pynmrstar 3.3.4__tar.gz → 3.3.5__tar.gz

{pynmrstar-3.3.4/pynmrstar.egg-info → pynmrstar-3.3.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pynmrstar
-Version: 3.3.4
+Version: 3.3.5
 Summary: PyNMR-STAR provides tools for reading, writing, modifying, and interacting with NMR-STAR files. Maintained by the BMRB.
 Home-page: https://github.com/uwbmrb/PyNMRSTAR
 Author: Jon Wedell
@@ -10,12 +10,12 @@ Keywords: bmrb,parser,nmr,nmrstar,biomagresbank,biological magnetic resonance ba
 Classifier: Development Status :: 6 - Mature
 Classifier: Environment :: Console
 Classifier: Programming Language :: Python :: 3 :: Only
-Classifier: Programming Language :: Python :: 3.7
 Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
 Classifier: Intended Audience :: Developers
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Natural Language :: English

{pynmrstar-3.3.4 → pynmrstar-3.3.5}/pynmrstar/_internal.py

@@ -13,7 +13,7 @@ from urllib.request import urlopen, Request
 
 import pynmrstar
 
-__version__: str = "3.3.4"
+__version__: str = "3.3.5"
 min_cnmrstar_version: str = "3.2.0"
 
 # If we have requests, open a session to reuse for the duration of the program run

{pynmrstar-3.3.4 → pynmrstar-3.3.5/pynmrstar.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pynmrstar
-Version: 3.3.4
+Version: 3.3.5
 Summary: PyNMR-STAR provides tools for reading, writing, modifying, and interacting with NMR-STAR files. Maintained by the BMRB.
 Home-page: https://github.com/uwbmrb/PyNMRSTAR
 Author: Jon Wedell
@@ -10,12 +10,12 @@ Keywords: bmrb,parser,nmr,nmrstar,biomagresbank,biological magnetic resonance ba
 Classifier: Development Status :: 6 - Mature
 Classifier: Environment :: Console
 Classifier: Programming Language :: Python :: 3 :: Only
-Classifier: Programming Language :: Python :: 3.7
 Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
 Classifier: Intended Audience :: Developers
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Natural Language :: English

{pynmrstar-3.3.4 → pynmrstar-3.3.5}/pynmrstar.egg-info/SOURCES.txt

@@ -1,5 +1,4 @@
 LICENSE
-MANIFEST.in
 README.rst
 setup.py
 c/cnmrstarmodule.c
@@ -10,7 +9,6 @@ pynmrstar/entry.py
 pynmrstar/exceptions.py
 pynmrstar/loop.py
 pynmrstar/parser.py
-pynmrstar/remove_non_nef_data.py
 pynmrstar/saveframe.py
 pynmrstar/schema.py
 pynmrstar/utils.py

{pynmrstar-3.3.4 → pynmrstar-3.3.5}/setup.py

@@ -46,12 +46,12 @@ setup(name='pynmrstar',
           'Development Status :: 6 - Mature',
           'Environment :: Console',
           'Programming Language :: Python :: 3 :: Only',
-          'Programming Language :: Python :: 3.7',
           'Programming Language :: Python :: 3.8',
           'Programming Language :: Python :: 3.9',
           'Programming Language :: Python :: 3.10',
           'Programming Language :: Python :: 3.11',
           'Programming Language :: Python :: 3.12',
+          'Programming Language :: Python :: 3.13',
           'Intended Audience :: Developers',
           'License :: OSI Approved :: MIT License',
           'Natural Language :: English',

pynmrstar-3.3.4/MANIFEST.in

@@ -1 +0,0 @@
-#recursive-include pynmrstar/unit_tests *

pynmrstar-3.3.4/pynmrstar/remove_non_nef_data.py

@@ -1,180 +0,0 @@
-#!/usr/bin/env python3
-
-import pynmrstar
-import logging
-
-
-def remove_software_specific_data(nef_file):
-    nef_tags = ['nef_nmr_meta_data', 'nef_molecular_system', 'nef_chemical_shift_list', 'nef_distance_restraint_list',
-                'nef_dihedral_restraint_list', 'nef_rdc_restraint_list', 'nef_nmr_spectrum', 'nef_peak_restraint_links',
-                'nef_related_entries', 'nef_program_script', 'nef_run_history', 'nef_sequence', 'nef_covalent_links',
-                'nef_chemical_shift', 'nef_distance_restraint', 'nef_dihedral_restraint', 'nef_rdc_restraint',
-                'nef_spectrum_dimension', 'nef_spectrum_dimension_transfer', 'nef_peak', 'nef_peak_restraint_link',
-                'audit', '_nef_program_script.program_name', '_nef_program_script.script_name',
-                '_nef_program_script.script',
-                '_nef_run_history.run_number', '_nef_run_history.program_name', '_nef_run_history.program_version',
-                '_nef_run_history.script_name', '_nef_run_history.script', '_nef_nmr_meta_data.sf_category',
-                '_nef_nmr_meta_data.sf_framecode', '_nef_nmr_meta_data.format_name',
-                '_nef_nmr_meta_data.format_version',
-                '_nef_nmr_meta_data.program_name', '_nef_nmr_meta_data.program_version',
-                '_nef_nmr_meta_data.creation_date',
-                '_nef_nmr_meta_data.uuid', '_nef_nmr_meta_data.coordinate_file_name',
-                '_nef_related_entries.database_name',
-                '_nef_related_entries.database_accession_code', '_nef_molecular_system.sf_category',
-                '_nef_molecular_system.sf_framecode', '_nef_sequence.index', '_nef_sequence.chain_code',
-                '_nef_sequence.sequence_code', '_nef_sequence.residue_name', '_nef_sequence.linking',
-                '_nef_sequence.residue_variant', '_nef_sequence.cis_peptide', '_nef_covalent_links.chain_code_1',
-                '_nef_covalent_links.sequence_code_1', '_nef_covalent_links.residue_name_1',
-                '_nef_covalent_links.atom_name_1', '_nef_covalent_links.chain_code_2',
-                '_nef_covalent_links.sequence_code_2',
-                '_nef_covalent_links.residue_name_2', '_nef_covalent_links.atom_name_2',
-                '_nef_chemical_shift_list.sf_category', '_nef_chemical_shift_list.sf_framecode',
-                '_nef_chemical_shift_list.atom_chemical_shift_units', '_nef_chemical_shift.chain_code',
-                '_nef_chemical_shift.sequence_code', '_nef_chemical_shift.residue_name',
-                '_nef_chemical_shift.atom_name', '_nef_chemical_shift.element', '_nef_chemical_shift.isotope_number',
-                '_nef_chemical_shift.value', '_nef_chemical_shift.value_uncertainty',
-                '_nef_distance_restraint_list.sf_category', '_nef_distance_restraint_list.sf_framecode',
-                '_nef_distance_restraint_list.potential_type', '_nef_distance_restraint_list.restraint_origin',
-                '_nef_distance_restraint.index', '_nef_distance_restraint.restraint_id',
-                '_nef_distance_restraint.restraint_combination_id', '_nef_distance_restraint.chain_code_1',
-                '_nef_distance_restraint.sequence_code_1', '_nef_distance_restraint.residue_name_1',
-                '_nef_distance_restraint.atom_name_1', '_nef_distance_restraint.chain_code_2',
-                '_nef_distance_restraint.sequence_code_2', '_nef_distance_restraint.residue_name_2',
-                '_nef_distance_restraint.atom_name_2', '_nef_distance_restraint.weight',
-                '_nef_distance_restraint.target_value', '_nef_distance_restraint.target_value',
-                '_nef_distance_restraint.target_value_uncertainty', '_nef_distance_restraint.lower_linear_limit',
-                '_nef_distance_restraint.lower_limit', '_nef_distance_restraint.upper_limit',
-                '_nef_distance_restraint.upper_linear_limit', '_nef_dihedral_restraint_list.sf_category',
-                '_nef_dihedral_restraint_list.sf_framecode', '_nef_dihedral_restraint_list.potential_type',
-                '_nef_dihedral_restraint_list.restraint_origin', '_nef_dihedral_restraint.index',
-                '_nef_dihedral_restraint.restraint_id', '_nef_dihedral_restraint.restraint_combination_id',
-                '_nef_dihedral_restraint.chain_code_1', '_nef_dihedral_restraint.sequence_code_1',
-                '_nef_dihedral_restraint.residue_name_1', '_nef_dihedral_restraint.atom_name_1',
-                '_nef_dihedral_restraint.chain_code_2', '_nef_dihedral_restraint.sequence_code_2',
-                '_nef_dihedral_restraint.residue_name_2', '_nef_dihedral_restraint.atom_name_2',
-                '_nef_dihedral_restraint.chain_code_3', '_nef_dihedral_restraint.sequence_code_3',
-                '_nef_dihedral_restraint.residue_name_3', '_nef_dihedral_restraint.atom_name_3',
-                '_nef_dihedral_restraint.chain_code_4', '_nef_dihedral_restraint.sequence_code_4',
-                '_nef_dihedral_restraint.residue_name_4', '_nef_dihedral_restraint.atom_name_4',
-                '_nef_dihedral_restraint.weight', '_nef_dihedral_restraint.target_value',
-                '_nef_dihedral_restraint.target_value_uncertainty', '_nef_dihedral_restraint.lower_linear_limit',
-                '_nef_dihedral_restraint.lower_limit', '_nef_dihedral_restraint.upper_limit',
-                '_nef_dihedral_restraint.upper_linear_limit', '_nef_dihedral_restraint.name',
-                '_nef_rdc_restraint_list.sf_category', '_nef_rdc_restraint_list.sf_framecode',
-                '_nef_rdc_restraint_list.potential_type', '_nef_rdc_restraint_list.restraint_origin',
-                '_nef_rdc_restraint_list.tensor_magnitude', '_nef_rdc_restraint_list.tensor_rhombicity',
-                '_nef_rdc_restraint_list.tensor_chain_code', '_nef_rdc_restraint_list.tensor_sequence_code',
-                '_nef_rdc_restraint_list.tensor_residue_name', '_nef_rdc_restraint.index',
-                '_nef_rdc_restraint.restraint_id', '_nef_rdc_restraint.restraint_combination_id',
-                '_nef_rdc_restraint.chain_code_1', '_nef_rdc_restraint.sequence_code_1',
-                '_nef_rdc_restraint.residue_name_1', '_nef_rdc_restraint.atom_name_1',
-                '_nef_rdc_restraint.chain_code_2', '_nef_rdc_restraint.sequence_code_2',
-                '_nef_rdc_restraint.residue_name_2', '_nef_rdc_restraint.atom_name_2',
-                '_nef_rdc_restraint.weight', '_nef_rdc_restraint.target_value',
-                '_nef_rdc_restraint.target_value', '_nef_rdc_restraint.target_value_uncertainty',
-                '_nef_rdc_restraint.target_value_uncertainty', '_nef_rdc_restraint.lower_linear_limit',
-                '_nef_rdc_restraint.lower_limit', '_nef_rdc_restraint.upper_limit',
-                '_nef_rdc_restraint.upper_linear_limit', '_nef_rdc_restraint.scale',
-                '_nef_rdc_restraint.distance_dependent', '_nef_nmr_spectrum.sf_category',
-                '_nef_nmr_spectrum.sf_framecode', '_nef_nmr_spectrum.num_dimensions',
-                '_nef_nmr_spectrum.chemical_shift_list', '_nef_nmr_spectrum.experiment_classification',
-                '_nef_nmr_spectrum.experiment_type', '_nef_spectrum_dimension.dimension_id',
-                '_nef_spectrum_dimension.axis_unit', '_nef_spectrum_dimension.axis_code',
-                '_nef_spectrum_dimension.spectrometer_frequency', '_nef_spectrum_dimension.spectral_width',
-                '_nef_spectrum_dimension.value_first_point', '_nef_spectrum_dimension.folding',
-                '_nef_spectrum_dimension.absolute_peak_positions', '_nef_spectrum_dimension.is_acquisition',
-                '_nef_spectrum_dimension_transfer.dimension_1', '_nef_spectrum_dimension_transfer.dimension_2',
-                '_nef_spectrum_dimension_transfer.transfer_type', '_nef_spectrum_dimension_transfer.is_indirect',
-                '_nef_peak.index', '_nef_peak.peak_id', '_nef_peak.volume',
-                '_nef_peak.volume_uncertainty', '_nef_peak.height', '_nef_peak.height_uncertainty',
-                '_nef_peak.position_1', '_nef_peak.position_uncertainty_1', '_nef_peak.position_2',
-                '_nef_peak.position_uncertainty_2', '_nef_peak.position_3', '_nef_peak.position_uncertainty_3',
-                '_nef_peak.position_4', '_nef_peak.position_uncertainty_4', '_nef_peak.position_5',
-                '_nef_peak.position_uncertainty_5', '_nef_peak.position_6', '_nef_peak.position_uncertainty_6',
-                '_nef_peak.position_7', '_nef_peak.position_uncertainty_7', '_nef_peak.position_8',
-                '_nef_peak.position_uncertainty_8', '_nef_peak.position_9', '_nef_peak.position_uncertainty_9',
-                '_nef_peak.position_10', '_nef_peak.position_uncertainty_10', '_nef_peak.position_11',
-                '_nef_peak.position_uncertainty_11', '_nef_peak.position_12', '_nef_peak.position_uncertainty_12',
-                '_nef_peak.position_13', '_nef_peak.position_uncertainty_13', '_nef_peak.position_14',
-                '_nef_peak.position_uncertainty_14', '_nef_peak.position_15', '_nef_peak.position_uncertainty_15',
-                '_nef_peak.chain_code_1', '_nef_peak.sequence_code_1', '_nef_peak.residue_name_1',
-                '_nef_peak.atom_name_1', '_nef_peak.chain_code_2', '_nef_peak.sequence_code_2',
-                '_nef_peak.residue_name_2',
-                '_nef_peak.atom_name_2', '_nef_peak.chain_code_3', '_nef_peak.sequence_code_3',
-                '_nef_peak.residue_name_3',
-                '_nef_peak.atom_name_3', '_nef_peak.chain_code_4', '_nef_peak.sequence_code_4',
-                '_nef_peak.residue_name_4',
-                '_nef_peak.atom_name_4', '_nef_peak.chain_code_5', '_nef_peak.sequence_code_5',
-                '_nef_peak.residue_name_5',
-                '_nef_peak.atom_name_5', '_nef_peak.chain_code_6', '_nef_peak.sequence_code_6',
-                '_nef_peak.residue_name_6',
-                '_nef_peak.atom_name_6', '_nef_peak.chain_code_7', '_nef_peak.sequence_code_7',
-                '_nef_peak.residue_name_7',
-                '_nef_peak.atom_name_7', '_nef_peak.chain_code_8', '_nef_peak.sequence_code_8',
-                '_nef_peak.residue_name_8',
-                '_nef_peak.atom_name_8', '_nef_peak.chain_code_9', '_nef_peak.sequence_code_9',
-                '_nef_peak.residue_name_9',
-                '_nef_peak.atom_name_9', '_nef_peak.chain_code_10', '_nef_peak.sequence_code_10',
-                '_nef_peak.residue_name_10',
-                '_nef_peak.atom_name_10', '_nef_peak.chain_code_11', '_nef_peak.sequence_code_11',
-                '_nef_peak.residue_name_11',
-                '_nef_peak.atom_name_11', '_nef_peak.chain_code_12', '_nef_peak.sequence_code_12',
-                '_nef_peak.residue_name_12',
-                '_nef_peak.atom_name_12', '_nef_peak.chain_code_13', '_nef_peak.sequence_code_13',
-                '_nef_peak.residue_name_13',
-                '_nef_peak.atom_name_13', '_nef_peak.chain_code_14', '_nef_peak.sequence_code_14',
-                '_nef_peak.residue_name_14',
-                '_nef_peak.atom_name_14', '_nef_peak.chain_code_15', '_nef_peak.sequence_code_15',
-                '_nef_peak.residue_name_15',
-                '_nef_peak.atom_name_15', '_nef_peak_restraint_links.sf_category',
-                '_nef_peak_restraint_links.sf_framecode',
-                '_nef_peak_restraint_link.nmr_spectrum_id', '_nef_peak_restraint_link.peak_id',
-                '_nef_peak_restraint_link.restraint_list_id', '_nef_peak_restraint_link.restraint_id',
-                '_audit.revision_id', '_audit.creation_date', '_audit.creation_method', '_audit.update_record']
-
-    # Suppress the parse notices, but then log everything after
-    logger = logging.getLogger('remove_non_nef_data')
-    logger.setLevel(logging.ERROR)
-    nef_data = pynmrstar.Entry.from_file(nef_file)
-    logger.setLevel(logging.DEBUG)
-
-    saveframe_index = 0
-    while saveframe_index < len(nef_data):
-        saveframe = nef_data[saveframe_index]
-        if not saveframe.category.lower().startswith('nef_'):
-            nef_data.remove_saveframe(saveframe)
-            logger.debug('Deleted entire saveframe: %s', saveframe.category)
-            continue
-
-        tags_to_remove = []
-        for tag in saveframe.tags:
-            if f'_{saveframe.category}.{tag[0]}'.lower() not in nef_tags:
-                tags_to_remove.append(tag)
-        saveframe.remove_tag(tags_to_remove)
-        logger.debug('Deleted saveframe tags: %s', tags_to_remove)
-
-        loop_index = 0
-        while loop_index < len(saveframe):
-            loop = saveframe[loop_index]
-            if not loop.category.lower().startswith('_nef'):
-                del (saveframe[loop_index])
-                logger.debug('Deleted entire loop: %s', loop.category)
-                continue
-            else:
-                for tag in loop.get_tag_names():
-                    if tag.lower() not in nef_tags:
-                        logger.debug('Deleted loop tag: %s', tag)
-                        loop.remove_tag(tag)
-            loop_index += 1
-        saveframe_index += 1
-
-    logger.debug('Finished removing saveframes/loops/tags.')
-    nef_data.remove_empty_saveframes()
-    out_file = 'cleaned.nef'
-    with open(out_file, 'w') as wstarfile:
-        wstarfile.write(str(nef_data))
-    return True
-
-
-if __name__ == "__main__":
-    remove_software_specific_data('gp78CnewHOME15_test.nef')