py-PACKMAN
1.3.5
py-PACKMAN
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W
A
AlphaShape() (in module packman.geometry.geometry)
ANM (class in packman.anm.anm)
,
[1]
Atom (class in packman.molecule.atom)
,
[1]
C
calc_dist() (packman.molecule.hetatom.HetAtom method)
,
[1]
calcualte_pymol_commands() (packman.apps.dci.DCI method)
calculate_CH_plot() (packman.apps.dci.DCI method)
calculate_cluster() (packman.apps.dci.DCI method)
calculate_cross_correlation() (packman.anm.hd_anm.hdANM method)
,
[1]
calculate_crosscorrelation() (packman.apps.dci.DCI method)
calculate_decomposition() (packman.anm.anm.ANM method)
,
[1]
(packman.anm.hd_anm.hdANM method)
,
[1]
(packman.apps.dci.DCI method)
calculate_distance() (packman.molecule.atom.Atom method)
,
[1]
calculate_entropy() (packman.entropy.entropy.PackingEntropy method)
,
[1]
(packman.molecule.chain.Chain method)
,
[1]
(packman.molecule.model.Model method)
,
[1]
(packman.molecule.residue.Residue method)
,
[1]
calculate_fluctuations() (packman.anm.anm.ANM method)
,
[1]
(packman.anm.hd_anm.hdANM method)
,
[1]
calculate_hessian() (packman.anm.anm.ANM method)
,
[1]
(packman.anm.hd_anm.hdANM method)
,
[1]
calculate_hessian_pseudoinverse() (packman.anm.hd_anm.hdANM method)
,
[1]
calculate_kirchoff() (packman.apps.dci.DCI method)
calculate_movie() (packman.anm.anm.ANM method)
,
[1]
(packman.anm.hd_anm.hdANM method)
,
[1]
calculate_RT_eigen_vectors() (packman.anm.hd_anm.hdANM method)
,
[1]
calculate_spherepoints() (packman.entropy.entropy.PackingEntropy method)
,
[1]
calculate_stiffness_compliance() (packman.anm.anm.ANM method)
,
[1]
calculate_surafacepoints() (packman.entropy.entropy.PackingEntropy method)
,
[1]
calculate_windows() (packman.apps.dci.DCI method)
Chain (class in packman.molecule.chain)
,
[1]
check_clashes() (packman.molecule.model.Model method)
,
[1]
Circumsphere() (in module packman.geometry.geometry)
D
DCI (class in packman.apps.dci)
dci_cli() (in module packman.apps.dci)
download_structure() (in module packman.molecule.molecule)
,
[1]
E
entropy_cli() (in module packman.apps.calculate_entropy)
,
[1]
G
get_alpha_value() (packman.molecule.annotations.Hinge method)
,
[1]
get_alternatelocationindicator() (packman.molecule.atom.Atom method)
,
[1]
(packman.molecule.hetatom.HetAtom method)
,
[1]
get_atom_byid() (packman.molecule.model.Model method)
,
[1]
get_atoms() (packman.molecule.chain.Chain method)
,
[1]
(packman.molecule.hetmol.HetMol method)
,
[1]
(packman.molecule.model.Model method)
,
[1]
(packman.molecule.residue.Residue method)
,
[1]
get_backbone() (packman.molecule.chain.Chain method)
,
[1]
(packman.molecule.model.Model method)
,
[1]
(packman.molecule.residue.Residue method)
,
[1]
get_bfactor() (packman.molecule.atom.Atom method)
,
[1]
(packman.molecule.hetatom.HetAtom method)
,
[1]
get_calpha() (packman.molecule.chain.Chain method)
,
[1]
(packman.molecule.model.Model method)
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[1]
(packman.molecule.residue.Residue method)
,
[1]
get_centerofgravity() (packman.molecule.hetmol.HetMol method)
,
[1]
(packman.molecule.residue.Residue method)
,
[1]
get_chain() (packman.molecule.model.Model method)
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[1]
get_chains() (packman.molecule.model.Model method)
,
[1]
get_charge() (packman.molecule.atom.Atom method)
,
[1]
get_cluster_labels() (packman.apps.dci.DCI method)
get_communities() (packman.apps.dci.DCI method)
get_compliance_map() (packman.anm.anm.ANM method)
,
[1]
get_compliance_profile() (packman.anm.anm.ANM method)
,
[1]
get_crosscorrelation() (packman.apps.dci.DCI method)
get_crosscorrelation_matrix() (packman.anm.hd_anm.hdANM method)
,
[1]
get_data() (packman.molecule.protein.Protein method)
,
[1]
get_domain_id() (packman.molecule.atom.Atom method)
,
[1]
(packman.molecule.hetmol.HetMol method)
,
[1]
(packman.molecule.residue.Residue method)
,
[1]
get_eigenvalues() (packman.anm.anm.ANM method)
,
[1]
(packman.anm.hd_anm.hdANM method)
,
[1]
get_eigenvectors() (packman.anm.anm.ANM method)
,
[1]
(packman.anm.hd_anm.hdANM method)
,
[1]
get_element() (packman.molecule.atom.Atom method)
,
[1]
get_elements() (packman.molecule.annotations.Hinge method)
,
[1]
get_elment() (packman.molecule.hetatom.HetAtom method)
,
[1]
get_entropy() (packman.molecule.chain.Chain method)
,
[1]
(packman.molecule.model.Model method)
,
[1]
(packman.molecule.residue.Residue method)
,
[1]
get_fluctuations() (packman.anm.anm.ANM method)
,
[1]
(packman.anm.hd_anm.hdANM method)
,
[1]
get_hessian() (packman.anm.anm.ANM method)
,
[1]
(packman.anm.hd_anm.hdANM method)
,
[1]
get_hessian_block() (packman.anm.hd_anm.hdANM method)
,
[1]
get_hessian_pseudoinverse() (packman.anm.hd_anm.hdANM method)
,
[1]
get_hetatoms() (packman.molecule.model.Model method)
,
[1]
get_hetmols() (packman.molecule.chain.Chain method)
,
[1]
(packman.molecule.model.Model method)
,
[1]
get_hinges() (packman.molecule.chain.Chain method)
,
[1]
get_id() (packman.molecule.annotations.Hinge method)
,
[1]
(packman.molecule.atom.Atom method)
,
[1]
(packman.molecule.chain.Chain method)
,
[1]
(packman.molecule.hetatom.HetAtom method)
,
[1]
(packman.molecule.hetmol.HetMol method)
,
[1]
(packman.molecule.model.Model method)
,
[1]
(packman.molecule.protein.Protein method)
,
[1]
(packman.molecule.residue.Residue method)
,
[1]
get_labels() (packman.apps.dci.DCI method)
get_location() (packman.molecule.atom.Atom method)
,
[1]
(packman.molecule.hetatom.HetAtom method)
,
[1]
get_n_communities() (packman.apps.dci.DCI method)
get_name() (packman.molecule.atom.Atom method)
,
[1]
(packman.molecule.hetatom.HetAtom method)
,
[1]
(packman.molecule.hetmol.HetMol method)
,
[1]
(packman.molecule.residue.Residue method)
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[1]
get_occupancy() (packman.molecule.atom.Atom method)
,
[1]
(packman.molecule.hetatom.HetAtom method)
,
[1]
get_parent() (packman.molecule.atom.Atom method)
,
[1]
(packman.molecule.chain.Chain method)
,
[1]
(packman.molecule.hetatom.HetAtom method)
,
[1]
(packman.molecule.hetmol.HetMol method)
,
[1]
(packman.molecule.model.Model method)
,
[1]
(packman.molecule.residue.Residue method)
,
[1]
get_property() (packman.molecule.atom.Atom method)
,
[1]
(packman.molecule.chain.Chain method)
,
[1]
(packman.molecule.hetmol.HetMol method)
,
[1]
(packman.molecule.model.Model method)
,
[1]
(packman.molecule.residue.Residue method)
,
[1]
get_pvalue() (packman.molecule.annotations.Hinge method)
,
[1]
get_range() (packman.apps.dci.DCI method)
get_residues() (packman.molecule.chain.Chain method)
,
[1]
(packman.molecule.model.Model method)
,
[1]
get_RT_eigen_vectors() (packman.anm.hd_anm.hdANM method)
,
[1]
get_segmentidentifier() (packman.molecule.atom.Atom method)
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[1]
(packman.molecule.hetatom.HetAtom method)
,
[1]
get_stats() (packman.molecule.annotations.Hinge method)
,
[1]
get_stiffness_map() (packman.anm.anm.ANM method)
,
[1]
get_stiffness_profile() (packman.anm.anm.ANM method)
,
[1]
get_surafacepoints() (packman.entropy.entropy.PackingEntropy method)
,
[1]
get_tip() (packman.molecule.residue.Residue method)
,
[1]
get_torsion() (packman.molecule.model.Model method)
,
[1]
get_total_chain_entropy() (packman.entropy.entropy.PackingEntropy method)
,
[1]
get_total_entropy() (packman.entropy.entropy.PackingEntropy method)
,
[1]
get_total_packing_fraction() (packman.entropy.entropy.PackingEntropy method)
,
[1]
H
hdANM (class in packman.anm.hd_anm)
,
[1]
hdanm_cli() (in module packman.apps.hdanm)
hdANM_GUI (class in packman.bin.GUI)
HetAtom (class in packman.molecule.hetatom)
,
[1]
HetMol (class in packman.molecule.hetmol)
,
[1]
hide() (packman.bin.GUI.hdANM_GUI method)
(packman.bin.GUI.HingePrediction method)
(packman.bin.GUI.HomePage method)
(packman.bin.GUI.Voronoi_Packing_Entropy_GUI method)
Hinge (class in packman.molecule.annotations)
,
[1]
hinge_cli() (in module packman.apps.predict_hinge)
,
[1]
HingePrediction (class in packman.bin.GUI)
HomePage (class in packman.bin.GUI)
I
IO() (in module packman.bin.PACKMAN)
,
[1]
L
load_cif() (in module packman.molecule.molecule)
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[1]
load_cli() (in module packman.bin.PACKMAN)
,
[1]
load_gui() (in module packman.bin.GUI)
load_hinge() (in module packman.utilities.utilities)
,
[1]
load_pdb() (in module packman.molecule.molecule)
,
[1]
load_structure() (in module packman.molecule.molecule)
,
[1]
M
main() (in module packman.bin.PACKMAN)
,
[1]
Model (class in packman.molecule.model)
,
[1]
P
PackingEntropy (class in packman.entropy.entropy)
,
[1]
packman (module)
,
[1]
packman.anm (module)
,
[1]
packman.anm.anm (module)
,
[1]
packman.anm.hd_anm (module)
,
[1]
packman.apps (module)
,
[1]
packman.apps.calculate_entropy (module)
,
[1]
packman.apps.dci (module)
packman.apps.hdanm (module)
packman.apps.predict_hinge (module)
,
[1]
packman.bin (module)
,
[1]
packman.bin.GUI (module)
packman.bin.PACKMAN (module)
,
[1]
packman.constants (module)
,
[1]
packman.constants.Constants (module)
,
[1]
packman.entropy (module)
,
[1]
packman.entropy.entropy (module)
,
[1]
packman.geometry (module)
packman.geometry.geometry (module)
packman.molecule (module)
,
[1]
packman.molecule.annotations (module)
,
[1]
packman.molecule.atom (module)
,
[1]
packman.molecule.chain (module)
,
[1]
packman.molecule.hetatom (module)
,
[1]
packman.molecule.hetmol (module)
,
[1]
packman.molecule.model (module)
,
[1]
packman.molecule.molecule (module)
,
[1]
packman.molecule.protein (module)
,
[1]
packman.molecule.residue (module)
,
[1]
packman.tests (module)
packman.tests.anm (module)
packman.tests.anm.test_anm (module)
packman.tests.data (module)
packman.tests.entropy (module)
packman.tests.entropy.test_entropy (module)
packman.tests.molecule (module)
packman.tests.molecule.test_molecule (module)
packman.utilities (module)
,
[1]
packman.utilities.utilities (module)
,
[1]
predict_hinge() (in module packman.apps.predict_hinge)
,
[1]
Protein (class in packman.molecule.protein)
,
[1]
R
Residue (class in packman.molecule.residue)
,
[1]
RMSD() (in module packman.utilities.utilities)
,
[1]
run_Entropy() (packman.bin.GUI.Voronoi_Packing_Entropy_GUI method)
run_hdANM() (packman.bin.GUI.hdANM_GUI method)
run_PACKMAN() (packman.bin.GUI.HingePrediction method)
S
set_alternatelocationindicator() (packman.molecule.atom.Atom method)
,
[1]
(packman.molecule.hetatom.HetAtom method)
,
[1]
set_bfactor() (packman.molecule.atom.Atom method)
,
[1]
(packman.molecule.hetatom.HetAtom method)
,
[1]
set_charge() (packman.molecule.atom.Atom method)
,
[1]
set_data() (packman.molecule.protein.Protein method)
,
[1]
set_domain_id() (packman.molecule.hetmol.HetMol method)
,
[1]
(packman.molecule.residue.Residue method)
,
[1]
set_elment() (packman.molecule.atom.Atom method)
,
[1]
(packman.molecule.hetatom.HetAtom method)
,
[1]
set_entropy() (packman.molecule.residue.Residue method)
,
[1]
set_hinges() (packman.molecule.chain.Chain method)
,
[1]
set_id() (packman.molecule.atom.Atom method)
,
[1]
(packman.molecule.chain.Chain method)
,
[1]
(packman.molecule.hetatom.HetAtom method)
,
[1]
(packman.molecule.hetmol.HetMol method)
,
[1]
(packman.molecule.model.Model method)
,
[1]
(packman.molecule.residue.Residue method)
,
[1]
set_location() (packman.molecule.atom.Atom method)
,
[1]
(packman.molecule.hetatom.HetAtom method)
,
[1]
set_name() (packman.molecule.atom.Atom method)
,
[1]
(packman.molecule.hetatom.HetAtom method)
,
[1]
(packman.molecule.hetmol.HetMol method)
,
[1]
(packman.molecule.residue.Residue method)
,
[1]
set_occupancy() (packman.molecule.atom.Atom method)
,
[1]
(packman.molecule.hetatom.HetAtom method)
,
[1]
set_parent() (packman.molecule.atom.Atom method)
,
[1]
(packman.molecule.chain.Chain method)
,
[1]
(packman.molecule.hetatom.HetAtom method)
,
[1]
(packman.molecule.hetmol.HetMol method)
,
[1]
(packman.molecule.model.Model method)
,
[1]
(packman.molecule.residue.Residue method)
,
[1]
set_property() (packman.molecule.atom.Atom method)
,
[1]
(packman.molecule.chain.Chain method)
,
[1]
(packman.molecule.hetmol.HetMol method)
,
[1]
(packman.molecule.model.Model method)
,
[1]
(packman.molecule.residue.Residue method)
,
[1]
set_segmentidentifier() (packman.molecule.atom.Atom method)
,
[1]
(packman.molecule.hetatom.HetAtom method)
,
[1]
set_torsion() (packman.molecule.model.Model method)
,
[1]
setUp() (packman.tests.anm.test_anm.TestMolecule method)
(packman.tests.entropy.test_entropy.TestMolecule method)
(packman.tests.molecule.test_molecule.TestMolecule method)
show() (packman.bin.GUI.hdANM_GUI method)
(packman.bin.GUI.HingePrediction method)
(packman.bin.GUI.HomePage method)
(packman.bin.GUI.Voronoi_Packing_Entropy_GUI method)
show_frame() (packman.bin.GUI.Skeleton method)
Skeleton (class in packman.bin.GUI)
superimporse() (in module packman.utilities.utilities)
,
[1]
T
tearDown() (packman.tests.anm.test_anm.TestMolecule method)
(packman.tests.entropy.test_entropy.TestMolecule method)
(packman.tests.molecule.test_molecule.TestMolecule method)
test_ANM_Compliance() (packman.tests.anm.test_anm.TestMolecule method)
test_Atom() (packman.tests.molecule.test_molecule.TestMolecule method)
test_Chain() (packman.tests.molecule.test_molecule.TestMolecule method)
test_hdANM() (packman.tests.anm.test_anm.TestMolecule method)
test_load_cif() (packman.tests.molecule.test_molecule.TestMolecule method)
test_load_pdb() (packman.tests.molecule.test_molecule.TestMolecule method)
test_Model() (packman.tests.molecule.test_molecule.TestMolecule method)
test_PackingEntropy() (packman.tests.entropy.test_entropy.TestMolecule method)
test_Protein() (packman.tests.molecule.test_molecule.TestMolecule method)
test_Residue() (packman.tests.molecule.test_molecule.TestMolecule method)
TestMolecule (class in packman.tests.anm.test_anm)
(class in packman.tests.entropy.test_entropy)
(class in packman.tests.molecule.test_molecule)
top_menu (class in packman.bin.GUI)
V
Voronoi_Packing_Entropy_GUI (class in packman.bin.GUI)
W
write_cif() (packman.molecule.protein.Protein method)
,
[1]
write_pdb() (packman.molecule.protein.Protein method)
,
[1]
write_structure() (packman.molecule.protein.Protein method)
,
[1]
WriteOBJ() (in module packman.utilities.utilities)
,
[1]
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v: 1.3.5
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