pdb2pqr
v3.6.1
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pdb2pqr
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Index
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A
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B
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C
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D
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E
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F
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G
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H
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I
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J
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K
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L
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M
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N
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O
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P
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Q
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R
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S
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T
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U
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V
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W
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__init__() (pdb2pqr.aa.ALA method)
(pdb2pqr.aa.ARG method)
(pdb2pqr.aa.ASN method)
(pdb2pqr.aa.ASP method)
(pdb2pqr.aa.Amino method)
(pdb2pqr.aa.CYS method)
(pdb2pqr.aa.GLN method)
(pdb2pqr.aa.GLU method)
(pdb2pqr.aa.GLY method)
(pdb2pqr.aa.HIS method)
(pdb2pqr.aa.ILE method)
(pdb2pqr.aa.LEU method)
(pdb2pqr.aa.LIG method)
(pdb2pqr.aa.LYS method)
(pdb2pqr.aa.MET method)
(pdb2pqr.aa.PHE method)
(pdb2pqr.aa.PRO method)
(pdb2pqr.aa.SER method)
(pdb2pqr.aa.THR method)
(pdb2pqr.aa.TRP method)
(pdb2pqr.aa.TYR method)
(pdb2pqr.aa.VAL method)
(pdb2pqr.aa.WAT method)
(pdb2pqr.biomolecule.Biomolecule method)
(pdb2pqr.cells.Cells method)
(pdb2pqr.debump.Debump method)
(pdb2pqr.definitions.Definition method)
(pdb2pqr.definitions.DefinitionAtom method)
(pdb2pqr.definitions.DefinitionHandler method)
(pdb2pqr.definitions.DefinitionResidue method)
(pdb2pqr.definitions.Patch method)
(pdb2pqr.forcefield.Forcefield method)
(pdb2pqr.forcefield.ForcefieldAtom method)
(pdb2pqr.forcefield.ForcefieldHandler method)
(pdb2pqr.forcefield.ForcefieldResidue method)
(pdb2pqr.hydrogens.HydrogenRoutines method)
(pdb2pqr.hydrogens.optimize.OptimizationHolder method)
(pdb2pqr.hydrogens.optimize.Optimize method)
(pdb2pqr.hydrogens.structures.Alcoholic method)
(pdb2pqr.hydrogens.structures.Carboxylic method)
(pdb2pqr.hydrogens.structures.Flip method)
(pdb2pqr.hydrogens.structures.Generic method)
(pdb2pqr.hydrogens.structures.HydrogenAmbiguity method)
(pdb2pqr.hydrogens.structures.HydrogenConformation method)
(pdb2pqr.hydrogens.structures.HydrogenDefinition method)
(pdb2pqr.hydrogens.structures.HydrogenHandler method)
(pdb2pqr.hydrogens.structures.PotentialBond method)
(pdb2pqr.hydrogens.structures.Water method)
(pdb2pqr.inputgen.Elec method)
(pdb2pqr.inputgen.Input method)
(pdb2pqr.io.DuplicateFilter method)
(pdb2pqr.ligand.mol2.Mol2Atom method)
(pdb2pqr.ligand.mol2.Mol2Bond method)
(pdb2pqr.ligand.mol2.Mol2Molecule method)
(pdb2pqr.ligand.topology.Topology method)
(pdb2pqr.na.ADE method)
(pdb2pqr.na.CYT method)
(pdb2pqr.na.GUA method)
(pdb2pqr.na.Nucleic method)
(pdb2pqr.na.THY method)
(pdb2pqr.na.URA method)
(pdb2pqr.pdb.ANISOU method)
(pdb2pqr.pdb.ATOM method)
(pdb2pqr.pdb.AUTHOR method)
(pdb2pqr.pdb.BaseRecord method)
(pdb2pqr.pdb.CAVEAT method)
(pdb2pqr.pdb.CISPEP method)
(pdb2pqr.pdb.COMPND method)
(pdb2pqr.pdb.CONECT method)
(pdb2pqr.pdb.CRYST1 method)
(pdb2pqr.pdb.DBREF method)
(pdb2pqr.pdb.END method)
(pdb2pqr.pdb.ENDMDL method)
(pdb2pqr.pdb.EXPDTA method)
(pdb2pqr.pdb.FORMUL method)
(pdb2pqr.pdb.HEADER method)
(pdb2pqr.pdb.HELIX method)
(pdb2pqr.pdb.HET method)
(pdb2pqr.pdb.HETATM method)
(pdb2pqr.pdb.HETNAM method)
(pdb2pqr.pdb.HETSYN method)
(pdb2pqr.pdb.HYDBND method)
(pdb2pqr.pdb.JRNL method)
(pdb2pqr.pdb.KEYWDS method)
(pdb2pqr.pdb.LINK method)
(pdb2pqr.pdb.MASTER method)
(pdb2pqr.pdb.MODEL method)
(pdb2pqr.pdb.MODRES method)
(pdb2pqr.pdb.MTRIXn method)
(pdb2pqr.pdb.NUMMDL method)
(pdb2pqr.pdb.OBSLTE method)
(pdb2pqr.pdb.ORIGXn method)
(pdb2pqr.pdb.REMARK method)
(pdb2pqr.pdb.REVDAT method)
(pdb2pqr.pdb.SCALEn method)
(pdb2pqr.pdb.SEQADV method)
(pdb2pqr.pdb.SEQRES method)
(pdb2pqr.pdb.SHEET method)
(pdb2pqr.pdb.SIGATM method)
(pdb2pqr.pdb.SIGUIJ method)
(pdb2pqr.pdb.SITE method)
(pdb2pqr.pdb.SLTBRG method)
(pdb2pqr.pdb.SOURCE method)
(pdb2pqr.pdb.SPRSDE method)
(pdb2pqr.pdb.SSBOND method)
(pdb2pqr.pdb.TER method)
(pdb2pqr.pdb.TITLE method)
(pdb2pqr.pdb.TURN method)
(pdb2pqr.pdb.TVECT method)
(pdb2pqr.psize.Psize method)
(pdb2pqr.residue.Residue method)
(pdb2pqr.structures.Atom method)
(pdb2pqr.structures.Chain method)
(pdb2pqr.topology.Topology method)
(pdb2pqr.topology.TopologyAtom method)
(pdb2pqr.topology.TopologyConformer method)
(pdb2pqr.topology.TopologyConformerAdd method)
(pdb2pqr.topology.TopologyConformerRemove method)
(pdb2pqr.topology.TopologyDihedral method)
(pdb2pqr.topology.TopologyHandler method)
(pdb2pqr.topology.TopologyReference method)
(pdb2pqr.topology.TopologyResidue method)
(pdb2pqr.topology.TopologyTautomer method)
(pdb2pqr.topology.TopologyTitrationState method)
A
A (in module pdb2pqr.na)
AA_DEF_PATH (in module pdb2pqr.config)
AA_NAMES (in module pdb2pqr.config)
add() (in module pdb2pqr.utilities)
add_atom() (pdb2pqr.aa.Amino method)
(pdb2pqr.aa.LIG method)
(pdb2pqr.aa.WAT method)
(pdb2pqr.forcefield.ForcefieldResidue method)
(pdb2pqr.hydrogens.structures.HydrogenConformation method)
(pdb2pqr.na.Nucleic method)
(pdb2pqr.residue.Residue method)
add_bond() (pdb2pqr.structures.Atom method)
add_cell() (pdb2pqr.cells.Cells method)
add_conf() (pdb2pqr.hydrogens.structures.HydrogenDefinition method)
add_dihedral_angle() (pdb2pqr.aa.Amino method)
(pdb2pqr.na.Nucleic method)
add_hydrogens() (pdb2pqr.biomolecule.Biomolecule method)
add_patch() (pdb2pqr.definitions.Definition method)
add_residue() (pdb2pqr.structures.Chain method)
ADE (class in pdb2pqr.na)
ALA (class in pdb2pqr.aa)
Alcoholic (class in pdb2pqr.hydrogens.structures)
Amino (class in pdb2pqr.aa)
analyze_connectivity() (in module pdb2pqr.utilities)
angle() (in module pdb2pqr.utilities)
ANGLE_CUTOFF (in module pdb2pqr.config)
ANISOU (class in pdb2pqr.pdb)
apply_force_field() (pdb2pqr.biomolecule.Biomolecule method)
apply_name_scheme() (pdb2pqr.biomolecule.Biomolecule method)
apply_patch() (pdb2pqr.biomolecule.Biomolecule method)
apply_pka_values() (pdb2pqr.biomolecule.Biomolecule method)
ARG (class in pdb2pqr.aa)
ASN (class in pdb2pqr.aa)
ASP (class in pdb2pqr.aa)
assign_cells() (pdb2pqr.cells.Cells method)
assign_charges() (pdb2pqr.ligand.mol2.Mol2Molecule method)
assign_parameters() (pdb2pqr.ligand.mol2.Mol2Molecule method)
assign_radii() (pdb2pqr.ligand.mol2.Mol2Molecule method)
assign_radius() (pdb2pqr.ligand.mol2.Mol2Atom method)
assign_termini() (pdb2pqr.biomolecule.Biomolecule method)
assign_terms() (in module pdb2pqr.ligand.peoe)
ATOM (class in pdb2pqr.pdb)
Atom (class in pdb2pqr.structures)
atom_names (pdb2pqr.ligand.mol2.Mol2Bond attribute)
atom_site() (in module pdb2pqr.cif)
atoms (pdb2pqr.biomolecule.Biomolecule attribute)
(pdb2pqr.structures.Chain attribute)
AUTHOR (class in pdb2pqr.pdb)
author() (in module pdb2pqr.cif)
AVOGADRO (in module pdb2pqr.config)
B
BACKBONE (in module pdb2pqr.config)
BaseRecord (class in pdb2pqr.pdb)
Biomolecule (class in pdb2pqr.biomolecule)
BOLTZMANN (in module pdb2pqr.config)
bond_order (pdb2pqr.ligand.mol2.Mol2Atom attribute)
bonded_atom_names (pdb2pqr.ligand.mol2.Mol2Atom attribute)
BONDED_SS_LIMIT (in module pdb2pqr.config)
build_main_parser() (in module pdb2pqr.main)
build_parser() (in module pdb2pqr.inputgen)
(in module pdb2pqr.psize)
BUMP_HEAVY_SIZE (in module pdb2pqr.config)
BUMP_HYDROGEN_SIZE (in module pdb2pqr.config)
C
C (in module pdb2pqr.na)
calculate_dihedral_angles() (pdb2pqr.biomolecule.Biomolecule method)
Carboxylic (class in pdb2pqr.hydrogens.structures)
CAVEAT (class in pdb2pqr.pdb)
CELL_SIZE (in module pdb2pqr.config)
Cells (class in pdb2pqr.cells)
center() (in module pdb2pqr.quatfit)
CFAC (in module pdb2pqr.psize)
Chain (class in pdb2pqr.structures)
characters() (pdb2pqr.definitions.DefinitionHandler method)
(pdb2pqr.forcefield.ForcefieldHandler method)
(pdb2pqr.hydrogens.structures.HydrogenHandler method)
(pdb2pqr.topology.TopologyHandler method)
charge (pdb2pqr.biomolecule.Biomolecule attribute)
(pdb2pqr.residue.Residue attribute)
CHARGE_ERROR (in module pdb2pqr.config)
check_files() (in module pdb2pqr.main)
check_options() (in module pdb2pqr.main)
CISPEP (class in pdb2pqr.pdb)
cispep() (in module pdb2pqr.cif)
CITATIONS (in module pdb2pqr.config)
cleanup() (pdb2pqr.hydrogens.HydrogenRoutines method)
complete() (pdb2pqr.hydrogens.structures.Alcoholic method)
(pdb2pqr.hydrogens.structures.Carboxylic method)
(pdb2pqr.hydrogens.structures.Flip method)
(pdb2pqr.hydrogens.structures.Generic method)
(pdb2pqr.hydrogens.structures.Water method)
COMPND (class in pdb2pqr.pdb)
compnd() (in module pdb2pqr.cif)
CONECT (class in pdb2pqr.pdb)
conect() (in module pdb2pqr.cif)
coords (pdb2pqr.ligand.mol2.Mol2Atom attribute)
(pdb2pqr.structures.Atom attribute)
count_models() (in module pdb2pqr.cif)
create_atom() (pdb2pqr.aa.Amino method)
(pdb2pqr.aa.LIG method)
(pdb2pqr.aa.WAT method)
(pdb2pqr.na.Nucleic method)
create_handler() (in module pdb2pqr.hydrogens)
create_html_typemap() (pdb2pqr.biomolecule.Biomolecule method)
create_residue() (pdb2pqr.biomolecule.Biomolecule method)
cross() (in module pdb2pqr.utilities)
CRYST1 (class in pdb2pqr.pdb)
cryst1() (in module pdb2pqr.cif)
CYS (class in pdb2pqr.aa)
CYT (class in pdb2pqr.na)
D
DA (in module pdb2pqr.na)
DBREF (class in pdb2pqr.pdb)
DC (in module pdb2pqr.na)
Debump (class in pdb2pqr.debump)
DEBUMP_ANGLE_STEP_SIZE (in module pdb2pqr.config)
DEBUMP_ANGLE_STEPS (in module pdb2pqr.config)
DEBUMP_ANGLE_TEST_COUNT (in module pdb2pqr.config)
debump_biomolecule() (pdb2pqr.debump.Debump method)
debump_residue() (pdb2pqr.debump.Debump method)
Definition (class in pdb2pqr.definitions)
DefinitionAtom (class in pdb2pqr.definitions)
DefinitionHandler (class in pdb2pqr.definitions)
DefinitionResidue (class in pdb2pqr.definitions)
DG (in module pdb2pqr.na)
dihedral() (in module pdb2pqr.utilities)
DIST_CUTOFF (in module pdb2pqr.config)
distance() (in module pdb2pqr.utilities)
(pdb2pqr.ligand.mol2.Mol2Atom method)
dot() (in module pdb2pqr.utilities)
drop_water() (in module pdb2pqr.main)
DT (in module pdb2pqr.na)
dump_apbs() (in module pdb2pqr.io)
dump_pickle() (pdb2pqr.inputgen.Input method)
DuplicateFilter (class in pdb2pqr.io)
dx_to_cube() (in module pdb2pqr.main)
E
Elec (class in pdb2pqr.inputgen)
ELEC_CHARGE (in module pdb2pqr.config)
electronegativity() (in module pdb2pqr.ligand.peoe)
element (pdb2pqr.ligand.mol2.Mol2Atom attribute)
ELEMENT_BY_GROUP (in module pdb2pqr.ligand)
END (class in pdb2pqr.pdb)
endElement() (pdb2pqr.definitions.DefinitionHandler method)
(pdb2pqr.forcefield.ForcefieldHandler method)
(pdb2pqr.hydrogens.structures.HydrogenHandler method)
(pdb2pqr.topology.TopologyHandler method)
ENDMDL (class in pdb2pqr.pdb)
equilibrate() (in module pdb2pqr.ligand.peoe)
expdata() (in module pdb2pqr.cif)
EXPDTA (class in pdb2pqr.pdb)
F
factorial() (in module pdb2pqr.utilities)
FADD (in module pdb2pqr.psize)
filter() (pdb2pqr.io.DuplicateFilter method)
FILTER_WARNINGS (in module pdb2pqr.config)
FILTER_WARNINGS_LIMIT (in module pdb2pqr.config)
finalize() (pdb2pqr.hydrogens.structures.Alcoholic method)
(pdb2pqr.hydrogens.structures.Carboxylic method)
(pdb2pqr.hydrogens.structures.Flip method)
(pdb2pqr.hydrogens.structures.Generic method)
(pdb2pqr.hydrogens.structures.Water method)
find_atom_torsions() (pdb2pqr.ligand.mol2.Mol2Molecule method)
find_coordinates() (in module pdb2pqr.quatfit)
find_matching_names() (pdb2pqr.forcefield.ForcefieldHandler class method)
find_nearby_atoms() (pdb2pqr.debump.Debump method)
find_new_rings() (pdb2pqr.ligand.mol2.Mol2Molecule method)
find_residue_conflicts() (pdb2pqr.debump.Debump method)
fix() (pdb2pqr.hydrogens.structures.Carboxylic method)
fix_flip() (pdb2pqr.hydrogens.structures.Flip method)
Flip (class in pdb2pqr.hydrogens.structures)
FORCE_FIELDS (in module pdb2pqr.config)
Forcefield (class in pdb2pqr.forcefield)
ForcefieldAtom (class in pdb2pqr.forcefield)
ForcefieldHandler (class in pdb2pqr.forcefield)
ForcefieldResidue (class in pdb2pqr.forcefield)
formal_charge (pdb2pqr.ligand.mol2.Mol2Atom attribute)
FORMUL (class in pdb2pqr.pdb)
from_pqr_line() (pdb2pqr.structures.Atom class method)
from_qcd_line() (pdb2pqr.structures.Atom class method)
G
G (in module pdb2pqr.na)
Generic (class in pdb2pqr.hydrogens.structures)
get() (pdb2pqr.forcefield.ForcefieldAtom method)
get_amber_params() (pdb2pqr.forcefield.Forcefield class method)
get_atom() (pdb2pqr.forcefield.ForcefieldResidue method)
(pdb2pqr.residue.Residue method)
get_bump_score() (pdb2pqr.debump.Debump method)
get_bump_score_atom() (pdb2pqr.debump.Debump method)
get_charmm_params() (pdb2pqr.forcefield.Forcefield class method)
get_closest_atom() (pdb2pqr.debump.Debump method)
get_common_string_rep() (pdb2pqr.structures.Atom method)
get_definitions() (in module pdb2pqr.io)
get_group() (pdb2pqr.forcefield.Forcefield method)
get_hbond_angle() (pdb2pqr.hydrogens.optimize.Optimize static method)
get_molecule() (in module pdb2pqr.io)
get_moveable_names() (pdb2pqr.residue.Residue method)
get_names() (pdb2pqr.forcefield.Forcefield method)
get_near_cells() (pdb2pqr.cells.Cells method)
get_nearest_bonds() (pdb2pqr.definitions.DefinitionResidue method)
get_old_header() (in module pdb2pqr.io)
get_pair_energy() (pdb2pqr.hydrogens.optimize.Optimize static method)
get_params() (pdb2pqr.forcefield.Forcefield method)
get_params1() (pdb2pqr.forcefield.Forcefield method)
get_parse_params() (pdb2pqr.forcefield.Forcefield class method)
get_pdb_file() (in module pdb2pqr.io)
get_pdb_string() (pdb2pqr.structures.Atom method)
get_position_with_three_bonds() (pdb2pqr.hydrogens.optimize.Optimize class method)
get_positions_with_two_bonds() (pdb2pqr.hydrogens.optimize.Optimize class method)
get_pqr_string() (pdb2pqr.structures.Atom method)
get_residue() (pdb2pqr.forcefield.Forcefield method)
GLN (class in pdb2pqr.aa)
GLU (class in pdb2pqr.aa)
GLY (class in pdb2pqr.aa)
GMEMCEIL (in module pdb2pqr.psize)
GMEMFAC (in module pdb2pqr.psize)
GUA (class in pdb2pqr.na)
H
has_atom() (pdb2pqr.forcefield.ForcefieldResidue method)
(pdb2pqr.residue.Residue method)
has_reference (pdb2pqr.structures.Atom attribute)
has_residue() (pdb2pqr.forcefield.Forcefield method)
HEADER (class in pdb2pqr.pdb)
header() (in module pdb2pqr.cif)
HELIX (class in pdb2pqr.pdb)
HET (class in pdb2pqr.pdb)
HETATM (class in pdb2pqr.pdb)
HETNAM (class in pdb2pqr.pdb)
HETSYN (class in pdb2pqr.pdb)
HIS (class in pdb2pqr.aa)
hold_residues() (pdb2pqr.biomolecule.Biomolecule method)
HYD_DEF_PATH (in module pdb2pqr.config)
HYDBND (class in pdb2pqr.pdb)
HydrogenAmbiguity (class in pdb2pqr.hydrogens.structures)
HydrogenConformation (class in pdb2pqr.hydrogens.structures)
HydrogenDefinition (class in pdb2pqr.hydrogens.structures)
HydrogenHandler (class in pdb2pqr.hydrogens.structures)
HydrogenRoutines (class in pdb2pqr.hydrogens)
I
ILE (class in pdb2pqr.aa)
initialize_full_optimization() (pdb2pqr.hydrogens.HydrogenRoutines method)
initialize_wat_optimization() (pdb2pqr.hydrogens.HydrogenRoutines method)
Input (class in pdb2pqr.inputgen)
is_backbone (pdb2pqr.definitions.DefinitionAtom attribute)
(pdb2pqr.structures.Atom attribute)
is_carboxylic_hbond() (pdb2pqr.hydrogens.structures.Carboxylic method)
is_hbond() (pdb2pqr.hydrogens.optimize.Optimize method)
is_hydrogen (pdb2pqr.structures.Atom attribute)
is_optimizeable() (pdb2pqr.hydrogens.HydrogenRoutines method)
is_repairable() (in module pdb2pqr.main)
J
jacobi() (in module pdb2pqr.quatfit)
JRNL (class in pdb2pqr.pdb)
K
KEYWDS (class in pdb2pqr.pdb)
keywds() (in module pdb2pqr.cif)
L
length (pdb2pqr.ligand.mol2.Mol2Bond attribute)
letter_code() (pdb2pqr.aa.ALA method)
(pdb2pqr.aa.ARG method)
(pdb2pqr.aa.ASN method)
(pdb2pqr.aa.ASP method)
(pdb2pqr.aa.CYS method)
(pdb2pqr.aa.GLN method)
(pdb2pqr.aa.GLU method)
(pdb2pqr.aa.GLY method)
(pdb2pqr.aa.HIS method)
(pdb2pqr.aa.ILE method)
(pdb2pqr.aa.LEU method)
(pdb2pqr.aa.LYS method)
(pdb2pqr.aa.MET method)
(pdb2pqr.aa.PHE method)
(pdb2pqr.aa.PRO method)
(pdb2pqr.aa.SER method)
(pdb2pqr.aa.THR method)
(pdb2pqr.aa.TRP method)
(pdb2pqr.aa.TYR method)
(pdb2pqr.aa.VAL method)
(pdb2pqr.na.ADE method)
(pdb2pqr.na.CYT method)
(pdb2pqr.na.GUA method)
(pdb2pqr.na.THY method)
(pdb2pqr.na.URA method)
(pdb2pqr.residue.Residue static method)
LEU (class in pdb2pqr.aa)
LIG (class in pdb2pqr.aa)
LINK (class in pdb2pqr.pdb)
LYS (class in pdb2pqr.aa)
M
main() (in module pdb2pqr.inputgen)
(in module pdb2pqr.main)
main_driver() (in module pdb2pqr.main)
make_atom_with_no_bonds() (pdb2pqr.hydrogens.optimize.Optimize method)
make_atom_with_one_bond_h() (pdb2pqr.hydrogens.optimize.Optimize class method)
make_atom_with_one_bond_lp() (pdb2pqr.hydrogens.optimize.Optimize class method)
make_water_with_one_bond() (pdb2pqr.hydrogens.optimize.Optimize class method)
MASTER (class in pdb2pqr.pdb)
MET (class in pdb2pqr.aa)
MODEL (class in pdb2pqr.pdb)
MODRES (class in pdb2pqr.pdb)
Mol2Atom (class in pdb2pqr.ligand.mol2)
Mol2Bond (class in pdb2pqr.ligand.mol2)
Mol2Molecule (class in pdb2pqr.ligand.mol2)
MTRIX1 (class in pdb2pqr.pdb)
MTRIX2 (class in pdb2pqr.pdb)
MTRIX3 (class in pdb2pqr.pdb)
MTRIXn (class in pdb2pqr.pdb)
N
NA_DEF_PATH (in module pdb2pqr.config)
NA_NAMES (in module pdb2pqr.config)
non_trivial() (in module pdb2pqr.main)
NONBONDED_BY_TYPE (in module pdb2pqr.ligand)
noninteger_charge() (in module pdb2pqr.utilities)
normalize() (in module pdb2pqr.utilities)
Nucleic (class in pdb2pqr.na)
num_bio_atoms (pdb2pqr.biomolecule.Biomolecule attribute)
num_bonded_heavy (pdb2pqr.ligand.mol2.Mol2Atom attribute)
num_bonded_hydrogen (pdb2pqr.ligand.mol2.Mol2Atom attribute)
num_heavy (pdb2pqr.biomolecule.Biomolecule attribute)
num_missing_heavy (pdb2pqr.biomolecule.Biomolecule attribute)
NUMMDL (class in pdb2pqr.pdb)
O
OBSLTE (class in pdb2pqr.pdb)
OFRAC (in module pdb2pqr.psize)
OptimizationHolder (class in pdb2pqr.hydrogens.optimize)
Optimize (class in pdb2pqr.hydrogens.optimize)
optimize_hydrogens() (pdb2pqr.hydrogens.HydrogenRoutines method)
ORIGX1 (class in pdb2pqr.pdb)
ORIGX2 (class in pdb2pqr.pdb)
ORIGX3 (class in pdb2pqr.pdb)
ORIGXn (class in pdb2pqr.pdb)
origxn() (in module pdb2pqr.cif)
P
parse_atoms() (pdb2pqr.ligand.mol2.Mol2Molecule method)
parse_bonds() (pdb2pqr.ligand.mol2.Mol2Molecule method)
parse_hydrogen() (pdb2pqr.hydrogens.HydrogenRoutines method)
parse_input() (pdb2pqr.psize.Psize method)
parse_lines() (pdb2pqr.psize.Psize method)
parse_string() (pdb2pqr.psize.Psize method)
Patch (class in pdb2pqr.definitions)
PATCH_DEF_PATH (in module pdb2pqr.config)
patch_map (pdb2pqr.biomolecule.Biomolecule attribute)
pdb2pqr (module)
pdb2pqr.aa (module)
pdb2pqr.biomolecule (module)
pdb2pqr.cells (module)
pdb2pqr.cif (module)
pdb2pqr.config (module)
pdb2pqr.debump (module)
pdb2pqr.definitions (module)
pdb2pqr.forcefield (module)
pdb2pqr.hydrogens (module)
pdb2pqr.hydrogens.optimize (module)
pdb2pqr.hydrogens.structures (module)
pdb2pqr.inputgen (module)
pdb2pqr.io (module)
pdb2pqr.ligand (module)
pdb2pqr.ligand.mol2 (module)
pdb2pqr.ligand.peoe (module)
pdb2pqr.ligand.topology (module)
pdb2pqr.main (module)
pdb2pqr.na (module)
pdb2pqr.pdb (module)
pdb2pqr.psize (module)
pdb2pqr.quatfit (module)
pdb2pqr.residue (module)
pdb2pqr.run (module)
pdb2pqr.structures (module)
pdb2pqr.topology (module)
pdb2pqr.utilities (module)
PEPTIDE_DIST (in module pdb2pqr.config)
PHE (class in pdb2pqr.aa)
pick_dihedral_angle() (pdb2pqr.residue.Residue method)
pka_switchstate() (pdb2pqr.hydrogens.HydrogenRoutines class method)
PotentialBond (class in pdb2pqr.hydrogens.structures)
print_biomolecule_atoms() (in module pdb2pqr.io)
print_input_files() (pdb2pqr.inputgen.Input method)
print_pdb() (in module pdb2pqr.main)
print_pqr() (in module pdb2pqr.main)
print_pqr_header() (in module pdb2pqr.io)
print_pqr_header_cif() (in module pdb2pqr.io)
print_splash_screen() (in module pdb2pqr.main)
PRO (class in pdb2pqr.aa)
Psize (class in pdb2pqr.psize)
Q
q2mat() (in module pdb2pqr.quatfit)
qchichange() (in module pdb2pqr.quatfit)
qfit() (in module pdb2pqr.quatfit)
qtransform() (in module pdb2pqr.quatfit)
qtrfit() (in module pdb2pqr.quatfit)
R
RA (in module pdb2pqr.na)
RADIANS_TO_DEGREES (in module pdb2pqr.config)
RADII (in module pdb2pqr.ligand)
RC (in module pdb2pqr.na)
read() (pdb2pqr.ligand.mol2.Mol2Molecule method)
read_atom() (in module pdb2pqr.pdb)
read_cif() (in module pdb2pqr.cif)
read_dx() (in module pdb2pqr.io)
read_hydrogen_def() (pdb2pqr.hydrogens.HydrogenRoutines method)
read_pdb() (in module pdb2pqr.pdb)
read_pqr() (in module pdb2pqr.io)
read_qcd() (in module pdb2pqr.io)
rebuild_tetrahedral() (pdb2pqr.aa.Amino method)
record_type() (pdb2pqr.pdb.BaseRecord method)
REDFAC (in module pdb2pqr.psize)
reference_map (pdb2pqr.biomolecule.Biomolecule attribute)
register_line_parser() (in module pdb2pqr.pdb)
REMARK (class in pdb2pqr.pdb)
remove_atom() (pdb2pqr.residue.Residue method)
remove_cell() (pdb2pqr.cells.Cells method)
remove_hydrogens() (pdb2pqr.biomolecule.Biomolecule method)
rename() (pdb2pqr.hydrogens.structures.Carboxylic method)
rename_atom() (pdb2pqr.residue.Residue method)
rename_residue() (pdb2pqr.residue.Residue method)
renumber_residues() (pdb2pqr.structures.Chain method)
reorder() (pdb2pqr.residue.Residue method)
repair_heavy() (pdb2pqr.biomolecule.Biomolecule method)
REPAIR_LIMIT (in module pdb2pqr.config)
reserialize() (pdb2pqr.biomolecule.Biomolecule method)
Residue (class in pdb2pqr.residue)
REVDAT (class in pdb2pqr.pdb)
RG (in module pdb2pqr.na)
RNA_MAPPING (in module pdb2pqr.config)
rotate_tetrahedral() (pdb2pqr.residue.Residue class method)
rotate_to_smallest() (pdb2pqr.ligand.mol2.Mol2Molecule static method)
rotmol() (in module pdb2pqr.quatfit)
RU (in module pdb2pqr.na)
run_pdb2pka() (in module pdb2pqr.run)
run_pdb2pqr() (in module pdb2pqr.run)
run_propka() (in module pdb2pqr.main)
run_psize() (pdb2pqr.psize.Psize method)
S
SCALE1 (class in pdb2pqr.pdb)
SCALE2 (class in pdb2pqr.pdb)
SCALE3 (class in pdb2pqr.pdb)
SCALEn (class in pdb2pqr.pdb)
scalen() (in module pdb2pqr.cif)
score_dihedral_angle() (pdb2pqr.debump.Debump method)
SEQADV (class in pdb2pqr.pdb)
SEQRES (class in pdb2pqr.pdb)
SER (class in pdb2pqr.aa)
set_all() (pdb2pqr.psize.Psize method)
set_center() (pdb2pqr.psize.Psize method)
set_chain_id() (pdb2pqr.residue.Residue method)
set_coarse_grid_dims() (pdb2pqr.psize.Psize method)
set_dihedral_angle() (pdb2pqr.debump.Debump method)
set_donors_acceptors() (pdb2pqr.biomolecule.Biomolecule method)
(pdb2pqr.residue.Residue method)
set_fine_grid_dims() (pdb2pqr.psize.Psize method)
set_fine_grid_points() (pdb2pqr.psize.Psize method)
set_focus() (pdb2pqr.psize.Psize method)
set_hip() (pdb2pqr.biomolecule.Biomolecule method)
set_length() (pdb2pqr.psize.Psize method)
set_optimizeable_hydrogens() (pdb2pqr.hydrogens.HydrogenRoutines method)
set_proc_grid() (pdb2pqr.psize.Psize method)
set_reference_distance() (pdb2pqr.biomolecule.Biomolecule method)
set_res_seq() (pdb2pqr.residue.Residue method)
set_rings() (pdb2pqr.ligand.mol2.Mol2Molecule method)
set_smallest() (pdb2pqr.psize.Psize method)
set_state() (pdb2pqr.aa.Amino method)
(pdb2pqr.aa.ARG method)
(pdb2pqr.aa.ASP method)
(pdb2pqr.aa.CYS method)
(pdb2pqr.aa.GLU method)
(pdb2pqr.aa.HIS method)
(pdb2pqr.aa.LYS method)
(pdb2pqr.aa.PRO method)
(pdb2pqr.aa.TYR method)
(pdb2pqr.na.ADE method)
(pdb2pqr.na.CYT method)
(pdb2pqr.na.GUA method)
(pdb2pqr.na.Nucleic method)
(pdb2pqr.na.THY method)
(pdb2pqr.na.URA method)
set_states() (pdb2pqr.biomolecule.Biomolecule method)
set_termini() (pdb2pqr.biomolecule.Biomolecule method)
set_torsions() (pdb2pqr.ligand.mol2.Mol2Molecule method)
setup_logger() (in module pdb2pqr.io)
setup_molecule() (in module pdb2pqr.main)
SHEET (class in pdb2pqr.pdb)
shortest_path() (in module pdb2pqr.utilities)
SIGATM (class in pdb2pqr.pdb)
SIGUIJ (class in pdb2pqr.pdb)
SITE (class in pdb2pqr.pdb)
SLTBRG (class in pdb2pqr.pdb)
SMALL_NUMBER (in module pdb2pqr.config)
sort_dict_by_value() (in module pdb2pqr.utilities)
SOURCE (class in pdb2pqr.pdb)
source() (in module pdb2pqr.cif)
SPACE (in module pdb2pqr.psize)
split_input() (in module pdb2pqr.inputgen)
SPRSDE (class in pdb2pqr.pdb)
SSBOND (class in pdb2pqr.pdb)
ssbond() (in module pdb2pqr.cif)
startElement() (pdb2pqr.definitions.DefinitionHandler method)
(pdb2pqr.forcefield.ForcefieldHandler method)
(pdb2pqr.hydrogens.structures.HydrogenHandler method)
(pdb2pqr.topology.TopologyHandler method)
subtract() (in module pdb2pqr.utilities)
switchstate() (pdb2pqr.hydrogens.HydrogenRoutines method)
T
TER (class in pdb2pqr.pdb)
test_dat_file() (in module pdb2pqr.io)
test_for_file() (in module pdb2pqr.io)
test_names_file() (in module pdb2pqr.io)
test_xml_file() (in module pdb2pqr.io)
THR (class in pdb2pqr.aa)
THY (class in pdb2pqr.na)
TITLE (class in pdb2pqr.pdb)
title() (in module pdb2pqr.cif)
TITLE_STR (in module pdb2pqr.config)
TITRATION_DICT (in module pdb2pqr.hydrogens)
Topology (class in pdb2pqr.ligand.topology)
(class in pdb2pqr.topology)
TOPOLOGY_DEF_PATH (in module pdb2pqr.config)
TopologyAtom (class in pdb2pqr.topology)
TopologyConformer (class in pdb2pqr.topology)
TopologyConformerAdd (class in pdb2pqr.topology)
TopologyConformerRemove (class in pdb2pqr.topology)
TopologyDihedral (class in pdb2pqr.topology)
TopologyHandler (class in pdb2pqr.topology)
TOPOLOGYPATH (in module pdb2pqr.topology)
TopologyReference (class in pdb2pqr.topology)
TopologyResidue (class in pdb2pqr.topology)
TopologyTautomer (class in pdb2pqr.topology)
TopologyTitrationState (class in pdb2pqr.topology)
transform_arguments() (in module pdb2pqr.main)
translate() (in module pdb2pqr.quatfit)
TRP (class in pdb2pqr.aa)
try_acceptor() (pdb2pqr.hydrogens.structures.Alcoholic method)
(pdb2pqr.hydrogens.structures.Carboxylic method)
(pdb2pqr.hydrogens.structures.Flip method)
(pdb2pqr.hydrogens.structures.Water method)
try_both() (pdb2pqr.hydrogens.structures.Alcoholic method)
(pdb2pqr.hydrogens.structures.Carboxylic method)
(pdb2pqr.hydrogens.structures.Flip method)
(pdb2pqr.hydrogens.structures.Water method)
try_donor() (pdb2pqr.hydrogens.structures.Alcoholic method)
(pdb2pqr.hydrogens.structures.Carboxylic method)
(pdb2pqr.hydrogens.structures.Flip method)
(pdb2pqr.hydrogens.structures.Water method)
try_positions_three_bonds_h() (pdb2pqr.hydrogens.optimize.Optimize method)
try_positions_three_bonds_lp() (pdb2pqr.hydrogens.optimize.Optimize method)
try_positions_with_two_bonds_h() (pdb2pqr.hydrogens.optimize.Optimize method)
try_positions_with_two_bonds_lp() (pdb2pqr.hydrogens.optimize.Optimize method)
try_single_alcoholic_h() (pdb2pqr.hydrogens.optimize.Optimize method)
try_single_alcoholic_lp() (pdb2pqr.hydrogens.optimize.Optimize method)
TURN (class in pdb2pqr.pdb)
TVECT (class in pdb2pqr.pdb)
TYR (class in pdb2pqr.aa)
U
U (in module pdb2pqr.na)
update_bonds() (pdb2pqr.biomolecule.Biomolecule method)
update_internal_bonds() (pdb2pqr.biomolecule.Biomolecule method)
update_map() (pdb2pqr.forcefield.ForcefieldHandler class method)
update_ss_bridges() (pdb2pqr.biomolecule.Biomolecule method)
update_terminus_status() (pdb2pqr.residue.Residue method)
URA (class in pdb2pqr.na)
V
VACUUM_PERMIT (in module pdb2pqr.config)
VAL (class in pdb2pqr.aa)
VALENCE_BY_ELEMENT (in module pdb2pqr.ligand)
VALENCE_BY_GROUP (in module pdb2pqr.ligand)
VERSION (in module pdb2pqr.config)
W
WAT (class in pdb2pqr.aa)
Water (class in pdb2pqr.hydrogens.structures)
water_residue_names (pdb2pqr.aa.WAT attribute)
write_cube() (in module pdb2pqr.io)
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