Index

A

add() (topology.CharmmTopology method) align() (operate.Move method) amino_acid_sld() (properties.Atomic method) amu() (properties.Atomic method) Atom (class in system)

atom() (system.Atom method) atom_charge() (system.Atom method) atom_vdw() (system.Atom method) Atomic (class in properties)

B

beta() (system.Atom method) betas() (system.Atom method)

betas_mask() (system.Atom method)

C

Calculate (class in calculate) calculate (module) calculate_angle() (in module linear_algebra) calculate_center_of_mass() (calculate.Calculate method) calculate_mass() (calculate.Calculate method) calculate_minimum_and_maximum() (calculate.Calculate method) calculate_molecular_formula() (calculate.Calculate method) calculate_principle_moments_of_inertia() (calculate.Calculate method) calculate_radius_of_gyration() (calculate.Calculate method) calculate_residue_charge() (calculate.Calculate method) calculate_root_mean_square_deviation() (calculate.Calculate method) center() (operate.Move method) chain() (system.Atom method)

chains() (system.Atom method) chains_mask() (system.Atom method) charge() (system.Atom method) charmm_names() (properties.Atomic method) charmm_type() (system.Atom method) CharmmTopology (class in topology) check_charmm_atomic_order_reorganize() (topology.CharmmTopology method) com() (system.Atom method) compare_list_ignore_order() (topology.CharmmTopology method) conect() (system.Atom method) coor() (system.Atom method) create_fasta() (properties.Atomic method) cross_product() (in module linear_algebra)

D

delete() (system.Atom method) delframes() (system.Atom method)

dihedral_angle() (in module linear_algebra) divide_molecule() (multiprocessing_sasmol.Multiprocessing_SasMol method)

E

effective_charge() (system.Atom method) effective_van_der_waals() (system.Atom method) element() (system.Atom method) elements() (system.Atom method)

elements_mask() (system.Atom method) energy() (system.Atom method) example_worker() (multiprocessing_sasmol.Multiprocessing_SasMol method)

F

fasta() (system.Atom method) filename() (system.Atom method)

find_u() (in module linear_algebra) formula() (system.Atom method)

G

get_frame_lists() (multiprocessing_sasmol.Multiprocessing_SasMol method)

H

header() (system.Atom method)

I

id() (system.Atom method)

index() (system.Atom method)

L

linear_algebra (module) load() (system.Atom method)

loc() (system.Atom method) long_range_potential() (system.Atom method)

M

maketop() (system.Atom method) mass() (system.Atom method) mass_check() (operate.Move method) matrix_multiply() (in module linear_algebra) maximum() (system.Atom method) minimum() (system.Atom method) Molecule (class in system)

Molecule_Maker (class in system) moltype() (system.Atom method) moltypes() (system.Atom method) Move (class in operate) Multiprocessing_SasMol (class in multiprocessing_sasmol) multiprocessing_sasmol (module)

N

name() (system.Atom method) names() (system.Atom method) names_mask() (system.Atom method) natoms() (system.Atom method) number_of_betas() (system.Atom method) number_of_chains() (system.Atom method) number_of_elements() (system.Atom method)

number_of_frames() (system.Atom method) number_of_moltypes() (system.Atom method) number_of_names() (system.Atom method) number_of_occupancies() (system.Atom method) number_of_resids() (system.Atom method) number_of_resnames() (system.Atom method) number_of_segnames() (system.Atom method)

O

occupancies() (system.Atom method) occupancies_mask() (system.Atom method) occupancy() (system.Atom method) one_letter_resname() (system.Atom method)

operate (module) original_index() (system.Atom method) original_resid() (system.Atom method)

P

patch_charmm_residue_atoms() (topology.CharmmTopology method) pmi() (system.Atom method)

properties (module)

R

read_charmm_topology() (topology.CharmmTopology method) rescode() (system.Atom method) resid() (system.Atom method) resids() (system.Atom method) resids_mask() (system.Atom method) residue_charge() (system.Atom method) residue_flag() (system.Atom method)

resname() (system.Atom method) resnames() (system.Atom method) resnames_mask() (system.Atom method) rg() (system.Atom method) rotate() (operate.Move method) rotate_euler() (operate.Move method) rotate_general_axis() (operate.Move method)

S

save() (system.Atom method) segname() (system.Atom method) segnames() (system.Atom method) segnames_mask() (system.Atom method) send_coordinates_to_vmd() (view.View method) set_average_vdw() (properties.Atomic method) setAtom() (system.Atom method) setAtom_charge() (system.Atom method) setAtom_vdw() (system.Atom method) setBeta() (system.Atom method) setBetas() (system.Atom method) setBetas_mask() (system.Atom method) setChain() (system.Atom method) setChains() (system.Atom method) setChains_mask() (system.Atom method) setCharge() (system.Atom method) setCharmm_type() (system.Atom method) setCom() (system.Atom method) setConect() (system.Atom method) setCoor() (system.Atom method) setEffective_charge() (system.Atom method) setEffective_van_der_waals() (system.Atom method) setElement() (system.Atom method) setElements() (system.Atom method) setElements_mask() (system.Atom method) setEnergy() (system.Atom method) setFasta() (system.Atom method) setFilename() (system.Atom method) setFormula() (system.Atom method) setHeader() (system.Atom method) setId() (system.Atom method) setIndex() (system.Atom method) setLoc() (system.Atom method) setLong_range_potential() (system.Atom method) setMass() (system.Atom method) setMaximum() (system.Atom method) setMinimum() (system.Atom method) setMoltype() (system.Atom method) setMoltypes() (system.Atom method) setName() (system.Atom method) setNames() (system.Atom method) setNames_mask() (system.Atom method) setNatoms() (system.Atom method)

setNumber_of_betas() (system.Atom method) setNumber_of_chains() (system.Atom method) setNumber_of_elements() (system.Atom method) setNumber_of_frames() (system.Atom method) setNumber_of_moltypes() (system.Atom method) setNumber_of_names() (system.Atom method) setNumber_of_occupancies() (system.Atom method) setNumber_of_resids() (system.Atom method) setNumber_of_resnames() (system.Atom method) setNumber_of_segnames() (system.Atom method) setOccupancies() (system.Atom method) setOccupancies_mask() (system.Atom method) setOccupancy() (system.Atom method) setOne_letter_resname() (system.Atom method) setOriginal_index() (system.Atom method) setOriginal_resid() (system.Atom method) setPmi() (system.Atom method) setRescode() (system.Atom method) setResid() (system.Atom method) setResids() (system.Atom method) setResids_mask() (system.Atom method) setResidue_charge() (system.Atom method) setResidue_flag() (system.Atom method) setResname() (system.Atom method) setResnames() (system.Atom method) setResnames_mask() (system.Atom method) setRg() (system.Atom method) setSegname() (system.Atom method) setSegnames() (system.Atom method) setSegnames_mask() (system.Atom method) setShape() (system.Atom method) setShort_range_potential() (system.Atom method) setTotal_mass() (system.Atom method) setType() (system.Atom method) setUnitcell() (system.Atom method) setup_charmm_residue_atoms() (topology.CharmmTopology method) setup_cys_patch_atoms_simple() (topology.CharmmTopology method) shape() (system.Atom method) short_range_potential() (system.Atom method) signed_angle() (in module linear_algebra) submit_jobs() (multiprocessing_sasmol.Multiprocessing_SasMol method) System (class in system) system (module)

T

topology (module) total_mass() (system.Atom method)

translate() (operate.Move method) type() (system.Atom method)

U

unitcell() (system.Atom method)

V

View (class in view)

view (module)