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PLAMS
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PLAMS
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Index
Index
_
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A
|
B
|
C
|
D
|
E
|
F
|
G
|
H
|
I
|
J
|
K
|
L
|
M
|
N
|
O
|
P
|
Q
|
R
|
S
|
T
|
U
|
V
|
W
|
X
|
Y
_
__add__() (Molecule method)
__array__() (Molecule method)
__call__() (DCDTrajectoryFile method)
(XYZTrajectoryFile method)
__contains__() (KFFile method)
(Results method)
(Settings method)
__delattr__() (Settings method)
__delitem__() (Settings method)
__getattr__() (Settings method)
__getitem__() (KFFile method)
(Molecule method)
(Results method)
(Settings method)
__getstate__() (Job method)
(Molecule method)
__iadd__() (Molecule method)
__init__() (AMSAnalysisJob method)
(AMSMDJob method)
(AMSMDScanDensityJob method)
(AMSMSDJob method)
(AMSNPTJob method)
(AMSNVEJob method)
(AMSNVESpawnerJob method)
(AMSNVTJob method)
(AMSRDFJob method)
(AMSVACFJob method)
(Atom method)
(Bond method)
(ConformersJob method)
(ConformersResults method)
(Cp2kJob method)
(CRSJob method)
(DCDTrajectoryFile method)
(DensfJob method)
(DiracJob method)
(FCFJob method)
(GridRunner method)
(Job method)
(JobManager method)
(JobRunner method)
(KFFile method)
(KFHistory method)
(KFReader method)
(Molecule method)
(MultiJob method)
(ORCAJob method)
(PeriodicTable method)
(RaspaJob method)
(Results method)
(RKFHistoryFile method)
(RKFTrajectoryFile method)
(SCMJob method)
(Settings method)
(SingleJob method)
(Units method)
(XYZHistoryFile method)
(XYZTrajectoryFile method)
__iter__() (Atom method)
(Bond method)
(KFFile method)
(KFReader method)
(Molecule method)
(MultiJob method)
(Settings method)
__len__() (Molecule method)
__missing__() (Settings method)
__new__() (_MetaResults static method)
(_MetaRunner static method)
(AMSCalculator static method)
__repr__() (Molecule method)
(Settings method)
__round__() (Molecule method)
__setattr__() (Settings method)
__setitem__() (KFFile method)
(Settings method)
__setstate__() (Molecule method)
__str__() (Atom method)
(Bond method)
(ConformersResults method)
(Molecule method)
(Settings method)
_atom_symbol() (SCMJob static method)
_atomic_numbers_input_order() (ADFResults method)
(MOPACResults method)
(SCMResults method)
_autodetect() (GridRunner method)
(KFReader method)
_caller_name_and_arg() (in module scm.plams.core.results)
_check_hash() (JobManager method)
_check_queue() (GridRunner method)
_clean() (JobManager method)
(Results method)
_construct_array_dict() (CRSResults method)
_convert_lattice() (ReaxFFJob static method)
_copy_to() (Results method)
_correct_chemical_system() (RKFHistoryFile method)
_create_index() (KFReader method)
_datablocks() (KFReader static method)
_dict_to_df() (CRSResults static method)
_execute() (Job method)
(MultiJob method)
(SingleJob method)
_export_attribute() (Results method)
(SCMResults method)
_extract_hessian() (ADFResults method)
_finalize() (Job method)
_flatten_variable() (RKFTrajectoryFile method)
_get_array_dict() (CRSResults method)
_get_bond_id() (Molecule method)
_get_data() (KFReader method)
_get_property() (PeriodicTable class method)
_get_ready() (Cp2kJob method)
(DiracJob method)
(Job method)
(MultiJob method)
(ORCAJob method)
(RaspaJob method)
(ReaxFFJob method)
(SingleJob method)
_get_single_value() (SCMResults method)
_in_thread() (in module scm.plams.core.jobrunner)
_int2inp() (ADFResults method)
(SCMResults method)
_kfpath() (SCMResults method)
_kfpresent() (SCMResults method)
_limit() (in module scm.plams.core.jobrunner)
_log_status() (Job method)
_MetaResults (class in scm.plams.core.results)
_MetaRunner (class in scm.plams.core.jobrunner)
_mol_from_rkf_section() (Molecule static method)
_notify() (MultiJob method)
_parse() (KFReader method)
_prepare() (Job method)
_privileged_access() (in module scm.plams.core.results)
_process_file() (Results method)
_read_block() (KFReader method)
_register() (JobManager method)
_remove_mol() (AMSAnalysisJob method)
(DensfJob method)
(FCFJob method)
(SCMJob method)
_replace_job_name() (Results static method)
_restrict() (in module scm.plams.core.results)
_result_type (ConformersJob attribute)
(Cp2kJob attribute)
(CRSJob attribute)
(ORCAJob attribute)
(RaspaJob attribute)
(VASPJob attribute)
_rewrite_molecule() (RKFHistoryFile method)
(RKFTrajectoryFile method)
_run_job() (JobRunner method)
_serialize_input() (SCMJob method)
_serialize_mol() (AMSAnalysisJob method)
(DensfJob method)
(FCFJob method)
(SCMJob method)
_set_energy() (RKFTrajectoryFile method)
_set_system_version_elements() (RKFHistoryFile method)
_split() (KFFile static method)
_store_historydata_for_step() (RKFTrajectoryFile method)
_str() (KFFile static method)
(Settings method)
_update_celldata() (RKFTrajectoryFile method)
_write_dictionary_to_history() (RKFTrajectoryFile method)
_write_ffield() (ReaxFFJob method)
_write_geofile() (ReaxFFJob method)
A
add_atom() (Molecule method)
add_bond() (Molecule method)
add_hatoms() (Molecule method)
add_Hs() (in module scm.plams.interfaces.molecule.rdkit)
add_molecule() (Molecule method)
add_to_class() (in module scm.plams.core.functions)
add_to_instance() (in module scm.plams.core.functions)
ADFResults (class in scm.plams.interfaces.adfsuite.adf)
align_lattice() (Molecule method)
AMSAnalysisJob (class in scm.plams.interfaces.adfsuite.amsanalysis)
AMSCalculator (class in scm.plams.interfaces.adfsuite.ase_calculator)
AMSJob (class in scm.plams.interfaces.adfsuite.ams)
AMSMDJob (class in scm.plams.recipes.md.amsmdjob)
AMSMDScanDensityJob (class in scm.plams.recipes.md.scandensity)
AMSMSDJob (class in scm.plams.recipes.md.trajectoryanalysis)
AMSNPTJob (class in scm.plams.recipes.md.amsmdjob)
AMSNPTResults (class in scm.plams.recipes.md.amsmdjob)
AMSNVEJob (class in scm.plams.recipes.md.amsmdjob)
AMSNVESpawnerJob (class in scm.plams.recipes.md.nvespawner)
AMSNVTJob (class in scm.plams.recipes.md.amsmdjob)
AMSRDFJob (class in scm.plams.recipes.md.trajectoryanalysis)
AMSResults (class in scm.plams.interfaces.adfsuite.ams)
AMSVACFJob (class in scm.plams.recipes.md.trajectoryanalysis)
AMSWorker (class in scm.plams.interfaces.adfsuite.amsworker)
AMSWorkerPool (class in scm.plams.interfaces.adfsuite.amsworker)
AMSWorkerResults (class in scm.plams.interfaces.adfsuite.amsworker)
angle() (Atom method)
(in module scm.plams.tools.geometry)
apply_reaction_smarts() (in module scm.plams.interfaces.molecule.rdkit)
apply_strain() (Molecule method)
apply_template() (in module scm.plams.interfaces.molecule.rdkit)
are_orbitals_fractionally_occupied() (AMSResults method)
as_array() (Molecule method)
as_dict() (Molecule method)
(Settings method)
as_vector() (Bond method)
ascii2unicode() (Units class method)
assign_chirality() (Molecule method)
Atom (class in scm.plams.mol.atom)
awk_file() (Results method)
awk_output() (Results method)
axis_rotation_matrix() (in module scm.plams.tools.geometry)
B
bend() (in module scm.plams.mol.identify)
Bond (class in scm.plams.mol.bond)
bond_matrix() (Molecule method)
C
calculate() (AMSCalculator method)
call() (GridRunner method)
(JobRunner method)
canonicalize_mol() (in module scm.plams.interfaces.molecule.rdkit)
cell_angles() (Molecule method)
cell_lengths() (Molecule method)
cell_shape() (in module scm.plams.tools.geometry)
cellvectors_from_shape() (in module scm.plams.tools.geometry)
check() (AMSAnalysisJob method)
(AMSJob method)
(ConformersJob method)
(Cp2kJob method)
(CrystalJob method)
(DensfJob method)
(DFTBPlusJob method)
(DiracJob method)
(Job method)
(MOPACJob method)
(MultiJob method)
(ORCAJob method)
(ORCAResults method)
(RaspaJob method)
(ReaxFFJob method)
(SCMJob method)
(SingleJob method)
(VASPJob method)
check_go() (Cp2kResults method)
check_scf() (Cp2kResults method)
clean_exit() (AMSCalculator method)
clear() (in module scm.plams.mol.identify)
close() (DCDTrajectoryFile method)
(RKFTrajectoryFile method)
(XYZTrajectoryFile method)
closest_atom() (Molecule method)
collect() (AMSResults method)
(ConformersResults method)
(DiracResults method)
(RaspaResults method)
(Results method)
(SCMResults method)
ConformersJob (class in scm.conformers)
ConformersResults (class in scm.conformers)
conversion_ratio() (Units class method)
convert() (Units class method)
copy() (Molecule method)
(Settings method)
cos_to_coskf() (CRSJob static method)
Cp2kJob (class in scm.plams.interfaces.thirdparty.cp2k)
Cp2kResults (class in scm.plams.interfaces.thirdparty.cp2k)
Cp2kSettings2Mol() (in module scm.plams.interfaces.thirdparty.cp2k)
CRSJob (class in scm.plams.interfaces.adfsuite.crs)
CRSResults (class in scm.plams.interfaces.adfsuite.crs)
CrystalJob (class in scm.plams.interfaces.thirdparty.crystal)
D
DCDTrajectoryFile (class in scm.plams.trajectories.dcdfile)
delete_all_bonds() (Molecule method)
delete_atom() (Molecule method)
delete_bond() (Molecule method)
delete_section() (KFFile method)
DensfJob (class in scm.plams.interfaces.adfsuite.densf)
DFTBPlusJob (class in scm.plams.interfaces.thirdparty.dftbplus)
DFTBPlusResults (class in scm.plams.interfaces.thirdparty.dftbplus)
dihedral() (in module scm.plams.tools.geometry)
DiracJob (class in scm.plams.interfaces.thirdparty.dirac)
DiracResults (class in scm.plams.interfaces.thirdparty.dirac)
distance_array() (in module scm.plams.tools.geometry)
distance_to() (Atom method)
distance_to_mol() (Molecule method)
distance_to_point() (Molecule method)
E
engine_names() (AMSResults method)
ensure_property() (AMSCalculator method)
F
FCFJob (class in scm.plams.interfaces.adfsuite.fcf)
file_to_traj() (in module scm.plams.tools.converters)
find_bond() (Molecule method)
find_case() (Settings method)
find_permutation() (Molecule method)
finish() (in module scm.plams.core.functions)
flatten() (Settings method)
forcefield_params_from_rkf() (Molecule method)
from_array() (Molecule method)
from_dict() (Molecule class method)
from_elements() (Molecule class method)
from_input() (AMSJob class method)
from_inputfile() (AMSJob class method)
(SCMJob class method)
from_rdmol() (in module scm.plams.interfaces.molecule.rdkit)
from_sequence() (in module scm.plams.interfaces.molecule.rdkit)
from_smarts() (in module scm.plams.interfaces.molecule.rdkit)
from_smiles() (in module scm.plams.interfaces.molecule.rdkit)
fromASE() (in module scm.plams.interfaces.molecule.ase)
full_runscript() (SingleJob method)
G
gaussian_output_to_ams() (in module scm.plams.tools.converters)
GeometryOptimization() (AMSWorker method)
GeometryOptimizations() (AMSWorkerPool method)
get() (Settings method)
get_activity_coefficient() (CRSResults method)
get_atomic_charges() (DFTBPlusResults method)
(ORCAResults method)
get_atomic_number() (PeriodicTable class method)
get_atomic_temperatures_at_step() (AMSResults method)
get_backbone_atoms() (in module scm.plams.interfaces.molecule.rdkit)
get_band_structure() (AMSResults method)
get_block_value() (RaspaResults method)
get_boltzmann_distribution() (ConformersResults method)
get_center_of_mass() (Molecule method)
get_charges() (AMSResults method)
(AMSWorkerResults method)
get_chirality() (Molecule method)
get_complete_molecules_within_threshold() (Molecule method)
get_conformations() (in module scm.plams.interfaces.molecule.rdkit)
get_conformers() (ConformersResults method)
get_connection_table() (Molecule method)
get_connectors() (PeriodicTable class method)
get_density() (Molecule method)
get_density_along_axis() (AMSResults method)
get_diffusion_coefficient_from_velocity_acf() (AMSResults method)
get_dipole() (ORCAResults method)
get_dipole_vector() (ADFResults method)
(ORCAResults method)
get_dipolegradients() (AMSResults method)
(AMSWorkerResults method)
get_dipolemoment() (AMSResults method)
(AMSWorkerResults method)
get_dispersion() (Cp2kResults method)
(ORCAResults method)
get_dispersion_energy() (VASPResults method)
get_elastictensor() (AMSResults method)
(AMSWorkerResults method)
get_electronegative() (PeriodicTable class method)
get_electrons() (ORCAResults method)
get_elements() (DCDTrajectoryFile method)
(XYZTrajectoryFile method)
get_energies() (ConformersResults method)
get_energy() (ADFResults method)
(AMSResults method)
(AMSWorkerResults method)
(Cp2kResults method)
(CRSResults method)
(DFTBPlusResults method)
(ORCAResults method)
(VASPResults method)
get_energy_decomposition() (ADFResults method)
get_energy_landscape() (AMSResults method)
get_engine_properties() (AMSResults method)
get_engine_results() (AMSResults method)
get_equilibrated_molecule() (AMSNPTResults method)
get_errormsg() (AMSJob method)
(AMSResults method)
(AMSWorkerResults method)
get_file_chunk() (Results method)
get_force_constants() (AMSResults method)
get_forcefield_params() (AMSResults method)
get_forces() (Cp2kResults method)
get_formula() (Molecule method)
get_fragment() (Molecule method)
get_frequencies() (ADFResults method)
(AMSResults method)
get_from_all_files() (RaspaResults method)
get_gradients() (ADFResults method)
(AMSResults method)
(AMSWorkerResults method)
(ORCAResults method)
get_green_kubo_viscosity() (AMSResults method)
get_hessian() (ADFResults method)
(AMSResults method)
(AMSWorkerResults method)
get_hirshfeld() (ORCAResults method)
get_hirshfeld_charges() (Cp2kResults method)
get_history_molecule() (AMSResults method)
get_history_property() (AMSResults method)
get_history_variables() (AMSResults method)
get_homo_energies() (AMSResults method)
get_input() (AMSJob method)
(ConformersJob method)
(Cp2kJob method)
(CrystalJob method)
(DFTBPlusJob method)
(DiracJob method)
(MOPACJob method)
(ORCAJob method)
(RaspaJob method)
(ReaxFFJob method)
(SCMJob method)
(SingleJob method)
(VASPJob method)
get_input_molecule() (ADFResults method)
(AMSResults method)
(AMSWorkerResults method)
get_isotherm() (RaspaResults method)
get_length() (DCDTrajectoryFile method)
(RKFTrajectoryFile method)
(XYZTrajectoryFile method)
get_lowest_conformer() (ConformersResults method)
get_lowest_energy() (ConformersResults method)
get_lumo_energies() (AMSResults method)
get_main_ase_atoms() (AMSResults method)
(AMSWorkerResults method)
get_main_molecule() (ADFResults method)
(AMSResults method)
(AMSWorkerResults method)
get_mass() (Molecule method)
(PeriodicTable class method)
get_md_cell_volumes() (Cp2kResults method)
get_md_infos() (Cp2kResults method)
get_md_pressure() (Cp2kResults method)
get_metallic() (PeriodicTable class method)
get_molecule() (AMSResults method)
(DFTBPlusResults method)
(SCMResults method)
get_molecule_indices() (Molecule method)
get_mulliken_charges() (Cp2kResults method)
get_multigrid_info() (Cp2kResults method)
get_multispecies_dist() (CRSResults method)
get_n_spin() (AMSResults method)
get_neb_results() (AMSResults method)
get_nested() (Settings method)
get_orbital_energies() (AMSResults method)
(ORCAResults method)
get_orbital_occupations() (AMSResults method)
get_output_chunk() (Results method)
get_pesscan_results() (AMSResults method)
get_plamsmol() (DCDTrajectoryFile method)
(RKFHistoryFile method)
(RKFTrajectoryFile method)
(XYZTrajectoryFile method)
get_power_spectrum() (AMSResults method)
get_prop_names() (CRSResults method)
get_properties() (ADFResults method)
(SCMResults method)
get_property_at_step() (AMSResults method)
get_radius() (PeriodicTable class method)
get_relative_energies() (ConformersResults method)
get_results() (CRSResults method)
get_rkf_skeleton() (AMSResults method)
get_runscript() (AMSJob method)
(ConformersJob method)
(Cp2kJob method)
(CrystalJob method)
(DFTBPlusJob method)
(DiracJob method)
(MOPACJob method)
(ORCAJob method)
(RaspaJob method)
(ReaxFFJob method)
(SCMJob method)
(SingleJob method)
(VASPJob method)
get_runtime() (Cp2kResults method)
(ORCAResults method)
get_scf_iterations() (ORCAResults method)
get_sigma_potential() (CRSResults method)
get_sigma_profile() (CRSResults method)
get_skeleton() (KFFile method)
get_smallest_homo_lumo_gap() (AMSResults method)
get_stresstensor() (AMSResults method)
(AMSWorkerResults method)
get_substructure() (in module scm.plams.interfaces.molecule.rdkit)
get_symbol() (PeriodicTable class method)
get_system_version() (AMSResults method)
get_task() (AMSJob method)
get_time_step() (AMSResults method)
get_timings() (ADFResults method)
(AMSResults method)
(Cp2kResults method)
(ORCAResults method)
get_unique_angles() (Molecule method)
get_unique_bonds() (Molecule method)
get_value() (RaspaResults method)
get_velocities_from() (AMSMDJob method)
get_velocity_acf() (AMSResults method)
grep_file() (Results method)
grep_output() (Results method)
GridRunner (class in scm.plams.core.jobrunner)
guess_atomic_charges() (Molecule method)
guess_bonds() (Molecule method)
guess_system_charge() (Molecule method)
H
hash() (Job method)
(MultiJob method)
(SingleJob method)
hash_input() (AMSJob method)
(ReaxFFJob method)
(SCMJob method)
(SingleJob method)
hash_runscript() (SingleJob method)
I
implemented_properties() (AMSCalculator property)
in_ring() (Molecule method)
index() (Molecule method)
init() (in module scm.plams.core.functions)
initialize() (in module scm.plams.mol.identify)
is_aromatic() (Bond method)
is_valid_stepnumber() (AMSResults method)
iter() (KFHistory method)
iter_optional() (KFHistory method)
iterate() (in module scm.plams.mol.identify)
J
Job (class in scm.plams.core.basejob)
JobManager (class in scm.plams.core.jobmanager)
JobRunner (class in scm.plams.core.jobrunner)
K
keys() (KFFile method)
KFFile (class in scm.plams.tools.kftools)
KFHistory (class in scm.plams.tools.kftools)
kfpath() (SCMResults method)
KFReader (class in scm.plams.tools.kftools)
knock() (in module scm.plams.mol.identify)
L
label() (Molecule method)
label_atoms() (in module scm.plams.mol.identify)
length() (Bond method)
load() (in module scm.plams.core.functions)
(SingleJob class method)
load_all() (in module scm.plams.core.functions)
load_external() (AMSJob class method)
(SingleJob class method)
load_job() (JobManager method)
load_reaxff_control() (in module scm.plams.interfaces.adfsuite.reaxff)
locate_rings() (Molecule method)
locate_rings_acm() (Molecule method)
locate_rings_networkx() (Molecule method)
log() (in module scm.plams.core.functions)
M
map_to_central_cell() (Molecule method)
merge() (Settings method)
modify_atom() (in module scm.plams.interfaces.molecule.rdkit)
module
scm.plams.interfaces.molecule.ase
scm.plams.interfaces.molecule.rdkit
scm.plams.tools.converters
scm.plams.tools.geometry
scm.plams.tools.plot
mol2CrystalConf() (in module scm.plams.interfaces.thirdparty.crystal)
Molecule (class in scm.plams.interfaces.molecule.ase)
(class in scm.plams.mol.molecule)
molecule() (DCDTrajectoryFile property)
(XYZTrajectoryFile property)
molecule_name() (in module scm.plams.mol.identify)
MOPACJob (class in scm.plams.interfaces.adfsuite.mopac)
MOPACResults (class in scm.plams.interfaces.adfsuite.mopac)
move_to() (Atom method)
MultiJob (class in scm.plams.core.basejob)
N
name() (AMSResults property)
(AMSWorkerResults property)
neighbors() (Atom method)
(Molecule method)
new_children() (MultiJob method)
new_name() (in module scm.plams.mol.identify)
newkf() (SCMResults method)
numbers() (Molecule property)
O
ok() (AMSResults method)
(AMSWorkerResults method)
(Job method)
ORCAJob (class in scm.plams.interfaces.thirdparty.orca)
ORCAResults (class in scm.plams.interfaces.thirdparty.orca)
order_ring() (Molecule method)
other_end() (Bond method)
other_jobs() (MultiJob method)
P
packmol() (in module scm.plams.interfaces.molecule.packmol)
packmol_microsolvation() (in module scm.plams.interfaces.molecule.packmol)
packmol_on_slab() (in module scm.plams.interfaces.molecule.packmol)
ParseInput() (AMSWorker method)
partition_protein() (in module scm.plams.interfaces.molecule.rdkit)
PeriodicTable (class in scm.plams.tools.periodic_table)
perturb_atoms() (Molecule method)
perturb_lattice() (Molecule method)
pickle() (Job method)
plot() (CRSResults method)
plot_band_structure() (in module scm.plams.tools.plot)
plot_molecule() (in module scm.plams.tools.plot)
pop() (Settings method)
popitem() (Settings method)
postrun() (AMSMSDJob method)
(AMSRDFJob method)
(AMSVACFJob method)
(Job method)
preoptimize() (in module scm.plams.interfaces.adfsuite.quickjobs)
prerun() (AMSMSDJob method)
(AMSNVESpawnerJob method)
(AMSRDFJob method)
(AMSVACFJob method)
(Job method)
print_molecule() (ORCAJob method)
Q
qe_output_to_ams() (in module scm.plams.tools.converters)
R
RaspaJob (class in scm.plams.interfaces.thirdparty.raspa)
RaspaResults (class in scm.plams.interfaces.thirdparty.raspa)
read() (KFFile method)
(KFReader method)
(Molecule method)
read_all() (KFHistory method)
read_all_molecules_in_xyz_file() (in module scm.plams.core.functions)
read_file() (Results method)
read_frame() (DCDTrajectoryFile method)
(RKFTrajectoryFile method)
(XYZTrajectoryFile method)
read_last_frame() (DCDTrajectoryFile method)
(RKFTrajectoryFile method)
(XYZTrajectoryFile method)
read_molecules() (in module scm.plams.core.functions)
read_next() (DCDTrajectoryFile method)
(RKFTrajectoryFile method)
(XYZTrajectoryFile method)
read_rkf_section() (AMSResults method)
read_section() (KFFile method)
readarray() (SCMResults method)
readase() (Molecule method)
,
[1]
readin() (Molecule method)
readkf() (SCMResults method)
readpdb() (in module scm.plams.interfaces.molecule.rdkit)
(Molecule method)
readrkf() (AMSResults method)
readxyz() (Molecule method)
ReaxFFJob (class in scm.plams.interfaces.adfsuite.reaxff)
recreate_molecule() (ADFResults method)
(AMSResults method)
(Results method)
recreate_settings() (ADFResults method)
(AMSResults method)
(Cp2kResults method)
(Results method)
refine_density() (in module scm.plams.interfaces.adfsuite.quickjobs)
refine_lattice() (in module scm.plams.interfaces.adfsuite.quickjobs)
refresh() (AMSResults method)
(Results method)
(SCMResults method)
regex_file() (Results method)
remove_child() (MultiJob method)
remove_job() (JobManager method)
rename() (Results method)
resize() (Bond method)
resize_bond() (Molecule method)
restart_from() (AMSMDJob class method)
Results (class in scm.plams.core.results)
rewind() (DCDTrajectoryFile method)
(RKFTrajectoryFile method)
(XYZTrajectoryFile method)
rkf_to_ase_atoms() (in module scm.plams.tools.converters)
rkf_to_ase_traj() (in module scm.plams.tools.converters)
RKFHistoryFile (class in scm.plams.trajectories.rkfhistoryfile)
rkfpath() (AMSResults method)
(ConformersResults method)
RKFTrajectoryFile (class in scm.plams.trajectories.rkffile)
rmsd() (Molecule static method)
rotate() (Atom method)
(Bond method)
(Molecule method)
rotate_bond() (Molecule method)
rotate_lattice() (Molecule method)
rotation_matrix() (in module scm.plams.tools.geometry)
round_coords() (Molecule method)
run() (AMSJob method)
(Job method)
run_analysis() (Trajectory method)
S
save() (KFFile method)
scm.plams.interfaces.molecule.ase
module
scm.plams.interfaces.molecule.rdkit
module
scm.plams.tools.converters
module
scm.plams.tools.geometry
module
scm.plams.tools.plot
module
SCMJob (class in scm.plams.interfaces.adfsuite.scmjob)
SCMResults (class in scm.plams.interfaces.adfsuite.scmjob)
sections() (KFFile method)
separate() (Molecule method)
set_atoms_id() (Molecule method)
set_byteorder() (DCDTrajectoryFile method)
set_connectors() (PeriodicTable class method)
set_density() (Molecule method)
set_elements() (DCDTrajectoryFile method)
(XYZTrajectoryFile method)
set_integer_bonds() (Molecule method)
set_local_labels() (Molecule method)
set_mass() (PeriodicTable class method)
set_name() (XYZTrajectoryFile method)
set_nested() (Settings method)
set_radius() (PeriodicTable class method)
setdefault() (Settings method)
Settings (class in scm.plams.core.settings)
settings_to_mol() (AMSJob static method)
(SCMJob static method)
shortest_path_dijkstra() (Molecule method)
SingleJob (class in scm.plams.core.basejob)
SinglePoint() (AMSWorker method)
SinglePoints() (AMSWorkerPool method)
soft_update() (Settings method)
stop() (AMSWorker method)
(AMSWorkerPool method)
stop_worker() (AMSCalculator method)
store_historydata() (RKFTrajectoryFile method)
(XYZTrajectoryFile method)
store_mddata() (RKFTrajectoryFile method)
str() (Atom method)
(Molecule method)
substitute() (Molecule method)
supercell() (Molecule method)
suppress_missing() (Settings class method)
symbols() (Molecule property)
T
to_input_order() (SCMResults method)
to_rdmol() (in module scm.plams.interfaces.molecule.rdkit)
to_smiles() (in module scm.plams.interfaces.molecule.rdkit)
toASE() (in module scm.plams.interfaces.molecule.ase)
traj_to_rkf() (in module scm.plams.tools.converters)
Trajectory (class in scm.plams.trajectories.trajectory)
translate() (Atom method)
(Molecule method)
twist() (in module scm.plams.mol.identify)
U
unflatten() (Settings method)
unique_atoms() (in module scm.plams.mol.identify)
unit_cell_volume() (Molecule method)
Units (class in scm.plams.tools.units)
unset_atoms_id() (Molecule method)
update() (Settings method)
V
variable_type() (KFReader method)
vasp_output_to_ams() (in module scm.plams.tools.converters)
VASPJob (class in scm.plams.interfaces.thirdparty.vasp)
VASPResults (class in scm.plams.interfaces.thirdparty.vasp)
vector_to() (Atom method)
W
wait() (Results method)
wrap() (Molecule method)
write() (KFFile method)
(Molecule method)
write_next() (DCDTrajectoryFile method)
(RKFHistoryFile method)
(RKFTrajectoryFile method)
(XYZHistoryFile method)
(XYZTrajectoryFile method)
writease() (Molecule method)
,
[1]
writein() (Molecule method)
writepdb() (in module scm.plams.interfaces.molecule.rdkit)
X
XYZHistoryFile (class in scm.plams.trajectories.xyzhistoryfile)
XYZTrajectoryFile (class in scm.plams.trajectories.xyzfile)
Y
yield_coords() (in module scm.plams.interfaces.molecule.rdkit)