Package schrodinger :: Package protein :: Module analysis_params

Module analysis_params

Variables

protonated_residues = {'ARG ': 'ARN ', 'ASP ': 'ASH ', 'GLU ':...

ideal_bond_lengths = {' ': {' C ': {' N ': (490.0, 1.329), '...
Dictionary containing ideal bond lengths for some bonds in residues; keys are residue names and values are dictionary B; dictionary B keys are atoms types and values are dictionary C; dictionary C keys are atom types and values are tuples of (G-factor coefficient, ideal bond length.

ideal_bond_angles = {' ': {' C ': {' N ': {' CA ': (50.0, 12...
Dictionary containing ideal bond angles for some bond angles in residues; keys are residue names and values are dictionary B; dictionary B keys are atoms types and values are dictionary C; dictionary C keys are atom types and values are dictionary D; dictionary D keys are atom types and values are tuples of (G-factor coefficient, ideal bond angle.

sidechain_dihedral_atomnames = {' ': [[' N ', ' CA ', ' CB ',...

planar_groups = {' ': [' CG ', ' CD ', ' OE1', ' OE2'], 'A': [...
Dictionary containing lists of groups that should be planar; keys are residue names and values are lists of atom names.

improper_torsions = {' ': [[' OE2', ' CG ', ' CD ', ' OE1']], ...
Dictionary containing lists of improper torsions; keys are residue names and values are lists of lists of atom names, one for each improper torsion in the residue.

backbone_dihedrals = {' ': {'-10.0,-60.0': 1.4e-05, '-100.0,-1...

sidechain_dihedrals = {' ': {'-100.0,-150.0': 0.000151, '-100....

pxp_vdwr = {1: 1.1, 6: 1.77, 7: 1.64, 8: 1.58, 9: 1.46, 15: 1....

__package__ = 'schrodinger.protein'

i = 1

normal_res = 'GLU '

num_chi = 2

protonated_res_list = 'GLH '

res = ' '

res_type = 'MET '

val_list = [[' N ', ' CA ', ' CB ', ' CG '], [' CA ', ' CB ',...

Variables Details

[hide private]

protonated_residues

Value:

{'ARG ': 'ARN ',
 'ASP ': 'ASH ',
 'GLU ': 'GLH ',
 'HIS ': ('HID ', 'HIE ', 'HIP '),
 'LYS ': 'LYN '}

ideal_bond_lengths

Dictionary containing ideal bond lengths for some bonds in residues; keys are residue names and values are dictionary B; dictionary B keys are atoms types and values are dictionary C; dictionary C keys are atom types and values are tuples of (G-factor coefficient, ideal bond length.

Value:

{' ': {' C  ': {' N  ': (490.0, 1.329), ' O  ': (570.0, 1.231)},
       ' CA ': {' C  ': (317.0, 1.525), ' CB ': (268.0, 1.53)},
       ' CB ': {' CG ': (268.0, 1.52)},
       ' CD ': {' OE1': (656.0, 1.249), ' OE2': (656.0, 1.249)},
       ' CG ': {' CD ': (317.0, 1.516)},
       ' N  ': {' CA ': (337.0, 1.458)}},
 'A': {' C  ': {' N  ': (490.0, 1.329), ' O  ': (570.0, 1.231)},
       ' CA ': {' C  ': (317.0, 1.525), ' CB ': (268.0, 1.53)},
...

ideal_bond_angles

Dictionary containing ideal bond angles for some bond angles in residues; keys are residue names and values are dictionary B; dictionary B keys are atoms types and values are dictionary C; dictionary C keys are atom types and values are dictionary D; dictionary D keys are atom types and values are tuples of (G-factor coefficient, ideal bond angle.

Value:

{' ': {' C  ': {' N  ': {' CA ': (50.0, 121.7)}},
       ' CA ': {' C  ': {' N  ': (70.0, 116.2)},
                ' CB ': {' CG ': (58.35, 114.1)}},
       ' CB ': {' CA ': {' C  ': (63.0, 110.1)},
                ' CG ': {' CD ': (63.0, 112.6)}},
       ' CG ': {' CD ': {' OE1': (70.0, 118.4), ' OE2': (70.0, 118.4)}
},
       ' N  ': {' C  ': {' O  ': (80.0, 123.0)}},
...

sidechain_dihedral_atomnames

Value:

{' ': [[' N  ', ' CA ', ' CB ', ' CG '],
       [' CA ', ' CB ', ' CG ', ' CD ']],
 'A': [[' N  ', ' CA ', ' CB ', ' CG '],
       [' CA ', ' CB ', ' CG ', ' CD ']],
 'ARG ': [[' N  ', ' CA ', ' CB ', ' CG '],
          [' CA ', ' CB ', ' CG ', ' CD ']],
 'ASN ': [[' N  ', ' CA ', ' CB ', ' CG '],
          [' CA ', ' CB ', ' CG ', ' OD1']],
...

planar_groups

Dictionary containing lists of groups that should be planar; keys are residue names and values are lists of atom names.

Value:

{' ': [' CG ', ' CD ', ' OE1', ' OE2'],
 'A': [' CD ', ' NE ', ' CZ ', ' NH1', ' NH2'],
 'ARG ': [' CD ', ' NE ', ' CZ ', ' NH1', ' NH2'],
 'ASN ': [' CB ', ' CG ', ' OD1', ' ND2'],
 'ASP ': [' CB ', ' CG ', ' OD1', ' OD2'],
 'G': [' CG ', ' CD ', ' OE1', ' OE2'],
 'GLN ': [' CG ', ' CD ', ' OE1', ' NE2'],
 'GLU ': [' CG ', ' CD ', ' OE1', ' OE2'],
...

improper_torsions

Dictionary containing lists of improper torsions; keys are residue names and values are lists of lists of atom names, one for each improper torsion in the residue.

Value:

{' ': [[' OE2', ' CG ', ' CD ', ' OE1']],
 'A': [[' HE ', ' CZ ', ' NE ', ' CD '],
       [' NE ', ' NH2', ' CZ ', ' NH1'],
       ['1HH1', '2HH1', ' NH1', ' CZ '],
       ['2HH2', ' CZ ', ' NH2', '1HH2'],
       ['HH11', 'HH12', ' NH1', ' CZ '],
       ['HH22', ' CZ ', ' NH2', 'HH21']],
 'ARG ': [[' HE ', ' CZ ', ' NE ', ' CD '], [' NE ', ' NH2', ' CZ ', '
...

backbone_dihedrals

Value:

{' ': {'-10.0,-60.0': 1.4e-05,
       '-100.0,-10.0': 0.003774,
       '-100.0,-100.0': 8.1e-05,
       '-100.0,-120.0': 2.7e-05,
       '-100.0,-130.0': 1.4e-05,
       '-100.0,-140.0': 4.1e-05,
       '-100.0,-150.0': 1.4e-05,
       '-100.0,-160.0': 1.4e-05,
...

sidechain_dihedrals

Value:

{' ': {'-100.0,-150.0': 0.000151,
       '-100.0,-160.0': 0.000356,
       '-100.0,-170.0': 0.000397,
       '-100.0,-50.0': 0.000164,
       '-100.0,-60.0': 0.000274,
       '-100.0,-70.0': 0.000439,
       '-100.0,-80.0': 0.000178,
       '-100.0,150.0': 0.000123,
...

pxp_vdwr

Value:

{1: 1.1,
 6: 1.77,
 7: 1.64,
 8: 1.58,
 9: 1.46,
 15: 1.8,
 16: 1.81,
 17: 1.76,
...

val_list

Value:

[[' N  ', ' CA ', ' CB ', ' CG '], [' CA ', ' CB ', ' CG ', ' SD ']]