- A
- Mathematical forms of restraints
- accessibility_type
- Model.write_data() write
| Restraints.make() make
- actions
- ConjugateGradients() optimize
| MolecularDynamics() optimize
| actions.WriteStructure() write
| actions.CHARMMTrajectory() write
- actions.CHARMMTrajectory()
- AutoModel.get_optimize_actions() get
| Model.write_psf() write
| actions.CHARMMTrajectory() write
- actions.Trace()
- AutoModel.trace_output control
| ConjugateGradients() optimize
| actions.Trace() write
| TOP to Python correspondence
- actions.WriteStructure()
- ConjugateGradients() optimize
| actions.WriteStructure() write
| actions.CHARMMTrajectory() write
- add
- Restraints.add() add
| Selection.add() add
- add_leading_gaps
- Residue.add_leading_gaps() add
- add_trailing_gaps
- Residue.add_trailing_gaps() add
- align
- Alignment.align() align
- align2d
- Alignment.align2d() align
- align3d
- Alignment.align3d() align
- align3d_repeat
- Alignment.align3d() align
- align3d_trf
- Alignment.align3d() align
| Features of proteins used
- align_alignment
- Alignment.write() write
- align_block
- Alignment.write() write
| Alignment.align() align
| Alignment.malign() align
| Alignment of protein sequences
| Alignment.get_suboptimals() parse
| Alignment.segment_matching() align
- align_code
- Chain.write() write
| Chain.atom_file_and_code() get
- align_codes
- Alignment.append() read
| Alignment.append_model() copy
- align_what
- Alignment.align() align
| Alignment of protein sequences
- Alignment
- Alignment file
| Alignment() create
- Alignment class
- The Alignment class: comparison
- alignment files
- format
- Alignment file (PIR)
- reading
- Alignment.append() read
- writing
- Alignment.write() write
- alignment Structure class
- The Structure class: a
- Alignment()
- Alignment() create
- Alignment.align()
- Alignment.write() write
| Alignment.align() align
| Alignment.align2d() align
| Alignment.malign() align
| Alignment.consensus() consensus
| Alignment.align3d() align
| Alignment.salign() align
| Alignment of protein sequences
| Alignment of protein structures
| Gap penalties and correcting
| SequenceDB.filter() cluster
| TOP to Python correspondence
- Alignment.align2d
- Residue.curvature Mainchain
- Alignment.align2d()
- Coordinate files and derivative
| Alignment.write() write
| Alignment.align2d() align
| Alignment.salign() align
| Alignment of protein structures
| TOP to Python correspondence
- Alignment.align3d()
- Selection.superpose() superpose
| Alignment.align3d() align
| Alignment.malign3d() align
| Alignment.salign() align
| Features of proteins used
| TOP to Python correspondence
- Alignment.append()
- Alignment() create
| Alignment.append() read
| Alignment.read_one() read
| Alignment.compare_with() compare
| Alignment.write() write
| Alignment.describe() describe
| Profile.build() Build
| Flowchart of comparative modeling
| TOP to Python correspondence
- Alignment.append_model()
- Selection.mutate() mutate
| Alignment.append_model() copy
| Alignment.malign3d() align
| Useful SALIGN information and
| Flowchart of comparative modeling
| TOP to Python correspondence
- Alignment.append_profile()
- Alignment.append_profile() add
| TOP to Python correspondence
- Alignment.append_sequence()
- Changes since release 10.5
| Model.build_sequence() build
| Alignment.append_sequence() add
- Alignment.check()
- Alignment file
| Running MODELLER
| Fully automated alignment and
| Frequently asked questions (FAQ)
| Alignment.check() check
| Structure.reread() reread
| Flowchart of comparative modeling
| TOP to Python correspondence
- Alignment.check_sequence_structure()
- Alignment.check_sequence_structure() check
| Alignment.check() check
- Alignment.check_structure_structure()
- Alignment.check_structure_structure() check
| Alignment.check() check
- Alignment.clear()
- Alignment.clear() delete
- Alignment.comments
- Alignment.comments alignment
- Alignment.compare_sequences()
- Environ.dendrogram() clustering
| Environ.principal_components() clustering
| Alignment.id_table() calculate
| Alignment.compare_sequences() compare
| TOP to Python correspondence
- Alignment.compare_structures()
- Coordinate files and derivative
| Environ.dendrogram() clustering
| Environ.principal_components() clustering
| Alignment.compare_structures() compare
| TOP to Python correspondence
- Alignment.compare_with()
- Alignment.compare_with() compare
| Alignment.align() align
| TOP to Python correspondence
- Alignment.consensus()
- Alignment.write() write
| Alignment.consensus() consensus
| TOP to Python correspondence
- Alignment.describe()
- Alignment.describe() describe
| TOP to Python correspondence
- Alignment.edit()
- Alignment.edit() edit
| TOP to Python correspondence
- Alignment.get_suboptimals()
- Sub-optimal alignments
| Alignment.get_suboptimals() parse
- Alignment.id_table()
- Environ.dendrogram() clustering
| Environ.principal_components() clustering
| Alignment.id_table() calculate
| Alignment.compare_sequences() compare
| Sequence.get_num_equiv() get
| Sequence.get_sequence_identity() get
| TOP to Python correspondence
- Alignment.malign()
- Alignment.malign() align
| Alignment.malign3d() align
| Alignment.salign() align
| Features of proteins used
| SequenceDB.search() search
| TOP to Python correspondence
- Alignment.malign3d()
- Coordinate files and derivative
| Model.transfer_xyz() copy
| Alignment.compare_structures() compare
| Alignment.malign3d() align
| Alignment.salign() align
| Features of proteins used
| Structure.read() read
| Flowchart of comparative modeling
| TOP to Python correspondence
- Alignment.positions
- Alignment.positions list
| Residue.get_aligned_residue() get
- Alignment.read_one()
- Alignment.read_one() read
| modfile.File() open
- Alignment.salign
- Residue.curvature Mainchain
- Alignment.salign()
- Alignment.align() align
| Alignment.align2d() align
| Alignment.malign() align
| Alignment.align3d() align
| Alignment.malign3d() align
| Alignment.salign() align
| Features of proteins used
| Alignment of protein structures
| Useful SALIGN information and
| Alignment.get_suboptimals() parse
| Structure.read() read
| The salign module: high-level
| iterative_structural_align() obtain
| TOP to Python correspondence
- Alignment.segment_matching()
- Alignment.segment_matching() align
| TOP to Python correspondence
- Alignment.to_profile
- Environ.make_pssmdb() Create
- Alignment.to_profile()
- Alignment.to_profile() convert
| Profile() create
| Profile.to_alignment() profile
| Profile.scan() Compare
| Profile.build() Build
| Profile file
| TOP to Python correspondence
- Alignment.write()
- Selection.mutate() mutate
| Alignment.write() write
| Alignment.align() align
| Alignment.align2d() align
| Alignment.consensus() consensus
| Alignment.malign3d() align
| Chain.write() write
| Profile.build() Build
| SequenceDB.search() search
| TOP to Python correspondence
- alignment_features
- Alignment.write() write
- alignment_format
- Alignment.write() write
- alignment_type
- Alignment of protein sequences
| Alignment of protein structures
- alignment_what
- Alignment of protein sequences
- AllHModel
- AllHModel() prepare
- AllHModel class
- AllHModel reference
- AllHModel()
- AllHModel() prepare
- allow_alternates
- Alignment.append() read
- aln
- AutoModel.special_restraints() add
| Model.get_insertions() return
| Model.get_deletions() return
| Model.patch_ss_templates() guess
| Model.transfer_xyz() copy
| Model.res_num_from() residue
| Model.color() color
| Restraints.make() make
| Selection.superpose() superpose
| Alignment.compare_with() compare
| SequenceDB.search() search
- aln_base_filename
- Profile.scan() Compare
- alnfile
- AutoModel() prepare
| LoopModel() prepare
- alnseq
- Model.generate_topology() generate
- Alpha
- Alpha() make
- Alpha()
- Alpha() make
- angular_step_size
- Density.grid_search() dock
- append
- Topology.append() append
| Parameters.append() append
| Restraints.append() read
| GroupRestraints.append() read
| Alignment.append() read
- append_model
- Alignment.append_model() copy
- append_profile
- Alignment.append_profile() add
- append_sequence
- Alignment.append_sequence() add
- asgl_output
- Selection.energy() evaluate
| Alignment.compare_structures() compare
- assess
- Selection.assess() assess
- assess_dope
- Selection.assess_dope() assess
- assess_dopehr
- Selection.assess_dopehr() assess
- assess_ga341
- Model.assess_ga341() assess
- assess_methods
- Getting a very fast
| AutoModel() prepare
- assess_normalized_dope
- Model.assess_normalized_dope() assess
- Assessor
- Selection.assess() assess
| soap_pp.Assessor() assess
- atmsel
- Restraints.make() make
| Restraints.pick() pick
- atmsel1
- Restraints.make_distance() make
- atmsel2
- Restraints.make_distance() make
- Atom class
- The Atom class: a
- atom classes
- Loop modeling method
- Atom.accessibility
- Model.write_data() write
| Atom.accessibility atomic
- Atom.biso
- Model.write_data() write
| Model.make_region() define
| Atom.biso isotropic
- Atom.charge
- Atom.charge electrostatic
- Atom.dvx
- Atom.dvx objective
- Atom.get_equivalent_atom()
- Restraints.make_distance() make
| Atom.get_equivalent_atom() get
- Atom.mass
- Atom.mass mass
- Atom.name
- Atom.name PDB
- Atom.occ
- Atom.occ occupancy
- Atom.residue
- Atom.residue residue
- Atom.type
- AutoModel.special_patches() add
| Block (BLK) residues with
| Atom.type CHARMM
- Atom.vx
- Atom.vx x
- atom1
- Sheet() make
- atom2
- Sheet() make
- atom_accessibility
- Model.make_region() define
- atom_file
- Structure.read() read
| Chain.write() write
| Chain.atom_file_and_code() get
- atom_file_and_code
- Chain.atom_file_and_code() get
- atom_files
- Alignment.append() read
| Alignment.append_model() copy
- atom_ids
- Specification of pseudo atoms
| Restraints.unpick() unselect
- atom_range
- Model.atom_range() return
- AtomScorer
- soap_pp.AtomScorer() create
- AtomType class
- The AtomType class: a
- AtomType.element
- AtomType.element element
- AtomType.mass
- AtomType.mass atomic
- AtomType.name
- AtomType.name CHARMM
- auto_align
- AutoModel.auto_align() generate
- auto_overhang
- Alignment of protein structures
- AutoModel
- AutoModel() prepare
| AutoModel.get_model_filename() get
- AutoModel class
- AutoModel reference
- AutoModel()
- AutoModel() prepare
| AllHModel() prepare
| LoopModel() prepare
- AutoModel.assess_methods
- LoopModel() prepare
| Model.assess_ga341() assess
| Model.assess_normalized_dope() assess
| Selection.assess_dope() assess
| Selection.assess_dopehr() assess
| soap_loop.Scorer() create
- AutoModel.auto_align()
- Fully automated alignment and
| AutoModel.auto_align() generate
- AutoModel.blank_single_chain
- AutoModel.blank_single_chain Control
- AutoModel.cluster()
- AutoModel.cluster() cluster
- AutoModel.deviation
- AutoModel.rand_method control
| Flowchart of comparative modeling
- AutoModel.ending_model
- Simple usage
| AutoModel.starting_model first
| AutoModel.ending_model last
| AutoModel.get_model_filename() get
| LoopModel.loop.ending_model last
| LoopModel.get_loop_model_filename() get
| Selection.assess_dope() assess
- AutoModel.final_malign3d
- AutoModel() prepare
| AutoModel.final_malign3d final
| LoopModel.loop.write_selection_only write
| Flowchart of comparative modeling
- AutoModel.generate_method
- Using your own initial
| AutoModel.generate_method control
- AutoModel.get_model_filename()
- AutoModel() prepare
| AutoModel.get_model_filename() get
| LoopModel.get_loop_model_filename() get
- AutoModel.get_optimize_actions()
- AutoModel.trace_output control
| AutoModel.get_optimize_actions() get
| AutoModel.get_refine_actions() get
- AutoModel.get_refine_actions()
- AutoModel.trace_output control
| AutoModel.get_refine_actions() get
- AutoModel.guess_atom_type()
- AutoModel.guess_atom_types() automatically
| AutoModel.guess_atom_type() automatically
- AutoModel.guess_atom_types()
- AutoModel.special_patches() add
| AutoModel.guess_atom_types() automatically
| AutoModel.guess_atom_type() automatically
| Block (BLK) residues with
- AutoModel.initial_malign3d
- Building a model from
| AutoModel() prepare
| AutoModel.initial_malign3d initial
| Model.transfer_xyz() copy
| Alignment.check_structure_structure() check
- AutoModel.library_schedule
- Changing the default optimization
| AutoModel() prepare
| AutoModel.library_schedule select
| AutoModel.very_fast() request
| LoopModel.loop.library_schedule select
- AutoModel.make()
- Simple usage
| Getting a very fast
| Accessing output data after
| Fully automated alignment and
| AutoModel.outputs all
| AutoModel.make() build
- AutoModel.max_ca_ca_distance
- AutoModel.max_ca_ca_distance Distance
| AutoModel.max_n_o_distance Distance
| AutoModel.max_sc_mc_distance Distance
| AutoModel.max_sc_sc_distance Distance
| AutoModel.very_fast() request
- AutoModel.max_molpdf
- Changing the default optimization
| AutoModel.max_molpdf objective
- AutoModel.max_n_o_distance
- AutoModel.max_ca_ca_distance Distance
| AutoModel.max_n_o_distance Distance
- AutoModel.max_sc_mc_distance
- AutoModel.max_ca_ca_distance Distance
| AutoModel.max_sc_mc_distance Distance
- AutoModel.max_sc_sc_distance
- AutoModel.max_ca_ca_distance Distance
| AutoModel.max_sc_sc_distance Distance
- AutoModel.max_var_iterations
- Changing the default optimization
| AutoModel.max_var_iterations select
| LoopModel.loop.max_var_iterations select
- AutoModel.md_level
- Changing the default optimization
| AutoModel.md_level control
| AutoModel.very_fast() request
| LoopModel.loop.md_level control
- AutoModel.nonstd_restraints()
- Including water molecules, HETATM
| AutoModel.nonstd_restraints() add
| Block (BLK) residues with
| Flowchart of comparative modeling
- AutoModel.outputs
- Accessing output data after
| AutoModel.outputs all
| LoopModel.loop.outputs all
- AutoModel.rand_method
- AutoModel() prepare
| AutoModel.rand_method control
| AutoModel.very_fast() request
- AutoModel.repeat_optimization
- Changing the default optimization
| AutoModel.repeat_optimization number
- AutoModel.select_atoms()
- Refining only part of
| AutoModel() prepare
| AutoModel.select_atoms() select
- AutoModel.set_output_model_format()
- Generating new-style PDBx/mmCIF outputs
| AutoModel.set_output_model_format() set
| AutoModel.get_model_filename() get
- AutoModel.special_patches()
- Including disulfide bridges
| Residues and chains in
| AutoModel.special_patches() add
| AutoModel.guess_atom_types() automatically
| Flowchart of comparative modeling
- AutoModel.special_restraints()
- Adding additional restraints to
| Building multi-chain models
| AutoModel.special_restraints() add
| Flowchart of comparative modeling
- AutoModel.starting_model
- Simple usage
| AutoModel.starting_model first
| AutoModel.ending_model last
| AutoModel.get_model_filename() get
| LoopModel.loop.starting_model first
| LoopModel.get_loop_model_filename() get
- AutoModel.trace_output
- AutoModel.trace_output control
| AutoModel.get_optimize_actions() get
- AutoModel.use_parallel_job()
- AutoModel.use_parallel_job() parallelize
- AutoModel.user_after_single_model()
- Building multi-chain models
| AutoModel.user_after_single_model() analyze
| LoopModel.user_after_single_loop_model() analyze
- AutoModel.very_fast()
- Getting a very fast
| AutoModel.max_ca_ca_distance Distance
| AutoModel.very_fast() request
- AutoModel.write_intermediates
- AutoModel.write_intermediates write
- B
- Mathematical forms of restraints
- base_align_codes
- Alignment.edit() edit
- basis_pdf_weight
- Restraints.make() make
- basis_relative_weight
- Restraints.make() make
- best_docked_models
- Density.grid_search() dock
- bibliography
- MODELLER bibliography
- blank_single_chain
- Model.build_sequence() build
| Model.generate_topology() generate
| Alignment.append_sequence() add
- BLOCK residues
- Block (BLK) residues with
- break_break_bonus
- Alignment.align() align
| Gap penalties and correcting
- breakpoint
- Controlling breakpoints and the
- bug reports
- Bug reports
- build
- Model.build() build
| Profile.build() Build
- build_ini_loop
- LoopModel.build_ini_loop() create
- build_method
- Model.build() build
- build_sequence
- Model.build_sequence() build
- by_chain
- Alignment.edit() edit
- by_residue
- Selection.by_residue() make
- cap_atom_shift
- MolecularDynamics() optimize
| Molecular dynamics
- ccf_func_type
- Density.read() read
- ccmatrix_offset
- Profile.scan() Compare
- Chain class
- The Chain class: a
- Chain.atom_file_and_code()
- Chain.write() write
| Chain.atom_file_and_code() get
- Chain.atoms
- Chain.atoms all
- Chain.filter()
- Model.make_chains() Fetch
| Chain.filter() check
| Chain.write() write
| Chain.atom_file_and_code() get
- Chain.join()
- Chain.join() join
- Chain.name
- Model.rename_segments() rename
| Chain.name chain
- Chain.residues
- Chain.residues all
- Chain.write()
- Model.make_chains() Fetch
| Chain.filter() check
| Chain.write() write
| Chain.atom_file_and_code() get
- chains_list
- SequenceDB.read() read
| SequenceDB.write() write
- change
- Selection.rotate_dihedrals() change
- CHARMMTrajectory
- actions.CHARMMTrajectory() write
- check
- Alignment.check() check
- check_profile
- Profile.build() Build
- check_sequence_structure
- Alignment.check_sequence_structure() check
- check_structure_structure
- Alignment.check_structure_structure() check
- chop_nonstd_termini
- Chain.filter() check
| Chain.write() write
- cispeptide
- cispeptide() creates
- cispeptide()
- Restraints.add() add
| Restraints.unpick() unselect
| cispeptide() creates
- classes
- GroupRestraints() create
| GroupRestraints.append() read
- clean_sequences
- SequenceDB.read() read
- clear
- Topology.clear() clear
| Parameters.clear() clear
| Restraints.clear() delete
| Alignment.clear() delete
- clear_topology
- Model.clear_topology() clear
- close
- SequenceDB.close() close
- cluster
- AutoModel.cluster() cluster
- cluster_cut
- AutoModel.cluster() cluster
| Model.transfer_xyz() copy
- cluster_method
- Model.transfer_xyz() copy
- color
- Model.color() color
- comment
- Chain.write() write
- Communicator.get_data()
- Parallel job support
| Job() create
| Communicator.send_data() send
| Communicator.get_data() get
- Communicator.send_data()
- Parallel job support
| Job() create
| Job.queue_task() submit
| Communicator.send_data() send
| Communicator.get_data() get
| Worker.run_cmd() run
- compactness
- Model.assess_ga341() assess
- compare_mode
- Alignment.compare_structures() compare
- compare_sequences
- Alignment.compare_sequences() compare
- compare_structures
- Alignment.compare_structures() compare
- compare_with
- Alignment.compare_with() compare
- comparison_type
- Alignment of protein sequences
- complete_pdb
- Model.write_psf() write
| complete_pdb() read
- complete_pdb()
- Model.read() read
| Model.write() write
| Selection.assess_dope() assess
| Chain.join() join
| complete_pdb() read
- compressed files
- Reading or writing files
- condense
- Restraints.condense() remove
- ConjugateGradients
- ConjugateGradients() optimize
- ConjugateGradients()
- AutoModel.max_var_iterations select
| Rigid bodies
| Restraints.make_distance() make
| ConjugateGradients() optimize
| QuasiNewton() optimize
| MolecularDynamics() optimize
| actions.WriteStructure() write
| actions.Trace() write
| actions.CHARMMTrajectory() write
| complete_pdb() read
| Flowchart of comparative modeling
| TOP to Python correspondence
- consensus
- Alignment.consensus() consensus
- contact_shell
- Feature types
- convert
- SequenceDB.convert() convert
- correls
- Mathematical forms of restraints
- Coulomb
- Block (BLK) residues with
| Static and dynamic restraints
| Mathematical forms of restraints
| Rigid bodies
| The EnergyData class: objective
| EnergyData.contact_shell nonbond
| EnergyData.dynamic_coulomb calculate
| EnergyData.coulomb_switch Coulomb
| EnergyData.relative_dielectric relative
| Model.read() read
| Restraints.make() make
| physical.Values() create
| Function
| Coulomb restraint
- csrfile
- AutoModel() prepare
- current_directory
- Alignment.malign3d() align
| Useful SALIGN information and
- cutoff
- gbsa.Scorer() create
- data_file
- SequenceDB.search() search
- debug_function
- Selection.debug_function() test
- debug_function_cutoff
- Selection.debug_function() test
- default
- modfile.default() generate
- delete
- modfile.delete() delete
- delta
- Mathematical forms of restraints
- dendrogram
- Environ.dendrogram() clustering
- dendrogram_file
- Alignment of protein structures
| Useful SALIGN information and
- Density
- Density() create
- Density class
- The Density class: handling
- Density()
- Density() create
- Density.grid
- Density.grid Density
- Density.grid_search()
- The Density class: handling
| Density() create
| Density.read() read
| Density.grid_search() dock
| TOP to Python correspondence
- Density.px
- Density.px Origin
- Density.py
- Density.py Origin
- Density.pz
- Density.pz Origin
- Density.read()
- Density() create
| Density.resolution Map
| Density.voxel_size Map
| Density.px Origin
| Density.py Origin
| Density.pz Origin
| Density.read() read
| Density.grid_search() dock
| TOP to Python correspondence
- Density.resolution
- Density.resolution Map
| Density.sigma_factor Sigma
- Density.sigma_factor
- Density.sigma_factor Sigma
- Density.voxel_size
- Density.voxel_size Map
- density_type
- Density.read() read
| Density.grid_search() dock
- describe
- Alignment.describe() describe
- detailed_debugging
- Selection.debug_function() test
- deviation
- AutoModel() prepare
| Restraints.symmetry.report() report
| Selection.randomize_xyz() randomize
- dih_lib_only
- Restraints.make() make
- Dihedral class
- The Dihedral class: a
- Dihedral.atoms
- Dihedral.atoms atoms
- Dihedral.dihclass
- Dihedral.dihclass integer
- Dihedral.value
- Dihedral.value current
- dihedrals
- Selection.rotate_dihedrals() change
- distance_rsr_model
- Restraints.make_distance() make
- disulfide bond restraints
- Including disulfide bridges
- dnr_accpt_lib
- Model.write_data() write
- DOPEHRLoopModel class
- DOPEHRLoopModel reference
- DOPELoopModel
- DOPELoopModel() prepare
- DOPELoopModel class
- DOPELoopModel reference
- DOPELoopModel()
- DOPELoopModel() prepare
| The gbsa module: implicit
- dr
- SAXSData.ini_saxs() Initialization
- dr_exp
- SAXSData.ini_saxs() Initialization
- e_native_comb
- Model.assess_ga341() assess
- e_native_pair
- Model.assess_ga341() assess
- e_native_surf
- Model.assess_ga341() assess
- edat
- Key for command descriptions
| Environ.edat default
| ConjugateGradients() optimize
| MolecularDynamics() optimize
- edit
- Alignment.edit() edit
- edit_align_codes
- Alignment.edit() edit
- edit_file_ext
- Alignment.malign3d() align
- electrostatics
- see Coulomb
- em_fit_output_file
- Density.grid_search() dock
- em_map_size
- Density.read() read
- em_pdb_name
- Density.grid_search() dock
- end
- Model.atom_range() return
| Model.residue_range() return
- end_of_file
- Alignment.append() read
- energy
- Selection.energy() evaluate
- EnergyData
- Key for command descriptions
| EnergyData() create
- EnergyData class
- The EnergyData class: objective
- EnergyData()
- EnergyData() create
- EnergyData.contact_shell
- EnergyData.contact_shell nonbond
| EnergyData.update_dynamic nonbond
| EnergyData.nlogn_use select
| Restraints.make() make
| Selection.assess_dope() assess
| ConjugateGradients() optimize
| gbsa.Scorer() create
| soap_loop.Scorer() create
| Atomic density
| TOP to Python correspondence
- EnergyData.coulomb_switch
- EnergyData.contact_shell nonbond
| EnergyData.coulomb_switch Coulomb
| gbsa.Scorer() create
| TOP to Python correspondence
- EnergyData.covalent_cys
- EnergyData.covalent_cys use
| TOP to Python correspondence
- EnergyData.density
- Static and dynamic restraints
- EnergyData.dynamic_coulomb
- Static and dynamic restraints
| EnergyData.contact_shell nonbond
| EnergyData.dynamic_coulomb calculate
| Restraints.make() make
| TOP to Python correspondence
- EnergyData.dynamic_lennard
- Static and dynamic restraints
| EnergyData.contact_shell nonbond
| EnergyData.dynamic_lennard calculate
| Restraints.make() make
| TOP to Python correspondence
- EnergyData.dynamic_modeller
- Block (BLK) residues with
| Static and dynamic restraints
| EnergyData.dynamic_modeller calculate
| EnergyData.covalent_cys use
| Model.group_restraints all
| The GroupRestraints class: restraints
| TOP to Python correspondence
- EnergyData.dynamic_sphere
- Static and dynamic restraints
| EnergyData.contact_shell nonbond
| EnergyData.sphere_stdv soft-sphere
| EnergyData.dynamic_sphere calculate
| Restraints.make() make
| TOP to Python correspondence
- EnergyData.energy_terms
- EnergyData.energy_terms user-defined
| gbsa.Scorer() create
| soap_loop.Scorer() create
| User-defined energy terms
- EnergyData.excl_local
- EnergyData.excl_local exclude
| Restraints.make_distance() make
| TOP to Python correspondence
- EnergyData.lennard_jones_switch
- EnergyData.contact_shell nonbond
| EnergyData.lennard_jones_switch Lennard-Jones
| TOP to Python correspondence
- EnergyData.max_nlogn_grid_cells
- EnergyData.nlogn_use select
| EnergyData.max_nlogn_grid_cells maximum
- EnergyData.nlogn_use
- EnergyData.nlogn_use select
| EnergyData.max_nlogn_grid_cells maximum
| ConjugateGradients() optimize
| TOP to Python correspondence
- EnergyData.nonbonded_sel_atoms
- Refining only part of
| EnergyData.nonbonded_sel_atoms control
| Restraints.make() make
| Restraints.pick() pick
| Selection.assess_dope() assess
| TOP to Python correspondence
- EnergyData.radii_factor
- EnergyData.contact_shell nonbond
| EnergyData.radii_factor scale
| Model.write_data() write
| TOP to Python correspondence
- EnergyData.relative_dielectric
- EnergyData.relative_dielectric relative
| Coulomb restraint
| TOP to Python correspondence
- EnergyData.saxsdata
- Static and dynamic restraints
- EnergyData.sphere_stdv
- EnergyData.sphere_stdv soft-sphere
| EnergyData.dynamic_sphere calculate
| TOP to Python correspondence
- EnergyData.update_dynamic
- EnergyData.contact_shell nonbond
| EnergyData.update_dynamic nonbond
| ConjugateGradients() optimize
| MolecularDynamics() optimize
| TOP to Python correspondence
- EnergyProfile class
- The EnergyProfile class: a
- EnergyProfile.get_normalized()
- EnergyProfile.get_normalized() get
- EnergyProfile.get_smoothed()
- EnergyProfile.get_smoothed() get
- EnergyProfile.heavy_rms
- EnergyProfile.heavy_rms heavy
- EnergyProfile.min_rms
- EnergyProfile.min_rms minimal
- EnergyProfile.write_to_file()
- EnergyProfile.write_to_file() write
- env.io.hetatm
- Including water molecules, HETATM
- env.io.hydrogen
- Including water molecules, HETATM
| Building an all hydrogen
- env.io.water
- Including water molecules, HETATM
- Environ
- Environ() create
- Environ class
- The Environ class: MODELLER
- Environ()
- Simple usage
| Frequently asked questions (FAQ)
| Environ() create
| TOP to Python correspondence
- Environ.dendrogram()
- Environ.dendrogram() clustering
| Model.transfer_xyz() copy
| Alignment.id_table() calculate
| Alignment.compare_structures() compare
| SequenceDB.search() search
| TOP to Python correspondence
- Environ.edat
- Key for command descriptions
| Environ.edat default
| EnergyData() create
- Environ.io
- Key for command descriptions
| Environ.io default
| IOData() create
- Environ.libs
- Environ.libs MODELLER
- Environ.make_pssmdb()
- Environ.make_pssmdb() Create
| Profile.scan() Compare
- Environ.principal_components()
- Environ.principal_components() clustering
| Alignment.id_table() calculate
| Alignment.compare_structures() compare
| TOP to Python correspondence
- Environ.schedule_scale
- Changing the default optimization
| Environ.schedule_scale energy
| Schedule() create
- Environ.system()
- Environ.system() execute
| TOP to Python correspondence
- equilibrate
- MolecularDynamics() optimize
| Molecular dynamics
- eqvdst
- Alignment.check_structure_structure() check
- errors
- EOFError
- Controlling breakpoints and the
- FileFormatError
- Controlling breakpoints and the
| Model.read() read
| Alignment.append() read
| Alignment.read_one() read
- handling and recovering
- Controlling breakpoints and the
- IndexError
- Controlling breakpoints and the
- IOError
- Controlling breakpoints and the
- MemoryError
- Controlling breakpoints and the
- ModellerError
- Controlling breakpoints and the
| Model.assess_ga341() assess
- NetworkError
- Communicator.send_data() send
- NotImplementedError
- Controlling breakpoints and the
| Restraints.spline() approximate
- RemoteError
- Communicator.send_data() send
- SequenceMismatchError
- Alignment.append() read
| Alignment.read_one() read
- standard Python
- Controlling breakpoints and the
- StatisticsError
- Profile.build() Build
- TypeError
- Controlling breakpoints and the
- UnicodeError
- Controlling breakpoints and the
| Unicode
- ValueError
- Controlling breakpoints and the
| Restraints.spline() approximate
| Alignment.append_model() copy
| Chain.join() join
- ZeroDivisionError
- Controlling breakpoints and the
- exclude_distance
- Restraints.make_distance() make
- excluded pairs
- Excluded pairs
- ExcludedPair
- Excluded pairs
- exit_stage
- AutoModel.make() build
- ext_tree_file
- Alignments using external restraints
- extend_by_residue
- Selection.extend_by_residue() extend
- extension
- Model.get_insertions() return
| Model.get_deletions() return
| Selection.extend_by_residue() extend
- extra_data
- Model.write() write
- factor
- Mathematical forms of restraints
- fast_search
- SequenceDB.search() search
- fast_search_cutoff
- SequenceDB.search() search
- feature
- Mathematical forms of restraints
| Restraints.spline() approximate
- feature_weight
- Features of proteins used
- feature_weights
- Alignment of protein sequences
| Useful SALIGN information and
- features.Angle
- Feature types
- features.Density
- Feature types
- features.Dihedral
- Feature types
- features.DihedralDiff
- Feature types
- features.Distance
- Feature types
- features.MinimalDistance
- Feature types
- features.SolventAccess
- Feature types
- features.XCoordinate
- Feature types
- features.YCoordinate
- Feature types
- features.ZCoordinate
- Feature types
- fh
- Schedule.write() write
- File
- Environ.principal_components() clustering
| Topology.append() append
| Parameters.append() append
| Topology.write() write
| Model.read() read
| Model.write() write
| Model.write_data() write
| Restraints.append() read
| Restraints.write() write
| GroupRestraints.append() read
| Alignment.append() read
| Alignment.read_one() read
| Alignment.write() write
| Alignment.segment_matching() align
| Structure.write() write
| Structure.read() read
| Chain.write() write
| Profile.read() read
| Profile.write() write
| Density.read() read
| modfile.File() open
- file naming
- File naming
- file types
- File types
- file_exists
- modfile.inquire() check
- file_ext
- AutoModel.get_model_filename() get
| LoopModel.get_loop_model_filename() get
| Alignment.segment_matching() align
| modfile.default() generate
- file_id
- Alignment.segment_matching() align
| modfile.default() generate
- filename
- SAXSData.ini_saxs() Initialization
| complete_pdb() read
- filepattern
- actions.WriteStructure() write
- filter
- Chain.filter() check
| SequenceDB.filter() cluster
- filter_type
- Density.read() read
- filter_values
- Density.read() read
- first
- actions.WriteStructure() write
| actions.CHARMMTrajectory() write
- fit
- Selection.superpose() superpose
| Alignment.write() write
| Alignment.align2d() align
| Alignment.compare_structures() compare
| Alignment.align3d() align
| Alignment.malign3d() align
| Features of proteins used
| Useful SALIGN information and
- fit_atoms
- Alignment.compare_structures() compare
| Alignment.align3d() align
| Alignment.malign3d() align
| Features of proteins used
- fit_on_first
- Features of proteins used
| Useful SALIGN information and
- fit_pdbnam
- Features of proteins used
- fix_offsets
- Alignments using external restraints
- form
- Restraints.spline() approximate
- format
- Chain.write() write
- forms.Cosine
- Mathematical forms of restraints
- forms.Coulomb
- Mathematical forms of restraints
- forms.Factor
- Mathematical forms of restraints
- forms.Gaussian
- Mathematical forms of restraints
- forms.LennardJones
- Mathematical forms of restraints
- forms.LowerBound
- Mathematical forms of restraints
- forms.MultiBinormal
- Mathematical forms of restraints
- forms.MultiGaussian
- Mathematical forms of restraints
- forms.NDSpline
- Mathematical forms of restraints
- forms.Spline
- Mathematical forms of restraints
- forms.UpperBound
- Mathematical forms of restraints
- frequently asked questions
- Frequently asked questions (FAQ)
- gap_function
- Alignment.salign() align
| Alignment of protein structures
| Sub-optimal alignments
| Residue.curvature Mainchain
- gap_gap_score
- Gap penalties and correcting
- gap_penalties_1d
- Alignment.align() align
| Alignment.align2d() align
| Alignment.malign() align
| Alignment.salign() align
| Gap penalties and correcting
| Profile.scan() Compare
| SequenceDB.search() search
| SequenceDB.filter() cluster
| Profile file
- gap_penalties_2d
- Alignment.align2d() align
| Alignment of protein structures
| Gap penalties and correcting
- gap_penalties_3d
- Alignment.align3d() align
| Alignment.malign3d() align
| Features of proteins used
| Gap penalties and correcting
- gap_residue_score
- Gap penalties and correcting
- gapdist
- Alignment.check_sequence_structure() check
- gaps_in_target
- Profile.build() Build
- GB/SA scoring
- gbsa.Scorer() create
- gbsa.Scorer()
- Block (BLK) residues with
| gbsa.Scorer() create
- generate_topology
- Model.generate_topology() generate
- get_aligned_residue
- Residue.get_aligned_residue() get
- get_data
- Communicator.get_data() get
- get_deletions
- Model.get_deletions() return
- get_dope_profile
- Selection.get_dope_profile() get
- get_dopehr_profile
- Selection.get_dopehr_profile() get
- get_equivalent_atom
- Atom.get_equivalent_atom() get
- get_insertions
- Model.get_insertions() return
- get_leading_gaps
- Residue.get_leading_gaps() get
- get_loop_model_filename
- LoopModel.get_loop_model_filename() get
- get_model_filename
- AutoModel.get_model_filename() get
- get_normalized
- EnergyProfile.get_normalized() get
- get_normalized_dope_profile
- Model.get_normalized_dope_profile() get
- get_num_equiv
- Sequence.get_num_equiv() get
- get_optimize_actions
- AutoModel.get_optimize_actions() get
- get_range
- Restraints.spline() approximate
- get_refine_actions
- AutoModel.get_refine_actions() get
- get_sequence_identity
- Sequence.get_sequence_identity() get
- get_smoothed
- EnergyProfile.get_smoothed() get
- get_suboptimals
- Alignment.get_suboptimals() parse
- get_trailing_gaps
- Residue.get_trailing_gaps() get
- grid_search
- Density.grid_search() dock
- group
- Restraints.spline() approximate
- GroupRestraints
- GroupRestraints() create
- GroupRestraints class
- The GroupRestraints class: restraints
- GroupRestraints()
- Block (BLK) residues with
| Model.group_restraints all
| GroupRestraints() create
| TOP to Python correspondence
- GroupRestraints.append()
- GroupRestraints() create
| GroupRestraints.append() read
| TOP to Python correspondence
- guess_atom_type
- AutoModel.guess_atom_type() automatically
- guess_atom_types
- AutoModel.guess_atom_types() automatically
- guide_factor
- MolecularDynamics() optimize
- guide_time
- MolecularDynamics() optimize
- high
- Mathematical forms of restraints
- highderiv
- Mathematical forms of restraints
- host
- Job() create
- hot_atoms
- Selection.hot_atoms() atoms
- hybrid-36
- IOData.hybrid36 whether
- id1
- AutoModel.get_model_filename() get
| LoopModel.get_loop_model_filename() get
| modfile.default() generate
- id2
- AutoModel.get_model_filename() get
| LoopModel.get_loop_model_filename() get
| modfile.default() generate
- id_table
- Alignment.id_table() calculate
- improve_alignment
- Features of proteins used
| Useful SALIGN information and
- include_termini
- Model.get_insertions() return
| Model.get_deletions() return
| Model.loops() return
- info.bindir
- info.bindir MODELLER
- info.build_date
- info.version the
| info.build_date the
- info.debug
- info.debug this
- info.exe_type
- info.exe_type the
- info.jobname
- info.jobname name
| Job() create
- info.time_mark()
- info.time_mark() print
| TOP to Python correspondence
- info.version
- info.version the
- info.version_info
- info.version the
| info.version_info the
- ini_saxs
- SAXSData.ini_saxs() Initialization
- inifile
- AutoModel() prepare
- inimodel
- LoopModel() prepare
- init_velocities
- MolecularDynamics() optimize
- initialize_xyz
- Model.build() build
- input_profile_file
- Alignment.align2d() align
- input_weights_file
- Features of proteins used
- inquire
- modfile.inquire() check
- installation
- Obtaining and installing the
- intersegment
- Restraints.make() make
- io
- Key for command descriptions
| Environ.io default
| Model.generate_topology() generate
| Alignment.append() read
| Alignment.edit() edit
- IOData
- IOData() create
- IOData class
- The IOData class: coordinate
- IOData()
- Key for command descriptions
| IOData() create
| Model.read() read
- IOData.atom_files_directory
- Simple usage
| Changes since release 10.4
| Coordinate files and derivative
| IOData.atom_files_directory search
| Alignment file (PIR)
| TOP to Python correspondence
- IOData.convert_modres
- IOData() create
| IOData.convert_modres whether
| Model.read() read
- IOData.hetatm
- Block (BLK) residues with
| IOData() create
| IOData.hetatm whether
| IOData.convert_modres whether
| TOP to Python correspondence
- IOData.hybrid36
- IOData() create
| IOData.hybrid36 whether
| IOData.two_char_chain whether
| Model.read() read
| Model.write() write
| Chain.name chain
- IOData.hydrogen
- IOData() create
| IOData.hydrogen whether
| TOP to Python correspondence
- IOData.two_char_chain
- IOData() create
| IOData.hybrid36 whether
| IOData.two_char_chain whether
| Model.read() read
| Model.write() write
- IOData.water
- IOData() create
| IOData.hetatm whether
| IOData.water whether
| TOP to Python correspondence
- iterative_structural_align
- iterative_structural_align() obtain
- iterative_structural_align()
- Alignment of protein structures
| iterative_structural_align() obtain
- Job
- Job() create
- Job class
- Parallel job support
- Job()
- Job() create
| SGEPEJob() create
| SGEQsubJob() create
- Job.queue_task()
- Parallel job support
| Job() create
| Job.queue_task() submit
- Job.run_all_tasks()
- Parallel job support
| Job() create
| Job.queue_task() submit
| Job.run_all_tasks() run
| Job.yield_tasks_unordered() run
- Job.start()
- Parallel job support
| Job() create
| Job.start() start
- Job.worker_startup_commands
- Job() create
| Job.worker_startup_commands Worker
- Job.yield_tasks_unordered()
- Parallel job support
| Job() create
| Job.queue_task() submit
| Job.run_all_tasks() run
| Job.yield_tasks_unordered() run
- join
- Chain.join() join
- keep_disulfides
- Model.read() read
- knowns
- Building a model from
| AutoModel() prepare
| LoopModel() prepare
| Alignment.check_structure_structure() check
- last
- actions.WriteStructure() write
| actions.CHARMMTrajectory() write
- last_scales
- Schedule() create
| Schedule.make_for_model() trim
- Lennard-Jones
- Frequently asked questions (FAQ)
| AutoModel.guess_atom_types() automatically
| DOPELoopModel reference
| Residues with defined topology,
| Block (BLK) residues with
| Static and dynamic restraints
| Mathematical forms of restraints
| Rigid bodies
| EnergyData.contact_shell nonbond
| EnergyData.dynamic_lennard calculate
| EnergyData.lennard_jones_switch Lennard-Jones
| Restraints.make() make
| Selection.assess_dope() assess
| physical.Values() create
| Function
| Lennard-Jones restraint
- level
- log.level() Set
- Libraries.parameters
- Libraries.parameters parameter
- Libraries.topology
- Libraries.topology topology
- library
- gbsa.Scorer() create
| soap_loop.Scorer() create
- library_schedule
- AutoModel() prepare
- local_alignment
- Alignment.align() align
| Alignment.salign() align
- LocalWorker
- LocalWorker() create
- LocalWorker()
- LocalWorker() create
- log object
- The log object: controlling
- log.level()
- log.level() Set
| TOP to Python correspondence
- log.minimal()
- log.minimal() display
- log.none()
- log.none() display
- log.verbose()
- Useful SALIGN information and
| log.verbose() display
- log.very_verbose()
- log.very_verbose() display
- loop modeling
- Loop optimization
| Loop modeling method
- loop_assess_methods
- LoopModel() prepare
- LoopModel
- LoopModel() prepare
| LoopModel.get_loop_model_filename() get
- LoopModel class
- LoopModel reference
- LoopModel()
- LoopModel() prepare
| DOPELoopModel() prepare
- LoopModel.build_ini_loop()
- LoopModel.build_ini_loop() create
| Loop modeling method
- LoopModel.get_loop_model_filename()
- AutoModel.get_model_filename() get
| LoopModel.get_loop_model_filename() get
- LoopModel.loop.assess_methods
- AutoModel() prepare
| Model.assess_ga341() assess
| Model.assess_normalized_dope() assess
| Selection.assess_dope() assess
| Selection.assess_dopehr() assess
| soap_loop.Scorer() create
- LoopModel.loop.ending_model
- Automatic loop refinement after
| LoopModel.loop.ending_model last
| LoopModel.get_loop_model_filename() get
| Loop modeling method
- LoopModel.loop.library_schedule
- LoopModel.loop.library_schedule select
- LoopModel.loop.max_var_iterations
- LoopModel.loop.max_var_iterations select
- LoopModel.loop.md_level
- LoopModel.loop.md_level control
- LoopModel.loop.outputs
- Accessing output data after
| LoopModel.loop.outputs all
- LoopModel.loop.starting_model
- Automatic loop refinement after
| LoopModel.loop.starting_model first
| LoopModel.get_loop_model_filename() get
| Loop modeling method
- LoopModel.loop.write_defined_only
- LoopModel.loop.write_defined_only only
- LoopModel.loop.write_selection_only
- LoopModel.loop.write_selection_only write
| LoopModel.loop.write_defined_only only
- LoopModel.read_potential()
- LoopModel.read_potential() read
- LoopModel.select_loop_atoms()
- Defining loop regions for
| Refining an existing PDB
| LoopModel() prepare
| LoopModel.select_loop_atoms() select
| Loop modeling method
- LoopModel.user_after_single_loop_model()
- AutoModel.user_after_single_model() analyze
| LoopModel.user_after_single_loop_model() analyze
- loops
- Model.loops() return
- low
- Mathematical forms of restraints
- lowderiv
- Mathematical forms of restraints
- make
- AutoModel.make() build
| Topology.make() make
| Restraints.make() make
- make_chains
- Model.make_chains() Fetch
- make_distance
- Restraints.make_distance() make
- make_for_model
- Schedule.make_for_model() trim
- make_pssmdb
- Environ.make_pssmdb() Create
- make_region
- Model.make_region() define
- make_valid_pdb_coordinates
- Model.make_valid_pdb_coordinates() make
- malign
- Alignment.malign() align
- malign3d
- Alignment.malign3d() align
- matrix_comparison
- Alignment of protein sequences
- matrix_file
- Alignment.id_table() calculate
| Alignment.compare_sequences() compare
| Alignment.compare_structures() compare
- matrix_offset
- Environ.make_pssmdb() Create
| Alignment.align() align
| Profile.scan() Compare
| SequenceDB.filter() cluster
| Profile file
- matrix_offset_3d
- Features of proteins used
- max_aln_evalue
- Profile.scan() Compare
| Profile.build() Build
- max_atom_shift
- QuasiNewton() optimize
- max_diff_res
- SequenceDB.filter() cluster
- max_gap_length
- Alignment.align2d() align
- max_gaps_match
- Alignment.compare_sequences() compare
- max_iterations
- AutoModel.max_var_iterations select
| ConjugateGradients() optimize
| MolecularDynamics() optimize
- max_nonstdres
- Chain.filter() check
- max_unaligned_res
- SequenceDB.filter() cluster
- max_var_iterations
- AutoModel.very_fast() request
- maximal_distance
- AutoModel.max_ca_ca_distance Distance
| Restraints.make_distance() make
- maxlength
- Model.get_insertions() return
- maxs
- SAXSData.ini_saxs() Initialization
- maxworker
- SGEQsubJob() create
- md_return
- MolecularDynamics() optimize
- md_time_step
- MolecularDynamics() optimize
- mdl
- Model.res_num_from() residue
| Model.orient() center
| Restraints.reindex() renumber
| Schedule.make_for_model() trim
| Alignment.append_model() copy
| Alignment.compare_sequences() compare
| complete_pdb() read
- mdl2
- Selection.superpose() superpose
- mean
- Mathematical forms of restraints
- means
- Mathematical forms of restraints
- memory
- log.level() Set
- method
- Method for comparative protein
- min_atom_shift
- ConjugateGradients() optimize
- min_base_entries
- Alignment.edit() edit
- min_loop_length
- Alignment.segment_matching() align
- minimal
- log.minimal() display
- minimal_chain_length
- Chain.filter() check
- minimal_resolution
- Chain.filter() check
- minimal_stdres
- Chain.filter() check
- minlength
- Model.get_insertions() return
- minmax_db_seq_len
- SequenceDB.read() read
- missing parameters
- Frequently asked questions (FAQ)
| Residues with defined topology,
- mixflag
- SAXSData.ini_saxs() Initialization
- mmCIF files
- in alignment files
- Alignment file (PIR)
- reading
- Model.read() read
- search path
- IOData.atom_files_directory search
- temperature factor
- Model.write() write
| Model.transfer_xyz() copy
| Model.write_data() write
| Model.make_region() define
| Model.color() color
| Selection.energy() evaluate
| Alignment.compare_sequences() compare
| Atom.biso isotropic
- writing
- Model.write() write
- mode
- modfile.File() open
- Model
- Model() create
- Model class
- The Model class: handling
- Model()
- Model() create
- Model.assess_ga341()
- AutoModel() prepare
| Model.seq_id sequence
| Model.assess_ga341() assess
| Selection.assess_dope() assess
- Model.assess_normalized_dope()
- AutoModel() prepare
| Model.assess_normalized_dope() assess
| Model.get_normalized_dope_profile() get
| Selection.assess_dope() assess
- Model.atom_range()
- Feature types
| Model.atoms all
| Model.atom_range() return
| The Selection class: handling
- Model.atoms
- Residues and chains in
| Feature types
| Model.atoms all
| Model.atom_range() return
| The Selection class: handling
| The Atom class: a
- Model.build()
- Residues with defined topology,
| Model.remark text
| Model.build_sequence() build
| Model.generate_topology() generate
| Model.build() build
| Model.transfer_xyz() copy
| Selection.only_defined() select
| Flowchart of comparative modeling
| TOP to Python correspondence
- Model.build_sequence()
- Model.build_sequence() build
| Alignment.append_sequence() add
- Model.clear_topology()
- Model.clear_topology() clear
| Model.generate_topology() generate
- Model.color()
- Model.color() color
| TOP to Python correspondence
- Model.generate_topology()
- Frequently asked questions (FAQ)
| EnergyData.dynamic_sphere calculate
| EnergyData.dynamic_lennard calculate
| Model.read() read
| Model.build_sequence() build
| Model.clear_topology() clear
| Model.generate_topology() generate
| Model.write_psf() write
| Model.patch() patch
| Model.patch_ss_templates() guess
| Restraints.make() make
| Selection.rotate_dihedrals() change
| Flowchart of comparative modeling
| TOP to Python correspondence
- Model.get_deletions()
- Changes since release 10.5
| Model.get_insertions() return
| Model.get_deletions() return
| Model.loops() return
| The Selection class: handling
- Model.get_insertions()
- Model.get_insertions() return
| Model.get_deletions() return
| Model.loops() return
| The Selection class: handling
- Model.get_normalized_dope_profile()
- Model.get_normalized_dope_profile() get
| The EnergyProfile class: a
- Model.group_restraints
- EnergyData.dynamic_modeller calculate
| Model.group_restraints all
- Model.last_energy
- Model.last_energy last
| Model.write() write
- Model.loops()
- LoopModel.select_loop_atoms() select
| Model.get_insertions() return
| Model.get_deletions() return
| Model.loops() return
| The Selection class: handling
- Model.make_chains()
- Model.make_chains() Fetch
| Chain.filter() check
| TOP to Python correspondence
- Model.make_region()
- Model.make_region() define
| Atom.biso isotropic
| TOP to Python correspondence
- Model.make_valid_pdb_coordinates()
- Model.make_valid_pdb_coordinates() make
- Model.orient()
- Model.orient() center
| TOP to Python correspondence
- Model.patch()
- Including disulfide bridges
| Frequently asked questions (FAQ)
| AutoModel.special_patches() add
| Topology.append() append
| Parameters.append() append
| Model.generate_topology() generate
| Model.patch() patch
| TOP to Python correspondence
- Model.patch_ss()
- Model.patch_ss() guess
| TOP to Python correspondence
- Model.patch_ss_templates()
- Including disulfide bridges
| Model.patch_ss_templates() guess
| Model.patch_ss() guess
| Flowchart of comparative modeling
| TOP to Python correspondence
- Model.point()
- Model.point() return
| The Point class: a
- Model.read()
- Residues with defined topology,
| Model() create
| Model.remark text
| Model.read() read
| Model.write() write
| Model.generate_topology() generate
| Model.patch_ss() guess
| Model.build() build
| Model.make_chains() Fetch
| Restraints.condense() remove
| Selection.rotate_dihedrals() change
| Sequence.range residue
| Sequence.rfactor R
| modfile.File() open
| complete_pdb() read
| Flowchart of comparative modeling
| TOP to Python correspondence
- Model.remark
- Model.remark text
| Model.write() write
- Model.rename_segments()
- Residues and chains in
| Model.rename_segments() rename
| TOP to Python correspondence
- Model.reorder_atoms()
- Model.reorder_atoms() standardize
| TOP to Python correspondence
- Model.res_num_from()
- Model.generate_topology() generate
| Model.res_num_from() residue
| TOP to Python correspondence
- Model.residue_range()
- Refining only part of
| Feature types
| Model.residue_range() return
| Alpha() make
| Strand() make
| The Selection class: handling
| Sequence.residues list
- Model.resolution
- Model.resolution resolution
- Model.restraints
- Model.restraints all
| The Restraints class: static
- Model.saxs_chifun()
- Model.saxs_chifun() Calculate
- Model.saxs_intens()
- Model.saxs_intens() Calculate
- Model.saxs_pr()
- Model.saxs_pr() Calculate
| SAXSData.saxs_pr_read() Read
- Model.seq_id
- Model.seq_id sequence
| Model.write() write
| Model.assess_ga341() assess
- Model.to_iupac()
- Model() create
| Model.to_iupac() standardize
| TOP to Python correspondence
- Model.transfer_xyz()
- AutoModel.cluster() cluster
| Residues with defined topology,
| Environ.dendrogram() clustering
| Model.seq_id sequence
| Model.generate_topology() generate
| Model.build() build
| Model.transfer_xyz() copy
| Selection.only_defined() select
| Alignment.malign3d() align
| Flowchart of comparative modeling
| TOP to Python correspondence
- Model.write()
- Model.seq_id sequence
| Model.last_energy last
| Model.read() read
| Model.write() write
| Model.write_data() write
| Model.make_region() define
| Model.color() color
| Selection.write() write
| Chain.join() join
| modfile.File() open
| Flowchart of comparative modeling
| TOP to Python correspondence
- Model.write_data
- Residue.curvature Mainchain
- Model.write_data()
- Feature types
| EnergyData.radii_factor scale
| Model.write() write
| Model.write_data() write
| Model.make_region() define
| Atom.biso isotropic
| Atom.accessibility atomic
| Atomic solvent accessibility
| TOP to Python correspondence
- Model.write_psf()
- Model.write_psf() write
| actions.CHARMMTrajectory() write
- model_format
- Model.write() write
- model_segment
- Model.read() read
| Sequence.range residue
| complete_pdb() read
| Alignment file (PIR)
- modeller_path
- Job() create
- modfile.default()
- modfile.default() generate
- modfile.delete()
- modfile.delete() delete
| TOP to Python correspondence
- modfile.File()
- AutoModel() prepare
| Reading or writing files
| Environ() create
| Topology.append() append
| Parameters.append() append
| Topology.write() write
| Model.read() read
| Model.write() write
| Model.write_psf() write
| Restraints.append() read
| Restraints.write() write
| Schedule.write() write
| GroupRestraints() create
| GroupRestraints.append() read
| Alignment.append() read
| Alignment.read_one() read
| Alignment.write() write
| Alignment.id_table() calculate
| Structure.write() write
| Structure.read() read
| Chain.write() write
| EnergyProfile.write_to_file() write
| Profile.read() read
| Profile.write() write
| Density.read() read
| modfile.File() open
- modfile.inquire()
- modfile.inquire() check
| TOP to Python correspondence
- MolecularDynamics
- MolecularDynamics() optimize
- MolecularDynamics()
- MolecularDynamics() optimize
| actions.WriteStructure() write
| actions.CHARMMTrajectory() write
| Flowchart of comparative modeling
| TOP to Python correspondence
- molpdf
- Selection.energy() evaluate
| Selection.assess_dope() assess
| Selection.assess_dopehr() assess
| ConjugateGradients() optimize
| QuasiNewton() optimize
| MolecularDynamics() optimize
- mutate
- Selection.mutate() mutate
- n_exceed
- Selection.debug_function() test
- n_prof_iterations
- Profile.build() Build
| Profile file
- n_subopt
- Sub-optimal alignments
- natomtyp
- SAXSData.ini_saxs() Initialization
- NDSpline.add_dimension
- Mathematical forms of restraints
- neighbor_cutoff
- Model.write_data() write
- ngap
- Residue.add_leading_gaps() add
| Residue.add_trailing_gaps() add
| Residue.remove_leading_gaps() remove
| Residue.remove_trailing_gaps() remove
- nmesh
- SAXSData.ini_saxs() Initialization
- no_ter
- Model.write() write
- nodename
- SGEPEWorker() create
| SSHWorker() create
- none
- log.none() display
- nonstd_restraints
- AutoModel.nonstd_restraints() add
- normalize_pp_scores
- Useful SALIGN information and
- normalize_profile
- Selection.energy() evaluate
- nr
- SAXSData.ini_saxs() Initialization
- nr_exp
- SAXSData.ini_saxs() Initialization
- number_of_steps
- Density.grid_search() dock
- obj
- Selection.add() add
- off_diagonal
- Alignment.align() align
- only_atom_types
- Selection.only_atom_types() select
- only_defined
- Selection.only_defined() select
- only_het_residues
- Selection.only_het_residues() select
- only_mainchain
- Selection.only_mainchain() select
- only_no_topology
- Selection.only_no_topology() select
- only_residue_types
- Selection.only_residue_types() select
- only_sidechain
- Selection.only_sidechain() select
- only_std_residues
- Selection.only_std_residues() select
- only_water_residues
- Selection.only_water_residues() select
- open
- Mathematical forms of restraints
- optimization
- conjugate gradients
- ConjugateGradients() optimize
- molecular dynamics
- MolecularDynamics() optimize
- quasi-Newton
- QuasiNewton() optimize
- user-defined
- User-defined optimizers
- variable target function method
- Schedule() create
- options
- SGEQsubJob() create
- orient
- Model.orient() center
- OrientData
- Model.orient() center
- outfile
- SequenceDB.convert() convert
- output
- Model.write_data() write
| Restraints.spline() approximate
| Selection.energy() evaluate
| ConjugateGradients() optimize
| actions.Trace() write
| Alignment.compare_structures() compare
| Alignment.align3d() align
| Alignment.malign3d() align
| Alignment.salign() align
| Useful SALIGN information and
| SequenceDB.search() search
- output_alignments
- Profile.scan() Compare
- output_cod_file
- SequenceDB.filter() cluster
- output_grp_file
- SequenceDB.filter() cluster
- output_score_file
- Profile.scan() Compare
| Profile.build() Build
- output_weights_file
- Useful SALIGN information and
- overhang
- Alignment.edit() edit
| Alignment.align() align
| Alignment of protein structures
- overhang_auto_limit
- Alignment of protein structures
- overhang_factor
- Alignment of protein structures
- PairScorer
- soap_pp.PairScorer() create
- parameters
- GroupRestraints() create
- Parameters.append()
- Libraries.parameters parameter
| Parameters.append() append
| Parameters.read() read
- Parameters.clear()
- Parameters.clear() clear
| Parameters.read() read
- Parameters.read()
- AutoModel() prepare
| Parameters.read() read
| TOP to Python correspondence
- patch
- Model.patch() patch
- patch_default
- Model.build_sequence() build
| Model.generate_topology() generate
| Model.patch() patch
| complete_pdb() read
- patch_ss
- Model.patch_ss() guess
- patch_ss_templates
- Model.patch_ss_templates() guess
- PDB files
- in alignment files
- Alignment file (PIR)
- reading
- Model.read() read
- search path
- IOData.atom_files_directory search
- temperature factor
- Model.write() write
| Model.transfer_xyz() copy
| Model.write_data() write
| Model.make_region() define
| Model.color() color
| Selection.energy() evaluate
| Alignment.compare_sequences() compare
| Atom.biso isotropic
- writing
- Model.write() write
- physical.Values class
- physical.Values() create
- physical.Values()
- Environ.schedule_scale energy
| Strand() make
| Sheet() make
| physical.Values() create
- pick
- Restraints.pick() pick
- pick_hot_cutoff
- Selection.hot_atoms() atoms
- PIR format
- Alignment file (PIR)
- point
- Model.point() return
- Point class
- The Point class: a
- Point.select_sphere()
- The Selection class: handling
| Selection.select_sphere() select
| Point.select_sphere() select
| The Atom class: a
- Point.x
- Point.x x
| The Atom class: a
- pr_smooth
- SAXSData.ini_saxs() Initialization
- prf
- Alignment.append_profile() add
- principal_components
- Environ.principal_components() clustering
- probe_radius
- Model.write_data() write
- Profile
- Profile() create
- Profile class
- The Profile class: using
- Profile()
- Profile() create
- Profile.build()
- Environ.make_pssmdb() Create
| The Profile class: using
| Profile.scan() Compare
| Profile.build() Build
| The SequenceDB class: using
| SequenceDB.read() read
| SequenceDB.write() write
| Profile file
| TOP to Python correspondence
- Profile.read()
- Environ.make_pssmdb() Create
| Alignment.to_profile() convert
| Profile() create
| Profile.read() read
| Profile.to_alignment() profile
| Profile.scan() Compare
| Profile.build() Build
| SequenceDB.read() read
| Profile file
| TOP to Python correspondence
- Profile.scan()
- Environ.make_pssmdb() Create
| The Profile class: using
| Profile() create
| Profile.scan() Compare
| PSSMDB() create
| PSSMDB.read() read
| TOP to Python correspondence
- Profile.to_alignment()
- Alignment.append_profile() add
| Profile.to_alignment() profile
| Profile.build() Build
| TOP to Python correspondence
- Profile.write()
- Profile.write() write
| Profile.build() Build
| TOP to Python correspondence
- profile_format
- Environ.make_pssmdb() Create
| Profile.scan() Compare
- profile_list_file
- Environ.make_pssmdb() Create
| Profile.scan() Compare
- program updates
- MODELLER updates
- protonation states
- Model.read() read
- psa_integration_step
- Model.write_data() write
- pseudo atoms
- Specification of pseudo atoms
- pseudo_atom.CH2
- Specification of pseudo atoms
- pseudo_atom.CH31
- Specification of pseudo atoms
- pseudo_atom.CH32
- Specification of pseudo atoms
- pseudo_atom.GravityCenter
- Specification of pseudo atoms
- PSF files
- writing
- Model.write_psf() write
- pssm_file
- Profile.build() Build
- PSSMDB
- PSSMDB() create
- PSSMDB()
- PSSMDB() create
- PSSMDB.read()
- PSSMDB() create
| PSSMDB.read() read
- pssmdb_name
- Environ.make_pssmdb() Create
- px
- Density.read() read
- py
- Density.read() read
- Python
- installation
- Obtaining and installing the
- license
- Copyright notice
- used by MODELLER
- Script file
- using MODELLER as a Python module
- Running MODELLER
- pz
- Density.read() read
- q1
- Mathematical forms of restraints
- q2
- Mathematical forms of restraints
- QuasiNewton
- QuasiNewton() optimize
- QuasiNewton()
- Rigid bodies
| QuasiNewton() optimize
- queue_task
- Job.queue_task() submit
- rand_seed
- Environ() create
- randomize_xyz
- Selection.randomize_xyz() randomize
- read
- Topology.read() read
| Parameters.read() read
| Model.read() read
| Structure.read() read
| Profile.read() read
| PSSMDB.read() read
| SequenceDB.read() read
| Density.read() read
- read_one
- Alignment.read_one() read
- read_potential
- LoopModel.read_potential() read
- reference_atom
- Selection.superpose() superpose
- reference_distance
- Selection.superpose() superpose
- refine_local
- Selection.superpose() superpose
- region_size
- Model.make_region() define
- reindex
- Restraints.reindex() renumber
- remove_gaps
- Alignment.append() read
| Alignment.read_one() read
- remove_leading_gaps
- Residue.remove_leading_gaps() remove
- remove_trailing_gaps
- Residue.remove_trailing_gaps() remove
- remove_unpicked
- Restraints.remove_unpicked() remove
- rename_segments
- Model.rename_segments() rename
- renumber_residues
- Model.rename_segments() rename
- reorder_atoms
- Model.reorder_atoms() standardize
- report
- Restraints.symmetry.report() report
- represtyp
- SAXSData.ini_saxs() Initialization
- reread
- Structure.reread() reread
- res_num_from
- Model.res_num_from() residue
- Residue class
- The Residue class: a
- Residue.add_leading_gaps()
- Residue.add_leading_gaps() add
- Residue.add_trailing_gaps()
- Residue.add_trailing_gaps() add
- Residue.alpha
- Residue.alpha α
- Residue.atoms
- Residue.atoms all
- Residue.chain
- Residue.chain chain
- Residue.chi1
- Residue.chi1 χ1
- Residue.chi2
- Residue.chi2 χ2
- Residue.chi3
- Residue.chi3 χ3
- Residue.chi4
- Residue.chi4 χ4
- Residue.chi5
- Residue.chi5 χ5
- Residue.code
- Residue.code One-letter
- Residue.curvature
- Residue.curvature Mainchain
- Residue.get_aligned_residue()
- Residue.get_aligned_residue() get
- Residue.get_leading_gaps()
- Residue.get_leading_gaps() get
- Residue.get_trailing_gaps()
- Residue.get_trailing_gaps() get
- Residue.hetatm
- Residue.hetatm HETATM
- Residue.index
- Residue.index internal
| Residue.num PDB-style
- Residue.inscode
- Residue.num PDB-style
| Residue.intnum PDB-style
| Residue.inscode PDB-style
- Residue.intnum
- Residue.num PDB-style
| Residue.intnum PDB-style
- Residue.name
- Residue.name internal
- Residue.num
- Residue.num PDB-style
| Residue.intnum PDB-style
- Residue.omega
- Residue.omega ω
- Residue.pdb_name
- Residue.pdb_name PDB
- Residue.phi
- Residue.phi φ
| Residue.psi ψ
| Residue.omega ω
| Residue.alpha α
| Residue.chi1 χ1
| Residue.chi2 χ2
| Residue.chi3 χ3
| Residue.chi4 χ4
| Residue.chi5 χ5
| The Dihedral class: a
- Residue.psi
- Residue.psi ψ
- Residue.remove_leading_gaps()
- Residue.remove_leading_gaps() remove
- Residue.remove_trailing_gaps()
- Residue.remove_trailing_gaps() remove
- residue_range
- Model.residue_range() return
- residue_span_range
- EnergyData.covalent_cys use
| Restraints.make() make
| Restraints.pick() pick
| ConjugateGradients() optimize
- residue_span_sign
- Restraints.make() make
- residue_type
- Model.patch() patch
| Selection.mutate() mutate
- residues
- Frequently asked questions (FAQ)
| Model.patch() patch
| Alpha() make
| Strand() make
- modified
- IOData.convert_modres whether
| Model.read() read
- noncanonical
- IOData.convert_modres whether
| Model.read() read
- resolution
- Density.read() read
- restraint_group
- Restraints.make() make
- restraint_sel_atoms
- Restraints.make() make
| Restraints.pick() pick
- restraint_stdev
- Restraints.make_distance() make
- restraint_stdev2
- Restraints.make_distance() make
- restraint_type
- Restraints.make() make
| Restraints.unpick_redundant() unselect
- restraints
- feature types
- Feature types
- mathematical forms
- Mathematical forms of restraints
- pseudo atoms
- Specification of pseudo atoms
- rigid bodies
- Rigid bodies
- static versus dynamic
- Static and dynamic restraints
- symmetry
- Symmetry restraints
- violations
- Restraint violations
- Restraints class
- The Restraints class: static
- Restraints.add()
- Frequently asked questions (FAQ)
| Static and dynamic restraints
| Restraints.make() make
| Restraints.add() add
| Restraints.unpick() unselect
| Alpha() make
| Strand() make
| Sheet() make
| cispeptide() creates
| TOP to Python correspondence
- Restraints.append()
- Frequently asked questions (FAQ)
| Restraints.append() read
| Restraints.write() write
| TOP to Python correspondence
- Restraints.clear()
- Restraints.pseudo_atoms all
| Restraints.clear() delete
| Restraints.append() read
- Restraints.condense()
- Frequently asked questions (FAQ)
| Restraints.unpick_redundant() unselect
| Restraints.remove_unpicked() remove
| Restraints.condense() remove
| Restraints.unpick() unselect
| Restraints.reindex() renumber
| Alpha() make
| Strand() make
| TOP to Python correspondence
- Restraints.excluded_pairs
- Excluded pairs
| Restraints.excluded_pairs all
- Restraints.make()
- Frequently asked questions (FAQ)
| Coordinate files and derivative
| Residues with defined topology,
| Static and dynamic restraints
| Model.patch_ss_templates() guess
| Restraints.make() make
| Restraints.make_distance() make
| Restraints.pick() pick
| Restraints.spline() approximate
| Restraints.append() read
| Restraints.write() write
| Atomic solvent accessibility
| Flowchart of comparative modeling
| TOP to Python correspondence
- Restraints.make_distance()
- Frequently asked questions (FAQ)
| AutoModel.max_ca_ca_distance Distance
| Block (BLK) residues with
| Restraints.make() make
| Restraints.make_distance() make
| Atom.get_equivalent_atom() get
| Atomic solvent accessibility
- Restraints.nonbonded_pairs
- Restraints.nonbonded_pairs all
- Restraints.pick()
- Frequently asked questions (FAQ)
| Restraints.pick() pick
| Selection.hot_atoms() atoms
| Schedule() create
| Flowchart of comparative modeling
| TOP to Python correspondence
- Restraints.pseudo_atoms
- Specification of pseudo atoms
| Restraints.pseudo_atoms all
- Restraints.reindex()
- Restraints.reindex() renumber
| TOP to Python correspondence
- Restraints.remove_unpicked()
- Restraints.pick() pick
| Restraints.remove_unpicked() remove
| Restraints.condense() remove
- Restraints.rigid_bodies
- Rigid bodies
| Restraints.rigid_bodies all
- Restraints.spline()
- Restraints.make() make
| Restraints.spline() approximate
| User-defined restraint forms
| TOP to Python correspondence
- Restraints.symmetry
- Symmetry restraints
| Restraints.symmetry all
- Restraints.symmetry.report()
- Restraints.symmetry.report() report
- Restraints.unpick()
- Frequently asked questions (FAQ)
| Restraints.unpick() unselect
| Alpha() make
| Strand() make
| TOP to Python correspondence
- Restraints.unpick_all()
- Restraints.unpick_all() unselect
| Restraints.pick() pick
- Restraints.unpick_redundant()
- Restraints.make() make
| Restraints.unpick_redundant() unselect
| Restraints.condense() remove
- Restraints.write()
- Static and dynamic restraints
| Restraints.write() write
| Flowchart of comparative modeling
| TOP to Python correspondence
- restraints_filter
- Restraints.pick() pick
- restyp_lib_file
- Environ() create
- rho_solv
- SAXSData.ini_saxs() Initialization
- rigid bodies
- Rigid bodies
- RigidBody
- Rigid bodies
- rms_cutoff
- Selection.superpose() superpose
| Useful SALIGN information and
- rms_cutoffs
- Alignment.compare_structures() compare
- root_name
- AutoModel() prepare
| AutoModel.get_model_filename() get
| LoopModel.get_loop_model_filename() get
| Alignment.segment_matching() align
| modfile.default() generate
- rotate_dihedrals
- Selection.rotate_dihedrals() change
- rotate_mass_center
- Selection.rotate_mass_center() rotate
- rotate_origin
- Selection.rotate_origin() rotate
- rr_file
- Environ.make_pssmdb() Create
| Alignment.compare_sequences() compare
| Alignment.align() align
| Alignment.align2d() align
| Alignment.malign() align
| Features of proteins used
| Useful SALIGN information and
| Alignment.segment_matching() align
| Profile.scan() Compare
| SequenceDB.search() search
| SequenceDB.filter() cluster
| Profile file
- run_all_tasks
- Job.run_all_tasks() run
- run_cmd
- Worker.run_cmd() run
- s_hi
- SAXSData.ini_saxs() Initialization
- s_hybrid
- SAXSData.ini_saxs() Initialization
- s_low
- SAXSData.ini_saxs() Initialization
- s_max
- SAXSData.ini_saxs() Initialization
- s_min
- SAXSData.ini_saxs() Initialization
- salign
- Alignment.salign() align
- SalignData
- Alignment.salign() align
- saxs_chifun
- Model.saxs_chifun() Calculate
- saxs_intens
- Model.saxs_intens() Calculate
- saxs_pr
- Model.saxs_pr() Calculate
- saxs_pr_read
- SAXSData.saxs_pr_read() Read
- saxs_read
- SAXSData.saxs_read() Read
- SAXSData
- SAXSData() create
- SAXSData class
- The SAXSData class: using
- SAXSData()
- SAXSData() create
- SAXSData.ini_saxs()
- SAXSData() create
| SAXSData.ini_saxs() Initialization
| SAXSData.saxs_read() Read
- SAXSData.saxs_pr_read()
- SAXSData.saxs_pr_read() Read
- SAXSData.saxs_read()
- SAXSData.saxs_read() Read
- scale_factor
- Rigid bodies
- scan
- Profile.scan() Compare
- Schedule
- Schedule() create
- Schedule class
- The Schedule class: variable
- Schedule()
- Schedule() create
| Schedule.make_for_model() trim
| Schedule.write() write
- Schedule.make_for_model()
- Schedule() create
| Schedule.make_for_model() trim
| TOP to Python correspondence
- Schedule.write()
- Schedule.write() write
| TOP to Python correspondence
- schedule_scale
- Selection.hot_atoms() atoms
| Selection.energy() evaluate
| Selection.debug_function() test
| Selection.assess_dope() assess
| Selection.assess() assess
| ConjugateGradients() optimize
- score
- Model.assess_ga341() assess
| Selection.assess() assess
- score_statistics
- Profile.scan() Compare
- Scorer
- gbsa.Scorer() create
| soap_loop.Scorer() create
| soap_peptide.Scorer() create
| soap_protein_od.Scorer() create
- script file
- Script file
- search
- SequenceDB.search() search
- search_group_list
- SequenceDB.search() search
- search_randomizations
- SequenceDB.search() search
- search_sort
- SequenceDB.search() search
- search_top_list
- SequenceDB.search() search
- segment_cutoff
- Alignment.segment_matching() align
- segment_growth_c
- Alignment.segment_matching() align
- segment_growth_n
- Alignment.segment_matching() align
- segment_ids
- Model.rename_segments() rename
- segment_matching
- Alignment.segment_matching() align
- segment_report
- Alignment.segment_matching() align
- segment_shift
- Alignment.segment_matching() align
- select_atoms
- AutoModel.select_atoms() select
- select_loop_atoms
- LoopModel.select_loop_atoms() select
- select_sphere
- Selection.select_sphere() select
| Point.select_sphere() select
- Selection
- Selection() create
| Selection.hot_atoms() atoms
- Selection class
- The Selection class: handling
- Selection()
- Refining only part of
| Model.point() return
| Model.get_insertions() return
| Model.get_deletions() return
| Model.loops() return
| The Selection class: handling
| Selection() create
| Selection.extend_by_residue() extend
| Selection.by_residue() make
| Selection.select_sphere() select
| Selection.only_atom_types() select
| Selection.only_residue_types() select
| Selection.translate() translate
| Selection.rotate_origin() rotate
| Selection.rotate_mass_center() rotate
| Point.select_sphere() select
- Selection.add()
- The Selection class: handling
| Selection.add() add
- Selection.assess()
- Selection.assess_dope() assess
| Selection.assess() assess
| soap_loop.Scorer() create
| soap_protein_od.Scorer() create
- Selection.assess_dope()
- AutoModel() prepare
| DOPELoopModel reference
| Rigid bodies
| Model.assess_normalized_dope() assess
| Selection.assess_dope() assess
| Selection.assess_dopehr() assess
| Selection.get_dope_profile() get
| Selection.assess() assess
| Sequence.chains list
- Selection.assess_dopehr()
- AutoModel() prepare
| DOPEHRLoopModel reference
| Selection.assess_dopehr() assess
| Selection.get_dopehr_profile() get
- Selection.by_residue()
- The Selection class: handling
| Selection.by_residue() make
- Selection.debug_function()
- Selection.debug_function() test
| physical.Values() create
| TOP to Python correspondence
- Selection.energy()
- Including disulfide bridges
| Frequently asked questions (FAQ)
| Mathematical forms of restraints
| Model.write() write
| Model.generate_topology() generate
| Restraints.nonbonded_pairs all
| Selection.energy() evaluate
| Selection.debug_function() test
| Selection.assess_dope() assess
| Selection.assess() assess
| Atom.biso isotropic
| EnergyProfile.get_smoothed() get
| complete_pdb() read
| Function
| Flowchart of comparative modeling
| TOP to Python correspondence
- Selection.extend_by_residue()
- Selection.extend_by_residue() extend
| Selection.by_residue() make
| Selection.hot_atoms() atoms
- Selection.get_dope_profile()
- Selection.get_dope_profile() get
| The EnergyProfile class: a
- Selection.get_dopehr_profile()
- Selection.get_dopehr_profile() get
| The EnergyProfile class: a
- Selection.hot_atoms()
- Model.generate_topology() generate
| Selection.hot_atoms() atoms
| Function
| TOP to Python correspondence
- Selection.mutate()
- Selection.mutate() mutate
| TOP to Python correspondence
- Selection.only_atom_types()
- The Selection class: handling
| Selection.only_atom_types() select
- Selection.only_defined()
- The Selection class: handling
| Selection.only_defined() select
- Selection.only_het_residues()
- The Selection class: handling
| Selection.only_het_residues() select
- Selection.only_mainchain()
- The Selection class: handling
| Selection.only_mainchain() select
| Selection.only_sidechain() select
- Selection.only_no_topology()
- The Selection class: handling
| Selection.only_no_topology() select
- Selection.only_residue_types()
- The Selection class: handling
| Selection.only_residue_types() select
- Selection.only_sidechain()
- The Selection class: handling
| Selection.only_sidechain() select
- Selection.only_std_residues()
- The Selection class: handling
| Selection.only_std_residues() select
- Selection.only_water_residues()
- The Selection class: handling
| Selection.only_water_residues() select
- Selection.randomize_xyz()
- Selection.randomize_xyz() randomize
| Schedule() create
| Flowchart of comparative modeling
| TOP to Python correspondence
- Selection.rotate_dihedrals()
- Selection.rotate_dihedrals() change
| TOP to Python correspondence
- Selection.rotate_mass_center()
- Selection.rotate_origin() rotate
| Selection.rotate_mass_center() rotate
- Selection.rotate_origin()
- Selection.rotate_origin() rotate
| Selection.rotate_mass_center() rotate
| TOP to Python correspondence
- Selection.select_sphere()
- The Selection class: handling
| Selection.select_sphere() select
| Point.select_sphere() select
- Selection.superpose()
- Selection.superpose() superpose
| Alignment.compare_structures() compare
| TOP to Python correspondence
- Selection.transform()
- Selection.rotate_origin() rotate
| Selection.rotate_mass_center() rotate
| Selection.transform() transform
| TOP to Python correspondence
- Selection.translate()
- Selection.translate() translate
| TOP to Python correspondence
- Selection.unbuild()
- Selection.unbuild() undefine
| TOP to Python correspondence
- Selection.write()
- Model.write() write
| Selection.write() write
- selection_segment
- Alignment file (PIR)
- send_data
- Communicator.send_data() send
- seq
- Sequence.get_num_equiv() get
| Sequence.get_sequence_identity() get
- seq_database_file
- SequenceDB.read() read
| SequenceDB.search() search
- seq_database_format
- SequenceDB.filter() cluster
- seqid_cut
- SequenceDB.filter() cluster
- sequence
- AutoModel() prepare
| AutoModel.get_model_filename() get
| LoopModel() prepare
| LoopModel.get_loop_model_filename() get
| Selection.rotate_dihedrals() change
- Sequence class
- The Sequence class: a
- Sequence.atom_file
- Model.generate_topology() generate
| Alignment.append_model() copy
| Alignment.malign3d() align
| Sequence.atom_file PDB
| Structure.reread() reread
| Structure.read() read
| TOP to Python correspondence
- Sequence.chains
- The Model class: handling
| Model.atoms all
| The Selection class: handling
| Sequence.chains list
| The Chain class: a
- Sequence.code
- Alignment.append_model() copy
| Sequence.code alignment
| Alignment file (PIR)
| Profile file
| TOP to Python correspondence
- Sequence.get_num_equiv()
- Sequence.get_num_equiv() get
- Sequence.get_sequence_identity()
- Sequence.get_sequence_identity() get
- Sequence.name
- Sequence.name protein
- Sequence.prottyp
- Sequence.prottyp protein
- Sequence.range
- Sequence.range residue
- Sequence.residues
- Residues and chains in
| Feature types
| The Model class: handling
| Model.atoms all
| Model.residue_range() return
| The Selection class: handling
| Sequence.residues list
| The Residue class: a
- Sequence.resolution
- Sequence.resolution structure
- Sequence.rfactor
- Model.read() read
| Sequence.rfactor R
- Sequence.source
- Sequence.source source
- Sequence.transfer_res_prop()
- Alignment.write() write
| Sequence.transfer_res_prop() transfer
- SequenceDB
- SequenceDB() create
- SequenceDB class
- The SequenceDB class: using
- SequenceDB()
- SequenceDB() create
- SequenceDB.close()
- SequenceDB.close() close
- SequenceDB.convert()
- SequenceDB.read() read
| SequenceDB.convert() convert
- SequenceDB.filter()
- The SequenceDB class: using
| SequenceDB() create
| SequenceDB.read() read
| SequenceDB.filter() cluster
| TOP to Python correspondence
- SequenceDB.read()
- Alignment.append() read
| Profile.build() Build
| SequenceDB() create
| SequenceDB.read() read
| SequenceDB.write() write
| SequenceDB.convert() convert
| SequenceDB.search() search
| SequenceDB.filter() cluster
| Profile file
| TOP to Python correspondence
- SequenceDB.search()
- The SequenceDB class: using
| SequenceDB.search() search
| TOP to Python correspondence
- SequenceDB.write()
- SequenceDB.write() write
| SequenceDB.convert() convert
| TOP to Python correspondence
- set_output_model_format
- AutoModel.set_output_model_format() set
- SGEPEJob
- SGEPEJob() create
- SGEPEJob()
- SGEPEJob() create
- SGEPEWorker
- SGEPEWorker() create
- SGEPEWorker()
- SGEPEWorker() create
- SGEQsubJob
- SGEQsubJob() create
- SGEQsubJob()
- SGEQsubJob() create
| Job.run_all_tasks() run
- SGEQsubWorker
- SGEQsubWorker() create
- SGEQsubWorker()
- SGEQsubWorker() create
- Sheet
- Sheet() make
- Sheet()
- Sheet() make
- sheet_h_bonds
- Sheet() make
- signif_cutoff
- SequenceDB.search() search
- similarity_flag
- Features of proteins used
| Alignment of protein sequences
| Sub-optimal alignments
| Alignments using external restraints
| Useful SALIGN information and
- skip
- actions.WriteStructure() write
| actions.Trace() write
| actions.CHARMMTrajectory() write
- smoothing_window
- Selection.energy() evaluate
- soap_loop.Scorer()
- AutoModel() prepare
| Selection.assess() assess
| soap_loop.Scorer() create
| soap_peptide.Scorer() create
| soap_pp.Assessor() assess
| soap_protein_od.Scorer() create
- soap_peptide.Scorer()
- soap_peptide.Scorer() create
- soap_pp.Assessor()
- soap_pp.Assessor() assess
- soap_pp.AtomScorer()
- soap_pp.AtomScorer() create
| soap_pp.Assessor() assess
- soap_pp.PairScorer()
- soap_pp.PairScorer() create
| soap_pp.AtomScorer() create
| soap_pp.Assessor() assess
- soap_protein_od.Scorer()
- AutoModel() prepare
| Selection.assess() assess
| soap_protein_od.Scorer() create
- soft-sphere
- Frequently asked questions (FAQ)
| AutoModel.guess_atom_types() automatically
| DOPELoopModel reference
| Block (BLK) residues with
| Static and dynamic restraints
| The EnergyData class: objective
| EnergyData.update_dynamic nonbond
| EnergyData.sphere_stdv soft-sphere
| EnergyData.dynamic_sphere calculate
| EnergyData.radii_factor scale
| Restraints.make() make
| physical.Values() create
| Schedule() create
| Function
- solvation_model
- gbsa.Scorer() create
- spaceflag
- SAXSData.ini_saxs() Initialization
- special_patches
- AutoModel.special_patches() add
| Model.build_sequence() build
| complete_pdb() read
- special_restraints
- AutoModel.special_restraints() add
- spline
- Restraints.spline() approximate
- spline_dx
- Restraints.make() make
| Restraints.spline() approximate
- spline_min_points
- Restraints.make() make
| Restraints.spline() approximate
- spline_on_site
- Restraints.make() make
- spline_range
- Restraints.make() make
- ssh_command
- SSHWorker() create
- SSHWorker
- SSHWorker() create
- SSHWorker()
- SSHWorker() create
- start
- Model.atom_range() return
| Model.residue_range() return
| actions.WriteStructure() write
| Job.start() start
- start_type
- Density.grid_search() dock
- statistical potential
- Loop modeling method
- stdev
- Mathematical forms of restraints
- stdevs
- Mathematical forms of restraints
- steps
- Schedule() create
- Strand
- Strand() make
- Strand()
- Strand() make
| Sheet() make
- Structure.read()
- Structure.read() read
- Structure.reread()
- Structure.reread() reread
| Structure.read() read
- Structure.write()
- Structure.write() write
- structure_types
- Chain.filter() check
- submodel
- Topology.make() make
- subopt_offset
- Sub-optimal alignments
- summary_file
- Profile.scan() Compare
- superpose
- Selection.superpose() superpose
- superpose_refine
- Selection.superpose() superpose
- SuperposeData
- Selection.superpose() superpose
- surftyp
- Model.write_data() write
- swap_atoms_in_res
- Selection.superpose() superpose
- Symmetry
- Symmetry restraints
- symmetry restraints
- Symmetry restraints
- system
- Environ.system() execute
- temperature
- MolecularDynamics() optimize
| Density.grid_search() dock
- terms
- Selection.energy() evaluate
- time_mark
- info.time_mark() print
- to_alignment
- Profile.to_alignment() profile
- to_iupac
- Model.to_iupac() standardize
- to_profile
- Alignment.to_profile() convert
- Topology.append()
- Libraries.topology topology
| Topology.append() append
| Topology.read() read
| Selection.rotate_dihedrals() change
| TOP to Python correspondence
- Topology.clear()
- Topology.append() append
| Topology.clear() clear
| Topology.read() read
- Topology.make()
- Topology.append() append
| Topology.make() make
| Topology.submodel select
| Topology.write() write
| TOP to Python correspondence
- Topology.read()
- AutoModel() prepare
| Topology.read() read
| Topology.submodel select
| TOP to Python correspondence
- Topology.submodel
- Frequently asked questions (FAQ)
| EnergyData.radii_factor scale
| Topology.append() append
| Topology.make() make
| Topology.submodel select
| Model.generate_topology() generate
| Model.patch_ss() guess
| Model.write_data() write
| TOP to Python correspondence
- Topology.write()
- Topology.write() write
| TOP to Python correspondence
- Trace
- actions.Trace() write
- transfer_res_num
- complete_pdb() read
- transfer_res_prop
- Sequence.transfer_res_prop() transfer
- transfer_xyz
- Model.transfer_xyz() copy
- transform
- Selection.transform() transform
- translate
- Selection.translate() translate
- translate_type
- Density.grid_search() dock
- tutorial
- Using MODELLER for comparative
- unbuild
- Selection.unbuild() undefine
- Unicode
- Unicode
- unpick
- Restraints.unpick() unselect
- unpick_all
- Restraints.unpick_all() unselect
- unpick_redundant
- Restraints.unpick_redundant() unselect
- use_conv
- SAXSData.ini_saxs() Initialization
- use_lookup
- SAXSData.ini_saxs() Initialization
- use_offset
- SAXSData.ini_saxs() Initialization
- use_parallel_job
- AutoModel.use_parallel_job() parallelize
- use_rolloff
- SAXSData.ini_saxs() Initialization
- user_after_single_loop_model
- LoopModel.user_after_single_loop_model() analyze
- user_after_single_model
- AutoModel.user_after_single_model() analyze
- UTF-8
- Unicode
- Values
- Mathematical forms of restraints
| physical.Values() create
- varatom
- Alignment.compare_structures() compare
- variability_file
- Alignment.compare_sequences() compare
- variable target function method
- Changing the default optimization
- verbose
- log.verbose() display
- very_fast
- AutoModel.very_fast() request
- very_verbose
- log.very_verbose() display
- viol_report_cut
- Selection.hot_atoms() atoms
| Selection.energy() evaluate
- viol_report_cut2
- Selection.energy() evaluate
- virtual_atom.CH1
- Specification of pseudo atoms
- virtual_atom.CH1A
- Specification of pseudo atoms
- virtual_atom.CH2
- Specification of pseudo atoms
- voxel_size
- Density.read() read
- VTFM
- see variable target function method
- weights
- Mathematical forms of restraints
- weights_type
- Features of proteins used
- window
- EnergyProfile.get_smoothed() get
- window_size
- Profile.build() Build
| SequenceDB.read() read
| SequenceDB.write() write
| SequenceDB.search() search
| SequenceDB.filter() cluster
- Worker.run_cmd()
- Parallel job support
| Job() create
| Communicator.send_data() send
| Worker.run_cmd() run
- write
- Topology.write() write
| Model.write() write
| Restraints.write() write
| Selection.write() write
| Schedule.write() write
| Alignment.write() write
| Structure.write() write
| Chain.write() write
| Profile.write() write
| SequenceDB.write() write
- write_all_atoms
- actions.WriteStructure() write
- write_data
- Model.write_data() write
- write_fit
- Alignment.malign3d() align
| Features of proteins used
| Useful SALIGN information and
- write_psf
- Model.write_psf() write
- write_to_file
- EnergyProfile.write_to_file() write
- write_whole_pdb
- Alignment.malign3d() align
| Useful SALIGN information and
- WriteStructure
- actions.WriteStructure() write
- wswitch
- SAXSData.ini_saxs() Initialization
- yield_tasks_unordered
- Job.yield_tasks_unordered() run
- Z-score
- Model.assess_normalized_dope() assess
- z_comb
- Model.assess_ga341() assess
- z_pair
- Model.assess_ga341() assess
- z_surf
- Model.assess_ga341() assess
- zero_width_break
- Alignment.append_sequence() add
