Dabble
2.7.6
Command-line Usage
System Building with Dabble
Parameterization with Dabble
Utility Programs
API Examples
Dabble
Docs
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Index
Index
A
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C
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D
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F
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G
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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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R
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S
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T
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W
A
add_molecule() (Dabble.DabbleBuilder method)
AmberMatcher (class in Dabble.param)
AmberWriter (class in Dabble.param)
atomsel_remaining() (in module Dabble.molutils)
C
center_system() (in module Dabble.molutils)
CharmmMatcher (class in Dabble.param)
CharmmWriter (class in Dabble.param)
check_out_type() (in module Dabble.fileutils)
check_write_ok() (in module Dabble.fileutils)
combine_molecules() (in module Dabble.molutils)
concatenate_mae_files() (in module Dabble.fileutils)
convert_ions() (Dabble.DabbleBuilder method)
D
Dabble.fileutils (module)
Dabble.molutils (module)
DabbleBuilder (class in Dabble)
diameter() (in module Dabble.molutils)
F
file (Dabble.param.CharmmWriter attribute)
G
get_cell_size() (Dabble.DabbleBuilder method)
get_disulfide() (Dabble.param.AmberMatcher method)
(Dabble.param.CharmmMatcher method)
get_element() (Dabble.param.MoleculeMatcher static method)
get_extraresidue_atoms() (Dabble.param.MoleculeMatcher method)
get_linkage() (Dabble.param.AmberMatcher method)
get_lipid_head() (Dabble.param.AmberMatcher method)
get_lipid_tails() (Dabble.param.AmberMatcher method)
get_names() (Dabble.param.AmberMatcher method)
(Dabble.param.CharmmMatcher method)
(Dabble.param.MoleculeMatcher method)
get_net_charge() (in module Dabble.molutils)
get_num_salt_ions_needed() (in module Dabble.molutils)
get_patches() (Dabble.param.CharmmMatcher method)
get_system_dimensions() (in module Dabble.molutils)
get_system_net_charge() (in module Dabble.molutils)
get_unit() (Dabble.param.AmberMatcher method)
K
known_pres (Dabble.param.CharmmMatcher attribute)
(Dabble.param.MoleculeMatcher attribute)
known_res (Dabble.param.AmberMatcher attribute)
(Dabble.param.CharmmMatcher attribute)
(Dabble.param.MoleculeMatcher attribute)
L
lipid_composition() (in module Dabble.molutils)
lipid_sel (Dabble.param.CharmmWriter attribute)
load_solute() (in module Dabble.fileutils)
M
matcher (Dabble.param.CharmmWriter attribute)
MoleculeMatcher (class in Dabble.param)
molid (Dabble.param.CharmmWriter attribute)
molids (Dabble.DabbleBuilder attribute)
N
nodenames (Dabble.param.AmberMatcher attribute)
(Dabble.param.CharmmMatcher attribute)
(Dabble.param.MoleculeMatcher attribute)
num_atoms_remaining() (in module Dabble.molutils)
num_lipids_remaining() (in module Dabble.molutils)
num_waters_remaining() (in module Dabble.molutils)
O
opts (Dabble.DabbleBuilder attribute)
P
parse_vmd_graph() (Dabble.param.MoleculeMatcher static method)
patches (Dabble.param.CharmmMatcher attribute)
(Dabble.param.MoleculeMatcher attribute)
print_lipid_composition() (in module Dabble.molutils)
prompt_topos (Dabble.param.CharmmWriter attribute)
psf_name (Dabble.param.CharmmWriter attribute)
R
remove_molecule() (Dabble.DabbleBuilder method)
S
set_cations() (in module Dabble.molutils)
set_ion() (in module Dabble.molutils)
size (Dabble.DabbleBuilder attribute)
solute_sel (Dabble.DabbleBuilder attribute)
solute_xy_diameter() (in module Dabble.molutils)
T
tile_system() (in module Dabble.molutils)
tmp_dir (Dabble.DabbleBuilder attribute)
(Dabble.param.CharmmWriter attribute)
topologies (Dabble.param.AmberMatcher attribute)
(Dabble.param.CharmmMatcher attribute)
(Dabble.param.CharmmWriter attribute)
(Dabble.param.MoleculeMatcher attribute)
W
water_only (Dabble.DabbleBuilder attribute)
write() (Dabble.DabbleBuilder method)
(Dabble.param.AmberWriter method)
(Dabble.param.CharmmWriter method)
write_ct_blocks() (in module Dabble.fileutils)
write_final_system() (in module Dabble.fileutils)