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_DENSITY | density.read() |
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() |
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 |
Automatic builds 2015-05-19