Index

A

add_atoms (AddBranch attribute) add_branches (Modification attribute) add_to_modification_log() (AnnotatedStructure method) AddBranch (class in viennaptm.modification.modification_library)

anchor_atoms (AddBranch attribute) AnnotatedStructure (class in viennaptm.dataclasses.annotatedstructure) apply_transform() (in module viennaptm.modification.calculation.align) atom_mapping (Modification attribute) atoms_to_array() (Modifier static method)

B

build_command() (GromacsCommand method) build_gromacs_cmd() (EditConf method) (GromacsCommand method) (Grompp method) (Mdrun method) (PDB2GMX method) (Trjconv method)

C

chainsep (PDB2GMXParameters attribute) check_branch() (AddBranch method) clean_pdb (PDB2GMXParameters attribute)

compute_alignment_transform() (in module viennaptm.modification.calculation.align) config (ModifierParameters attribute) custom_library (ModificationLibraryMetadata attribute)

D

date (ModificationLibraryMetadata attribute) debug (ModifierParameters attribute)

delete_log_entry() (AnnotatedStructure method) dump_resolved_config() (ModifierParameters method)

E

EditConf (class in viennaptm.gromacs.editconf) ensure_paths() (PDB2GMXParameters class method) expected_outputs() (EditConf method) (GromacsCommand method) (Grompp method) (Mdrun method) (PDB2GMX method) (Trjconv method)

F

forcefield (PDB2GMXParameters attribute) from_cif() (AnnotatedStructure class method)

from_pdb() (AnnotatedStructure class method) from_rcsb() (AnnotatedStructure class method)

G

get_library() (Modifier method) get_log() (AnnotatedStructure method)

gromacs (ModifierParameters attribute) GromacsCommand (class in viennaptm.gromacs.gromacs_command) Grompp (class in viennaptm.gromacs.grompp)

I

ignore_h (PDB2GMXParameters attribute) index_file (PDB2GMXParameters attribute) input (ModifierParameters attribute) (PDB2GMXParameters attribute)

inspect_result() (GromacsCommand method) is_console_logging() (ModifierParameters method)

L

load_config_file() (ModifierParameters class method) load_residue_from_pdb() (ModificationLibrary method)

log_file_path() (ModifierParameters method) logger (ModifierParameters attribute)

M

Mdrun (class in viennaptm.gromacs.mdrun) merge (PDB2GMXParameters attribute) metadata (Modification attribute) (ModificationLibrary attribute) minimize_and_write_pdb() (in module viennaptm.gromacs.minimization_pipeline) model_config (AddBranch attribute) (Modification attribute) (ModificationLibrary attribute) (ModificationLibraryMetadata attribute) (Modifier attribute) (ModifierParameters attribute) (PDB2GMXParameters attribute)

Modification (class in viennaptm.modification.modification_library) ModificationLibrary (class in viennaptm.modification.modification_library) ModificationLibraryMetadata (class in viennaptm.modification.modification_library) modifications (ModificationLibrary attribute) Modifier (class in viennaptm.modification.application.modifier) ModifierParameters (class in viennaptm.entrypoints.viennaptm) modify (ModifierParameters attribute) modify() (Modifier method) mpi_prefix() (GromacsCommand method)

O

output (ModifierParameters attribute)

output_gro (PDB2GMXParameters attribute)

P

PDB2GMX (class in viennaptm.gromacs.pdb2gmx) PDB2GMXParameters (class in viennaptm.gromacs.pdb2gmx) posre_itp (PDB2GMXParameters attribute)

post_run_checks() (GromacsCommand method) print_log() (AnnotatedStructure method) ptm_list (ModifierParameters attribute)

R

remove_hydrogens() (Modifier static method) residue_modified_abbreviation (Modification attribute)

residue_original_abbreviation (Modification attribute) run() (GromacsCommand method)

T

target_templates (ModificationLibrary attribute) to_cif() (AnnotatedStructure method)

to_pdb() (AnnotatedStructure method) topology (PDB2GMXParameters attribute) Trjconv (class in viennaptm.gromacs.trjconv)

V

validate_file_input() (ModifierParameters class method) validate_input_modification() (ModifierParameters class method)

validate_output() (ModifierParameters class method) verbose (PDB2GMXParameters attribute) Visualizer() (in module viennaptm.utils.visualizer)

W

water (PDB2GMXParameters attribute)

weights (AddBranch attribute)