molUtils

Utilities for handling structures and sequences

Functions Overview

allAA
return:list of all 20 ‘exact’ single AA codes.
allAACodes
return:list of all single AA codes, including B, Z, X :rtype: [str]
cmpAtoms Comparison function for bringing atoms into standard order within residues as defined by atomDic.
elementType Classify an atom as polar or unpolar:: atomType( eLetter ) -> list of types this element belongs to
resType Classify residues as aromatic (a), charged (c) or polar (p).
single2longAA Convert string of 1-letter AA code into list of 3-letter AA codes.
singleAA convert list with 3-letter AA code to list with 1-letter code
sortAtomsOfModel Sort atoms within residues into the standard order defined in atomDic.

Classes Overview

Exceptions Defined in this Module

MolUtilError

molUtils Module Details

exception biskit.molUtils.MolUtilError[source]
biskit.molUtils.aaDicStandard = {'ala': 'A', 'arg': 'R', 'asn': 'N', 'asp': 'D', 'asx': 'B', 'cys': 'C', 'gln': 'Q', 'glu': 'E', 'glx': 'Z', 'gly': 'G', 'his': 'H', 'ile': 'I', 'leu': 'L', 'lys': 'K', 'met': 'M', 'phe': 'F', 'pro': 'P', 'ser': 'S', 'thr': 'T', 'trp': 'W', 'tyr': 'Y', 'val': 'V'}

translate PDB amino acid names to single letter code

biskit.molUtils.nsDicStandard = {'a': 'a', 'a3': 'a', 'a5': 'a', 'c': 'c', 'c3': 'c', 'c5': 'c', 'da': 'a', 'da3': 'a', 'da5': 'a', 'dc': 'c', 'dc3': 'c', 'dc5': 'c', 'dg': 'g', 'dg3': 'g', 'dg5': 'g', 'dt': 't', 'dt3': 't', 'dt5': 't', 'g': 'g', 'g3': 'g', 'g5': 'g', 't': 't', 't3': 't', 't5': 't', 'u': 'u', 'u3': 'u', 'u5': 'u'}

same for nucleic acids (incomplete)

biskit.molUtils.aaDic = {'ace': 'X', 'ala': 'A', 'arg': 'R', 'asn': 'N', 'asp': 'D', 'asx': 'B', 'cys': 'C', 'cyx': 'C', 'gln': 'Q', 'glu': 'E', 'glx': 'Z', 'gly': 'G', 'hid': 'H', 'hie': 'H', 'hip': 'H', 'his': 'H', 'ile': 'I', 'leu': 'L', 'lys': 'K', 'met': 'M', 'nme': 'X', 'phe': 'F', 'pro': 'P', 'ser': 'S', 'thr': 'T', 'trp': 'W', 'tyr': 'Y', 'unk': 'X', 'val': 'V'}

extend aaDicStandard with non-standard residues

biskit.molUtils.nsDic = {'a': 'a', 'a3': 'a', 'a5': 'a', 'adp': 'a', 'amp': 'a', 'atp': 'a', 'c': 'c', 'c3': 'c', 'c5': 'c', 'cdp': 'c', 'ctp': 'c', 'da': 'a', 'da3': 'a', 'da5': 'a', 'dc': 'c', 'dc3': 'c', 'dc5': 'c', 'dg': 'g', 'dg3': 'g', 'dg5': 'g', 'dt': 't', 'dt3': 't', 'dt5': 't', 'fad': 'f', 'fmp': 'f', 'g': 'g', 'g3': 'g', 'g5': 'g', 'gdp': 'g', 'gmp': 'g', 'gtp': 'g', 'nad': 'n', 't': 't', 't3': 't', 't5': 't', 'tdp': 't', 'ttp': 't', 'u': 'u', 'u3': 'u', 'u5': 'u', 'udp': 'u', 'utp': 'u'}

extend nsDicStandard with non-standard residues

biskit.molUtils.xxDic = {'ca': '+', 'cl-': '-', 'hoh': '~', 'na+': '+', 'nap': 'X', 'ndp': 'X', 'tip3': '~', 'wat': '~'}

translate common hetero residues to pseudo single letter code

biskit.molUtils.resDicStandard = {'a': 'a', 'a3': 'a', 'a5': 'a', 'ala': 'A', 'arg': 'R', 'asn': 'N', 'asp': 'D', 'asx': 'B', 'c': 'c', 'c3': 'c', 'c5': 'c', 'cys': 'C', 'da': 'a', 'da3': 'a', 'da5': 'a', 'dc': 'c', 'dc3': 'c', 'dc5': 'c', 'dg': 'g', 'dg3': 'g', 'dg5': 'g', 'dt': 't', 'dt3': 't', 'dt5': 't', 'g': 'g', 'g3': 'g', 'g5': 'g', 'gln': 'Q', 'glu': 'E', 'glx': 'Z', 'gly': 'G', 'his': 'H', 'ile': 'I', 'leu': 'L', 'lys': 'K', 'met': 'M', 'phe': 'F', 'pro': 'P', 'ser': 'S', 't': 't', 't3': 't', 't5': 't', 'thr': 'T', 'trp': 'W', 'tyr': 'Y', 'u': 'u', 'u3': 'u', 'u5': 'u', 'val': 'V'}

translate standard PDB amino and nucleic acid names to single letter code

biskit.molUtils.aaAtoms = {'ALA': ['N', 'CA', 'C', 'O', 'CB', 'OXT'], 'ARG': ['N', 'CA', 'C', 'O', 'CB', 'CG', 'CD', 'NE', 'CZ', 'NH1', 'NH2', 'OXT'], 'ASN': ['N', 'CA', 'C', 'O', 'CB', 'CG', 'OD1', 'ND2', 'OXT'], 'ASP': ['N', 'CA', 'C', 'O', 'CB', 'CG', 'OD1', 'OD2', 'OXT'], 'CYS': ['N', 'CA', 'C', 'O', 'CB', 'SG', 'OXT'], 'GLN': ['N', 'CA', 'C', 'O', 'CB', 'CG', 'CD', 'OE1', 'NE2', 'OXT'], 'GLU': ['N', 'CA', 'C', 'O', 'CB', 'CG', 'CD', 'OE1', 'OE2', 'OXT'], 'GLY': ['N', 'CA', 'C', 'O', 'OXT'], 'HIS': ['N', 'CA', 'C', 'O', 'CB', 'CG', 'ND1', 'CD2', 'CE1', 'NE2', 'OXT'], 'ILE': ['N', 'CA', 'C', 'O', 'CB', 'CG1', 'CG2', 'CD1', 'OXT'], 'LEU': ['N', 'CA', 'C', 'O', 'CB', 'CG', 'CD1', 'CD2', 'OXT'], 'LYS': ['N', 'CA', 'C', 'O', 'CB', 'CG', 'CD', 'CE', 'NZ', 'OXT'], 'MET': ['N', 'CA', 'C', 'O', 'CB', 'CG', 'SD', 'CE', 'OXT'], 'PHE': ['N', 'CA', 'C', 'O', 'CB', 'CG', 'CD1', 'CD2', 'CE1', 'CE2', 'CZ', 'OXT'], 'PRO': ['N', 'CA', 'C', 'O', 'CB', 'CG', 'CD', 'OXT'], 'SER': ['N', 'CA', 'C', 'O', 'CB', 'OG', 'OXT'], 'THR': ['N', 'CA', 'C', 'O', 'CB', 'OG1', 'CG2', 'OXT'], 'TRP': ['N', 'CA', 'C', 'O', 'CB', 'CG', 'CD1', 'CD2', 'NE1', 'CE2', 'CE3', 'CZ2', 'CZ3', 'CH2', 'OXT'], 'TYR': ['N', 'CA', 'C', 'O', 'CB', 'CG', 'CD1', 'CD2', 'CE1', 'CE2', 'CZ', 'OH', 'OXT'], 'VAL': ['N', 'CA', 'C', 'O', 'CB', 'CG1', 'CG2', 'OXT']}

heavy atoms of amino acids in standard order, OXT applies to C term only

biskit.molUtils.elements = {'carbon': ['C', 'CD2', 'CZ2', 'CB', 'CA', 'CG', 'CE', 'CD', 'CZ', 'CH2', 'CE3', 'CD1', 'CE1', 'CZ3', 'CG1', 'CG2', 'CE2'], 'clustering_AB': ['C', 'CA', 'CB'], 'clustering_ABD': ['C', 'CA', 'CB', 'CD', 'CD1', 'OD1', 'SD'], 'clustering_ABDZ': ['C', 'CA', 'CB', 'CD', 'CD1', 'CD2', 'CZ', 'CZ2', 'CZ3', 'ND1', 'ND2', 'NZ', 'OD1', 'OD2', 'SD'], 'clustering_AG': ['C', 'CA', 'CG', 'CG1', 'OG', 'OG1', 'SG'], 'clustering_AGE': ['C', 'CA', 'CG', 'CG1', 'OG', 'OG1', 'SG', 'NE', 'OE1', 'CE1', 'CE', 'CE3'], 'clustering_B': ['C', 'CB'], 'clustering_BD': ['C', 'CB', 'CD', 'CD1', 'OD1', 'SD'], 'clustering_BDZ': ['C', 'CB', 'CD', 'CD1', 'CD2', 'CZ', 'CZ2', 'CZ3', 'ND1', 'ND2', 'NZ', 'OD1', 'OD2', 'SD'], 'clustering_G': ['C', 'CG', 'CG1', 'OG', 'OG1', 'SG'], 'nitrogen': ['NZ', 'ND2', 'NH1', 'NH2', 'ND1', 'NE1', 'NE2', 'NE', 'N'], 'oxygen': ['OG', 'OE2', 'OXT', 'OD1', 'OE1', 'OH', 'OG1', 'OD2', 'O'], 'suplphur': ['SG', 'SD']}

dictionary of elements

biskit.molUtils.aaAtomsH = {'ALA': {'CA': 1, 'C': 0, 'OXT': 0, 'N': 1, 'O': 0, 'CB': 3}, 'ARG': {'CA': 1, 'NH1': 2, 'CG': 2, 'CZ': 0, 'CD': 2, 'NE': 1, 'N': 1, 'O': 0, 'CB': 2, 'C': 0, 'NH2': 2, 'OXT': 0}, 'ASN': {'CA': 1, 'CG': 0, 'N': 1, 'O': 0, 'CB': 2, 'C': 0, 'ND2': 2, 'OXT': 0, 'OD1': 0}, 'ASP': {'CA': 1, 'OD2': 0, 'CG': 0, 'N': 1, 'O': 0, 'CB': 2, 'C': 0, 'OXT': 0, 'OD1': 0}, 'CYS': {'CA': 1, 'C': 0, 'OXT': 0, 'N': 1, 'O': 0, 'SG': 1, 'CB': 2}, 'GLN': {'CA': 1, 'CG': 2, 'CD': 0, 'OE1': 0, 'N': 1, 'O': 0, 'CB': 2, 'C': 0, 'NE2': 2, 'OXT': 0}, 'GLU': {'CA': 1, 'OE2': 0, 'CG': 2, 'CD': 0, 'OE1': 0, 'N': 1, 'O': 0, 'CB': 2, 'C': 0, 'OXT': 0}, 'GLY': {'CA': 1, 'C': 0, 'N': 1, 'O': 0, 'OXT': 0}, 'HIS': {'CA': 1, 'ND1': 1, 'N': 1, 'O': 0, 'CD2': 1, 'CB': 2, 'CE1': 1, 'C': 0, 'NE2': 0, 'OXT': 0, 'CG': 0}, 'ILE': {'CA': 1, 'N': 1, 'O': 0, 'CB': 0, 'C': 0, 'CG1': 1, 'CG2': 3, 'OXT': 0, 'CD1': 3}, 'LEU': {'CA': 1, 'CG': 0, 'N': 1, 'O': 0, 'CD2': 3, 'CB': 2, 'C': 0, 'OXT': 0, 'CD1': 3}, 'LYS': {'CA': 1, 'CG': 2, 'CD': 2, 'N': 1, 'O': 0, 'CB': 2, 'C': 0, 'CE': 2, 'OXT': 0, 'NZ': 3}, 'MET': {'CA': 1, 'CG': 2, 'N': 1, 'O': 0, 'CB': 2, 'C': 0, 'SD': 0, 'CE': 3, 'OXT': 0}, 'PHE': {'CA': 1, 'CG': 0, 'CZ': 1, 'CD2': 1, 'N': 1, 'O': 0, 'CE2': 1, 'CB': 2, 'CE1': 1, 'C': 0, 'OXT': 0, 'CD1': 1}, 'PRO': {'CA': 1, 'CG': 2, 'CD': 2, 'N': 0, 'O': 0, 'CB': 2, 'C': 0, 'OXT': 0}, 'SER': {'CA': 1, 'C': 0, 'OG': 1, 'OXT': 0, 'N': 1, 'O': 0, 'CB': 2}, 'THR': {'CA': 1, 'N': 1, 'O': 0, 'CB': 0, 'C': 0, 'CG2': 3, 'OXT': 0, 'OG1': 1}, 'TRP': {'CA': 1, 'CG': 0, 'NE1': 1, 'CD2': 0, 'N': 1, 'O': 0, 'CE2': 0, 'CB': 2, 'CZ2': 1, 'C': 0, 'CZ3': 1, 'CE3': 1, 'OXT': 0, 'CD1': 1, 'CH2': 1}, 'TYR': {'CA': 1, 'CG': 0, 'CZ': 0, 'CD2': 1, 'N': 1, 'O': 0, 'CE2': 1, 'CB': 2, 'CE1': 1, 'C': 0, 'OXT': 0, 'OH': 1, 'CD1': 1}, 'VAL': {'CA': 1, 'N': 1, 'O': 0, 'CB': 0, 'C': 0, 'CG1': 3, 'CG2': 3, 'OXT': 0}, 'XXX': {'CA': 1, 'N': 1, 'O': 0, 'C': 0, 'OXT': 0}}

number of attached H for each heavy atom in each amino acid

biskit.molUtils.resDic = {'a': 'a', 'a3': 'a', 'a5': 'a', 'ace': 'X', 'ala': 'A', 'arg': 'R', 'asn': 'N', 'asp': 'D', 'asx': 'B', 'c': 'c', 'c3': 'c', 'c5': 'c', 'cys': 'C', 'cyx': 'C', 'da': 'a', 'da3': 'a', 'da5': 'a', 'dc': 'c', 'dc3': 'c', 'dc5': 'c', 'dg': 'g', 'dg3': 'g', 'dg5': 'g', 'dt': 't', 'dt3': 't', 'dt5': 't', 'g': 'g', 'g3': 'g', 'g5': 'g', 'gln': 'Q', 'glu': 'E', 'glx': 'Z', 'gly': 'G', 'hid': 'H', 'hie': 'H', 'hip': 'H', 'his': 'H', 'ile': 'I', 'leu': 'L', 'lys': 'K', 'met': 'M', 'nme': 'X', 'phe': 'F', 'pro': 'P', 'ser': 'S', 't': 't', 't3': 't', 't5': 't', 'thr': 'T', 'trp': 'W', 'tyr': 'Y', 'u': 'u', 'u3': 'u', 'u5': 'u', 'unk': 'X', 'val': 'V'}

map AA and NS and some other residue names to single letter code

biskit.molUtils.atomDic = {'ALA': ['N', 'CA', 'C', 'O', 'CB', 'OXT'], 'ARG': ['N', 'CA', 'C', 'O', 'CB', 'CG', 'CD', 'NE', 'CZ', 'NH1', 'NH2', 'OXT'], 'ASN': ['N', 'CA', 'C', 'O', 'CB', 'CG', 'OD1', 'ND2', 'OXT'], 'ASP': ['N', 'CA', 'C', 'O', 'CB', 'CG', 'OD1', 'OD2', 'OXT'], 'ATP': ['PG', 'O1G', 'O2G', 'O3G', 'PB', 'O1B', 'O2B', 'O3B', 'PA', 'O1A', 'O2A', 'O3A', 'O5*', 'C5*', 'C4*', 'O4*', 'C3*', 'O3*', 'C2*', 'O2*', 'C1*', 'N9', 'C8', 'N7', 'C5', 'C6', 'N6', 'N1', 'C2', 'N3', 'C4'], 'CYS': ['N', 'CA', 'C', 'O', 'CB', 'SG', 'OXT'], 'DA': ['P', 'O1P', 'O2P', "O5'", "C5'", "C4'", "O4'", "C1'", 'N9', 'C8', 'N7', 'C5', 'C6', 'N6', 'N1', 'C2', 'N3', 'C4', "C3'", "C2'", "O3'"], 'DA3': ['P', 'O1P', 'O2P', "O5'", "C5'", "C4'", "O4'", "C1'", 'N9', 'C8', 'N7', 'C5', 'C6', 'N6', 'N1', 'C2', 'N3', 'C4', "C3'", "C2'", "O3'", 'H3T'], 'DA5': ['H5T', "O5'", "C5'", "C4'", "O4'", "C1'", 'N9', 'C8', 'N7', 'C5', 'C6', 'N6', 'N1', 'C2', 'N3', 'C4', "C3'", "C2'", "O3'"], 'DC': ['P', 'O1P', 'O2P', "O5'", "C5'", "C4'", "O4'", "C1'", 'N1', 'C6', 'C5', 'C4', 'N4', 'N3', 'C2', 'O2', "C3'", "C2'", "O3'"], 'DC3': ['P', 'O1P', 'O2P', "O5'", "C5'", "C4'", "O4'", "C1'", 'N1', 'C6', 'C5', 'C4', 'N4', 'N3', 'C2', 'O2', "C3'", "C2'", "O3'", 'H3T'], 'DC5': ['H5T', "O5'", "C5'", "C4'", "O4'", "C1'", 'N1', 'C6', 'C5', 'C4', 'N4', 'N3', 'C2', 'O2', "C3'", "C2'", "O3'"], 'DG': ['P', 'O1P', 'O2P', "O5'", "C5'", "C4'", "O4'", "C1'", 'N9', 'C8', 'N7', 'C5', 'C6', 'O6', 'N1', 'C2', 'N2', 'N3', 'C4', "C3'", "C2'", "O3'"], 'DG3': ['P', 'O1P', 'O2P', "O5'", "C5'", "C4'", "O4'", "C1'", 'N9', 'C8', 'N7', 'C5', 'C6', 'O6', 'N1', 'C2', 'N2', 'N3', 'C4', "C3'", "C2'", "O3'", 'H3T'], 'DG5': ['H5T', "O5'", "C5'", "C4'", "O4'", "C1'", 'N9', 'C8', 'N7', 'C5', 'C6', 'O6', 'N1', 'C2', 'N2', 'N3', 'C4', "C3'", "C2'", "O3'"], 'DT': ['P', 'O1P', 'O2P', "O5'", "C5'", "C4'", "O4'", "C1'", 'N1', 'C6', 'C5', 'C7', 'C4', 'O4', 'N3', 'C2', 'O2', "C3'", "C2'", "O3'"], 'DT3': ['P', 'O1P', 'O2P', "O5'", "C5'", "C4'", "O4'", "C1'", 'N1', 'C6', 'C5', 'C7', 'C4', 'O4', 'N3', 'C2', 'O2', "C3'", "C2'", "O3'", 'H3T'], 'DT5': ['H5T', "O5'", "C5'", "C4'", "O4'", "C1'", 'N1', 'C6', 'C5', 'C7', 'C4', 'O4', 'N3', 'C2', 'O2', "C3'", "C2'", "O3'"], 'GLN': ['N', 'CA', 'C', 'O', 'CB', 'CG', 'CD', 'OE1', 'NE2', 'OXT'], 'GLU': ['N', 'CA', 'C', 'O', 'CB', 'CG', 'CD', 'OE1', 'OE2', 'OXT'], 'GLY': ['N', 'CA', 'C', 'O', 'OXT'], 'GTP': ['PG', 'O1G', 'O2G', 'O3G', 'PB', 'O1B', 'O2B', 'O3B', 'PA', 'O1A', 'O2A', 'O3A', 'O5*', 'C5*', 'C4*', 'O4*', 'C3*', 'O3*', 'C2*', 'O2*', 'C1*', 'N9', 'C8', 'N7', 'C5', 'C6', 'O6', 'N1', 'C2', 'N2', 'N3', 'C4'], 'HIS': ['N', 'CA', 'C', 'O', 'CB', 'CG', 'ND1', 'CD2', 'CE1', 'NE2', 'OXT'], 'ILE': ['N', 'CA', 'C', 'O', 'CB', 'CG1', 'CG2', 'CD1', 'OXT'], 'LEU': ['N', 'CA', 'C', 'O', 'CB', 'CG', 'CD1', 'CD2', 'OXT'], 'LYS': ['N', 'CA', 'C', 'O', 'CB', 'CG', 'CD', 'CE', 'NZ', 'OXT'], 'MET': ['N', 'CA', 'C', 'O', 'CB', 'CG', 'SD', 'CE', 'OXT'], 'MG': ['MG'], 'NAP': None, 'NDP': ['P1', 'O1', 'O2', 'O5R', 'C5R', 'O1R', 'C4R', 'C3R', 'O3R', 'C2R', 'O2R', 'C1R', 'N9', 'C8', 'N7', 'C5', 'C6', 'N6', 'N1', 'C2', 'N3', 'C4', 'O10', 'P2', 'O11', 'O21', 'O51R', 'C51R', 'O11R', 'C41R', 'C31R', 'O31R', 'C21R', 'O21R', 'C11R', 'N11', 'C61', 'C51', 'C71', 'O71', 'N71', 'C41', 'C31', 'C21', 'P3', 'O3', 'O4', 'O5', 'H8', 'H9', 'H7', 'H6', 'H1', 'H5', 'H4', 'H13', 'H11', 'H12', 'H10', 'H18', 'H19', 'H17', 'H16', 'H3', 'H15', 'H2', 'H14', 'H23', 'H24', 'H25', 'H22', 'H21', 'H20'], 'PHE': ['N', 'CA', 'C', 'O', 'CB', 'CG', 'CD1', 'CD2', 'CE1', 'CE2', 'CZ', 'OXT'], 'PRO': ['N', 'CA', 'C', 'O', 'CB', 'CG', 'CD', 'OXT'], 'RA': ['P', 'O1P', 'O2P', "O5'", "C5'", "C4'", "O4'", "C1'", 'N9', 'C8', 'N7', 'C5', 'C6', 'N6', 'N1', 'C2', 'N3', 'C4', "C3'", "C2'", "O2'", "O3'"], 'RA3': ['P', 'O1P', 'O2P', "O5'", "C5'", "C4'", "O4'", "C1'", 'N9', 'C8', 'N7', 'C5', 'C6', 'N6', 'N1', 'C2', 'N3', 'C4', "C3'", "C2'", "O2'", "O3'", 'H3T'], 'RA5': ['H5T', "O5'", "C5'", "C4'", "O4'", "C1'", 'N9', 'C8', 'N7', 'C5', 'C6', 'N6', 'N1', 'C2', 'N3', 'C4', "C3'", "C2'", "O2'", "O3'"], 'RC': ['P', 'O1P', 'O2P', "O5'", "C5'", "C4'", "O4'", "C1'", 'N1', 'C6', 'C5', 'C4', 'N4', 'N3', 'C2', 'O2', "C3'", "C2'", "O2'", "O3'"], 'RC3': ['P', 'O1P', 'O2P', "O5'", "C5'", "C4'", "O4'", "C1'", 'N1', 'C6', 'C5', 'C4', 'N4', 'N3', 'C2', 'O2', "C3'", "C2'", "O2'", "O3'", 'H3T'], 'RC5': ['H5T', "O5'", "C5'", "C4'", "O4'", "C1'", 'N1', 'C6', 'C5', 'C4', 'N4', 'N3', 'C2', 'O2', "C3'", "C2'", "O2'", "O3'"], 'RG': ['P', 'O1P', 'O2P', "O5'", "C5'", "C4'", "O4'", "C1'", 'N9', 'C8', 'N7', 'C5', 'C6', 'O6', 'N1', 'C2', 'N2', 'N3', 'C4', "C3'", "C2'", "O2'", "O3'"], 'RG3': ['P', 'O1P', 'O2P', "O5'", "C5'", "C4'", "O4'", "C1'", 'N9', 'C8', 'N7', 'C5', 'C6', 'O6', 'N1', 'C2', 'N2', 'N3', 'C4', "C3'", "C2'", "O2'", "O3'", 'H3T'], 'RG5': ['H5T', "O5'", "C5'", "C4'", "O4'", "C1'", 'N9', 'C8', 'N7', 'C5', 'C6', 'O6', 'N1', 'C2', 'N2', 'N3', 'C4', "C3'", "C2'", "O2'", "O3'"], 'RU': ['P', 'O1P', 'O2P', "O5'", "C5'", "C4'", "O4'", "C1'", 'N1', 'C6', 'C5', 'C4', 'O4', 'N3', 'C2', 'O2', "C3'", "C2'", "O2'", "O3'"], 'RU3': ['P', 'O1P', 'O2P', "O5'", "C5'", "C4'", "O4'", "C1'", 'N1', 'C6', 'C5', 'C4', 'O4', 'N3', 'C2', 'O2', "C3'", "C2'", "O2'", "O3'", 'H3T'], 'RU5': ['H5T', "O5'", "C5'", "C4'", "O4'", "C1'", 'N1', 'C6', 'C5', 'C4', 'O4', 'N3', 'C2', 'O2', "C3'", "C2'", "O2'", "O3'"], 'SER': ['N', 'CA', 'C', 'O', 'CB', 'OG', 'OXT'], 'THR': ['N', 'CA', 'C', 'O', 'CB', 'OG1', 'CG2', 'OXT'], 'TRP': ['N', 'CA', 'C', 'O', 'CB', 'CG', 'CD1', 'CD2', 'NE1', 'CE2', 'CE3', 'CZ2', 'CZ3', 'CH2', 'OXT'], 'TYR': ['N', 'CA', 'C', 'O', 'CB', 'CG', 'CD1', 'CD2', 'CE1', 'CE2', 'CZ', 'OH', 'OXT'], 'VAL': ['N', 'CA', 'C', 'O', 'CB', 'CG1', 'CG2', 'OXT']}

map AA and NS residue names to list of allowed heavy atoms

biskit.molUtils.atomSynonyms = {'CD': 'CD1', "O'": 'O', "O''": 'OXT', 'O1': 'O', 'O2': 'OXT', 'OT1': 'O', 'OT2': 'OXT'}

some common synonyms of atom names

biskit.molUtils.atomMasses = {'C': 12.01115, 'H': 1.00797, 'N': 14.0067, 'O': 15.9994, 'P': 30.9738, 'S': 32.064, 'ZN': 65.39}

**dictionary with relative atomic mass of elements {‘H’* – 1.01, ‘ZN’* – 65.39, …}

biskit.molUtils.allAACodes()[source]
Returns:list of all single AA codes, including B, Z, X
Return type:[str]
biskit.molUtils.allAA()[source]
Returns:list of all 20 ‘exact’ single AA codes.
Return type:[str]
biskit.molUtils.elementType(eLetter)[source]
Classify an atom as polar or unpolar::
atomType( eLetter ) -> list of types this element belongs to
Parameters:eLetter (str) – atom name
Returns:return ‘p’ for polar, ‘u’ for unpolar and None if not in classified
Return type:p|u OR None
biskit.molUtils.resType(resCode)[source]

Classify residues as aromatic (a), charged (c) or polar (p).

Parameters:resCode (str) – amino acid code
Returns:list of types this residue belongs to…
Return type:a|c|p OR None
biskit.molUtils.singleAA(seq, xtable=None, nonstandard=True, unknown='?')[source]

convert list with 3-letter AA code to list with 1-letter code

Parameters:
  • seq ([str]) – amino acid sequence in 3-letter code
  • xtable (dict) – dictionary with additional str:single_char mapping
  • nonstandard (bool) – support non-standard residue names (default True)
  • unknown (str) – letter to use for unknown residues [default: ‘?’]
Returns:

list with 1-letter code; C{ [‘A’,’C’,’L’,’A’…]}

Return type:

[str]

biskit.molUtils.single2longAA(seq)[source]

Convert string of 1-letter AA code into list of 3-letter AA codes.

Parameters:seq (str) – amino acid sequence in 1-letter code
Returns:list with the amino acids in 3-letter code
Return type:[str]
biskit.molUtils.cmpAtoms(a1, a2)[source]

Comparison function for bringing atoms into standard order within residues as defined by atomDic.

Parameters:
  • a1 (CrossView or equivalent dictionary) – atom dictionary
  • a2 (CrossView or equivalent dictionary) – atom dictionary
Returns:

int or list of matching positions

Return type:

[-1|0|1]

biskit.molUtils.sortAtomsOfModel(model)[source]

Sort atoms within residues into the standard order defined in atomDic.

Parameters:model (PDBModel) – model to sort
Returns:model with sorted atoms
Return type:PDBModel