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

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Files changed (53) hide show
  1. mimicpy/__init__.py +1 -1
  2. mimicpy/__main__.py +726 -2
  3. mimicpy/_authors.py +2 -2
  4. mimicpy/_version.py +2 -2
  5. mimicpy/coords/__init__.py +1 -1
  6. mimicpy/coords/base.py +1 -1
  7. mimicpy/coords/cpmdgeo.py +1 -1
  8. mimicpy/coords/gro.py +1 -1
  9. mimicpy/coords/pdb.py +1 -1
  10. mimicpy/core/__init__.py +1 -1
  11. mimicpy/core/prepare.py +3 -3
  12. mimicpy/core/selector.py +1 -1
  13. mimicpy/force_matching/__init__.py +34 -0
  14. mimicpy/force_matching/bonded_forces.py +628 -0
  15. mimicpy/force_matching/compare_top.py +809 -0
  16. mimicpy/force_matching/dresp.py +435 -0
  17. mimicpy/force_matching/nonbonded_forces.py +32 -0
  18. mimicpy/force_matching/opt_ff.py +2114 -0
  19. mimicpy/force_matching/qm_region.py +1960 -0
  20. mimicpy/plugins/__main_installer__.py +76 -0
  21. mimicpy/{__main_vmd__.py → plugins/__main_vmd__.py} +2 -2
  22. mimicpy/plugins/pymol.py +56 -0
  23. mimicpy/plugins/vmd.tcl +78 -0
  24. mimicpy/scripts/__init__.py +1 -1
  25. mimicpy/scripts/cpmd.py +1 -1
  26. mimicpy/scripts/fm_input.py +265 -0
  27. mimicpy/scripts/fmdata.py +120 -0
  28. mimicpy/scripts/mdp.py +1 -1
  29. mimicpy/scripts/ndx.py +1 -1
  30. mimicpy/scripts/script.py +1 -1
  31. mimicpy/topology/__init__.py +1 -1
  32. mimicpy/topology/itp.py +603 -35
  33. mimicpy/topology/mpt.py +1 -1
  34. mimicpy/topology/top.py +254 -15
  35. mimicpy/topology/topol_dict.py +233 -4
  36. mimicpy/utils/__init__.py +1 -1
  37. mimicpy/utils/atomic_numbers.py +1 -1
  38. mimicpy/utils/constants.py +17 -3
  39. mimicpy/utils/elements.py +1 -1
  40. mimicpy/utils/errors.py +1 -1
  41. mimicpy/utils/file_handler.py +1 -1
  42. mimicpy/utils/strings.py +1 -1
  43. mimicpy-0.3.0.dist-info/METADATA +156 -0
  44. mimicpy-0.3.0.dist-info/RECORD +50 -0
  45. {mimicpy-0.2.0.dist-info → mimicpy-0.3.0.dist-info}/WHEEL +1 -1
  46. mimicpy-0.3.0.dist-info/entry_points.txt +4 -0
  47. mimicpy-0.2.0.dist-info/METADATA +0 -86
  48. mimicpy-0.2.0.dist-info/RECORD +0 -38
  49. mimicpy-0.2.0.dist-info/entry_points.txt +0 -3
  50. {mimicpy-0.2.0.dist-info → mimicpy-0.3.0.dist-info/licenses}/COPYING +0 -0
  51. {mimicpy-0.2.0.dist-info → mimicpy-0.3.0.dist-info/licenses}/COPYING.LESSER +0 -0
  52. {mimicpy-0.2.0.dist-info → mimicpy-0.3.0.dist-info}/top_level.txt +0 -0
  53. {mimicpy-0.2.0.dist-info → mimicpy-0.3.0.dist-info}/zip-safe +0 -0
mimicpy/_authors.py CHANGED
@@ -1,6 +1,6 @@
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  #
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  # MiMiCPy: Python Based Tools for MiMiC
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- # Copyright (C) 2020-2021 Bharath Raghavan,
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+ # Copyright (C) 2020-2023 Bharath Raghavan,
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  # Florian Schackert
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  #
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  # This file is part of MiMiCPy.
@@ -19,4 +19,4 @@
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  # along with this program. If not, see <http://www.gnu.org/licenses/>.
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  #
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- __authors__ = 'Bharath Raghavan and Florian Schackert'
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+ __authors__ = 'Bharath Raghavan, Florian Schackert, Sachin Shivakumar'
mimicpy/_version.py CHANGED
@@ -1,6 +1,6 @@
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  #
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  # MiMiCPy: Python Based Tools for MiMiC
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- # Copyright (C) 2020-2021 Bharath Raghavan,
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+ # Copyright (C) 2020-2023 Bharath Raghavan,
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  # Florian Schackert
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  #
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  # This file is part of MiMiCPy.
@@ -19,4 +19,4 @@
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  # along with this program. If not, see <http://www.gnu.org/licenses/>.
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  #
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- __version__ = '0.2.0'
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+ __version__ = '0.3.0'
mimicpy/coords/__init__.py CHANGED
@@ -1,6 +1,6 @@
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  #
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  # MiMiCPy: Python Based Tools for MiMiC
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- # Copyright (C) 2020-2021 Bharath Raghavan,
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+ # Copyright (C) 2020-2023 Bharath Raghavan,
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  # Florian Schackert
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  #
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  # This file is part of MiMiCPy.
mimicpy/coords/base.py CHANGED
@@ -1,6 +1,6 @@
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  #
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  # MiMiCPy: Python Based Tools for MiMiC
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- # Copyright (C) 2020-2021 Bharath Raghavan,
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+ # Copyright (C) 2020-2023 Bharath Raghavan,
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  # Florian Schackert
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  #
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  # This file is part of MiMiCPy.
mimicpy/coords/cpmdgeo.py CHANGED
@@ -1,6 +1,6 @@
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  #
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  # MiMiCPy: Python Based Tools for MiMiC
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- # Copyright (C) 2020-2021 Bharath Raghavan,
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+ # Copyright (C) 2020-2023 Bharath Raghavan,
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  # Florian Schackert
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  #
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  # This file is part of MiMiCPy.
mimicpy/coords/gro.py CHANGED
@@ -1,6 +1,6 @@
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  #
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  # MiMiCPy: Python Based Tools for MiMiC
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- # Copyright (C) 2020-2021 Bharath Raghavan,
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+ # Copyright (C) 2020-2023 Bharath Raghavan,
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  # Florian Schackert
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  #
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  # This file is part of MiMiCPy.
mimicpy/coords/pdb.py CHANGED
@@ -1,6 +1,6 @@
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  #
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  # MiMiCPy: Python Based Tools for MiMiC
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- # Copyright (C) 2020-2021 Bharath Raghavan,
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+ # Copyright (C) 2020-2023 Bharath Raghavan,
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  # Florian Schackert
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  #
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  # This file is part of MiMiCPy.
mimicpy/core/__init__.py CHANGED
@@ -1,6 +1,6 @@
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  #
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  # MiMiCPy: Python Based Tools for MiMiC
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- # Copyright (C) 2020-2021 Bharath Raghavan,
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+ # Copyright (C) 2020-2023 Bharath Raghavan,
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  # Florian Schackert
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  #
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  # This file is part of MiMiCPy.
mimicpy/core/prepare.py CHANGED
@@ -1,6 +1,6 @@
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  #
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  # MiMiCPy: Python Based Tools for MiMiC
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- # Copyright (C) 2020-2021 Bharath Raghavan,
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+ # Copyright (C) 2020-2023 Bharath Raghavan,
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  # Florian Schackert
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  #
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  # This file is part of MiMiCPy.
@@ -53,7 +53,7 @@ class Preparation:
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  def add(self, selection=None, is_bound=False):
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  qdf = Preparation.__clean_qdf(self.selector.select(selection))
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  qdf.insert(2, 'is_bound', [int(is_bound)]*len(qdf))
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- self.__qm_atoms = self.__qm_atoms.append(qdf)
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+ self.__qm_atoms = pd.concat([self.__qm_atoms, qdf])
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  def delete(self, selection=None):
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  qdf = Preparation.__clean_qdf(self.selector.select(selection))
@@ -130,7 +130,7 @@ class Preparation:
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  pp_info = pd.read_csv(pp_info_file_name,
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  header=None,
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  names=['element','pp_name','pp_bound_name','labels','lmax','loc'],
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- delim_whitespace=True,
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+ sep=r'\s+',
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  comment='#')
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  pp_info = pp_info.set_index('element')
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  pp_info = pp_info.drop_duplicates(keep='first')
mimicpy/core/selector.py CHANGED
@@ -1,6 +1,6 @@
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  #
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  # MiMiCPy: Python Based Tools for MiMiC
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- # Copyright (C) 2020-2021 Bharath Raghavan,
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+ # Copyright (C) 2020-2023 Bharath Raghavan,
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  # Florian Schackert
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  #
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  # This file is part of MiMiCPy.
mimicpy/force_matching/__init__.py ADDED
@@ -0,0 +1,34 @@
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+ """
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+ Force matching module for MiMiCPy.
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+
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+ This module provides functionality for force matching in molecular dynamics simulations.
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+ """
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+
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+ from .qm_region import QMRegion
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+
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+ from .dresp import opt_dresp, compute_sd, get_configurations
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+ from .opt_ff import (
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+ ParameterOptimizer,
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+ get_optimize_ff_parameters,
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+ get_configurations_optff,
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+ optimization_ff,
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+ check_bond_equivalence,
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+ check_angle_equivalence,
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+ check_dihedral_equivalence
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+ )
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+
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+ __all__ = [
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+ # Classes
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+ 'ParameterOptimizer',
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+ 'QMRegion',
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+ # Functions
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+ 'get_configurations',
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+ 'get_optimize_ff_parameters',
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+ 'get_configurations_optff',
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+ 'optimization_ff',
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+ 'opt_dresp',
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+ 'compute_sd',
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+ 'check_bond_equivalence',
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+ 'check_angle_equivalence',
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+ 'check_dihedral_equivalence'
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+ ]