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| # Copyright 2019-22 by Robert T. Miller. All rights reserved. | |
| # This file is part of the Biopython distribution and governed by your | |
| # choice of the "Biopython License Agreement" or the "BSD 3-Clause License". | |
| # Please see the LICENSE file that should have been included as part of this | |
| # package. | |
| """Per residue backbone and sidechain hedra and dihedra definitions. | |
| Find this file in <your biopython distribution>/Bio/PDB/ic_data.py | |
| Listed in order of output for internal coordinates (.pic) output file. | |
| Require sufficient overlap to link all defined dihedra. Entries in these | |
| tables without corresponding atom coordinates are ignored. | |
| <http://www.imgt.org/IMGTeducation/Aide-memoire/_UK/aminoacids/formuleAA/> | |
| for naming of individual atoms | |
| """ | |
| # Backbone hedra and dihedra - within residue, no next or prev (no psi, phi, omg). | |
| ic_data_backbone = ( | |
| ("N", "CA", "C", "O"), # locate backbone O | |
| ("O", "C", "CA", "CB"), # locate CB | |
| ("CA", "C", "O"), | |
| ("CB", "CA", "C"), | |
| ("CA", "C", "OXT"), # OXT if present | |
| ("N", "CA", "C", "OXT"), | |
| ("H", "N", "CA"), # amide proton if present | |
| ("C", "CA", "N", "H"), | |
| ("HA", "CA", "C"), # CA proton | |
| ("O", "C", "CA", "HA"), | |
| ("HA2", "CA", "C"), # gly CA proton | |
| ("O", "C", "CA", "HA2"), | |
| ("HA3", "CA", "C"), # gly CA proton | |
| ("O", "C", "CA", "HA3"), | |
| ("N", "CA", "CB"), | |
| ("N", "CA", "CB", "HB"), # CB protons | |
| ("N", "CA", "CB", "HB1"), | |
| ("N", "CA", "CB", "HB2"), | |
| ("N", "CA", "CB", "HB3"), | |
| ("CA", "CB", "HB"), | |
| ("CA", "CB", "HB1"), | |
| ("CA", "CB", "HB2"), | |
| ("CA", "CB", "HB3"), | |
| ("H1", "N", "CA"), # chain start protons | |
| ("H2", "N", "CA"), | |
| ("H3", "N", "CA"), | |
| ("C", "CA", "N", "H1"), | |
| ("C", "CA", "N", "H2"), | |
| ("C", "CA", "N", "H3"), | |
| ) | |
| # Sidechain hedra and dihedra. | |
| # see http://www.mlb.co.jp/linux/science/garlic/doc/commands/dihedrals.html | |
| # for official chi angles | |
| ic_data_sidechains = { | |
| "V": ( | |
| ("CA", "CB", "CG1"), | |
| ("N", "CA", "CB", "CG1", "chi1"), # chi1 | |
| ("CA", "CB", "CG2"), | |
| ("N", "CA", "CB", "CG2"), | |
| ("CB", "CG1", "HG11"), | |
| ("CB", "CG1", "HG12"), | |
| ("CB", "CG1", "HG13"), | |
| ("CB", "CG2", "HG21"), | |
| ("CB", "CG2", "HG22"), | |
| ("CB", "CG2", "HG23"), | |
| ("CA", "CB", "CG1", "HG11"), | |
| ("CA", "CB", "CG1", "HG12"), | |
| ("CA", "CB", "CG1", "HG13"), | |
| ("CA", "CB", "CG2", "HG21"), | |
| ("CA", "CB", "CG2", "HG22"), | |
| ("CA", "CB", "CG2", "HG23"), | |
| ), | |
| "L": ( | |
| ("CA", "CB", "CG"), | |
| ("N", "CA", "CB", "CG", "chi1"), # chi1 | |
| ("CB", "CG", "CD1"), | |
| ("CA", "CB", "CG", "CD1", "chi2"), # chi2 | |
| ("CB", "CG", "CD2"), | |
| ("CA", "CB", "CG", "CD2"), | |
| ("CB", "CG", "HG"), | |
| ("CA", "CB", "CG", "HG"), | |
| ("CG", "CD1", "HD11"), | |
| ("CG", "CD1", "HD12"), | |
| ("CG", "CD1", "HD13"), | |
| ("CG", "CD2", "HD21"), | |
| ("CG", "CD2", "HD22"), | |
| ("CG", "CD2", "HD23"), | |
| ("CB", "CG", "CD1", "HD11"), | |
| ("CB", "CG", "CD1", "HD12"), | |
| ("CB", "CG", "CD1", "HD13"), | |
| ("CB", "CG", "CD2", "HD21"), | |
| ("CB", "CG", "CD2", "HD22"), | |
| ("CB", "CG", "CD2", "HD23"), | |
| ), | |
| "I": ( | |
| ("CA", "CB", "CG1"), | |
| ("N", "CA", "CB", "CG1", "chi1"), # chi1 | |
| ("CB", "CG1", "CD1"), | |
| ("CA", "CB", "CG1", "CD1", "chi2"), # chi2 | |
| ("CA", "CB", "CG2"), | |
| ("N", "CA", "CB", "CG2"), | |
| ("CB", "CG1", "HG12"), | |
| ("CB", "CG1", "HG13"), | |
| ("CB", "CG2", "HG21"), | |
| ("CB", "CG2", "HG22"), | |
| ("CB", "CG2", "HG23"), | |
| ("CA", "CB", "CG1", "HG12"), | |
| ("CA", "CB", "CG1", "HG13"), | |
| ("CA", "CB", "CG2", "HG21"), | |
| ("CA", "CB", "CG2", "HG22"), | |
| ("CA", "CB", "CG2", "HG23"), | |
| ("CG1", "CD1", "HD11"), | |
| ("CG1", "CD1", "HD12"), | |
| ("CG1", "CD1", "HD13"), | |
| ("CB", "CG1", "CD1", "HD11"), | |
| ("CB", "CG1", "CD1", "HD12"), | |
| ("CB", "CG1", "CD1", "HD13"), | |
| ), | |
| "M": ( | |
| ("CA", "CB", "CG"), | |
| ("N", "CA", "CB", "CG", "chi1"), # chi1 | |
| ("CB", "CG", "SD"), | |
| ("CA", "CB", "CG", "SD", "chi2"), # chi2 | |
| ("CG", "SD", "CE"), | |
| ("CB", "CG", "SD", "CE", "chi3"), # chi3 | |
| ("CB", "CG", "HG2"), | |
| ("CB", "CG", "HG3"), | |
| ("CA", "CB", "CG", "HG2"), | |
| ("CA", "CB", "CG", "HG3"), | |
| ("SD", "CE", "HE1"), | |
| ("SD", "CE", "HE2"), | |
| ("SD", "CE", "HE3"), | |
| ("CG", "SD", "CE", "HE1"), | |
| ("CG", "SD", "CE", "HE2"), | |
| ("CG", "SD", "CE", "HE3"), | |
| ), | |
| "F": ( | |
| ("CA", "CB", "CG"), | |
| ("N", "CA", "CB", "CG", "chi1"), # chi1 | |
| ("CB", "CG", "CD1"), | |
| ("CA", "CB", "CG", "CD1", "chi2"), # chi2 | |
| ("CG", "CD1", "CE1"), | |
| ("CB", "CG", "CD1", "CE1"), | |
| ("CD1", "CE1", "CZ"), | |
| ("CG", "CD1", "CE1", "CZ"), | |
| ("CB", "CG", "CD2"), | |
| ("CA", "CB", "CG", "CD2"), | |
| ("CG", "CD2", "CE2"), | |
| ("CB", "CG", "CD2", "CE2"), | |
| ("CG", "CD1", "HD1"), | |
| ("CB", "CG", "CD1", "HD1"), | |
| ("CG", "CD2", "HD2"), | |
| ("CB", "CG", "CD2", "HD2"), | |
| ("CD1", "CE1", "HE1"), | |
| ("CG", "CD1", "CE1", "HE1"), | |
| ("CD2", "CE2", "HE2"), | |
| ("CG", "CD2", "CE2", "HE2"), | |
| ("CE1", "CZ", "HZ"), | |
| ("CD1", "CE1", "CZ", "HZ"), | |
| ), | |
| "P": ( | |
| ("CA", "CB", "CG"), | |
| ("N", "CA", "CB", "CG", "chi1"), # chi1 | |
| ("CB", "CG", "CD"), | |
| ("CA", "CB", "CG", "CD", "chi2"), # chi2 | |
| ("CB", "CG", "HG2"), | |
| ("CB", "CG", "HG3"), | |
| ("CA", "CB", "CG", "HG2"), | |
| ("CA", "CB", "CG", "HG3"), | |
| ("CG", "CD", "HD2"), | |
| ("CG", "CD", "HD3"), | |
| ("CB", "CG", "CD", "HD2"), | |
| ("CB", "CG", "CD", "HD3"), | |
| ), | |
| "S": ( | |
| ("CA", "CB", "OG"), | |
| ("N", "CA", "CB", "OG", "chi1"), # chi1 | |
| ("CB", "OG", "HG"), | |
| ("CA", "CB", "OG", "HG"), | |
| ), | |
| "T": ( | |
| ("CA", "CB", "OG1"), | |
| ("N", "CA", "CB", "OG1", "chi1"), # chi1 | |
| ("CA", "CB", "CG2"), | |
| ("N", "CA", "CB", "CG2"), | |
| ("CB", "OG1", "HG1"), | |
| ("CA", "CB", "OG1", "HG1"), | |
| ("CB", "CG2", "HG21"), | |
| ("CB", "CG2", "HG22"), | |
| ("CB", "CG2", "HG23"), | |
| ("CA", "CB", "CG2", "HG21"), | |
| ("CA", "CB", "CG2", "HG22"), | |
| ("CA", "CB", "CG2", "HG23"), | |
| ), | |
| "C": ( | |
| ("CA", "CB", "SG"), | |
| ("N", "CA", "CB", "SG", "chi1"), # chi1 | |
| ("CB", "SG", "HG"), | |
| ("CA", "CB", "SG", "HG"), | |
| ), | |
| "N": ( | |
| ("CA", "CB", "CG"), | |
| ("N", "CA", "CB", "CG", "chi1"), # chi1 | |
| ("CB", "CG", "OD1"), | |
| ("CA", "CB", "CG", "OD1", "chi2"), # chi2 | |
| ("CB", "CG", "ND2"), | |
| ("CA", "CB", "CG", "ND2"), | |
| ("CG", "ND2", "HD21"), | |
| ("CG", "ND2", "HD22"), | |
| ("CB", "CG", "ND2", "HD21"), | |
| ("CB", "CG", "ND2", "HD22"), | |
| ), | |
| "Q": ( | |
| ("CA", "CB", "CG"), | |
| ("N", "CA", "CB", "CG", "chi1"), # chi1 | |
| ("CB", "CG", "CD"), | |
| ("CA", "CB", "CG", "CD", "chi2"), # chi2 | |
| ("CG", "CD", "OE1"), | |
| ("CB", "CG", "CD", "OE1", "chi3"), # chi3 | |
| ("CG", "CD", "NE2"), | |
| ("CB", "CG", "CD", "NE2"), | |
| ("CB", "CG", "HG2"), | |
| ("CB", "CG", "HG3"), | |
| ("CA", "CB", "CG", "HG2"), | |
| ("CA", "CB", "CG", "HG3"), | |
| ("CD", "NE2", "HE21"), | |
| ("CD", "NE2", "HE22"), | |
| ("CG", "CD", "NE2", "HE21"), | |
| ("CG", "CD", "NE2", "HE22"), | |
| ), | |
| "Y": ( | |
| ("CA", "CB", "CG"), | |
| ("N", "CA", "CB", "CG", "chi1"), # chi1 | |
| ("CB", "CG", "CD1"), | |
| ("CA", "CB", "CG", "CD1", "chi2"), # chi2 | |
| ("CG", "CD1", "CE1"), | |
| ("CB", "CG", "CD1", "CE1"), | |
| ("CD1", "CE1", "CZ"), | |
| ("CG", "CD1", "CE1", "CZ"), | |
| ("CE1", "CZ", "OH"), | |
| ("CD1", "CE1", "CZ", "OH"), | |
| ("CB", "CG", "CD2"), | |
| ("CA", "CB", "CG", "CD2"), | |
| ("CG", "CD2", "CE2"), | |
| ("CB", "CG", "CD2", "CE2"), | |
| ("CG", "CD1", "HD1"), | |
| ("CB", "CG", "CD1", "HD1"), | |
| ("CG", "CD2", "HD2"), | |
| ("CB", "CG", "CD2", "HD2"), | |
| ("CD1", "CE1", "HE1"), | |
| ("CG", "CD1", "CE1", "HE1"), | |
| ("CD2", "CE2", "HE2"), | |
| ("CG", "CD2", "CE2", "HE2"), | |
| ("CZ", "OH", "HH"), | |
| ("CE1", "CZ", "OH", "HH"), | |
| ), | |
| "W": ( | |
| ("CA", "CB", "CG"), | |
| ("N", "CA", "CB", "CG", "chi1"), # chi1 | |
| ("CB", "CG", "CD1"), | |
| ("CA", "CB", "CG", "CD1", "chi2"), # chi2 | |
| ("CG", "CD1", "NE1"), | |
| ("CB", "CG", "CD1", "NE1"), | |
| ("CB", "CG", "CD2"), | |
| ("CA", "CB", "CG", "CD2"), | |
| ("CG", "CD2", "CE2"), | |
| ("CB", "CG", "CD2", "CE2"), | |
| ("CD2", "CE2", "CZ2"), | |
| ("CG", "CD2", "CE2", "CZ2"), | |
| ("CE2", "CZ2", "CH2"), | |
| ("CD2", "CE2", "CZ2", "CH2"), | |
| ("CE2", "CZ2", "HZ2"), | |
| ("CD2", "CE2", "CZ2", "HZ2"), | |
| ("CG", "CD2", "CE3"), | |
| ("CB", "CG", "CD2", "CE3"), | |
| ("CZ2", "CH2", "CZ3"), | |
| ("CE2", "CZ2", "CH2", "CZ3"), | |
| ("CG", "CD1", "HD1"), | |
| ("CB", "CG", "CD1", "HD1"), | |
| ("CD1", "NE1", "HE1"), | |
| ("CG", "CD1", "NE1", "HE1"), | |
| ("CD2", "CE3", "HE3"), | |
| ("CG", "CD2", "CE3", "HE3"), | |
| ("CH2", "CZ3", "HZ3"), | |
| ("CZ2", "CH2", "CZ3", "HZ3"), | |
| ("CZ2", "CH2", "HH2"), | |
| ("CE2", "CZ2", "CH2", "HH2"), | |
| ), | |
| "D": ( | |
| ("CA", "CB", "CG"), | |
| ("N", "CA", "CB", "CG", "chi1"), # chi1 | |
| ("CB", "CG", "OD1"), | |
| ("CA", "CB", "CG", "OD1", "chi2"), # chi2 | |
| ("CB", "CG", "OD2"), | |
| ("CA", "CB", "CG", "OD2"), | |
| ("CG", "OD2", "HD2"), | |
| ("CB", "CG", "OD2", "HD2"), | |
| ), | |
| "E": ( | |
| ("CA", "CB", "CG"), | |
| ("N", "CA", "CB", "CG", "chi1"), # chi1 | |
| ("CB", "CG", "CD"), | |
| ("CA", "CB", "CG", "CD", "chi2"), # chi2 | |
| ("CG", "CD", "OE1"), | |
| ("CB", "CG", "CD", "OE1", "chi3"), # chi3 | |
| ("CG", "CD", "OE2"), | |
| ("CB", "CG", "CD", "OE2"), | |
| ("CB", "CG", "HG2"), | |
| ("CB", "CG", "HG3"), | |
| ("CA", "CB", "CG", "HG2"), | |
| ("CA", "CB", "CG", "HG3"), | |
| ("CD", "OE2", "HE2"), | |
| ("CG", "CD", "OE2", "HE2"), | |
| ), | |
| "H": ( | |
| ("CA", "CB", "CG"), | |
| ("N", "CA", "CB", "CG", "chi1"), # chi1 | |
| ("CB", "CG", "ND1"), | |
| ("CA", "CB", "CG", "ND1", "chi2"), # chi2 | |
| ("CG", "ND1", "CE1"), | |
| ("CB", "CG", "ND1", "CE1"), | |
| ("CB", "CG", "CD2"), | |
| ("CA", "CB", "CG", "CD2"), | |
| ("CG", "CD2", "NE2"), | |
| ("CB", "CG", "CD2", "NE2"), | |
| ("CG", "ND1", "HD1"), | |
| ("CB", "CG", "ND1", "HD1"), | |
| ("CG", "CD2", "HD2"), | |
| ("CB", "CG", "CD2", "HD2"), | |
| ("ND1", "CE1", "HE1"), | |
| ("CG", "ND1", "CE1", "HE1"), | |
| ("CD2", "NE2", "HE2"), | |
| ("CG", "CD2", "NE2", "HE2"), | |
| ), | |
| "K": ( | |
| ("CA", "CB", "CG"), | |
| ("N", "CA", "CB", "CG", "chi1"), # chi1 | |
| ("CB", "CG", "CD"), | |
| ("CA", "CB", "CG", "CD", "chi2"), # chi2 | |
| ("CG", "CD", "CE"), | |
| ("CB", "CG", "CD", "CE", "chi3"), # chi3 | |
| ("CD", "CE", "NZ"), | |
| ("CG", "CD", "CE", "NZ", "chi4"), # chi4 | |
| ("CB", "CG", "HG2"), | |
| ("CB", "CG", "HG3"), | |
| ("CA", "CB", "CG", "HG2"), | |
| ("CA", "CB", "CG", "HG3"), | |
| ("CG", "CD", "HD2"), | |
| ("CG", "CD", "HD3"), | |
| ("CB", "CG", "CD", "HD2"), | |
| ("CB", "CG", "CD", "HD3"), | |
| ("CD", "CE", "HE2"), | |
| ("CD", "CE", "HE3"), | |
| ("CG", "CD", "CE", "HE2"), | |
| ("CG", "CD", "CE", "HE3"), | |
| ("CE", "NZ", "HZ1"), | |
| ("CE", "NZ", "HZ2"), | |
| ("CE", "NZ", "HZ3"), | |
| ("CD", "CE", "NZ", "HZ1"), | |
| ("CD", "CE", "NZ", "HZ2"), | |
| ("CD", "CE", "NZ", "HZ3"), | |
| ), | |
| "R": ( | |
| ("CA", "CB", "CG"), | |
| ("N", "CA", "CB", "CG", "chi1"), # chi1 | |
| ("CB", "CG", "CD"), | |
| ("CA", "CB", "CG", "CD", "chi2"), # chi2 | |
| ("CG", "CD", "NE"), | |
| ("CB", "CG", "CD", "NE", "chi3"), # chi3 | |
| ("CD", "NE", "CZ"), | |
| ("CG", "CD", "NE", "CZ", "chi4"), # chi4 | |
| ("NE", "CZ", "NH1"), | |
| ("CD", "NE", "CZ", "NH1", "chi5"), # chi5 | |
| ("NE", "CZ", "NH2"), | |
| ("CD", "NE", "CZ", "NH2"), | |
| ("CB", "CG", "HG2"), | |
| ("CB", "CG", "HG3"), | |
| ("CA", "CB", "CG", "HG2"), | |
| ("CA", "CB", "CG", "HG3"), | |
| ("CG", "CD", "HD2"), | |
| ("CG", "CD", "HD3"), | |
| ("CB", "CG", "CD", "HD2"), | |
| ("CB", "CG", "CD", "HD3"), | |
| ("CD", "NE", "HE"), | |
| ("CG", "CD", "NE", "HE"), | |
| ("CZ", "NH1", "HH11"), | |
| ("CZ", "NH1", "HH12"), | |
| ("NE", "CZ", "NH1", "HH11"), | |
| ("NE", "CZ", "NH1", "HH12"), | |
| ("CZ", "NH2", "HH21"), | |
| ("CZ", "NH2", "HH22"), | |
| ("NE", "CZ", "NH2", "HH21"), | |
| ("NE", "CZ", "NH2", "HH22"), | |
| ), | |
| } | |
| # Additional sidechain entries for explicit bonds. | |
| # OpenSCAD output requires specification of bonds to be rendered as cylinders. | |
| # These entries define hedra and dihedra to explicitly cover all bonds in | |
| # rings, otherwise the entries above only capture atoms. | |
| ic_data_sidechain_extras = { | |
| "F": (("CE1", "CZ", "CE2"), ("CD1", "CE1", "CZ", "CE2")), | |
| "P": (("CG", "CD", "N"), ("CB", "CG", "CD", "N")), | |
| "Y": (("CE1", "CZ", "CE2"), ("CD1", "CE1", "CZ", "CE2")), | |
| "W": ( | |
| ("CD2", "CE3", "CZ3"), | |
| ("CG", "CD2", "CE3", "CZ3"), | |
| ("CD1", "NE1", "CE2"), | |
| ("CG", "CD1", "NE1", "CE2"), | |
| ), | |
| "H": (("ND1", "CE1", "NE2"), ("CG", "ND1", "CE1", "NE2")), | |
| } | |
| # sidechain primary angles dictionary | |
| # """ | |
| primary_angles = { | |
| "CACBCG1CD1", | |
| "CACBCGCD", | |
| "CACBCGCD1", | |
| "CACBCGND1", | |
| "CACBCGOD1", | |
| "CACBCGSD", | |
| "CBCGCDCE", | |
| "CBCGCDNE", | |
| "CBCGCDOE1", | |
| "CBCGSDCE", | |
| "CDNECZNH1", | |
| "CGCDCENZ", | |
| "CGCDNECZ", | |
| "NCACBCG", | |
| "NCACBCG1", | |
| "NCACBOG", | |
| "NCACBOG1", | |
| "NCACBSG", | |
| "NCACOXT", | |
| # non-standard because considered constant | |
| "CBCGCD1CE1", # phe, tyr | |
| "CGCD1CE1CZ", # phe, tyr | |
| "CBCGCD2CE2", # phe, tyr | |
| "CBCGND1CE1", # his | |
| "CBCGCD2NE2", # his | |
| "CD1CE1CZOH", # tyr | |
| "CBCGCD1NE1", # trp | |
| "CGCD2CE2CZ2", # trp | |
| "CD2CE2CZ2CH2", # trp | |
| "CE2CZ2CH2CZ3", # trp | |
| } | |
| # """ | |
| # Covalent radii for OpenSCAD output. | |
| # Covalent radii from Heyrovska, Raji : 'Atomic Structures of all the Twenty | |
| # Essential Amino Acids and a Tripeptide, with Bond Lengths as Sums of Atomic | |
| # Covalent Radii' <https://arxiv.org/pdf/0804.2488.pdf> | |
| # Adding Ores between Osb and Odb for Asp and Glu, Nres between Nsb and Ndb | |
| # for Arg, as PDB does not specify | |
| covalent_radii = { | |
| "Csb": 0.77, | |
| "Cres": 0.72, | |
| "Cdb": 0.67, | |
| "Osb": 0.67, | |
| "Ores": 0.635, | |
| "Odb": 0.60, | |
| "Nsb": 0.70, | |
| "Nres": 0.66, | |
| "Ndb": 0.62, | |
| "Ssb": 1.04, | |
| "Hsb": 0.37, | |
| } | |
| # Atom classes based on Heyrovska, Raji covalent radii paper. | |
| residue_atom_bond_state = { | |
| "X": { | |
| "N": "Nsb", | |
| "CA": "Csb", | |
| "C": "Cdb", | |
| "O": "Odb", | |
| "OXT": "Osb", | |
| "CB": "Csb", | |
| "H": "Hsb", | |
| }, | |
| "V": {"CG1": "Csb", "CG2": "Csb"}, | |
| "L": {"CG": "Csb", "CD1": "Csb", "CD2": "Csb"}, | |
| "I": {"CG1": "Csb", "CG2": "Csb", "CD1": "Csb"}, | |
| "M": {"CG": "Csb", "SD": "Ssb", "CE": "Csb"}, | |
| "F": { | |
| "CG": "Cdb", | |
| "CD1": "Cres", | |
| "CD2": "Cres", | |
| "CE1": "Cdb", | |
| "CE2": "Cdb", | |
| "CZ": "Cres", | |
| }, | |
| "P": {"CG": "Csb", "CD": "Csb"}, | |
| "S": {"OG": "Osb"}, | |
| "T": {"OG1": "Osb", "CG2": "Csb"}, | |
| "C": {"SG": "Ssb"}, | |
| "N": {"CG": "Csb", "OD1": "Odb", "ND2": "Ndb"}, | |
| "Q": {"CG": "Csb", "CD": "Csb", "OE1": "Odb", "NE2": "Ndb"}, | |
| "Y": { | |
| "CG": "Cdb", | |
| "CD1": "Cres", | |
| "CD2": "Cres", | |
| "CE1": "Cdb", | |
| "CE2": "Cdb", | |
| "CZ": "Cres", | |
| "OH": "Osb", | |
| }, | |
| "W": { | |
| "CG": "Cdb", | |
| "CD1": "Cdb", | |
| "CD2": "Cres", | |
| "NE1": "Nsb", | |
| "CE2": "Cdb", | |
| "CE3": "Cdb", | |
| "CZ2": "Cres", | |
| "CZ3": "Cres", | |
| "CH2": "Cdb", | |
| }, | |
| "D": {"CG": "Csb", "OD1": "Ores", "OD2": "Ores"}, | |
| "E": {"CG": "Csb", "CD": "Csb", "OE1": "Ores", "OE2": "Ores"}, | |
| "H": {"CG": "Cdb", "CD2": "Cdb", "ND1": "Nsb", "CE1": "Cdb", "NE2": "Ndb"}, | |
| "K": {"CG": "Csb", "CD": "Csb", "CE": "Csb", "NZ": "Nsb"}, | |
| "R": { | |
| "CG": "Csb", | |
| "CD": "Csb", | |
| "NE": "Nsb", | |
| "CZ": "Cdb", | |
| "NH1": "Nres", | |
| "NH2": "Nres", | |
| }, | |
| } | |
| # atomic weights of C,O,N,H,S | |
| atomic_weight = { | |
| "C": 12.0107, | |
| "O": 15.9994, | |
| "N": 14.0067, | |
| "H": 1.0079, | |
| "S": 32.065, | |
| } | |
| # electronegativity values for C,O,N,H,S | |
| electronegativity = {"C": 2.55, "O": 3.44, "N": 3.04, "H": 2.20, "S": 2.58} | |
| # hedra and dihedra default values reference database: | |
| # | |
| # generated from Pisces cullpdb cullpdb_pc20_res2.2_R1.0_d190812_chains8767.gz | |
| # (Aug 2019) https://dunbrack.fccc.edu/pisces | |
| # G. Wang and R. L. Dunbrack, Jr. PISCES: a protein sequence culling server. | |
| # Bioinformatics, 19:1589-1591, 2003. | |
| # | |
| # hedra defaults based on residue-atom classes from reference database | |
| # | |
| # entry format is | |
| # [(len1, angle, len3 averages), angle_sd] # len1, len3 std dev, [total count] | |
| # | |
| # angle standard deviation is used by :func:`ic_data.write_PIC` | |
| # | |
| # N.B. these are just intended as reasonable starting values. Despite the low | |
| # standard deviations, structures degrade quickly with any variation from true | |
| # measurements. | |
| # 226 total entries | |
| hedra_defaults = { | |
| # [(averages), angle_sd] # len1, len3 std dev, [total count] | |
| "ACAACAO": [ | |
| (1.52579, 120.49833, 1.23331), | |
| 0.91020, | |
| ], # 0.01155 0.01086 [37394] | |
| "ACAACAOXT": [ | |
| (1.52535, 119.74925, 1.24174), | |
| 2.62360, | |
| ], # 0.01142 0.01116 [81] | |
| "ACAACXN": [ | |
| (1.52577, 116.69299, 1.33094), | |
| 1.11553, | |
| ], # 0.01152 0.00834 [36750] | |
| "ACBACAAC": [ | |
| (1.52608, 110.28430, 1.52579), | |
| 0.94952, | |
| ], # 0.01629 0.01155 [37388] | |
| "AHANACA": [ | |
| (0.86805, 114.48737, 1.45832), | |
| 1.27049, | |
| ], # 0.03005 0.00756 [2765] | |
| "ANACAAC": [ | |
| (1.46120, 111.05839, 1.52579), | |
| 2.18854, | |
| ], # 0.01140 0.01155 [37398] | |
| "ANACAACB": [ | |
| (1.46120, 110.40921, 1.52608), | |
| 0.88125, | |
| ], # 0.01140 0.01629 [37388] | |
| "CCACCBCSG": [ | |
| (1.52946, 113.86203, 1.80753), | |
| 2.04695, | |
| ], # 0.01183 0.02318 [5998] | |
| "CCACCCO": [ | |
| (1.52388, 120.45381, 1.23272), | |
| 0.96573, | |
| ], # 0.01181 0.01089 [6007] | |
| "CCACCCOXT": [ | |
| (1.52380, 118.37897, 1.24397), | |
| 1.65356, | |
| ], # 0.01273 0.01088 [14] | |
| "CCACCXN": [ | |
| (1.52384, 116.58489, 1.33066), | |
| 1.24455, | |
| ], # 0.01182 0.00862 [5926] | |
| "CCBCCACC": [ | |
| (1.52946, 109.94838, 1.52388), | |
| 1.64395, | |
| ], # 0.01183 0.01181 [6003] | |
| "CHCNCCA": [ | |
| (0.87646, 114.49849, 1.45766), | |
| 1.61226, | |
| ], # 0.04363 0.00890 [520] | |
| "CNCCACC": [ | |
| (1.45964, 110.93113, 1.52388), | |
| 2.48827, | |
| ], # 0.01157 0.01181 [6007] | |
| "CNCCACCB": [ | |
| (1.45963, 110.53598, 1.52946), | |
| 1.28524, | |
| ], # 0.01158 0.01183 [6003] | |
| "DCADCBDCG": [ | |
| (1.53233, 113.01339, 1.51951), | |
| 1.09007, | |
| ], # 0.01090 0.01684 [27365] | |
| "DCADCDO": [ | |
| (1.52681, 120.45665, 1.23263), | |
| 0.97342, | |
| ], # 0.01191 0.01077 [27641] | |
| "DCADCDOXT": [ | |
| (1.52718, 120.50013, 1.24705), | |
| 4.69659, | |
| ], # 0.01149 0.05767 [39] | |
| "DCADCXN": [ | |
| (1.52680, 116.74172, 1.33107), | |
| 1.21325, | |
| ], # 0.01191 0.00855 [27228] | |
| "DCBDCADC": [ | |
| (1.53235, 110.14545, 1.52681), | |
| 1.77412, | |
| ], # 0.01090 0.01191 [27628] | |
| "DCBDCGDOD1": [ | |
| (1.51951, 119.15528, 1.25091), | |
| 1.65280, | |
| ], # 0.01685 0.02470 [27345] | |
| "DCBDCGDOD2": [ | |
| (1.51951, 118.08816, 1.25102), | |
| 1.70244, | |
| ], # 0.01685 0.02107 [27345] | |
| "DHDNDCA": [ | |
| (0.86939, 114.26667, 1.45930), | |
| 1.22719, | |
| ], # 0.03380 0.00813 [1934] | |
| "DNDCADC": [ | |
| (1.46141, 111.03743, 1.52681), | |
| 2.63643, | |
| ], # 0.01184 0.01191 [27642] | |
| "DNDCADCB": [ | |
| (1.46141, 110.56192, 1.53235), | |
| 1.31965, | |
| ], # 0.01184 0.01090 [27628] | |
| "ECAECBECG": [ | |
| (1.53167, 113.93062, 1.52189), | |
| 1.86367, | |
| ], # 0.01056 0.01867 [31977] | |
| "ECAECEO": [ | |
| (1.52593, 120.44996, 1.23262), | |
| 0.95085, | |
| ], # 0.01185 0.01072 [32752] | |
| "ECAECEOXT": [ | |
| (1.52528, 119.67583, 1.24355), | |
| 2.10431, | |
| ], # 0.01091 0.02096 [73] | |
| "ECAECXN": [ | |
| (1.52591, 116.74841, 1.33073), | |
| 1.16616, | |
| ], # 0.01183 0.00811 [32144] | |
| "ECBECAEC": [ | |
| (1.53172, 110.13602, 1.52593), | |
| 1.58401, | |
| ], # 0.01052 0.01184 [32734] | |
| "ECBECGECD": [ | |
| (1.52187, 113.25685, 1.52165), | |
| 1.74528, | |
| ], # 0.01868 0.02069 [31790] | |
| "ECGECDEOE1": [ | |
| (1.52164, 118.96293, 1.25216), | |
| 1.47937, | |
| ], # 0.02070 0.01122 [31755] | |
| "ECGECDEOE2": [ | |
| (1.52164, 118.11536, 1.25165), | |
| 1.45495, | |
| ], # 0.02070 0.01301 [31752] | |
| "EHENECA": [ | |
| (0.86888, 114.41246, 1.45880), | |
| 1.49683, | |
| ], # 0.03581 0.01978 [2274] | |
| "ENECAEC": [ | |
| (1.46058, 111.15787, 1.52593), | |
| 2.27719, | |
| ], # 0.01226 0.01185 [32753] | |
| "ENECAECB": [ | |
| (1.46059, 110.55046, 1.53172), | |
| 1.23650, | |
| ], # 0.01226 0.01052 [32734] | |
| "FCAFCBFCG": [ | |
| (1.53345, 113.82114, 1.50431), | |
| 1.13141, | |
| ], # 0.01162 0.01303 [18987] | |
| "FCAFCFO": [ | |
| (1.52456, 120.49095, 1.23299), | |
| 0.92876, | |
| ], # 0.01188 0.01129 [19038] | |
| "FCAFCFOXT": [ | |
| (1.52401, 119.63248, 1.24271), | |
| 1.73167, | |
| ], # 0.01429 0.01193 [42] | |
| "FCAFCXN": [ | |
| (1.52453, 116.58552, 1.33064), | |
| 1.20900, | |
| ], # 0.01187 0.00855 [18775] | |
| "FCBFCAFC": [ | |
| (1.53345, 110.10780, 1.52457), | |
| 1.76722, | |
| ], # 0.01161 0.01188 [19036] | |
| "FCBFCGFCD1": [ | |
| (1.50431, 120.70752, 1.38869), | |
| 0.74543, | |
| ], # 0.01303 0.01110 [18983] | |
| "FCBFCGFCD2": [ | |
| (1.50431, 120.54385, 1.38836), | |
| 0.68888, | |
| ], # 0.01303 0.01104 [18983] | |
| "FCD1FCE1FCZ": [ | |
| (1.39121, 119.89822, 1.38441), | |
| 0.58792, | |
| ], # 0.01538 0.01516 [18982] | |
| "FCGFCD1FCE1": [ | |
| (1.38869, 120.78060, 1.39121), | |
| 0.56650, | |
| ], # 0.01110 0.01538 [18982] | |
| "FCGFCD2FCE2": [ | |
| (1.38836, 120.79762, 1.39086), | |
| 0.57719, | |
| ], # 0.01104 0.01495 [18982] | |
| "FHFNFCA": [ | |
| (0.86889, 114.28542, 1.45775), | |
| 1.24716, | |
| ], # 0.03367 0.00836 [1374] | |
| "FNFCAFC": [ | |
| (1.46000, 110.81237, 1.52457), | |
| 2.47224, | |
| ], # 0.01149 0.01188 [19039] | |
| "FNFCAFCB": [ | |
| (1.46000, 110.60289, 1.53345), | |
| 1.35478, | |
| ], # 0.01150 0.01161 [19037] | |
| "GCAGCGO": [ | |
| (1.51677, 120.48820, 1.23313), | |
| 1.09788, | |
| ], # 0.00984 0.01079 [31845] | |
| "GCAGCGOXT": [ | |
| (1.51836, 120.01750, 1.24928), | |
| 4.04221, | |
| ], # 0.01201 0.03755 [57] | |
| "GCAGCXN": [ | |
| (1.51675, 116.65649, 1.33072), | |
| 1.35033, | |
| ], # 0.00983 0.00853 [31254] | |
| "GHGNGCA": [ | |
| (0.86934, 114.35896, 1.45001), | |
| 1.33528, | |
| ], # 0.03309 0.00781 [2219] | |
| "GNGCAGC": [ | |
| (1.45534, 113.13469, 1.51677), | |
| 2.73621, | |
| ], # 0.01227 0.00984 [31847] | |
| "HCAHCBHCG": [ | |
| (1.53191, 113.63847, 1.49588), | |
| 1.08749, | |
| ], # 0.01218 0.00823 [10862] | |
| "HCAHCHO": [ | |
| (1.52435, 120.44439, 1.23267), | |
| 0.98586, | |
| ], # 0.01258 0.01107 [10943] | |
| "HCAHCHOXT": [ | |
| (1.51933, 119.63321, 1.24306), | |
| 1.32706, | |
| ], # 0.01541 0.01146 [30] | |
| "HCAHCXN": [ | |
| (1.52433, 116.66524, 1.33078), | |
| 1.24379, | |
| ], # 0.01261 0.00914 [10708] | |
| "HCBHCAHC": [ | |
| (1.53191, 110.12661, 1.52435), | |
| 1.69525, | |
| ], # 0.01215 0.01258 [10944] | |
| "HCBHCGHCD2": [ | |
| (1.49588, 131.02926, 1.35512), | |
| 0.88822, | |
| ], # 0.00823 0.00773 [10855] | |
| "HCBHCGHND1": [ | |
| (1.49588, 122.63934, 1.37822), | |
| 0.85608, | |
| ], # 0.00823 0.00799 [10855] | |
| "HCGHCD2HNE2": [ | |
| (1.35512, 107.18603, 1.37374), | |
| 0.46636, | |
| ], # 0.00773 0.00737 [10854] | |
| "HCGHND1HCE1": [ | |
| (1.37822, 109.16038, 1.32333), | |
| 0.81076, | |
| ], # 0.00799 0.00842 [10854] | |
| "HHHNHCA": [ | |
| (0.86918, 114.34031, 1.45782), | |
| 1.46340, | |
| ], # 0.03246 0.00853 [815] | |
| "HNHCAHC": [ | |
| (1.46046, 111.09335, 1.52435), | |
| 2.58066, | |
| ], # 0.01208 0.01258 [10946] | |
| "HNHCAHCB": [ | |
| (1.46046, 110.46512, 1.53191), | |
| 1.38925, | |
| ], # 0.01208 0.01215 [10944] | |
| "ICAICBICG1": [ | |
| (1.54567, 110.42270, 1.53337), | |
| 1.28403, | |
| ], # 0.01493 0.01361 [27238] | |
| "ICAICBICG2": [ | |
| (1.54567, 110.72098, 1.53061), | |
| 1.04463, | |
| ], # 0.01493 0.01830 [27237] | |
| "ICAICIO": [ | |
| (1.52636, 120.50872, 1.23343), | |
| 0.88888, | |
| ], # 0.01177 0.01089 [27316] | |
| "ICAICIOXT": [ | |
| (1.52902, 119.47607, 1.24279), | |
| 3.18851, | |
| ], # 0.01090 0.01223 [46] | |
| "ICAICXN": [ | |
| (1.52634, 116.66184, 1.33089), | |
| 1.13349, | |
| ], # 0.01179 0.00937 [26993] | |
| "ICBICAIC": [ | |
| (1.54566, 110.43886, 1.52636), | |
| 1.73720, | |
| ], # 0.01492 0.01177 [27314] | |
| "ICBICG1ICD1": [ | |
| (1.53337, 113.96450, 1.51990), | |
| 1.43141, | |
| ], # 0.01361 0.02677 [27229] | |
| "IHINICA": [ | |
| (0.86749, 114.20034, 1.45804), | |
| 1.26213, | |
| ], # 0.03137 0.00805 [1899] | |
| "INICAIC": [ | |
| (1.46029, 109.82832, 1.52636), | |
| 2.41611, | |
| ], # 0.01165 0.01177 [27316] | |
| "INICAICB": [ | |
| (1.46029, 111.38983, 1.54566), | |
| 1.29388, | |
| ], # 0.01165 0.01492 [27314] | |
| "KCAKCBKCG": [ | |
| (1.53126, 114.04683, 1.52169), | |
| 1.74391, | |
| ], # 0.01054 0.01758 [26244] | |
| "KCAKCKO": [ | |
| (1.52595, 120.47261, 1.23256), | |
| 0.95867, | |
| ], # 0.01341 0.01075 [27000] | |
| "KCAKCKOXT": [ | |
| (1.52688, 119.77013, 1.24180), | |
| 2.43662, | |
| ], # 0.01084 0.01157 [93] | |
| "KCAKCXN": [ | |
| (1.52593, 116.70069, 1.33064), | |
| 1.17674, | |
| ], # 0.01345 0.00816 [26509] | |
| "KCBKCAKC": [ | |
| (1.53130, 110.09100, 1.52595), | |
| 1.49272, | |
| ], # 0.01049 0.01342 [26987] | |
| "KCBKCGKCD": [ | |
| (1.52167, 111.57829, 1.52379), | |
| 1.94916, | |
| ], # 0.01759 0.02433 [25968] | |
| "KCDKCEKNZ": [ | |
| (1.52230, 111.75306, 1.49305), | |
| 2.32602, | |
| ], # 0.01893 0.01971 [25629] | |
| "KCGKCDKCE": [ | |
| (1.52369, 111.62887, 1.52231), | |
| 1.75651, | |
| ], # 0.02411 0.01892 [25714] | |
| "KHKNKCA": [ | |
| (0.86934, 114.33829, 1.45890), | |
| 1.23454, | |
| ], # 0.03511 0.02392 [1822] | |
| "KNKCAKC": [ | |
| (1.46080, 111.08063, 1.52595), | |
| 2.33744, | |
| ], # 0.01278 0.01341 [27001] | |
| "KNKCAKCB": [ | |
| (1.46080, 110.54772, 1.53130), | |
| 1.17805, | |
| ], # 0.01278 0.01049 [26987] | |
| "LCALCBLCG": [ | |
| (1.53140, 116.33839, 1.53041), | |
| 2.65234, | |
| ], # 0.01072 0.01173 [43982] | |
| "LCALCLO": [ | |
| (1.52503, 120.41783, 1.23287), | |
| 0.90118, | |
| ], # 0.01180 0.01101 [44095] | |
| "LCALCLOXT": [ | |
| (1.52511, 119.77807, 1.24171), | |
| 2.96371, | |
| ], # 0.01649 0.01938 [97] | |
| "LCALCXN": [ | |
| (1.52501, 116.73371, 1.33088), | |
| 1.11117, | |
| ], # 0.01162 0.01016 [43450] | |
| "LCBLCALC": [ | |
| (1.53140, 109.99081, 1.52503), | |
| 1.43419, | |
| ], # 0.01072 0.01180 [44095] | |
| "LCBLCGLCD1": [ | |
| (1.53041, 110.43155, 1.52397), | |
| 1.76987, | |
| ], # 0.01173 0.01785 [43971] | |
| "LCBLCGLCD2": [ | |
| (1.53041, 110.63050, 1.52450), | |
| 1.73888, | |
| ], # 0.01173 0.01808 [43969] | |
| "LHLNLCA": [ | |
| (0.87043, 114.38647, 1.45799), | |
| 1.36194, | |
| ], # 0.03526 0.00840 [3044] | |
| "LNLCALC": [ | |
| (1.46035, 110.90523, 1.52503), | |
| 2.36226, | |
| ], # 0.01171 0.01180 [44096] | |
| "LNLCALCB": [ | |
| (1.46035, 110.50322, 1.53140), | |
| 1.14993, | |
| ], # 0.01171 0.01072 [44095] | |
| "MCAMCBMCG": [ | |
| (1.53120, 113.86413, 1.52052), | |
| 2.01777, | |
| ], # 0.01199 0.02222 [7201] | |
| "MCAMCMO": [ | |
| (1.52499, 120.43685, 1.23294), | |
| 0.98426, | |
| ], # 0.01184 0.01131 [7251] | |
| "MCAMCMOXT": [ | |
| (1.52632, 119.62203, 1.24398), | |
| 1.70106, | |
| ], # 0.01036 0.00862 [7] | |
| "MCAMCXN": [ | |
| (1.52498, 116.72073, 1.33086), | |
| 1.22277, | |
| ], # 0.01186 0.00891 [7191] | |
| "MCBMCAMC": [ | |
| (1.53120, 110.04147, 1.52500), | |
| 1.60511, | |
| ], # 0.01199 0.01184 [7248] | |
| "MCBMCGMSD": [ | |
| (1.52051, 112.65759, 1.80619), | |
| 2.73841, | |
| ], # 0.02223 0.02344 [7198] | |
| "MCGMSDMCE": [ | |
| (1.80620, 100.62190, 1.78579), | |
| 2.41850, | |
| ], # 0.02344 0.03908 [7196] | |
| "MHMNMCA": [ | |
| (0.86915, 114.41773, 1.45852), | |
| 1.45978, | |
| ], # 0.03366 0.00880 [595] | |
| "MNMCAMC": [ | |
| (1.46091, 110.97184, 1.52499), | |
| 2.26945, | |
| ], # 0.01368 0.01184 [7251] | |
| "MNMCAMCB": [ | |
| (1.46091, 110.56896, 1.53120), | |
| 1.27435, | |
| ], # 0.01368 0.01199 [7248] | |
| "NCANCBNCG": [ | |
| (1.53197, 112.64738, 1.51608), | |
| 1.12454, | |
| ], # 0.01524 0.01660 [19907] | |
| "NCANCNO": [ | |
| (1.52569, 120.44938, 1.23255), | |
| 0.99273, | |
| ], # 0.01205 0.01104 [20064] | |
| "NCANCNOXT": [ | |
| (1.52885, 119.91220, 1.24238), | |
| 2.46382, | |
| ], # 0.01806 0.01795 [40] | |
| "NCANCXN": [ | |
| (1.52568, 116.69676, 1.33090), | |
| 1.23077, | |
| ], # 0.01206 0.00847 [19740] | |
| "NCBNCANC": [ | |
| (1.53197, 110.30885, 1.52570), | |
| 1.73927, | |
| ], # 0.01521 0.01205 [20053] | |
| "NCBNCGNND2": [ | |
| (1.51608, 116.47117, 1.32781), | |
| 1.19956, | |
| ], # 0.01661 0.02243 [19898] | |
| "NCBNCGNOD1": [ | |
| (1.51608, 120.89146, 1.23316), | |
| 1.20758, | |
| ], # 0.01660 0.02656 [19899] | |
| "NHNNNCA": [ | |
| (0.86984, 114.38896, 1.45812), | |
| 1.48714, | |
| ], # 0.03532 0.00825 [1331] | |
| "NNNCANC": [ | |
| (1.46048, 111.52947, 1.52569), | |
| 2.76559, | |
| ], # 0.01161 0.01205 [20066] | |
| "NNNCANCB": [ | |
| (1.46048, 110.53625, 1.53197), | |
| 1.33219, | |
| ], # 0.01161 0.01521 [20054] | |
| "PCAPCBPCG": [ | |
| (1.53273, 104.39244, 1.49426), | |
| 1.38197, | |
| ], # 0.00986 0.02559 [20886] | |
| "PCAPCPO": [ | |
| (1.52595, 120.19725, 1.23340), | |
| 1.18822, | |
| ], # 0.01193 0.01091 [20902] | |
| "PCAPCPOXT": [ | |
| (1.52734, 119.54010, 1.24292), | |
| 2.65747, | |
| ], # 0.00925 0.01366 [37] | |
| "PCAPCXN": [ | |
| (1.52593, 116.77550, 1.33171), | |
| 1.40651, | |
| ], # 0.01183 0.23591 [20372] | |
| "PCBPCAPC": [ | |
| (1.53273, 110.90929, 1.52595), | |
| 1.33990, | |
| ], # 0.00986 0.01193 [20903] | |
| "PCBPCGPCD": [ | |
| (1.49426, 105.28138, 1.50552), | |
| 2.19879, | |
| ], # 0.02559 0.01875 [20886] | |
| "PHPNPCA": [ | |
| (0.96061, 109.46806, 1.47178), | |
| 0.00000, | |
| ], # 0.00000 0.00000 [1] | |
| "PNPCAPC": [ | |
| (1.46668, 112.64045, 1.52595), | |
| 2.33215, | |
| ], # 0.01057 0.01193 [20906] | |
| "PNPCAPCB": [ | |
| (1.46669, 103.26041, 1.53273), | |
| 0.69882, | |
| ], # 0.01057 0.00986 [20904] | |
| "QCAQCBQCG": [ | |
| (1.53106, 113.89466, 1.52254), | |
| 1.83279, | |
| ], # 0.01201 0.08019 [18045] | |
| "QCAQCQO": [ | |
| (1.52562, 120.46310, 1.23271), | |
| 0.91801, | |
| ], # 0.01217 0.01129 [18318] | |
| "QCAQCQOXT": [ | |
| (1.52576, 120.40130, 1.24054), | |
| 2.17575, | |
| ], # 0.01525 0.01248 [39] | |
| "QCAQCXN": [ | |
| (1.52559, 116.71033, 1.33069), | |
| 1.15544, | |
| ], # 0.01217 0.00840 [17980] | |
| "QCBQCAQC": [ | |
| (1.53109, 110.07668, 1.52562), | |
| 1.64027, | |
| ], # 0.01196 0.01217 [18315] | |
| "QCBQCGQCD": [ | |
| (1.52256, 112.72750, 1.51803), | |
| 1.63202, | |
| ], # 0.08033 0.02059 [17972] | |
| "QCGQCDQNE2": [ | |
| (1.51802, 116.43791, 1.32835), | |
| 1.06786, | |
| ], # 0.02060 0.01347 [17952] | |
| "QCGQCDQOE1": [ | |
| (1.51802, 120.93630, 1.23433), | |
| 1.02076, | |
| ], # 0.02059 0.01374 [17953] | |
| "QHQNQCA": [ | |
| (0.87040, 114.46502, 1.45862), | |
| 1.42022, | |
| ], # 0.03559 0.00758 [1282] | |
| "QNQCAQC": [ | |
| (1.46078, 111.10228, 1.52562), | |
| 2.34770, | |
| ], # 0.01404 0.01217 [18320] | |
| "QNQCAQCB": [ | |
| (1.46078, 110.56616, 1.53109), | |
| 1.41193, | |
| ], # 0.01404 0.01196 [18315] | |
| "RCARCBRCG": [ | |
| (1.53122, 113.88552, 1.52077), | |
| 1.85845, | |
| ], # 0.01119 0.02076 [23691] | |
| "RCARCRO": [ | |
| (1.52541, 120.47935, 1.23270), | |
| 0.91912, | |
| ], # 0.01164 0.01058 [24114] | |
| "RCARCROXT": [ | |
| (1.52634, 120.17987, 1.24104), | |
| 2.50707, | |
| ], # 0.01129 0.01042 [61] | |
| "RCARCXN": [ | |
| (1.52538, 116.68310, 1.33064), | |
| 1.13002, | |
| ], # 0.01164 0.00810 [23688] | |
| "RCBRCARC": [ | |
| (1.53126, 110.10652, 1.52542), | |
| 1.56579, | |
| ], # 0.01116 0.01165 [24103] | |
| "RCBRCGRCD": [ | |
| (1.52076, 111.73051, 1.52227), | |
| 2.04838, | |
| ], # 0.02076 0.01978 [23622] | |
| "RCDRNERCZ": [ | |
| (1.46073, 124.72448, 1.33067), | |
| 1.50694, | |
| ], # 0.01228 0.00806 [23496] | |
| "RCGRCDRNE": [ | |
| (1.52225, 111.67959, 1.46073), | |
| 2.20249, | |
| ], # 0.01979 0.01227 [23556] | |
| "RHRNRCA": [ | |
| (0.86985, 114.36013, 1.45821), | |
| 1.27468, | |
| ], # 0.03443 0.00757 [1811] | |
| "RNERCZRNH1": [ | |
| (1.33067, 120.61365, 1.32922), | |
| 1.16135, | |
| ], # 0.00806 0.00988 [23489] | |
| "RNERCZRNH2": [ | |
| (1.33067, 119.72946, 1.32726), | |
| 1.06991, | |
| ], # 0.00806 0.00957 [23487] | |
| "RNRCARC": [ | |
| (1.46051, 111.01141, 1.52541), | |
| 2.33294, | |
| ], # 0.01136 0.01164 [24114] | |
| "RNRCARCB": [ | |
| (1.46051, 110.57356, 1.53126), | |
| 1.25022, | |
| ], # 0.01135 0.01116 [24103] | |
| "SCASCBSOG": [ | |
| (1.53013, 110.77341, 1.41685), | |
| 1.52308, | |
| ], # 0.01158 0.01304 [28300] | |
| "SCASCSO": [ | |
| (1.52539, 120.46650, 1.23290), | |
| 1.01182, | |
| ], # 0.01529 0.01088 [28433] | |
| "SCASCSOXT": [ | |
| (1.52807, 120.91469, 1.24202), | |
| 2.64919, | |
| ], # 0.01641 0.01578 [51] | |
| "SCASCXN": [ | |
| (1.52530, 116.64870, 1.33098), | |
| 1.28030, | |
| ], # 0.01214 0.01498 [27939] | |
| "SCBSCASC": [ | |
| (1.53014, 109.87197, 1.52539), | |
| 1.52276, | |
| ], # 0.01158 0.01529 [28425] | |
| "SHSNSCA": [ | |
| (0.86951, 114.30447, 1.45799), | |
| 1.36681, | |
| ], # 0.03443 0.02922 [1952] | |
| "SNSCASC": [ | |
| (1.46027, 111.24019, 1.52539), | |
| 2.45592, | |
| ], # 0.01472 0.01529 [28434] | |
| "SNSCASCB": [ | |
| (1.46027, 110.50165, 1.53014), | |
| 1.23020, | |
| ], # 0.01472 0.01158 [28425] | |
| "TCATCBTCG2": [ | |
| (1.54072, 111.14321, 1.52457), | |
| 1.13578, | |
| ], # 0.01532 0.02075 [25482] | |
| "TCATCBTOG1": [ | |
| (1.54072, 109.25291, 1.43241), | |
| 1.13095, | |
| ], # 0.01532 0.00917 [25489] | |
| "TCATCTO": [ | |
| (1.52573, 120.48233, 1.23318), | |
| 0.98286, | |
| ], # 0.01190 0.01096 [25576] | |
| "TCATCTOXT": [ | |
| (1.52755, 119.66033, 1.23887), | |
| 1.40536, | |
| ], # 0.01034 0.00954 [30] | |
| "TCATCXN": [ | |
| (1.52571, 116.64426, 1.33079), | |
| 1.22228, | |
| ], # 0.01189 0.00878 [25220] | |
| "TCBTCATC": [ | |
| (1.54072, 109.68682, 1.52573), | |
| 1.87880, | |
| ], # 0.01537 0.01190 [25569] | |
| "THTNTCA": [ | |
| (0.86832, 114.26435, 1.45680), | |
| 1.25833, | |
| ], # 0.03213 0.00785 [1853] | |
| "TNTCATC": [ | |
| (1.45979, 110.71436, 1.52573), | |
| 2.46117, | |
| ], # 0.01171 0.01190 [25576] | |
| "TNTCATCB": [ | |
| (1.45979, 111.20333, 1.54072), | |
| 1.44118, | |
| ], # 0.01171 0.01537 [25569] | |
| "VCAVCBVCG1": [ | |
| (1.54600, 110.76896, 1.52671), | |
| 1.05246, | |
| ], # 0.01458 0.01806 [31953] | |
| "VCAVCBVCG2": [ | |
| (1.54600, 110.48323, 1.52593), | |
| 1.13183, | |
| ], # 0.01458 0.01841 [31953] | |
| "VCAVCVO": [ | |
| (1.52633, 120.53418, 1.23364), | |
| 0.88058, | |
| ], # 0.01147 0.01072 [32001] | |
| "VCAVCVOXT": [ | |
| (1.52365, 119.91629, 1.24178), | |
| 2.30810, | |
| ], # 0.01742 0.01279 [58] | |
| "VCAVCXN": [ | |
| (1.52632, 116.61840, 1.33078), | |
| 1.12023, | |
| ], # 0.01146 0.00830 [31561] | |
| "VCBVCAVC": [ | |
| (1.54599, 110.37127, 1.52633), | |
| 1.67136, | |
| ], # 0.01458 0.01147 [32000] | |
| "VHVNVCA": [ | |
| (0.86865, 114.22727, 1.45822), | |
| 1.30080, | |
| ], # 0.03224 0.00769 [2372] | |
| "VNVCAVC": [ | |
| (1.46011, 109.79444, 1.52633), | |
| 2.41989, | |
| ], # 0.01146 0.01147 [32003] | |
| "VNVCAVCB": [ | |
| (1.46011, 111.50512, 1.54599), | |
| 1.33066, | |
| ], # 0.01146 0.01458 [32000] | |
| "WCAWCBWCG": [ | |
| (1.53282, 113.97168, 1.49904), | |
| 2.24736, | |
| ], # 0.01277 0.01963 [6670] | |
| "WCAWCWO": [ | |
| (1.52458, 120.45502, 1.23347), | |
| 1.04358, | |
| ], # 0.01632 0.01110 [6686] | |
| "WCAWCWOXT": [ | |
| (1.52011, 119.00257, 1.24155), | |
| 1.69651, | |
| ], # 0.01311 0.01121 [13] | |
| "WCAWCXN": [ | |
| (1.52456, 116.66104, 1.33076), | |
| 1.27754, | |
| ], # 0.01636 0.00901 [6603] | |
| "WCBWCAWC": [ | |
| (1.53282, 110.03494, 1.52458), | |
| 1.68844, | |
| ], # 0.01277 0.01632 [6686] | |
| "WCBWCGWCD1": [ | |
| (1.49905, 127.04161, 1.36776), | |
| 0.82872, | |
| ], # 0.01961 0.01209 [6667] | |
| "WCBWCGWCD2": [ | |
| (1.49905, 126.62363, 1.43264), | |
| 0.78472, | |
| ], # 0.01961 0.01052 [6667] | |
| "WCD2WCE2WCZ2": [ | |
| (1.41285, 122.37162, 1.39683), | |
| 0.39598, | |
| ], # 0.01076 0.01110 [6667] | |
| "WCE2WCZ2WCH2": [ | |
| (1.39683, 117.46338, 1.37181), | |
| 0.48283, | |
| ], # 0.01110 0.01002 [6667] | |
| "WCGWCD1WNE1": [ | |
| (1.36776, 110.09367, 1.37511), | |
| 0.60391, | |
| ], # 0.01209 0.01180 [6667] | |
| "WCGWCD2WCE2": [ | |
| (1.43264, 107.20412, 1.41285), | |
| 0.45148, | |
| ], # 0.01052 0.01076 [6667] | |
| "WCGWCD2WCE3": [ | |
| (1.43264, 133.89457, 1.40061), | |
| 0.46905, | |
| ], # 0.01052 0.00787 [6667] | |
| "WCZ2WCH2WCZ3": [ | |
| (1.37181, 121.52060, 1.40362), | |
| 0.48184, | |
| ], # 0.01002 0.01255 [6667] | |
| "WHWNWCA": [ | |
| (0.87227, 114.45217, 1.45809), | |
| 1.56347, | |
| ], # 0.03567 0.00824 [502] | |
| "WNWCAWC": [ | |
| (1.46029, 110.90325, 1.52458), | |
| 2.40138, | |
| ], # 0.01173 0.01632 [6686] | |
| "WNWCAWCB": [ | |
| (1.46029, 110.55141, 1.53282), | |
| 1.35224, | |
| ], # 0.01173 0.01277 [6686] | |
| "XCANACA": [ | |
| (1.33090, 121.43998, 1.46106), | |
| 1.42147, | |
| ], # 0.00858 0.01120 [36738] | |
| "XCCNCCA": [ | |
| (1.33032, 121.51876, 1.45957), | |
| 1.56672, | |
| ], # 0.00808 0.01146 [5949] | |
| "XCDNDCA": [ | |
| (1.33068, 121.56274, 1.46130), | |
| 1.61419, | |
| ], # 0.00823 0.01171 [27198] | |
| "XCENECA": [ | |
| (1.33029, 121.45065, 1.46048), | |
| 1.51425, | |
| ], # 0.00786 0.01216 [32234] | |
| "XCFNFCA": [ | |
| (1.33047, 121.57766, 1.45994), | |
| 1.60046, | |
| ], # 0.00787 0.01139 [18837] | |
| "XCGNGCA": [ | |
| (1.32948, 121.38416, 1.45504), | |
| 1.48756, | |
| ], # 0.01404 0.01181 [30946] | |
| "XCHNHCA": [ | |
| (1.33052, 121.56887, 1.46026), | |
| 1.70772, | |
| ], # 0.00842 0.01180 [10739] | |
| "XCINICA": [ | |
| (1.32998, 121.58807, 1.46022), | |
| 1.51501, | |
| ], # 0.00789 0.01155 [26996] | |
| "XCKNKCA": [ | |
| (1.33029, 121.55854, 1.46068), | |
| 1.49435, | |
| ], # 0.00786 0.01264 [26578] | |
| "XCLNLCA": [ | |
| (1.33033, 121.48377, 1.46027), | |
| 1.44799, | |
| ], # 0.00783 0.01161 [43582] | |
| "XCMNMCA": [ | |
| (1.33037, 121.38091, 1.46012), | |
| 1.61882, | |
| ], # 0.00840 0.01278 [6955] | |
| "XCNNNCA": [ | |
| (1.33062, 121.61726, 1.46036), | |
| 1.69745, | |
| ], # 0.00820 0.01139 [19720] | |
| "XCPNPCA": [ | |
| (1.34101, 120.33021, 1.46667), | |
| 2.55702, | |
| ], # 0.01068 0.01051 [20520] | |
| "XCQNQCA": [ | |
| (1.33224, 121.45675, 1.46058), | |
| 1.77761, | |
| ], # 0.25095 0.01136 [17998] | |
| "XCRNRCA": [ | |
| (1.33033, 121.45120, 1.46045), | |
| 1.54197, | |
| ], # 0.00792 0.01125 [23753] | |
| "XCSNSCA": [ | |
| (1.33027, 121.49507, 1.45999), | |
| 1.58653, | |
| ], # 0.00803 0.01432 [27790] | |
| "XCTNTCA": [ | |
| (1.32996, 121.53022, 1.45965), | |
| 1.53181, | |
| ], # 0.00828 0.01146 [25119] | |
| "XCVNVCA": [ | |
| (1.32997, 121.61608, 1.46006), | |
| 1.51000, | |
| ], # 0.01029 0.01136 [31661] | |
| "XCWNWCA": [ | |
| (1.33060, 121.52771, 1.46022), | |
| 1.60459, | |
| ], # 0.00834 0.01156 [6627] | |
| "XCYNYCA": [ | |
| (1.33039, 121.64133, 1.45990), | |
| 1.67930, | |
| ], # 0.00870 0.01180 [16676] | |
| "YCAYCBYCG": [ | |
| (1.53316, 113.73017, 1.51069), | |
| 2.10543, | |
| ], # 0.01194 0.01218 [16797] | |
| "YCAYCXN": [ | |
| (1.52434, 116.57590, 1.33050), | |
| 1.23191, | |
| ], # 0.01245 0.00901 [16620] | |
| "YCAYCYO": [ | |
| (1.52434, 120.49480, 1.23293), | |
| 0.93410, | |
| ], # 0.01247 0.01112 [16834] | |
| "YCAYCYOXT": [ | |
| (1.52321, 119.49565, 1.24463), | |
| 2.34968, | |
| ], # 0.01606 0.01854 [36] | |
| "YCBYCAYC": [ | |
| (1.53316, 110.02329, 1.52434), | |
| 1.69072, | |
| ], # 0.01193 0.01247 [16834] | |
| "YCBYCGYCD1": [ | |
| (1.51069, 120.93847, 1.39171), | |
| 0.68236, | |
| ], # 0.01218 0.01060 [16794] | |
| "YCBYCGYCD2": [ | |
| (1.51069, 120.85238, 1.39117), | |
| 0.65315, | |
| ], # 0.01218 0.01080 [16794] | |
| "YCD1YCE1YCZ": [ | |
| (1.38947, 119.53062, 1.38197), | |
| 0.62808, | |
| ], # 0.01503 0.01268 [16793] | |
| "YCE1YCZYOH": [ | |
| (1.38198, 119.78227, 1.37715), | |
| 1.31664, | |
| ], # 0.01268 0.01162 [16792] | |
| "YCGYCD1YCE1": [ | |
| (1.39171, 121.13695, 1.38947), | |
| 0.53265, | |
| ], # 0.01060 0.01503 [16794] | |
| "YCGYCD2YCE2": [ | |
| (1.39117, 121.14721, 1.38918), | |
| 0.55038, | |
| ], # 0.01080 0.01471 [16793] | |
| "YHYNYCA": [ | |
| (0.86913, 114.22549, 1.45737), | |
| 1.30753, | |
| ], # 0.03360 0.00806 [1204] | |
| "YNYCAYC": [ | |
| (1.45996, 110.93364, 1.52434), | |
| 2.48714, | |
| ], # 0.01187 0.01247 [16834] | |
| "YNYCAYCB": [ | |
| (1.45996, 110.58072, 1.53316), | |
| 1.29512, | |
| ], # 0.01187 0.01193 [16835] | |
| } | |
| # primary dihedra defaults based on residue-atom classes from reference | |
| # database. | |
| # | |
| # primary dihedra are those not feasible to measure as a rotation from another | |
| # dihedral angle: psi, omega, phi, sidechain chi angles, and a few more for | |
| # aromatic sidechains as required by the algorithm. These are the ones you | |
| # really need to specify. | |
| # | |
| # each entry is the most common rounded int value observed over the class, | |
| # followed by standard deviation (used by :func:`ic_data.write_PIC`) | |
| # | |
| # numbers in comments after each entry are count of dihedra in class and average | |
| # angle | |
| # | |
| # N.B. these are just intended as reasonable starting values, in practice they | |
| # generate a helical backbone with a kink at proline residues | |
| # 134 total primary entries | |
| dihedra_primary_defaults = { | |
| # [most common int(value), std_dev] # count average | |
| "ANACAACAOXT": [169, 95.25474], # 81 -165.46932 | |
| "ANACAACXN": [-42, 98.15673], # 36750 -29.47243 | |
| "CNCCACCBCSG": [-70, 81.01579], # 5998 -85.23394 | |
| "CNCCACCCOXT": [-176, 80.00406], # 14 140.50216 | |
| "CNCCACCXN": [-44, 91.42604], # 5926 94.93048 | |
| "DCADCBDCGDOD1": [-13, 52.88900], # 27345 -11.84937 | |
| "DNDCADCBDCG": [-70, 79.12777], # 27365 -96.25186 | |
| "DNDCADCDOXT": [-7, 95.85319], # 39 158.65904 | |
| "DNDCADCXN": [-41, 83.80110], # 27228 14.67151 | |
| "ECAECBECGECD": [178, 65.34682], # 31790 -176.30888 | |
| "ECBECGECDEOE1": [-10, 68.20002], # 31755 -5.06398 | |
| "ENECAECBECG": [-68, 70.35756], # 31977 -98.71636 | |
| "ENECAECEOXT": [-25, 99.97143], # 73 -168.10401 | |
| "ENECAECXN": [-42, 92.43985], # 32144 -24.04536 | |
| "FCAFCBFCGFCD1": [85, 79.85765], # 18983 25.61167 | |
| "FCBFCGFCD1FCE1": [179, 1.83591], # 18982 -179.99254 | |
| "FCBFCGFCD2FCE2": [-179, 1.84368], # 18982 179.99540 | |
| "FCGFCD1FCE1FCZ": [0, 1.47424], # 18982 -0.02249 | |
| "FNFCAFCBFCG": [-65, 76.22754], # 18987 -102.70403 | |
| "FNFCAFCFOXT": [-6, 99.25114], # 42 158.48470 | |
| "FNFCAFCXN": [-47, 87.47370], # 18775 63.18666 | |
| "GNGCAGCGOXT": [171, 104.01396], # 57 -179.22384 | |
| "GNGCAGCXN": [-42, 101.30511], # 31254 -26.19519 | |
| "HCAHCBHCGHND1": [-73, 105.57152], # 10855 -80.79397 | |
| "HCBHCGHCD2HNE2": [-179, 2.10579], # 10854 -179.94222 | |
| "HCBHCGHND1HCE1": [179, 1.85979], # 10854 179.94389 | |
| "HNHCAHCBHCG": [-65, 76.36890], # 10862 -96.99583 | |
| "HNHCAHCHOXT": [178, 89.67199], # 30 -141.00653 | |
| "HNHCAHCXN": [-42, 84.52974], # 10708 37.08787 | |
| "ICAICBICG1ICD1": [169, 56.74755], # 27229 176.16728 | |
| "INICAICBICG1": [-63, 55.70911], # 27238 -61.62701 | |
| "INICAICIOXT": [-70, 89.44826], # 46 51.25035 | |
| "INICAICXN": [-46, 88.35710], # 26993 73.43770 | |
| "KCAKCBKCGKCD": [178, 53.85008], # 25968 -175.38550 | |
| "KCBKCGKCDKCE": [179, 56.41606], # 25714 -179.94658 | |
| "KCGKCDKCEKNZ": [-179, 67.53216], # 25629 -179.61758 | |
| "KNKCAKCBKCG": [-69, 68.26710], # 26244 -100.50122 | |
| "KNKCAKCKOXT": [-47, 103.08025], # 93 161.30451 | |
| "KNKCAKCXN": [-42, 95.81378], # 26509 -16.93019 | |
| "LCALCBLCGLCD1": [174, 58.10966], # 43971 141.93425 | |
| "LNLCALCBLCG": [-67, 56.26252], # 43982 -96.34969 | |
| "LNLCALCLOXT": [156, 98.73531], # 97 178.42308 | |
| "LNLCALCXN": [-41, 95.14039], # 43450 -14.58895 | |
| "MCAMCBMCGMSD": [178, 70.69856], # 7198 -161.34475 | |
| "MCBMCGMSDMCE": [-73, 97.48432], # 7196 -30.14847 | |
| "MNMCAMCBMCG": [-66, 66.26181], # 7201 -91.32003 | |
| "MNMCAMCMOXT": [-178, 72.38494], # 7 -102.91898 | |
| "MNMCAMCXN": [-42, 98.49678], # 7191 -11.35059 | |
| "NCANCBNCGNOD1": [-16, 67.43697], # 19899 -18.72551 | |
| "NNNCANCBNCG": [-68, 73.98113], # 19907 -92.41878 | |
| "NNNCANCNOXT": [147, 89.25031], # 40 152.04805 | |
| "NNNCANCXN": [-40, 77.32702], # 19740 27.97970 | |
| "PCAPCBPCGPCD": [36, 34.61280], # 20886 1.80409 | |
| "PNPCAPCBPCG": [-28, 25.95226], # 20886 0.27287 | |
| "PNPCAPCPOXT": [-56, 102.31786], # 37 160.48791 | |
| "PNPCAPCXN": [148, 99.98739], # 20372 127.77237 | |
| "QCAQCBQCGQCD": [176, 68.87188], # 17972 -175.20642 | |
| "QCBQCGQCDQOE1": [-51, 71.82863], # 17953 -4.14997 | |
| "QNQCAQCBQCG": [-67, 66.94384], # 18045 -94.68057 | |
| "QNQCAQCQOXT": [-179, 95.53036], # 39 -177.40254 | |
| "QNQCAQCXN": [-42, 93.49684], # 17980 -18.74463 | |
| "RCARCBRCGRCD": [177, 49.67635], # 23622 -176.16102 | |
| "RCBRCGRCDRNE": [179, 84.50289], # 23556 -173.50404 | |
| "RCDRNERCZRNH1": [0, 54.62565], # 23489 0.04129 | |
| "RCGRCDRNERCZ": [-88, 69.24645], # 23496 -175.95812 | |
| "RNRCARCBRCG": [-68, 71.72865], # 23691 -102.63698 | |
| "RNRCARCROXT": [171, 99.50938], # 61 -177.32361 | |
| "RNRCARCXN": [-41, 96.71025], # 23688 -14.55186 | |
| "SNSCASCBSOG": [66, 89.69619], # 28300 63.90162 | |
| "SNSCASCSOXT": [-30, 89.77697], # 51 -140.58823 | |
| "SNSCASCXN": [-42, 92.34618], # 27939 34.90087 | |
| "TNTCATCBTOG1": [-61, 75.97906], # 25489 0.35355 | |
| "TNTCATCTOXT": [-4, 85.80840], # 30 116.33387 | |
| "TNTCATCXN": [-43, 97.81897], # 25220 103.78844 | |
| "VNVCAVCBVCG1": [177, 60.41895], # 31953 -176.53074 | |
| "VNVCAVCVOXT": [162, 100.62799], # 58 139.89586 | |
| "VNVCAVCXN": [-44, 97.87826], # 31561 111.78211 | |
| "WCAWCBWCGWCD1": [90, 96.85361], # 6667 65.40881 | |
| "WCBWCGWCD1WNE1": [-179, 2.16184], # 6667 -179.84187 | |
| "WCBWCGWCD2WCE2": [179, 2.19723], # 6667 179.84352 | |
| "WCD2WCE2WCZ2WCH2": [0, 1.44032], # 6667 0.01803 | |
| "WCE2WCZ2WCH2WCZ3": [0, 1.38967], # 6667 -0.01231 | |
| "WCGWCD2WCE2WCZ2": [180, 1.02636], # 6667 179.96302 | |
| "WNWCAWCBWCG": [-71, 83.39480], # 6670 -103.58680 | |
| "WNWCAWCWOXT": [-178, 93.40045], # 13 131.22360 | |
| "WNWCAWCXN": [-43, 94.36376], # 6603 12.91505 | |
| "XCANACAAC": [-63, 34.11665], # 36738 -77.24348 | |
| "XCAXCANACA": [179, 5.71694], # 36738 179.41421 | |
| "XCAXCCNCCA": [179, 7.65580], # 5949 179.50458 | |
| "XCAXCDNDCA": [179, 7.69439], # 27198 179.07623 | |
| "XCAXCENECA": [179, 6.37868], # 32234 179.34942 | |
| "XCAXCFNFCA": [179, 6.19707], # 18837 179.35525 | |
| "XCAXCGNGCA": [179, 8.86313], # 30946 178.98640 | |
| "XCAXCHNHCA": [179, 7.15842], # 10739 179.50565 | |
| "XCAXCINICA": [179, 5.72861], # 26996 178.85749 | |
| "XCAXCKNKCA": [179, 6.23316], # 26578 179.16930 | |
| "XCAXCLNLCA": [179, 5.44198], # 43582 179.13937 | |
| "XCAXCMNMCA": [179, 6.15780], # 6955 179.29453 | |
| "XCAXCNNNCA": [179, 7.94004], # 19720 179.28144 | |
| "XCAXCPNPCA": [-180, 38.10480], # 20520 179.72853 | |
| "XCAXCQNQCA": [179, 5.98589], # 17998 179.17709 | |
| "XCAXCRNRCA": [179, 6.13625], # 23753 179.08276 | |
| "XCAXCSNSCA": [179, 7.81457], # 27790 179.45259 | |
| "XCAXCTNTCA": [179, 6.63019], # 25119 179.08898 | |
| "XCAXCVNVCA": [179, 6.28535], # 31661 178.92630 | |
| "XCAXCWNWCA": [179, 8.05982], # 6627 179.45312 | |
| "XCAXCYNYCA": [179, 6.42966], # 16676 179.66147 | |
| "XCCNCCACC": [-63, 39.85404], # 5949 -93.17092 | |
| "XCDNDCADC": [-63, 42.66497], # 27198 -81.36742 | |
| "XCENECAEC": [-64, 33.27969], # 32234 -78.04899 | |
| "XCFNFCAFC": [-64, 37.53881], # 18836 -92.58604 | |
| "XCGNGCAGC": [-62, 105.46218], # 30945 84.19701 | |
| "XCHNHCAHC": [-62, 44.74280], # 10739 -90.93838 | |
| "XCINICAIC": [-63, 28.64344], # 26996 -90.03017 | |
| "XCKNKCAKC": [-63, 37.33533], # 26577 -80.74953 | |
| "XCLNLCALC": [-63, 28.04783], # 43580 -81.71257 | |
| "XCMNMCAMC": [-63, 33.98800], # 6955 -83.88604 | |
| "XCNNNCANC": [-64, 56.30326], # 19719 -85.16140 | |
| "XCPNPCAPC": [-60, 10.60764], # 20519 -65.25196 | |
| "XCQNQCAQC": [-64, 36.43753], # 17998 -81.03040 | |
| "XCRNRCARC": [-64, 37.52840], # 23753 -83.03807 | |
| "XCSNSCASC": [-63, 39.99619], # 27790 -88.27000 | |
| "XCTNTCATC": [-62, 31.66804], # 25119 -95.01154 | |
| "XCVNVCAVC": [-62, 29.95014], # 31661 -94.87235 | |
| "XCWNWCAWC": [-64, 35.41390], # 6627 -87.28116 | |
| "XCYNYCAYC": [-63, 37.42074], # 16675 -93.61795 | |
| "YCAYCBYCGYCD1": [83, 79.95637], # 16794 21.14006 | |
| "YCBYCGYCD1YCE1": [-179, 1.95641], # 16794 -179.91379 | |
| "YCBYCGYCD2YCE2": [179, 1.97956], # 16793 179.92677 | |
| "YCD1YCE1YCZYOH": [180, 1.22077], # 16792 179.99504 | |
| "YCGYCD1YCE1YCZ": [0, 1.43861], # 16793 -0.02863 | |
| "YNYCAYCBYCG": [-67, 76.72110], # 16797 -102.49923 | |
| "YNYCAYCXN": [-46, 88.47760], # 16620 72.07880 | |
| "YNYCAYCYOXT": [132, 87.47211], # 36 155.93068 | |
| } | |
| # secondary dihedra defaults based on residue-atom classes from reference | |
| # database. | |
| # | |
| # secondary dihedra are those with relatively constant rotations from other | |
| # (primary) dihedra, such as the planar orientation of the amide O atom | |
| # (N-Ca-C-O) relative to the second N atom in the psi backbone dihedral | |
| # (N-CA-C-N). | |
| # | |
| # each entry is the primary angle to rotate from and the average rotation | |
| # observed over the class | |
| # | |
| # numbers in comments after each entry are count of dihedra in class and | |
| # standard deviation. | |
| # | |
| # N.B. these are just intended as reasonable starting values, but sufficient to | |
| # achieve <1.0 angstrom RMSD from the original structure in limited testing | |
| # using ChimeraX matchmaker | |
| dihedra_secondary_defaults = { | |
| # primary angle to rotate from, average rotation # count std dev | |
| "ANACAACAO": [("N", "CA", "C", "N"), 179.92568], # 36749 1.98809 | |
| "AOACACAACB": [("N", "CA", "C", "N"), -57.30099], # 36740 2.54018 | |
| "CNCCACCCO": [("N", "CA", "C", "N"), 179.94158], # 5926 2.20422 | |
| "COCCCCACCB": [("N", "CA", "C", "N"), -57.44056], # 5923 2.99793 | |
| "DCADCBDCGDOD2": [ | |
| ("CA", "CB", "CG", "OD1"), | |
| -179.86172, | |
| ], # 27344 2.38528 | |
| "DNDCADCDO": [("N", "CA", "C", "N"), -179.97109], # 27227 2.11112 | |
| "DODCDCADCB": [("N", "CA", "C", "N"), -57.07933], # 27214 3.07908 | |
| "ECBECGECDEOE2": [ | |
| ("CB", "CG", "CD", "OE1"), | |
| -179.97281, | |
| ], # 31751 2.90866 | |
| "ENECAECEO": [("N", "CA", "C", "N"), 179.92920], # 32144 2.23044 | |
| "EOECECAECB": [("N", "CA", "C", "N"), -57.13533], # 32127 3.00382 | |
| "FCAFCBFCGFCD2": [("CA", "CB", "CG", "CD1"), 179.97232], # 18983 2.66092 | |
| "FNFCAFCFO": [("N", "CA", "C", "N"), 179.86787], # 18775 2.24567 | |
| "FOFCFCAFCB": [("N", "CA", "C", "N"), -57.36288], # 18773 3.19500 | |
| "GNGCAGCGO": [("N", "CA", "C", "N"), 179.87864], # 31254 1.93653 | |
| "HCAHCBHCGHCD2": [("CA", "CB", "CG", "ND1"), 179.92892], # 10855 3.13324 | |
| "HNHCAHCHO": [("N", "CA", "C", "N"), 179.88083], # 10707 2.13861 | |
| "HOHCHCAHCB": [("N", "CA", "C", "N"), -57.32474], # 10705 3.15196 | |
| "INICAICBICG2": [("N", "CA", "CB", "CG1"), -123.20171], # 27237 2.42092 | |
| "INICAICIO": [("N", "CA", "C", "N"), -179.99219], # 26993 2.09900 | |
| "IOICICAICB": [("N", "CA", "C", "N"), -56.67074], # 26992 2.87033 | |
| "KNKCAKCKO": [("N", "CA", "C", "N"), 179.91063], # 26508 1.98813 | |
| "KOKCKCAKCB": [("N", "CA", "C", "N"), -57.24410], # 26495 2.74225 | |
| "LCALCBLCGLCD2": [("CA", "CB", "CG", "CD1"), 122.93111], # 43968 2.16725 | |
| "LNLCALCLO": [("N", "CA", "C", "N"), 179.91619], # 43450 2.02277 | |
| "LOLCLCALCB": [("N", "CA", "C", "N"), -57.47486], # 43450 2.83489 | |
| "MNMCAMCMO": [("N", "CA", "C", "N"), 179.89452], # 7191 2.16025 | |
| "MOMCMCAMCB": [("N", "CA", "C", "N"), -57.33882], # 7188 2.97285 | |
| "NCANCBNCGNND2": [("CA", "CB", "CG", "OD1"), 179.94543], # 19898 2.12515 | |
| "NNNCANCNO": [("N", "CA", "C", "N"), 179.92115], # 19739 2.13981 | |
| "NONCNCANCB": [("N", "CA", "C", "N"), -56.76402], # 19726 3.06823 | |
| "PNPCAPCPO": [("N", "CA", "C", "N"), 179.99101], # 20371 2.09744 | |
| "POPCPCAPCB": [("N", "CA", "C", "N"), -64.77747], # 20369 2.66024 | |
| "QCBQCGQCDQNE2": [ | |
| ("CB", "CG", "CD", "OE1"), | |
| -179.98865, | |
| ], # 17951 2.77403 | |
| "QNQCAQCQO": [("N", "CA", "C", "N"), 179.92706], # 17980 2.08396 | |
| "QOQCQCAQCB": [("N", "CA", "C", "N"), -57.18151], # 17976 3.18161 | |
| "RCDRNERCZRNH2": [("CD", "NE", "CZ", "NH1"), 179.99965], # 23487 3.02813 | |
| "RNRCARCRO": [("N", "CA", "C", "N"), 179.92085], # 23688 2.06352 | |
| "RORCRCARCB": [("N", "CA", "C", "N"), -57.21965], # 23677 3.05380 | |
| "SNSCASCSO": [("N", "CA", "C", "N"), 179.87018], # 27939 2.11127 | |
| "SOSCSCASCB": [("N", "CA", "C", "N"), -57.37555], # 27932 3.02066 | |
| "TNTCATCBTCG2": [("N", "CA", "CB", "OG1"), -120.62370], # 25482 2.72546 | |
| "TNTCATCTO": [("N", "CA", "C", "N"), 179.93709], # 25220 2.08437 | |
| "TOTCTCATCB": [("N", "CA", "C", "N"), -56.91727], # 25214 2.98795 | |
| "VNVCAVCBVCG2": [("N", "CA", "CB", "CG1"), 122.92482], # 31953 1.99439 | |
| "VNVCAVCVO": [("N", "CA", "C", "N"), -179.91262], # 31561 2.06055 | |
| "VOVCVCAVCB": [("N", "CA", "C", "N"), -56.53189], # 31558 2.84749 | |
| "WCAWCBWCGWCD2": [("CA", "CB", "CG", "CD1"), -179.77249], # 6667 3.15519 | |
| "WCBWCGWCD2WCE3": [ | |
| ("CB", "CG", "CD2", "CE2"), | |
| 179.97400, | |
| ], # 6667 1.70848 | |
| "WNWCAWCWO": [("N", "CA", "C", "N"), 179.79740], # 6603 2.20883 | |
| "WOWCWCAWCB": [("N", "CA", "C", "N"), -57.49156], # 6603 3.27149 | |
| "YCAYCBYCGYCD2": [ | |
| ("CA", "CB", "CG", "CD1"), | |
| -179.94185, | |
| ], # 16794 2.64007 | |
| "YNYCAYCYO": [("N", "CA", "C", "N"), 179.83537], # 16620 2.14952 | |
| "YOYCYCAYCB": [("N", "CA", "C", "N"), -57.40953], # 16620 3.10134 | |
| } # 53 total secondary default entries | |
| # secondary dihedra defaults based on residue-atom classes from reference | |
| # database. | |
| # | |
| # as above, but this table is for limited set of secondary dihedra which are | |
| # defined by rotation from chain terminal OXT or use the alternate CB locator | |
| # dihedral C(i-1)-C-N-CA-CB when the amide O is missing | |
| dihedra_secondary_xoxt_defaults = { | |
| # primary angle to rotate from, average rotation # count std dev | |
| "ANACAACAO": [("N", "CA", "C", "OXT"), 179.94094], # 81 2.11763 | |
| "AOACACAACB": [("N", "CA", "C", "OXT"), -57.60123], # 81 2.80240 | |
| "CNCCACCCO": [("N", "CA", "C", "OXT"), -179.80335], # 14 1.44006 | |
| "COCCCCACCB": [("N", "CA", "C", "OXT"), -56.72357], # 14 2.10630 | |
| "DNDCADCDO": [("N", "CA", "C", "OXT"), 179.49564], # 39 2.90408 | |
| "DODCDCADCB": [("N", "CA", "C", "OXT"), -57.21308], # 39 3.78367 | |
| "ENECAECEO": [("N", "CA", "C", "OXT"), 179.92513], # 73 5.63173 | |
| "EOECECAECB": [("N", "CA", "C", "OXT"), -57.23113], # 73 6.62931 | |
| "FNFCAFCFO": [("N", "CA", "C", "OXT"), -179.59346], # 42 3.26581 | |
| "FOFCFCAFCB": [("N", "CA", "C", "OXT"), -57.03927], # 42 4.29847 | |
| "GNGCAGCGO": [("N", "CA", "C", "OXT"), 179.69001], # 57 1.64200 | |
| "HNHCAHCHO": [("N", "CA", "C", "OXT"), -179.75032], # 30 1.44791 | |
| "HOHCHCAHCB": [("N", "CA", "C", "OXT"), -56.67577], # 30 2.65028 | |
| "INICAICIO": [("N", "CA", "C", "OXT"), 179.93893], # 46 1.77873 | |
| "IOICICAICB": [("N", "CA", "C", "OXT"), -56.65160], # 45 3.62735 | |
| "KNKCAKCKO": [("N", "CA", "C", "OXT"), 179.71490], # 93 18.78315 | |
| "KOKCKCAKCB": [("N", "CA", "C", "OXT"), -57.20240], # 93 19.02926 | |
| "LNLCALCLO": [("N", "CA", "C", "OXT"), 179.77678], # 97 1.98355 | |
| "LOLCLCALCB": [("N", "CA", "C", "OXT"), -57.59144], # 97 2.75152 | |
| "MNMCAMCMO": [("N", "CA", "C", "OXT"), -179.97795], # 7 1.96286 | |
| "MOMCMCAMCB": [("N", "CA", "C", "OXT"), -55.77939], # 7 4.32745 | |
| "NNNCANCNO": [("N", "CA", "C", "OXT"), 179.71084], # 40 1.95590 | |
| "NONCNCANCB": [("N", "CA", "C", "OXT"), -57.09828], # 40 3.22053 | |
| "PNPCAPCPO": [("N", "CA", "C", "OXT"), -179.53729], # 37 1.61467 | |
| "POPCPCAPCB": [("N", "CA", "C", "OXT"), -64.53147], # 37 2.37847 | |
| "QNQCAQCQO": [("N", "CA", "C", "OXT"), 179.58623], # 37 3.13328 | |
| "QOQCQCAQCB": [("N", "CA", "C", "OXT"), -57.50893], # 36 4.43485 | |
| "RNRCARCRO": [("N", "CA", "C", "OXT"), 179.93106], # 61 4.38718 | |
| "RORCRCARCB": [("N", "CA", "C", "OXT"), -57.72993], # 61 5.16366 | |
| "SNSCASCSO": [("N", "CA", "C", "OXT"), 179.56523], # 51 2.65719 | |
| "SOSCSCASCB": [("N", "CA", "C", "OXT"), -57.18238], # 51 3.57789 | |
| "TNTCATCTO": [("N", "CA", "C", "OXT"), -179.79984], # 30 1.33044 | |
| "TOTCTCATCB": [("N", "CA", "C", "OXT"), -56.58614], # 30 2.06022 | |
| "VNVCAVCVO": [("N", "CA", "C", "OXT"), -179.70350], # 57 3.55209 | |
| "VOVCVCAVCB": [("N", "CA", "C", "OXT"), -56.23549], # 57 4.14683 | |
| "WNWCAWCWO": [("N", "CA", "C", "OXT"), -179.82426], # 13 1.83266 | |
| "WOWCWCAWCB": [("N", "CA", "C", "OXT"), -57.66758], # 13 2.36066 | |
| "XCANACAACB": [("C", "N", "CA", "C"), -122.64404], # 4 0.71089 | |
| "XCDNDCADCB": [("C", "N", "CA", "C"), -129.79903], # 1 0.00000 | |
| "XCENECAECB": [("C", "N", "CA", "C"), -130.15620], # 1 0.00000 | |
| "XCFNFCAFCB": [("C", "N", "CA", "C"), -121.28140], # 1 0.00000 | |
| "XCHNHCAHCB": [("C", "N", "CA", "C"), -123.67335], # 3 1.41030 | |
| "XCKNKCAKCB": [("C", "N", "CA", "C"), -123.09741], # 1 0.00000 | |
| "XCLNLCALCB": [("C", "N", "CA", "C"), -122.14996], # 1 0.00000 | |
| "XCNNNCANCB": [("C", "N", "CA", "C"), -123.45323], # 2 1.53987 | |
| "XCPNPCAPCB": [("C", "N", "CA", "C"), -122.07120], # 4 3.14794 | |
| "XCQNQCAQCB": [("C", "N", "CA", "C"), -124.41558], # 2 1.44826 | |
| "XCSNSCASCB": [("C", "N", "CA", "C"), -121.29809], # 1 0.00000 | |
| "XCVNVCAVCB": [("C", "N", "CA", "C"), -122.15680], # 2 0.50441 | |
| "YNYCAYCYO": [("N", "CA", "C", "OXT"), 179.55952], # 36 13.58661 | |
| "YOYCYCAYCB": [("N", "CA", "C", "OXT"), -57.28932], # 36 13.86761 | |
| } # 51 total secondary X / OXT default entries | |