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TOP to Python correspondence

Please use the tables below to see which Python commands and variables correspond to old TOP commands and variables. Variables which are not listed in these tables have the same names as the old TOP equivalents (albeit in lower case).

Table C.1: Correspondence between TOP and Python commands.
TOP command Python equivalent
ADD_RESTRAINT Restraints.add()
ALIGN alignment.align()
ALIGN2D alignment.align2d()
ALIGN3D alignment.align3d()
ALIGN_CONSENSUS alignment.consensus()
ALN_TO_PROF alignment.to_profile()
BUILD_MODEL model.build()
BUILD_PROFILE profile.build()
CALL use Python subroutines
CHECK_ALIGNMENT alignment.check()
CLOSE use Python file object
COLOR_ALN_MODEL model.color()
COMPARE alignment.compare_structures()
COMPARE_ALIGNMENTS alignment.compare_with()
CONDENSE_RESTRAINTS Restraints.condense()
DEBUG_FUNCTION selection.debug_function()
DEFINE_INTEGER use Python 'int' variables
DEFINE_LOGICAL use Python 'bool' variables
DEFINE_REAL use Python 'float' variables
DEFINE_STRING use Python 'str' variables
DEFINE_SYMMETRY Restraints.add()
DELETE_ALIGNMENT del(alignment)
DELETE_FILE modfile.delete()
DELETE_RESTRAINT Restraints.unpick()
DENDROGRAM environ.dendrogram()
DESCRIBE alignment.describe()
DO use Python while or for loops
EDIT_ALIGNMENT alignment.edit()
EM_GRID_SEARCH density.grid_search()
END_SUBROUTINE use Python subroutines
ENERGY selection.energy()
EXIT use Python while or for loops
EXPAND_ALIGNMENT use alignment.append_model() in a loop
GENERATE_TOPOLOGY model.generate_topology()
ID_TABLE alignment.id_table()
IF use Python if statement
INCLUDE use Python import statement
INQUIRE modfile.inquire()
IUPAC_MODEL model.to_iupac()
MAKE_CHAINS model.make_chains()
MAKE_REGION model.make_region()
MAKE_RESTRAINTS Restraints.make()
MAKE_SCHEDULE schedule.make_for_model()
MAKE_TOPOLOGY_MODEL Topology.make()
MALIGN alignment.malign()
MALIGN3D alignment.malign3d()
MUTATE_MODEL selection.mutate()
OPEN use Python file object
OPERATE use Python arithmetic
OPTIMIZE conjugate_gradients() or molecular_dynamics(), or <schedule> objects
ORIENT_MODEL model.orient()
PATCH model.patch()
PATCH_SS_MODEL model.patch_ss()
PATCH_SS_TEMPLATES model.patch_ss_templates()
PICK_ATOMS Use <selection> objects
PICK_HOT_ATOMS selection.hot_atoms()
PICK_RESTRAINTS Restraints.pick()
PRINCIPAL_COMPONENTS environ.principal_components()
PROFILE_PROFILE_SCAN profile.scan()
PROF_TO_ALN alignment.append_profile() or profile.to_alignment()
RANDOMIZE_XYZ selection.randomize_xyz()
READ use Python file object
READ_ALIGNMENT alignment.append()
READ_ALIGNMENT2 alignment.append()
READ_ATOM_CLASSES group_restraints()
READ_MODEL model.read()
READ_MODEL2 model.read()
READ_PARAMETERS Parameters.read() or group_restraints.append()
READ_PROFILE profile.read()
READ_RESTRAINTS Restraints.append()
READ_RESTYP_LIB environ()
READ_SCHEDULE Use <schedule> objects
READ_SEQUENCE_DB sequence_db.read()
READ_TOPOLOGY Topology.read() or Topology.append()
REINDEX_RESTRAINTS Restraints.reindex()
RENAME_SEGMENTS model.rename_segments()
REORDER_ATOMS model.reorder_atoms()
RESET do not use
RETURN use Python subroutines
ROTATE_DIHEDRALS selection.rotate_dihedrals()
ROTATE_MODEL selection.translate(), selection.transform(), or selection.rotate_origin()
SALIGN alignment.salign()
SEGMENT_MATCHING alignment.segment_matching()
SEQFILTER sequence_db.filter()
SEQUENCE_COMPARISON alignment.compare_sequences()
SEQUENCE_SEARCH sequence_db.search()
SEQUENCE_TO_ALI alignment.append_model()
SET use Python variables
SPLINE_RESTRAINTS Restraints.spline()
STOP do not use
STRING_IF use Python if statement
STRING_OPERATE use Python arithmetic
SUBROUTINE use Python subroutines
SUPERPOSE selection.superpose()
SWITCH_TRACE actions.trace()
SYSTEM environ.system()
TIME_MARK info.time_mark()
TRANSFER_RES_NUMB model.res_num_from()
TRANSFER_XYZ model.transfer_xyz()
UNBUILD_MODEL selection.unbuild()
WRITE use Python file object
WRITE_ALIGNMENT alignment.write()
WRITE_DATA model.write_data()
WRITE_MODEL model.write()
WRITE_MODEL2 model.write()
WRITE_PDB_XREF use <residue> objects
WRITE_PROFILE profile.write()
WRITE_RESTRAINTS Restraints.write()
WRITE_SCHEDULE schedule.write()
WRITE_SEQUENCE_DB sequence_db.write()
WRITE_TOP do not use
WRITE_TOPOLOGY_MODEL Topology.write()

Table C.2: Correspondence between TOP and Python variables.
TOP variable Python equivalent
ALIGN_CODES Sequence.code
ATOM_FILES Sequence.atom_file
ATOM_FILES_DIRECTORY io_data.atom_files_directory
CONTACT_SHELL energy_data.contact_shell
COULOMB_SWITCH energy_data.coulomb_switch
COVALENT_CYS energy_data.covalent_cys
DYNAMIC_ACCESS do not use
DYNAMIC_COULOMB energy_data.dynamic_coulomb
DYNAMIC_LENNARD energy_data.dynamic_lennard
DYNAMIC_MODELLER energy_data.dynamic_modeller
DYNAMIC_PAIRS set automatically; do not use
DYNAMIC_SPHERE energy_data.dynamic_sphere
EXCL_LOCAL energy_data.excl_local
HETATM_IO io_data.hetatm
HYDROGEN_IO io_data.hydrogen
LENNARD_JONES_SWITCH energy_data.lennard_jones_switch
MOLPDF return value from selection.energy()
NLOGN_USE energy_data.nlogn_use
NONBONDED_SEL_ATOMS energy_data.nonbonded_sel_atoms
NUMB_OF_SEQUENCES len(alignment)
N_SCHEDULE len(schedule)
OUTPUT_CONTROL use log.level()
RADII_FACTOR energy_data.radii_factor
RELATIVE_DIELECTRIC energy_data.relative_dielectric
SCHEDULE_STEP do not use
SPHERE_STDV energy_data.sphere_stdv
TOPOLOGY_MODEL Topology.submodel
UPDATE_DYNAMIC energy_data.update_dynamic
WATER_IO io_data.water


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