pestifer.core package

The core package of the Pestifer project. It provides the base classes and utilities for handling molecular objects, script writing, and YAML serialization. It also provides an interface to the resources, like examples, the CHARMM force field, custom TcL scripts and packages, among others.

Submodules

• pestifer.core.artifacts module
  • Artifact
    • Artifact.copy()
    • Artifact.data
    • Artifact.has_stamp()
    • Artifact.key
    • Artifact.produced_by
    • Artifact.provenance
    • Artifact.stamp()
  • ArtifactDict
    • ArtifactDict.clear()
    • ArtifactDict.filter_by_produced_by()
    • ArtifactDict.from_list()
    • ArtifactDict.get()
    • ArtifactDict.items()
    • ArtifactDict.keys()
    • ArtifactDict.pop()
    • ArtifactDict.stamp()
    • ArtifactDict.to_list()
    • ArtifactDict.update_item()
    • ArtifactDict.values()
  • ArtifactList
    • ArtifactList.append()
    • ArtifactList.extend()
    • ArtifactList.filter_by_artifact_type()
    • ArtifactList.filter_by_key()
    • ArtifactList.filter_by_produced_by()
    • ArtifactList.from_dict()
    • ArtifactList.remove()
    • ArtifactList.sort()
    • ArtifactList.stamp()
    • ArtifactList.to_dict()
  • CIFFileArtifact
    • CIFFileArtifact.description
    • CIFFileArtifact.ext
  • CSVDataFileArtifact
    • CSVDataFileArtifact.description
    • CSVDataFileArtifact.ext
  • CSVDataFileArtifactList
    • CSVDataFileArtifactList.description
  • CharmmffFileArtifact
    • CharmmffFileArtifact.description
  • CharmmffFileArtifactList
    • CharmmffFileArtifactList.append()
    • CharmmffFileArtifactList.description
    • CharmmffFileArtifactList.extend()
    • CharmmffFileArtifactList.key
  • CharmmffParFileArtifact
    • CharmmffParFileArtifact.description
    • CharmmffParFileArtifact.ext
  • CharmmffParFileArtifacts
    • CharmmffParFileArtifacts.append()
    • CharmmffParFileArtifacts.description
  • CharmmffStreamFileArtifact
    • CharmmffStreamFileArtifact.description
    • CharmmffStreamFileArtifact.ext
  • CharmmffStreamFileArtifacts
    • CharmmffStreamFileArtifacts.append()
    • CharmmffStreamFileArtifacts.description
  • CharmmffTopFileArtifact
    • CharmmffTopFileArtifact.description
    • CharmmffTopFileArtifact.ext
  • CharmmffTopFileArtifacts
    • CharmmffTopFileArtifacts.append()
    • CharmmffTopFileArtifacts.description
    • CharmmffTopFileArtifacts.key
  • DataArtifact
    • DataArtifact.description
  • DataFileArtifact
    • DataFileArtifact.description
    • DataFileArtifact.ext
  • DataFileArtifactList
    • DataFileArtifactList.description
  • FileArtifact
    • FileArtifact.compare()
    • FileArtifact.data
    • FileArtifact.description
    • FileArtifact.diff()
    • FileArtifact.exists()
    • FileArtifact.ext
    • FileArtifact.keep
    • FileArtifact.mime_type
    • FileArtifact.name
    • FileArtifact.nonstate_results
    • FileArtifact.path
    • FileArtifact.pytestable
    • FileArtifact.remove()
    • FileArtifact.validate()
  • FileArtifactDict
  • FileArtifactList
    • FileArtifactList.all_exist()
    • FileArtifactList.make_tarball()
    • FileArtifactList.paths_to_list()
    • FileArtifactList.unique_paths()
  • InputFileArtifact
    • InputFileArtifact.description
    • InputFileArtifact.ext
  • JSONFileArtifact
    • JSONFileArtifact.description
    • JSONFileArtifact.ext
    • JSONFileArtifact.mime_type
  • LogFileArtifact
    • LogFileArtifact.description
    • LogFileArtifact.ext
  • LogFileArtifactList
    • LogFileArtifactList.description
  • NAMDColvarsConfigArtifact
    • NAMDColvarsConfigArtifact.description
    • NAMDColvarsConfigArtifact.ext
  • NAMDColvarsStateArtifact
    • NAMDColvarsStateArtifact.description
    • NAMDColvarsStateArtifact.ext
  • NAMDColvarsTrajectoryArtifact
    • NAMDColvarsTrajectoryArtifact.description
    • NAMDColvarsTrajectoryArtifact.ext
  • NAMDConfigFileArtifact
    • NAMDConfigFileArtifact.compare()
    • NAMDConfigFileArtifact.description
    • NAMDConfigFileArtifact.ext
  • NAMDCoorFileArtifact
    • NAMDCoorFileArtifact.description
    • NAMDCoorFileArtifact.ext
  • NAMDCoorFileArtifactList
    • NAMDCoorFileArtifactList.description
  • NAMDDcdFileArtifact
    • NAMDDcdFileArtifact.description
    • NAMDDcdFileArtifact.ext
  • NAMDExtraBondsFileArtifact
    • NAMDExtraBondsFileArtifact.description
    • NAMDExtraBondsFileArtifact.ext
  • NAMDLogFileArtifact
    • NAMDLogFileArtifact.description
  • NAMDLogFileArtifactList
    • NAMDLogFileArtifactList.description
  • NAMDOutputFileArtifact
    • NAMDOutputFileArtifact.description
    • NAMDOutputFileArtifact.mime_type
  • NAMDOutputFileArtifactList
    • NAMDOutputFileArtifactList.description
  • NAMDVelFileArtifact
    • NAMDVelFileArtifact.description
    • NAMDVelFileArtifact.ext
  • NAMDXscFileArtifact
    • NAMDXscFileArtifact.description
    • NAMDXscFileArtifact.ext
  • NAMDXstFileArtifact
    • NAMDXstFileArtifact.description
    • NAMDXstFileArtifact.ext
  • PDBFileArtifact
    • PDBFileArtifact.compare()
    • PDBFileArtifact.description
    • PDBFileArtifact.ext
  • PDBFileArtifactList
    • PDBFileArtifactList.description
  • PNGImageFileArtifact
    • PNGImageFileArtifact.description
    • PNGImageFileArtifact.ext
    • PNGImageFileArtifact.mime_type
    • PNGImageFileArtifact.nonstate_results
  • PNGImageFileArtifactList
    • PNGImageFileArtifactList.description
  • PQRFileArtifact
    • PQRFileArtifact.description
    • PQRFileArtifact.ext
  • PSFFileArtifact
    • PSFFileArtifact.compare()
    • PSFFileArtifact.description
    • PSFFileArtifact.ext
  • PSFFileArtifactList
    • PSFFileArtifactList.description
  • PackMolPDBForcedFileArtifact
    • PackMolPDBForcedFileArtifact.description
    • PackMolPDBForcedFileArtifact.ext
  • PackmolInputScriptArtifact
    • PackmolInputScriptArtifact.description
    • PackmolInputScriptArtifact.ext
  • PackmolLogFileArtifact
    • PackmolLogFileArtifact.description
  • PsfgenInputScriptArtifact
    • PsfgenInputScriptArtifact.description
  • PsfgenLogFileArtifact
    • PsfgenLogFileArtifact.description
  • StateArtifacts
    • StateArtifacts.coor
    • StateArtifacts.description
    • StateArtifacts.key
    • StateArtifacts.minimal_prm
    • StateArtifacts.pdb
    • StateArtifacts.psf
    • StateArtifacts.stamp()
    • StateArtifacts.to_list()
    • StateArtifacts.vel
    • StateArtifacts.xsc
  • TXTFileArtifact
    • TXTFileArtifact.description
    • TXTFileArtifact.ext
    • TXTFileArtifact.mime_type
  • TclScriptArtifact
    • TclScriptArtifact.description
    • TclScriptArtifact.ext
    • TclScriptArtifact.mime_type
  • VMDLogFileArtifact
    • VMDLogFileArtifact.description
  • VMDScriptArtifact
    • VMDScriptArtifact.description
  • YAMLFileArtifact
    • YAMLFileArtifact.description
    • YAMLFileArtifact.ext
    • YAMLFileArtifact.mime_type
• pestifer.core.baseobj module
  • BaseObj
    • BaseObj.assign_obj_to_attr()
    • BaseObj.copy()
    • BaseObj.copy_attr()
    • BaseObj.dump()
    • BaseObj.inlist()
    • BaseObj.map_attr()
    • BaseObj.model_config
    • BaseObj.objcat
    • BaseObj.serialize()
    • BaseObj.set()
    • BaseObj.set_nested()
    • BaseObj.strhash()
    • BaseObj.swap_attr()
    • BaseObj.update_attr_from_obj_attr()
    • BaseObj.update_attr_from_objlist_elem_attr()
    • BaseObj.weak_lt()
    • BaseObj.wildmatch()
  • BaseObjList
    • BaseObjList.append()
    • BaseObjList.assign_objs_to_attr()
    • BaseObjList.binnify()
    • BaseObjList.describe()
    • BaseObjList.dict_to_condition()
    • BaseObjList.extend()
    • BaseObjList.filter()
    • BaseObjList.get()
    • BaseObjList.give_item()
    • BaseObjList.ifilter()
    • BaseObjList.iget()
    • BaseObjList.insert()
    • BaseObjList.map_attr()
    • BaseObjList.prune_exclusions()
    • BaseObjList.puniq()
    • BaseObjList.puniquify()
    • BaseObjList.remove_and_return()
    • BaseObjList.remove_duplicates()
    • BaseObjList.remove_instance()
    • BaseObjList.set()
    • BaseObjList.sort()
    • BaseObjList.take_item()
    • BaseObjList.uniqattrs()
    • BaseObjList.update_attr_from_obj_attr()
    • BaseObjList.update_attr_from_objlist_elem_attr()
    • BaseObjList.validate()
  • GenericListMeta
• pestifer.core.command module
  • Command
    • Command.divider_line_length
    • Command.run()
• pestifer.core.config module
  • Config
    • Config.configure()
    • Config.configure_new()
    • Config.get_scripter()
    • Config.taskless_subconfig()
• pestifer.core.controller module
  • Controller
    • Controller.configure()
    • Controller.do_tasks()
    • Controller.provision_tasks()
    • Controller.reconfigure_tasks()
    • Controller.spawn_subcontroller()
    • Controller.write_complete_config()
• pestifer.core.errors module
  • PestiferBuildError
  • PestiferError
• pestifer.core.example module
  • Example
    • Example.author_email
    • Example.author_name
    • Example.auxiliary_inputs
    • Example.db_id
    • Example.example_id
    • Example.folder_name_format
    • Example.input
    • Example.inputs_subdir
    • Example.inputspath
    • Example.model_config
    • Example.model_post_init()
    • Example.outputs
    • Example.outputs_subdir
    • Example.outputspath
    • Example.report_line()
    • Example.rootfolderpath
    • Example.scriptname
    • Example.scriptpath
    • Example.shortname
    • Example.title
    • Example.to_dict()
    • Example.to_yaml()
    • Example.update_options()
  • ExampleList
    • ExampleList.append()
    • ExampleList.describe()
    • ExampleList.from_list_of_dicts()
    • ExampleList.from_yaml()
    • ExampleList.get_example_by_example_id()
    • ExampleList.get_example_by_shortname()
    • ExampleList.read_yaml()
    • ExampleList.to_list_of_dicts()
    • ExampleList.to_yaml()
• pestifer.core.examplemanager module
  • ExampleManager
    • ExampleManager.append_example()
    • ExampleManager.checkin_example()
    • ExampleManager.checkout_example()
    • ExampleManager.clone()
    • ExampleManager.copy_from()
    • ExampleManager.delete_example()
    • ExampleManager.examplefolderpath()
    • ExampleManager.inputspath()
    • ExampleManager.new_example_yaml()
    • ExampleManager.outputspath()
    • ExampleManager.rename_example()
    • ExampleManager.report_examples()
    • ExampleManager.scriptpath()
    • ExampleManager.set_example_author()
    • ExampleManager.update_example()
• pestifer.core.labels module
  • LabelMappers
    • LabelMappers.update_alias_mappings()
    • LabelMappers.update_aliases()
    • LabelMappers.update_atomselect_macros()
    • LabelMappers.update_segtypes()
  • Labels
• pestifer.core.objmanager module
  • ObjManager
    • ObjManager.used
    • ObjManager.counts_by_header()
    • ObjManager.expel()
    • ObjManager.filter_copy()
    • ObjManager.ingest()
    • ObjManager.retire()
• pestifer.core.pipeline module
  • PipelineContext
    • PipelineContext.head
    • PipelineContext.history
    • PipelineContext.controller_index
    • PipelineContext.bury()
    • PipelineContext.context_to_string()
    • PipelineContext.get_all_file_artifacts()
    • PipelineContext.get_artifact_series_by_key()
    • PipelineContext.get_current_artifact()
    • PipelineContext.get_current_artifact_data()
    • PipelineContext.get_state_artifact()
    • PipelineContext.history_to_string()
    • PipelineContext.import_artifacts()
    • PipelineContext.register()
    • PipelineContext.register_if_exists()
    • PipelineContext.rekey()
    • PipelineContext.show_artifact()
    • PipelineContext.show_artifacts()
    • PipelineContext.stash()
• pestifer.core.resourcemanager module
  • ResourceManager
    • ResourceManager.append_example()
    • ResourceManager.charmmff_content
    • ResourceManager.charmmff_version_dirs()
    • ResourceManager.charmmff_version_path()
    • ResourceManager.delete_example()
    • ResourceManager.example_manager
    • ResourceManager.get_charmmff_customdir()
    • ResourceManager.get_resource_path()
    • ResourceManager.get_tcl_pkgdir()
    • ResourceManager.get_tcl_scriptsdir()
    • ResourceManager.get_tcldir()
    • ResourceManager.rename_example()
    • ResourceManager.set_example_author()
    • ResourceManager.show()
    • ResourceManager.update_atomselect_macros()
    • ResourceManager.update_example()
  • USER_TOPPAR_DIR