Merge pull request #127 from SCM-NV/scripts

Quantum dot builder removal

CHANGELOG.md

@@ -1,3 +1,9 @@
+# 08/01/2019
+
+## Removed
+*  Quantum Dots builder functionality moved to [CAT](https://github.com/BvB93/CAT)
+
+
 
 # 19/10/2018
 

README.rst

@@ -101,13 +101,6 @@ Now you are ready to use *qmflows*.
   - Once the libraries and the virtual environment are installed, you only need to type
     ``conda activate qmflows`` each time that you want to use the software.
 
-
-.. _Quantum Dots builder:
-
-Quantum Dots builder
---------------------
-An example input file (including documentation) is located in qd-example_.
-Once the path, input ligands and input cores have been specified the job can be run with ``python qd_input.py``
 
 .. _documentation: https://qmflows.readthedocs.io/en/latest/
 .. _miniconda: http://conda.pydata.org/miniconda.html
@@ -121,4 +114,3 @@ Once the path, input ligands and input cores have been specified the job can be
 .. _tutorial-qmflows: https://github.com/SCM-NV/qmflows/tree/master/jupyterNotebooks
 .. _examples: https://github.com/SCM-NV/qmflows/tree/master/src/qmflows/examples
 .. _PLAMS: https://github.com/SCM-NV/PLAMS
-.. _qd-example: https://github.com/SCM-NV/qmflows/blob/master/test/QD_input_examples

setup.py

@@ -14,7 +14,7 @@ def readme():
     description='Automation of computations in quantum chemistry',
     license='Apache 2.0',
     url='https://github.com/SCM-NV/qmflows',
-    author=['Felipe Zapata', 'Bas van Beek'],
+    author=['Felipe Zapata'],
     author_email='f.zapata@esciencecenter.nl',
     keywords='chemistry workflows simulation materials',
     long_description=readme(),
@@ -23,7 +23,6 @@ def readme():
               "qmflows.components",
               "qmflows.data",
               "qmflows.data.dictionaries",
-              "qmflows.data.coskf",
               "qmflows.examples",
               "qmflows.examples.Conditional_workflows",
               "qmflows.examples.Constrained_and_TS_optimizations",
@@ -33,7 +32,7 @@ def readme():
               "qmflows.parsers",
               "qmflows.templates"],
     package_data={
-        "qmflows": ['data/templates/*json', 'data/dictionaries/*json', 'data/coskf/*coskf']
+        "qmflows": ['data/templates/*json', 'data/dictionaries/*json']
     },
     classifiers=[
         'Intended Audience :: Science/Research',
@@ -43,7 +42,7 @@ def readme():
         'Topic :: Scientific/Engineering :: Chemistry'
     ],
     install_requires=['h5py', 'numpy', 'noodles==0.3.1', 'plams>=1.2', 'pymonad',
-                      'pyparsing', 'filelock', 'openpyxl', 'pyyaml', 'xlrd', 'scipy'],
+                      'pyparsing', 'filelock'],
     dependency_links=[
         "git+https://github.com/SCM-NV/PLAMS@master#egg=plams-1.2"],
 

src/qmflows/__init__.py

@@ -1,13 +1,6 @@
 from .components import (
     Angle, Dihedral, Distance,
-    find_first_job, select_max, select_min,
-    read_database, compare_database, write_database,
-    read_mol, set_prop, create_dir,
-    find_substructure, find_substructure_split, merge_mol, qd_int,
-    adf_connectivity, fix_h, fix_carboxyl, from_iterable,
-    check_sys_var, ams_job_mopac_sp, qd_opt, get_time,
-    optimize_ligand,
-    ligand_to_qd)
+    find_first_job, select_max, select_min)
 
 from .packages import (
     adf, cp2k, dftb, dirac, gamess, orca, run)
@@ -24,10 +17,4 @@
     'example_ADF3FDE_Cystine', 'example_ADF3FDE_Dialanine', 'example_FDE_fragments',
     'example_H2O2_TS', 'example_freqs', 'example_generic_constraints',
     'example_partial_geometry_opt', 'freq', 'geometry', 'singlepoint', 'ts', 'get_template',
-    'find_first_job', 'select_max', 'select_min',
-    'read_mol', 'set_prop', 'create_dir',
-    'find_substructure', 'find_substructure_split',
-    'merge_mol', 'qd_int', 'adf_connectivity', 'fix_h', 'fix_carboxyl', 'from_iterable',
-    'check_sys_var', 'ams_job_mopac_sp', 'qd_opt', 'get_time',
-    'optimize_ligand',
-    'ligand_to_qd']
+    'find_first_job', 'select_max', 'select_min']

src/qmflows/components/__init__.py

@@ -2,22 +2,7 @@
 from .operations import (find_first_job, select_max, select_min)
 
 from .reactivity import (Distance, Angle, Dihedral)
-from .qd_database import (read_database, compare_database, write_database)
-from .qd_import_export import (read_mol, set_prop, create_dir)
-from .qd_ams import (check_sys_var, qd_opt, ams_job_mopac_sp)
-from .qd_functions import (find_substructure, find_substructure_split,
-                           merge_mol, qd_int, adf_connectivity, fix_h,
-                           fix_carboxyl, from_iterable, get_time)
-from .qd_ligand_opt import optimize_ligand
-from .qd_ligand_rotate import ligand_to_qd
 
 __all__ = [
     'ADF3FDE_Result', 'Fragment', 'MFCC_Result', 'adf3fde', 'adf_fragmentsjob', 'mfcc',
-    'find_first_job', 'select_max', 'select_min', 'Distance', 'Angle', 'Dihedral',
-    'read_database', 'compare_database', 'write_database',
-    'read_mol', 'set_prop', 'create_dir',
-    'check_sys_var', 'qd_opt', 'ams_job_mopac_sp',
-    'find_substructure', 'find_substructure_split', 'merge_mol',
-    'qd_int', 'adf_connectivity', 'fix_h', 'fix_carboxyl', 'from_iterable', 'get_time',
-    'optimize_ligand',
-    'ligand_to_qd']
+    'find_first_job', 'select_max', 'select_min', 'Distance', 'Angle', 'Dihedral']