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A
add_patch_definition() (pygen_structures.charmm_containers.CHARMMResidueTopologyFile method)
add_residue_definition() (pygen_structures.charmm_containers.CHARMMResidueTopologyFile method)
apply() (pygen_structures.charmm_containers.CHARMMPatchResidueDefinition method)
Atom (class in pygen_structures.mol_containers.atom)
C
CHARMMParameterFile (class in pygen_structures.charmm_containers)
CHARMMPatchResidueDefinition (class in pygen_structures.charmm_containers)
CHARMMResidue (class in pygen_structures.charmm_containers)
CHARMMResidueData (class in pygen_structures.charmm_containers)
CHARMMResidueDefinition (class in pygen_structures.charmm_containers)
CHARMMResidueTopologyFile (class in pygen_structures.charmm_containers)
check_parameters() (pygen_structures.charmm_containers.CHARMMParameterFile method)
(pygen_structures.mol_containers.molecule.Molecule method)
code_to_mol() (in module pygen_structures.convenience_functions)
F
finalize() (pygen_structures.mol_containers.molecule.Molecule method)
from_block() (pygen_structures.charmm_containers.CHARMMPatchResidueDefinition class method)
(pygen_structures.charmm_containers.CHARMMResidueDefinition class method)
from_file() (pygen_structures.charmm_containers.CHARMMParameterFile class method)
(pygen_structures.charmm_containers.CHARMMResidueTopologyFile class method)
from_pdb_line() (pygen_structures.mol_containers.atom.Atom class method)
from_residue_definition() (pygen_structures.charmm_containers.CHARMMResidue class method)
from_sequence() (pygen_structures.mol_containers.molecule.Molecule class method)
G
generate_coordinates() (pygen_structures.mol_containers.structure.Structure method)
get_adjacency_matrix() (pygen_structures.mol_containers.molecule.Molecule method)
get_conect_records() (pygen_structures.mol_containers.molecule.Molecule method)
get_unmatched() (pygen_structures.charmm_containers.CHARMMParameterFile method)
I
is_applicable_to() (pygen_structures.charmm_containers.CHARMMPatchResidueDefinition method)
L
load_charmm_dir() (in module pygen_structures.convenience_functions)
M
Molecule (class in pygen_structures.mol_containers.molecule)
P
pdb_to_mol() (in module pygen_structures.convenience_functions)
pygen_structures (module)
pygen_structures.charmm_containers (module)
pygen_structures.convenience_functions (module)
pygen_structures.mol_containers (module)
pygen_structures.mol_containers.atom (module)
pygen_structures.mol_containers.molecule (module)
pygen_structures.mol_containers.structure (module)
R
read_file() (pygen_structures.charmm_containers.CHARMMParameterFile method)
(pygen_structures.charmm_containers.CHARMMResidueTopologyFile method)
reorder_atoms() (pygen_structures.mol_containers.structure.Structure method)
S
sequence_to_mol() (in module pygen_structures.convenience_functions)
set_formal_charges() (pygen_structures.mol_containers.structure.Structure method)
Structure (class in pygen_structures.mol_containers.structure)
T
to_fragment_mol() (pygen_structures.charmm_containers.CHARMMResidueDefinition method)
to_mol() (pygen_structures.mol_containers.molecule.Molecule method)
(pygen_structures.mol_containers.structure.Structure method)
to_pdb_block() (pygen_structures.mol_containers.molecule.Molecule method)
to_pdb_file() (pygen_structures.mol_containers.molecule.Molecule method)
to_pdb_line() (pygen_structures.mol_containers.atom.Atom method)
to_psf_block() (pygen_structures.mol_containers.molecule.Molecule method)
to_psf_file() (pygen_structures.mol_containers.molecule.Molecule method)
to_psf_line() (pygen_structures.mol_containers.atom.Atom method)
to_residue() (pygen_structures.charmm_containers.CHARMMResidueDefinition method)
to_smarts() (pygen_structures.charmm_containers.CHARMMResidueDefinition method)
to_structure() (pygen_structures.charmm_containers.CHARMMResidueDefinition method)
(pygen_structures.mol_containers.molecule.Molecule method)
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