descripytor 0.3.1__tar.gz

descripytor-0.3.1/Getting_started_with_examples/descriptor_extraction_toolkit/config_example.json

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+{
+  "root_dir": null,
+  "feather_dir": "../feather_example",
+  "xyz_dir": "path/to/your/xyz",
+  "output_csv": "merged_features.csv",
+  "atoms_file": null,
+  "engines": {
+    "descripytor_full": {
+      "enabled": true,
+      "save_as": true,
+      "csv_file_name": "descripytor_full_features",
+      "prefix": "",
+      "atoms": {
+        "ring_vibration": [],
+        "stretch_threshold": 1600,
+        "stretching_vibration": [],
+        "bend_threshold": 3000,
+        "bending_vibration": [],
+        "center_atoms_dipole": [],
+        "dipole": [
+          [
+            23,
+            1,
+            3
+          ],
+          [
+            2,
+            1,
+            23
+          ]
+        ],
+        "charges": [
+          8,
+          1
+        ],
+        "charge_diff": [
+          [
+            8,
+            3
+          ],
+          [
+            8,
+            1
+          ]
+        ],
+        "sterimol": [
+          [
+            1,
+            23
+          ],
+          [
+            1,
+            3
+          ]
+        ],
+        "drop_atoms": [],
+        "bond_length": [
+          [
+            1,
+            2
+          ],
+          [
+            1,
+            23
+          ]
+        ],
+        "bond_angle": [
+          [
+            23,
+            1,
+            3
+          ],
+          [
+            23,
+            1,
+            2,
+            3
+          ]
+        ]
+      }
+    },
+    "descripytor_steric": {
+      "enabled": false,
+      "pairs": [
+        [
+          2,
+          19
+        ],
+        [
+          2,
+          4
+        ],
+        [
+          6,
+          5
+        ]
+      ],
+      "prefix": "steric_"
+    },
+    "xyz_sterimol": {
+      "enabled": false,
+      "pairs": [
+        [
+          6,
+          7
+        ],
+        [
+          6,
+          4
+        ]
+      ],
+      "radii": "CPK",
+      "prefix": "xyz_"
+    },
+    "xyz_geometry": {
+      "enabled": false,
+      "angles": [
+        [
+          2,
+          1,
+          5
+        ],
+        [
+          5,
+          1,
+          8,
+          6
+        ]
+      ],
+      "bond_lengths": [
+        [
+          1,
+          5
+        ],
+        [
+          5,
+          7
+        ]
+      ],
+      "prefix": "geom_"
+    },
+    "xyz_buried_volume": {
+      "enabled": false,
+      "metal_index": 18,
+      "radius": 3.5,
+      "prefix": "bv_"
+    },
+    "morfeus_sterimol": {
+      "enabled": false,
+      "pairs": [
+        [
+          6,
+          4
+        ]
+      ],
+      "prefix": ""
+    },
+    "morfeus_suite": {
+      "enabled": false,
+      "descriptors": [
+        "sterimol",
+        "buried_volume",
+        "sasa",
+        "dispersion"
+      ],
+      "sterimol_pairs": [
+        [
+          6,
+          4
+        ]
+      ],
+      "metal_index": null,
+      "cone_atoms": null,
+      "bv_radius": 3.5,
+      "pyramid_atoms": null,
+      "prefix": ""
+    },
+    "rdkit": {
+      "enabled": false,
+      "embed": true,
+      "prefix": "rdkit_"
+    },
+    "rdkit_fp": {
+      "enabled": false,
+      "n_bits": 256,
+      "include_usrcat": true,
+      "prefix": ""
+    },
+    "mordred": {
+      "enabled": false,
+      "ignore_3d": true,
+      "prefix": ""
+    },
+    "deepchem": {
+      "enabled": false,
+      "n_bits": 256,
+      "prefix": ""
+    },
+    "rafbl": {
+      "enabled": false,
+      "mult": 1.2,
+      "prefix": "rafbl_"
+    },
+    "qm": {
+      "enabled": false,
+      "log_dir": "C:\\path\\to\\your\\gaussian_logs",
+      "prefix": "qm_"
+    },
+    "aqme_qdescp": {
+      "enabled": false,
+      "level": "full",
+      "atoms": [],
+      "charge": 0,
+      "mult": 1,
+      "solvent": null,
+      "xtb_opt": true,
+      "nprocs": 1,
+      "prefix": "aqme_"
+    }
+  }
+}

descripytor-0.3.1/Getting_started_with_examples/input_example.json

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+{
+    "Ring Vibration atoms - by order -> Pick one  atom from a six member ring\n example: 13": "9",
+    "Stretch Threshold": 1400,
+    "Stretching Vibration atoms- enter bonded atom pairs: \n example: 1,2 4,5": "",
+    "Bend Threshold": 1300,
+    "Bending Vibration atoms - enter atom pairs that have a common atom: \n example: 4,7": "5,6",
+    "Dipole atoms - indices for coordination transformation: \n example: 4,5,6 - origin, y-axis, new xy plane": "1,2,19 20,19,27",
+    "charges values - Insert atoms to show charge: \n example: 1,2,3,4": "3,5,11,12,4,6,20,21,22,7",
+    "charge_diff - Insert atoms to show charge difference: \n example: 1,2 3,4": "3,5 11,12",
+    "Sterimol atoms - Primary axis along: \n example: 7,8": "1,4 4,1",
+    "Bond_length - Atom pairs to calculate difference: \n example: 1,2 4,5": "1,2 4,7",
+    "Bond_angle - Atom triplets to calculate difference: \n example: 1,2,3 4,5,6": "8,7,4,1 1,2,19"
+}

descripytor-0.3.1/LICENSE

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+MIT License
+
+Copyright (c) 2026 Eden Specktor
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

descripytor-0.3.1/M1_pre_calculations/esp_grid_driver.py

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+"""
+Command line driver for cylindrical ESP sampling, called by esp_grid_job.sh.
+
+Split into a write step and a read step because xtb runs between them. The
+geometry is rotated into the Sterimol frame BEFORE xtb sees it, and the rotated
+geometry is what gets submitted: the potential is a scalar field, so rotating
+the molecule does not change it, and having xtb and the grid share one frame
+removes any chance of the grid being expressed in different axes than the
+structure it is meant to sample.
+"""
+
+import argparse
+import pickle
+
+import pandas as pd
+
+from M2_data_extractor.extractor_utils.esp_grid_utils import (
+    angular_moments,
+    build_cylindrical_grid,
+    read_xtb_esp,
+    write_esp_coord,
+)
+from M2_data_extractor.extractor_utils.sterimol_utils import (
+    preform_coordination_transformation,
+)
+from utils.help_functions import get_df_from_file
+
+
+def write_step(args) -> None:
+    xyz_df = get_df_from_file(args.xyz)
+    xyz_df[['x', 'y', 'z']] = xyz_df[['x', 'y', 'z']].astype(float)
+
+    base_atoms = [int(i) for i in args.base_atoms.split(',')] if args.base_atoms else None
+    framed = preform_coordination_transformation(xyz_df, indices=base_atoms,
+                                                 origin=args.origin)
+
+    grid = build_cylindrical_grid(framed, n_phi=args.n_phi, n_axial=args.n_axial,
+                                  probe_offset=args.probe_offset, radii=args.radii)
+    n_points = write_esp_coord(grid, args.coord)
+
+    # The frame the grid lives in is the frame xtb must be given.
+    with open(args.framed_xyz, 'w') as handle:
+        handle.write(f'{len(framed)}\n')
+        handle.write('rotated into the Sterimol frame for ESP sampling\n')
+        for _, row in framed.iterrows():
+            handle.write(f'{row["atom"]:<3s} {row["x"]:>15.8f} '
+                         f'{row["y"]:>15.8f} {row["z"]:>15.8f}\n')
+
+    with open(args.grid, 'wb') as handle:
+        pickle.dump(grid, handle)
+
+    print(f'wrote {n_points} grid points to {args.coord} '
+          f'({args.n_axial} levels x {args.n_phi} azimuths)')
+
+
+def read_step(args) -> None:
+    with open(args.grid, 'rb') as handle:
+        grid = pickle.load(handle)
+
+    # Raises if the point count or the coordinates disagree, which is how a
+    # stale esp_coord surfaces as an error instead of as quiet wrong numbers.
+    sampled = read_xtb_esp(grid, args.esp)
+    sampled.to_csv(args.out, index=False)
+
+    moments = angular_moments(sampled, beta=args.beta)
+    moments.to_csv(args.moments, index=False)
+
+    # |Z| near zero means the field has no angular structure to align, so it is
+    # worth seeing before any descriptor built on the phases is believed.
+    summary = moments[['Z_S_1', 'Z_S_2', 'Z_E_1', 'Z_E_2']].abs().mean()
+    print(f'sampled {len(sampled)} points; mean |Z|: '
+          + ', '.join(f'{k}={v:.3f}' for k, v in summary.items()))
+
+
+def main() -> None:
+    parser = argparse.ArgumentParser(description=__doc__)
+    sub = parser.add_subparsers(dest='step', required=True)
+
+    write = sub.add_parser('write', help='build the grid and write esp_coord')
+    write.add_argument('--xyz', required=True)
+    write.add_argument('--grid', default='grid.pkl')
+    write.add_argument('--coord', default='esp_coord')
+    write.add_argument('--framed-xyz', default='framed.xyz')
+    write.add_argument('--base-atoms', default=None,
+                       help='comma separated indices defining the Sterimol frame')
+    write.add_argument('--origin', default=None)
+    write.add_argument('--n-phi', type=int, default=36)
+    write.add_argument('--n-axial', type=int, default=20)
+    write.add_argument('--probe-offset', type=float, default=0.5)
+    write.add_argument('--radii', default='bondi', choices=['bondi', 'CPK'])
+    write.set_defaults(func=write_step)
+
+    read = sub.add_parser('read', help='attach xtb_esp.dat to the grid')
+    read.add_argument('--grid', default='grid.pkl')
+    read.add_argument('--esp', default='xtb_esp.dat')
+    read.add_argument('--out', required=True)
+    read.add_argument('--moments', required=True)
+    read.add_argument('--beta', type=float, default=1.0)
+    read.set_defaults(func=read_step)
+
+    args = parser.parse_args()
+    args.func(args)
+
+
+if __name__ == '__main__':
+    main()

descripytor-0.3.1/M1_pre_calculations/main.py

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+import sys
+import os
+sys.path.append(os.path.dirname(os.path.abspath(__file__)))
+from utils.constants import *
+from utils.file_handlers import *
+from M1_pre_calculations.outwards_senders import *
+
+from typing import List, Tuple
+
+class Module1Handler:
+    """
+    A handler class for managing molecular calculations using Gaussian input files.
+
+    Attributes:
+        names_list (List[str]): List of molecule names extracted from the CSV file.
+        identifier_list (List[str]): List of molecular identifiers (e.g., SMILES strings).
+        working_dir (str): Directory path for working with files.
+        smiles_list (List[str]): List of SMILES strings, representing molecules.
+        inital_xyz_list (List[str]): List of file paths or data for initial XYZ coordinates.
+        calculation_method (str): Method of calculation, e.g., 'gaussian'.
+    """
+
+    def __init__(self, id_csv_filepath: str, working_dir: str = None, calculation_method: str = 'gaussian'):
+        """
+        Initializes the Module1Handler with necessary parameters.
+
+        Args:
+            id_csv_filepath (str): File path to the CSV file containing molecular identifiers.
+            working_dir (str, optional): Working directory for file operations. Defaults to the current directory.
+            calculation_method (str): The method of calculation to be used. Defaults to 'gaussian'.
+        """
+                  
+
+        
+        self.names_list, self.identifier_list = process_identifiers_csv_file(id_csv_filepath)
+        self.working_dir =os.path.dirname(id_csv_filepath) if working_dir is None else working_dir
+        self.smiles_list = self.identifier_list  # Update this if the identifier isn't SMILES
+        self.inital_xyz_list = smiles_to_coordinates(self.identifier_list)
+        self.calculation_method = calculation_method
+
+    def make_gaussian_input(self) -> None:
+        """
+        Generates Gaussian input files from the initial XYZ list.
+        """
+        xyz_files_list_to_gaussian_files(self.inital_xyz_list)
+
+    def submit_to_calculation(self) -> None:
+        """
+        Submits the generated Gaussian input for calculation.
+        """
+        submit_to_calculation(self.calculation_method)
+
+    def execute_full_operation(self) -> None:
+        """
+        Executes the full operation from generating Gaussian input to submitting for calculation.
+        """
+        self.make_gaussian_input()
+        self.submit_to_calculation()
+
+if __name__ == '__main__':
+    csv_filepath = r'smiles_list.csv'  # Replace with get_csv_filepath() if necessary
+    calculation_method = 'gaussian'
+    module_handler = Module1Handler(csv_filepath, calculation_method)
+    module_handler.execute_full_operation()

descripytor-0.3.1/M1_pre_calculations/outwards_senders.py

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+import sys
+import os
+sys.path.append(os.path.dirname(os.path.abspath(__file__)))
+#lib imports
+from utils.constants import LinuxCommands
+from utils.file_handlers import *
+
+from typing import List, Optional
+
+def run_gaussian_calculation(xyz_filename: str) -> None:
+    """
+    Placeholder for running a Gaussian calculation.
+
+    Args:
+        xyz_filename (str): The filename of the XYZ file.
+    """
+    pass
+
+def run_xtb_calcuation(xyz_filename: str, detailed_input: Optional[str] = None) -> None:
+    """
+    Runs an xTB calculation on a given XYZ file with optional detailed input.
+
+    Args:
+        xyz_filename (str): The filename of the XYZ file.
+        detailed_input (str, optional): Detailed input string for the xTB calculation. Defaults to None.
+    """
+    command = LinuxCommands.XTB_INPUT_PREFIX.value + detailed_input + ' ' + xyz_filename + LinuxCommands.XTB_SUFIX.value if detailed_input else LinuxCommands.XTB_PREFIX.value + xyz_filename + LinuxCommands.XTB_SUFIX.value
+    os.system(command)
+
+def run_crest_calculation(xyz_filename: str, detailed_input: Optional[str] = None) -> None:
+    """
+    Runs a CREST calculation on a given XYZ file with optional detailed input.
+
+    Args:
+        xyz_filename (str): The filename of the XYZ file.
+        detailed_input (str, optional): Detailed input string for the CREST calculation. Defaults to None.
+    """
+    command = LinuxCommands.CREST_INPUT_PREFIX.value + detailed_input + ' ' + xyz_filename + LinuxCommands.CREST_SUFIX.value if detailed_input else LinuxCommands.CREST_PREFIX.value + xyz_filename + LinuxCommands.CREST_SUFIX.value
+    os.system(command)
+
+def submit_to_gaussian_calculation(path=None) -> None:
+    """
+    Submits files to Gaussian calculation. Assumes .com files are located in the 'com' directory.
+    """
+    os.chdir(path) if path else os.chdir(os.getcwd())
+    os.system(LinuxCommands.COPY.value + ' ' + LinuxCommands.GAUSS_SUFIX.value + ' .')
+    for file in os.listdir():
+        if file.endswith('.com'):
+            output_name = file.split('.')[0] + '.log'
+            os.system(f'./g16 {file} {output_name} -q m')
+    os.remove('g16')
+    os.chdir('..')
+
+def submit_to_xtb_calculation(files_to_send: List[str]) -> str:
+    """
+    Submits files to xTB calculation.
+
+    Args:
+        files_to_send (List[str]): List of file names to be sent for xTB calculation.
+
+    Returns:
+        str: Path to the output folder.
+    """
+    output_folder_filepath = ''
+    # Implementation for xTB calculation submission
+    return output_folder_filepath
+
+def submit_to_crest_calculation(files_to_send: List[str]) -> str:
+    """
+    Submits files to CREST calculation.
+
+    Args:
+        files_to_send (List[str]): List of file names to be sent for CREST calculation.
+
+    Returns:
+        str: Path to the output folder.
+    """
+    output_folder_filepath = ''
+    # Implementation for CREST calculation submission
+    return output_folder_filepath
+
+def submit_to_calculation(calculation_method: str = 'gaussian') -> Optional[str]:
+    """
+    Submits files to a specified calculation method.
+
+    Args:
+        calculation_method (str): The calculation method to use. Defaults to 'gaussian'.
+
+    Returns:
+        Optional[str]: Path to the output folder, if applicable.
+    """
+    if calculation_method == 'gaussian':
+        return submit_to_gaussian_calculation()
+    elif calculation_method == 'xtb':
+        return submit_to_xtb_calculation([])
+    elif calculation_method == 'crest':
+        return submit_to_crest_calculation([])
+    return None

descripytor-0.3.1/M1_pre_calculations/pipeline/__init__.py

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+"""SMILES -> numbered structures -> chained cluster stages (GOAT, UMA, xTB, ORCA, Gaussian).
+
+    from M1_pre_calculations.pipeline import load, build_all, submit, status, retry, watch, fetch
+    p = load("protocol.json")
+    build_all(p); submit(p)
+
+See docs/PIPELINE.md.
+"""
+from .adopt import adopt, permutation, read_sources
+from .build import BuildError, build_all, build_one
+from .cluster import ClusterError, Remote, fetch, plan_lines, reset, retry, status, submit, summarize, watch
+from .protocol import Protocol, ProtocolError, load
+from .stages import render_all, render_stage