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buildH 1.6.1 documentation
Installation
Usage
Command line options
Lipid def file format
Lipid json file format
Tutorials
Notebook01: Compute Order Parameters
Notebook02: Export the reconstructed trajectory
Notebook03: POPC/POPE mixture
Notebook04: Use
buildH
as a module
Notebook05: POPC/cholesterol mixture
Algorithms & validation
Algorithms for building hydrogens
Order parameters and statistics
Validation of buildH
API Reference
API reference for
UI
submodule
API reference for
core
submodule
API reference for
geometry
submodule
API reference for
hydrogens
submodule
API reference for
init_dics
submodule
API reference for
lipids
submodule
API reference for
utils
submodule
API reference for
writers
submodule
Changelog
Index
A
|
B
|
C
|
E
|
F
|
G
|
I
|
L
|
M
|
N
|
P
|
R
|
V
|
W
A
apply_rotation() (in module buildh.geometry)
B
build_all_Hs_calc_OP() (in module buildh.core)
build_system_hydrogens() (in module buildh.core)
buildh.core
module
buildh.geometry
module
buildh.hydrogens
module
buildh.init_dics
module
buildh.lipids
module
buildh.UI
module
buildh.utils
module
buildh.writers
module
BuildHError
buildHs_on_1C() (in module buildh.core)
C
calc_angle() (in module buildh.geometry)
calc_OP() (in module buildh.geometry)
calc_rotation_matrix() (in module buildh.geometry)
check_atom() (in module buildh.utils)
check_def_file() (in module buildh.utils)
check_def_topol_consistency() (in module buildh.utils)
check_slice_options() (in module buildh.utils)
check_topology() (in module buildh.lipids)
cross_product() (in module buildh.geometry)
E
entry_point() (in module buildh.UI)
F
fast_build_all_Hs_calc_OP() (in module buildh.core)
G
gen_coordinates_calcOP() (in module buildh.core)
get_CH() (in module buildh.hydrogens)
get_CH2() (in module buildh.hydrogens)
get_CH3() (in module buildh.hydrogens)
get_CH_double_bond() (in module buildh.hydrogens)
get_indexes() (in module buildh.core)
I
init_dic_OP() (in module buildh.init_dics)
is_allHs_present() (in module buildh.utils)
isfile() (in module buildh.UI)
L
launch() (in module buildh.UI)
M
main() (in module buildh.UI)
make_dic_atname2genericname() (in module buildh.init_dics)
make_dic_Cname2Hnames() (in module buildh.init_dics)
make_dic_lipids_with_indexes() (in module buildh.core)
module
buildh.core
buildh.geometry
buildh.hydrogens
buildh.init_dics
buildh.lipids
buildh.UI
buildh.utils
buildh.writers
N
norm() (in module buildh.geometry)
normalize() (in module buildh.geometry)
P
pandasdf2pdb() (in module buildh.writers)
parse_cli() (in module buildh.UI)
R
read_lipids_topH() (in module buildh.lipids)
V
vec2quaternion() (in module buildh.geometry)
W
write_OP() (in module buildh.writers)
write_OP_alternate() (in module buildh.writers)