from __future__ import absolute_import, division, print_function class FormatError(RuntimeError): pass def chain_id_strip(id): if (id[0] == " "): return id[1] return id class _base(object): def __init__(self, pdb_str): if (len(pdb_str) < 80): pdb_str += " " * (80-len(pdb_str)) self.pdb_str = pdb_str def raise_FormatError(self, msg): raise FormatError('%s:\n "%s"' % (msg, self.pdb_str)) class header(_base): def __init__(self, pdb_str): # 11 - 50 String(40) classification Classifies the molecule(s) # 51 - 59 Date depDate Deposition date. This is the date # the coordinates were received by # the PDB # 63 - 66 IDcode idCode This identifier is unique within # PDB _base.__init__(self, pdb_str) self.classification = self.pdb_str[10:50] self.depdate = self.pdb_str[50:59] self.idcode = self.pdb_str[62:66] class expdta(_base): def __init__(self, pdb_str): # 9 - 10 Continuation continuation Allows concatenation of # multiple records. # 11 - 70 List technique The experimental technique(s) # with optional comment # describing the sample # or experiment. _base.__init__(self, pdb_str) self.continuation = self.pdb_str[8:10] self.technique = self.pdb_str[10:70] TECH = self.technique.upper() self.keywords = [] for keyword in ("ELECTRON DIFFRACTION", "FIBER DIFFRACTION", "FLUORESCENCE TRANSFER", "NEUTRON DIFFRACTION", "NMR", "THEORETICAL MODEL", "X-RAY DIFFRACTION"): if (TECH.find(keyword) >= 0): self.keywords.append(keyword) class remark_002(_base): def __init__(self, pdb_str): _base.__init__(self, pdb_str) self.text = self.pdb_str[11:70] flds = self.pdb_str[11:38].split() self.resolution = None if ( len(flds) == 3 and flds[0].upper() == "RESOLUTION." and flds[2].upper() == "ANGSTROMS."): try: self.resolution = float(flds[1]) except ValueError: pass class cryst1(_base): def __init__(self, pdb_str): # 7 - 15 Real(9.3) a a (Angstroms). # 16 - 24 Real(9.3) b b (Angstroms). # 25 - 33 Real(9.3) c c (Angstroms). # 34 - 40 Real(7.2) alpha alpha (degrees). # 41 - 47 Real(7.2) beta beta (degrees). # 48 - 54 Real(7.2) gamma gamma (degrees). # 56 - 66 LString sGroup Space group. # 67 - 70 Integer z Z value. _base.__init__(self, pdb_str) ps = self.pdb_str self.ucparams = [ps[ 6:15], ps[15:24], ps[24:33], ps[33:40], ps[40:47], ps[47:54]] self.sgroup = ps[55:66].strip() z = ps[66:70] if (len(" ".join(self.ucparams).strip()) == 0): self.ucparams = None else: try: self.ucparams = [float(u) for u in self.ucparams] except ValueError: self.raise_FormatError("Corrupt unit cell parameters") if (len(self.sgroup) == 0): self.sgroup = None if (z.strip()): try: self.z = int(z) except ValueError: self.raise_FormatError("Corrupt Z value") else: self.z = None class scalen(_base): def __init__(self, pdb_str): # 1 - 6 Record name "SCALEn" n=1, 2, or 3 # 11 - 20 Real(10.6) s[n][1] Sn1 # 21 - 30 Real(10.6) s[n][2] Sn2 # 31 - 40 Real(10.6) s[n][3] Sn3 # 46 - 55 Real(10.5) u[n] Un _base.__init__(self, pdb_str) self.n = int(self.pdb_str[5]) values = [] for i in [10,20,30,45]: fld = self.pdb_str[i:i+10] if (len(fld.strip()) == 0): value = 0 else: try: value = float(fld) except ValueError: raise self.raise_FormatError("Invalid floating-point value") values.append(value) self.sn1, self.sn2, self.sn3, self.un = values class conect(_base): def __init__(self, pdb_str): # 7 - 11 Integer serial Atom serial number # 12 - 16 Integer serial Serial number of bonded atom # 17 - 21 Integer serial Serial number of bonded atom # 22 - 26 Integer serial Serial number of bonded atom # 27 - 31 Integer serial Serial number of bonded atom # 32 - 36 Integer serial Serial number of hydrogen bonded atom # 37 - 41 Integer serial Serial number of hydrogen bonded atom # 42 - 46 Integer serial Serial number of salt bridged atom # 47 - 51 Integer serial Serial number of hydrogen bonded atom # 52 - 56 Integer serial Serial number of hydrogen bonded atom # 57 - 61 Integer serial Serial number of salt bridged atom _base.__init__(self, pdb_str) self.serial = self.pdb_str[6:11] ba = [] hba = [] sba = [] for i,l in [(11, ba), (16, ba), (21, ba), (26, ba), (31, hba), (36, hba), (41, sba), (46, hba), (51, hba), (56, sba)]: fld = self.pdb_str[i:i+5] if (fld != " "): l.append(fld) self.serial_numbers_bonded_atoms = ba self.serial_numbers_hydrogen_bonded_atoms = hba self.serial_numbers_salt_bridged_atoms = sba class link(_base): def __init__(self, pdb_str): # 13 - 16 Atom name1 Atom name. # 17 Character altLoc1 Alternate location indicator. # 18 - 20 Residue name resName1 Residue name. # 21 - 22 chainID1 Chain identifier. # 23 - 26 resSeq1 Residue sequence number. # 27 AChar iCode1 Insertion code. # 31 - 40 distance (REFMAC extension: F10.5) # 43 - 46 Atom name2 Atom name. # 47 Character altLoc2 Alternate location indicator. # 48 - 50 Residue name resName2 Residue name. # 51 - 52 chainID2 Chain identifier. # 53 - 56 resSeq2 Residue sequence number. # 57 AChar iCode2 Insertion code. # 60 - 65 SymOP sym1 Symmetry operator for 1st atom. # 67 - 72 SymOP sym2 Symmetry operator for 2nd atom. # 73 - 80 margin (REFMAC extension: _chem_link.id) _base.__init__(self, pdb_str) self.name1 = self.pdb_str[12:16] self.altloc1 = self.pdb_str[16] self.resname1 = self.pdb_str[17:20] self.chain_id1 = chain_id_strip(self.pdb_str[20:22]) self.resseq1 = self.pdb_str[22:26] self.icode1 = self.pdb_str[26] try: self.distance = float(self.pdb_str[30:40]) except ValueError: self.distance = None self.name2 = self.pdb_str[42:46] self.altloc2 = self.pdb_str[46] self.resname2 = self.pdb_str[47:50] self.chain_id2 = chain_id_strip(self.pdb_str[50:52]) self.resseq2 = self.pdb_str[52:56] self.icode2 = self.pdb_str[56] self.sym1 = self.pdb_str[59:65] self.sym2 = self.pdb_str[66:72] self.margin = self.pdb_str[72:80] class sltbrg(link): pass class ssbond(_base): def __init__(self, pdb_str): # 8 - 10 Integer serNum Serial number. # 12 - 14 LString(3) "CYS" Residue name. # 15 - 16 chainID1 Chain identifier. # 18 - 21 seqNum1 Residue sequence number. # 22 AChar icode1 Insertion code. # 26 - 28 LString(3) "CYS" Residue name. # 29 - 30 chainID2 Chain identifier. # 32 - 35 seqNum2 Residue sequence number. # 36 AChar icode2 Insertion code. # 60 - 65 SymOP sym1 Symmetry operator for 1st residue. # 67 - 72 SymOP sym2 Symmetry operator for 2nd residue. # 73 - 80 margin (REFMAC extension: _chem_link.id) _base.__init__(self, pdb_str) self.sernum = self.pdb_str[7:10] self.resname1 = self.pdb_str[11:14] self.chain_id1 = chain_id_strip(self.pdb_str[14:16]) self.resseq1 = self.pdb_str[17:21] self.icode1 = self.pdb_str[21] self.resname2 = self.pdb_str[25:28] self.chain_id2 = chain_id_strip(self.pdb_str[28:30]) self.resseq2 = self.pdb_str[31:35] self.icode2 = self.pdb_str[35] self.sym1 = self.pdb_str[59:65] self.sym2 = self.pdb_str[66:72] self.margin = self.pdb_str[72:80]