comp_chem_py
latest
Contents:
Developer guide
comp_chem_utils
cpmd_scritps
PDOS
comp_chem_py
Docs
»
Index
Edit on GitLab
Index
A
|
B
|
C
|
D
|
E
|
F
|
G
|
H
|
I
|
K
|
L
|
M
|
N
|
O
|
P
|
Q
|
R
|
S
|
T
|
U
|
V
|
W
|
X
A
add_atom() (residue method)
add_db_entry() (atom_type method)
add_row() (mol_info_table method)
(mol_xyz_table method)
atom (class in comp_chem_utils.pdbfile)
atom_name (class in comp_chem_utils.pdbfile)
atom_type (class in comp_chem_utils.molecule_data)
ATOMIC_MASS_AU (in module comp_chem_utils.conversions)
AU_TO_FS (in module comp_chem_utils.conversions)
AU_TO_JOULES (in module comp_chem_utils.conversions)
AU_TO_KELVIN (in module comp_chem_utils.conversions)
AU_TO_PS (in module comp_chem_utils.conversions)
AU_TO_S (in module comp_chem_utils.conversions)
avail_progs() (in module comp_chem_utils.program_info)
B
BOHR_TO_ANG (in module comp_chem_utils.conversions)
C
CAL_TO_JOULES (in module comp_chem_utils.conversions)
calculate_and_plot_pdos() (in module PDOS.PDOS_module)
center_of_mass() (in module comp_chem_utils.utils)
change_atom() (pdb_file method)
(residue method)
(structure method)
change_bond_length() (pdb_file method)
(residue method)
(structure method)
change_vector_norm() (in module comp_chem_utils.utils)
change_vector_norm_sym() (in module comp_chem_utils.utils)
check() (mol_data method)
(mol_file method)
(xyz_file method)
choose_exec() (in module comp_chem_utils.program_info)
comp_chem_utils.amino_acids (module)
comp_chem_utils.conversions (module)
comp_chem_utils.cpmd_utils (module)
comp_chem_utils.molecule_data (module)
comp_chem_utils.mts_md_turbo (module)
comp_chem_utils.mysql_tables (module)
comp_chem_utils.pdbfile (module)
comp_chem_utils.periodic (module)
comp_chem_utils.physcon (module)
comp_chem_utils.program_info (module)
comp_chem_utils.qmmm_utils (module)
comp_chem_utils.read_gaussian (module)
comp_chem_utils.sbatch_info (module)
comp_chem_utils.spectrum (module)
comp_chem_utils.utils (module)
convert() (in module comp_chem_utils.conversions)
cpmd_scripts.cell_size (module)
cpmd_scripts.cpmd_spec (module)
cpmd_scripts.get_cp_group (module)
cpmd_scripts.read_orbs_info (module)
cpmd_scripts.vmd_plot_cube (module)
create_scripts() (in module cpmd_scripts.vmd_plot_cube)
create_table() (mol_info_table method)
(mol_xyz_table method)
cross_section() (in module comp_chem_utils.spectrum)
D
data_update() (in module comp_chem_utils.mts_md_turbo)
delete_row() (mol_info_table method)
delete_table() (mol_xyz_table method)
descr() (in module comp_chem_utils.physcon)
detailed_output() (sbatch_option method)
E
Element (class in comp_chem_utils.periodic)
element() (in module comp_chem_utils.periodic)
EV_TO_JOULES (in module comp_chem_utils.conversions)
executable (class in comp_chem_utils.program_info)
export_xyz() (structure method)
F
find_duplicates() (mol_info_table method)
G
gauss_atom (class in comp_chem_utils.read_gaussian)
get_all() (Search method)
get_angle() (in module comp_chem_utils.utils)
get_chem_name() (mol_data method)
get_clean_atom_types() (in module comp_chem_utils.molecule_data)
get_col() (mol_info_table method)
get_dihedral_angle() (in module comp_chem_utils.utils)
get_distance() (in module comp_chem_utils.qmmm_utils)
(in module comp_chem_utils.utils)
get_distance_matrix() (in module comp_chem_utils.utils)
get_distance_matrix_2() (in module comp_chem_utils.utils)
get_env() (executable method)
get_exe() (executable method)
get_exec_line() (executable method)
get_file_as_list() (in module comp_chem_utils.utils)
get_forces_and_energy() (in module comp_chem_utils.mts_md_turbo)
get_gaussian_info() (in module comp_chem_utils.read_gaussian)
get_line() (in module comp_chem_utils.read_gaussian)
get_list_of_res() (structure method)
get_lmax_from_atomic_charge() (in module comp_chem_utils.utils)
get_natoms() (in module comp_chem_utils.cpmd_utils)
get_orbital_energies() (in module cpmd_scripts.read_orbs_info)
get_QM_region() (in module comp_chem_utils.qmmm_utils)
get_res_num() (in module comp_chem_utils.pdbfile)
get_rmsd() (in module comp_chem_utils.utils)
get_row() (mol_info_table method)
get_single() (Search method)
get_table() (mol_xyz_table method)
get_time_info() (in module comp_chem_utils.cpmd_utils)
get_transition_orbitals() (in module cpmd_scripts.read_orbs_info)
H
help() (in module comp_chem_utils.physcon)
I
init_from_db() (mol_data method)
init_from_mol() (mol_data method)
init_from_xyz() (mol_data method)
initialization() (in module comp_chem_utils.mts_md_turbo)
K
KCALMOL_TO_JOULES (in module comp_chem_utils.conversions)
keep_only() (pdb_file method)
(structure method)
L
load() (turbo_settings method)
M
make_new_dir() (in module comp_chem_utils.utils)
md_driver() (in module comp_chem_utils.mts_md_turbo)
md_settings (class in comp_chem_utils.mts_md_turbo)
modify_from_user() (sbatch_option method)
mol_data (class in comp_chem_utils.molecule_data)
mol_file (class in comp_chem_utils.molecule_data)
mol_info_table (class in comp_chem_utils.mysql_tables)
mol_xyz_table (class in comp_chem_utils.mysql_tables)
mysql_add_row() (in module comp_chem_utils.mysql_tables)
mysql_create_table() (in module comp_chem_utils.mysql_tables)
N
nres() (structure method)
nstr() (pdb_file method)
O
out() (atom_name method)
out_pdbfile() (pdb_file method)
out_to_db() (mol_data method)
out_to_file() (mol_file method)
(xyz_file method)
out_to_mol() (mol_data method)
out_to_xyz() (mol_data method)
output() (atom method)
(atom_type method)
(gauss_atom method)
(md_settings method)
(mol_data method)
(mol_file method)
(pdb_file method)
(residue method)
(sbatch_option method)
(structure method)
(xyz_file method)
P
pdb_file (class in comp_chem_utils.pdbfile)
PDOS.PDOS_module (module)
plot_dos_and_pdos() (in module PDOS.PDOS_module)
plot_spectrum() (in module comp_chem_utils.spectrum)
plot_stick_spectrum() (in module comp_chem_utils.spectrum)
print_constants() (in module comp_chem_utils.conversions)
print_spectrum() (in module comp_chem_utils.spectrum)
Q
qmmm_cpmd_atoms() (in module comp_chem_utils.cpmd_utils)
R
read() (atom method)
(atom_name method)
(pdb_file method)
(residue method)
(structure method)
read_atom_and_basis() (in module comp_chem_utils.read_gaussian)
read_basis() (in module comp_chem_utils.read_gaussian)
read_boolean() (in module comp_chem_utils.read_gaussian)
read_ENERGIES() (in module comp_chem_utils.cpmd_utils)
read_from_mol() (atom_type method)
read_from_table() (xyz_file method)
read_FTRAJECTORY() (in module comp_chem_utils.cpmd_utils)
read_GEOMETRY() (in module comp_chem_utils.cpmd_utils)
read_GEOMETRY_xyz() (in module comp_chem_utils.cpmd_utils)
read_mol() (mol_file method)
read_MTS_EXC_ENERG() (in module comp_chem_utils.cpmd_utils)
read_orbitals_and_coefs() (in module comp_chem_utils.read_gaussian)
read_SH_ENERG() (in module comp_chem_utils.cpmd_utils)
read_spectrum() (in module comp_chem_utils.spectrum)
read_standard_file() (in module comp_chem_utils.cpmd_utils)
read_table_spectrum() (in module comp_chem_utils.spectrum)
read_TRAJEC_xyz() (in module comp_chem_utils.cpmd_utils)
read_TRAJECTORY() (in module comp_chem_utils.cpmd_utils)
read_triangular_block() (in module comp_chem_utils.read_gaussian)
read_triangular_matrix() (in module comp_chem_utils.read_gaussian)
read_xyz() (xyz_file method)
read_xyz_structure() (in module comp_chem_utils.qmmm_utils)
read_xyz_table() (in module comp_chem_utils.molecule_data)
relsd() (in module comp_chem_utils.physcon)
rename_h_atoms() (residue method)
residue (class in comp_chem_utils.pdbfile)
return_xyz_table() (atom_type method)
S
sbatch_line() (in module comp_chem_utils.sbatch_info)
sbatch_option (class in comp_chem_utils.sbatch_info)
sd() (in module comp_chem_utils.physcon)
Search (class in comp_chem_utils.spectrum)
search_exc() (in module comp_chem_utils.spectrum)
search_osc() (in module comp_chem_utils.spectrum)
set() (sbatch_option method)
set_default() (sbatch_option method)
set_from_GUI() (atom_type method)
SIGMA_TO_EPS (in module comp_chem_utils.conversions)
SPEC_TO_SIGMA (in module comp_chem_utils.conversions)
spectral_function() (in module comp_chem_utils.spectrum)
split_TRAJEC_data() (in module comp_chem_utils.cpmd_utils)
structure (class in comp_chem_utils.pdbfile)
system_settings (class in comp_chem_utils.mts_md_turbo)
T
temperature_effect() (in module comp_chem_utils.spectrum)
test_conversion() (in module comp_chem_utils.conversions)
to_angstrom() (atom_type method)
(mol_file method)
turbo_settings (class in comp_chem_utils.mts_md_turbo)
type_() (in module comp_chem_utils.periodic)
U
update() (atom method)
(mol_info_table method)
V
value() (in module comp_chem_utils.physcon)
vel_auto_corr() (in module comp_chem_utils.utils)
vel_update() (in module comp_chem_utils.mts_md_turbo)
W
write_energies() (in module comp_chem_utils.mts_md_turbo)
write_TRAJEC_xyz() (in module comp_chem_utils.cpmd_utils)
write_xyz_data() (in module comp_chem_utils.mts_md_turbo)
X
xyz_data_to_np() (in module comp_chem_utils.cpmd_utils)
xyz_file (class in comp_chem_utils.molecule_data)
xyz_to_cpmd_atoms() (in module comp_chem_utils.cpmd_utils)
Read the Docs
v: latest
Versions
latest
Downloads
pdf
html
epub
On Read the Docs
Project Home
Builds
Free document hosting provided by
Read the Docs
.