------------------+
-
-**Reading coordinates**  |Done
-
-Please enter selection below. For more information type 'help'
-> add resname is ACT
-> q
-Using default values for maxstep and timestep
-Wrote Gromacs index file to index.ndx
-Wrote new CPMD input script to cpmd.inp
-
-=====> Done <=====
-
-```

mimicpy-0.2.0.dist-info/RECORD

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-mimicpy-0.2.0.dist-info/METADATA,sha256=AMeA5fN6iTsUePCi6GZvjdKx0vsvnjMuBuPni8bmV2A,2971
-mimicpy-0.2.0.dist-info/WHEEL,sha256=2wepM1nk4DS4eFpYrW1TTqPcoGNfHhhO_i5m4cOimbo,92
-mimicpy-0.2.0.dist-info/entry_points.txt,sha256=2mJU1oYBxmxN94dwnnRstFF7ucaguvT64YRmA-R07c8,90
-mimicpy-0.2.0.dist-info/top_level.txt,sha256=0EOwttsQadsiIEMxQf3yPwXZ8OpdurbfQOsn6o-5a9Y,8
-mimicpy-0.2.0.dist-info/zip-safe,sha256=AbpHGcgLb-kRsJGnwFEktk7uzpZOCcBY74-YBdrKVGs,1
-mimicpy-0.2.0.dist-info/RECORD,,

mimicpy-0.2.0.dist-info/entry_points.txt

@@ -1,3 +0,0 @@
-[console_scripts]
-mimicpy = mimicpy.__main__:main
-mimicpy_vmd = mimicpy.__main_vmd__:main