/usr/lib/python2.7/dist-packages/Scientific/IO/PDB.py is in python-scientific 2.9.4-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675 676 677 678 679 680 681 682 683 684 685 686 687 688 689 690 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705 706 707 708 709 710 711 712 713 714 715 716 717 718 719 720 721 722 723 724 725 726 727 728 729 730 731 732 733 734 735 736 737 738 739 740 741 742 743 744 745 746 747 748 749 750 751 752 753 754 755 756 757 758 759 760 761 762 763 764 765 766 767 768 769 770 771 772 773 774 775 776 777 778 779 780 781 782 783 784 785 786 787 788 789 790 791 792 793 794 795 796 797 798 799 800 801 802 803 804 805 806 807 808 809 810 811 812 813 814 815 816 817 818 819 820 821 822 823 824 825 826 827 828 829 830 831 832 833 834 835 836 837 838 839 840 841 842 843 844 845 846 847 848 849 850 851 852 853 854 855 856 857 858 859 860 861 862 863 864 865 866 867 868 869 870 871 872 873 874 875 876 877 878 879 880 881 882 883 884 885 886 887 888 889 890 891 892 893 894 895 896 897 898 899 900 901 902 903 904 905 906 907 908 909 910 911 912 913 914 915 916 917 918 919 920 921 922 923 924 925 926 927 928 929 930 931 932 933 934 935 936 937 938 939 940 941 942 943 944 945 946 947 948 949 950 951 952 953 954 955 956 957 958 959 960 961 962 963 964 965 966 967 968 969 970 971 972 973 974 975 976 977 978 979 980 981 982 983 984 985 986 987 988 989 990 991 992 993 994 995 996 997 998 999 1000 1001 1002 1003 1004 1005 1006 1007 1008 1009 1010 1011 1012 1013 1014 1015 1016 1017 1018 1019 1020 1021 1022 1023 1024 1025 1026 1027 1028 1029 1030 1031 1032 1033 1034 1035 1036 1037 1038 1039 1040 1041 1042 1043 1044 1045 1046 1047 1048 1049 1050 1051 1052 1053 1054 1055 1056 1057 1058 1059 1060 1061 1062 1063 1064 1065 1066 1067 1068 1069 1070 1071 1072 1073 1074 1075 1076 1077 1078 1079 1080 1081 1082 1083 1084 1085 1086 1087 1088 1089 1090 1091 1092 1093 1094 1095 1096 1097 1098 1099 1100 1101 1102 1103 1104 1105 1106 1107 1108 1109 1110 1111 1112 1113 1114 1115 1116 1117 1118 1119 1120 1121 1122 1123 1124 1125 1126 1127 1128 1129 1130 1131 1132 1133 1134 1135 1136 1137 1138 1139 1140 1141 1142 1143 1144 1145 1146 1147 1148 1149 1150 1151 1152 1153 1154 1155 1156 1157 1158 1159 1160 1161 1162 1163 1164 1165 1166 1167 1168 1169 1170 1171 1172 1173 1174 1175 1176 1177 1178 1179 1180 1181 1182 1183 1184 1185 1186 1187 1188 1189 1190 1191 1192 1193 1194 1195 1196 1197 1198 1199 1200 1201 1202 1203 1204 1205 1206 1207 1208 1209 1210 1211 1212 1213 1214 1215 1216 1217 1218 1219 1220 1221 1222 1223 1224 1225 1226 1227 1228 1229 1230 1231 1232 1233 1234 1235 1236 1237 1238 1239 1240 1241 1242 1243 1244 1245 1246 1247 1248 1249 1250 1251 1252 1253 1254 1255 1256 1257 1258 1259 1260 1261 1262 1263 1264 1265 1266 1267 1268 1269 1270 1271 1272 1273 1274 1275 1276 1277 1278 1279 1280 1281 1282 1283 1284 1285 1286 1287 1288 1289 1290 1291 1292 1293 1294 1295 1296 1297 1298 1299 1300 1301 1302 1303 1304 1305 1306 1307 1308 1309 1310 1311 1312 1313 1314 1315 1316 1317 1318 1319 1320 1321 1322 1323 1324 1325 1326 1327 1328 1329 1330 1331 1332 1333 1334 1335 1336 1337 1338 1339 1340 1341 1342 1343 1344 1345 1346 1347 1348 1349 1350 1351 1352 1353 1354 1355 1356 1357 1358 1359 1360 1361 1362 1363 1364 1365 1366 1367 1368 1369 1370 1371 1372 1373 1374 1375 1376 1377 1378 1379 1380 1381 1382 1383 1384 1385 1386 1387 1388 1389 1390 1391 1392 1393 1394 1395 1396 1397 1398 1399 1400 1401 1402 1403 1404 1405 1406 1407 1408 1409 1410 1411 1412 1413 1414 1415 1416 1417 1418 1419 1420 1421 1422 1423 1424 1425 1426 1427 1428 1429 1430 1431 1432 1433 1434 1435 1436 1437 1438 1439 1440 1441 1442 1443 1444 1445 1446 1447 1448 1449 1450 1451 1452 1453 1454 1455 1456 1457 1458 1459 1460 1461 1462 1463 1464 1465 1466 1467 1468 1469 1470 1471 1472 1473 1474 1475 1476 1477 1478 1479 1480 1481 1482 1483 1484 1485 1486 1487 1488 1489 1490 1491 1492 1493 1494 1495 1496 1497 1498 1499 1500 1501 1502 1503 1504 1505 1506 1507 1508 1509 1510 1511 1512 1513 1514 1515 1516 1517 1518 1519 1520 1521 1522 1523 1524 1525 1526 1527 1528 1529 1530 1531 1532 1533 1534 1535 | # This module handles input and output of PDB files.
#
# Written by Konrad Hinsen <hinsen@cnrs-orleans.fr>
# Last revision: 2012-10-17
#
"""
Parsing and writing of Protein Data Bank (PDB) files
This module provides classes that represent PDB (Protein Data Bank)
files and configurations contained in PDB files. It provides access to
PDB files on two levels: low-level (line by line) and high-level
(chains, residues, and atoms).
Caution: The PDB file format has been heavily abused, and it is
probably impossible to write code that can deal with all variants
correctly. This modules tries to read the widest possible range of PDB
files, but gives priority to a correct interpretation of the PDB
format as defined by the Brookhaven National Laboratory.
A special problem are atom names. The PDB file format specifies that
the first two letters contain the right-justified chemical element
name. A later modification allowed the initial space in hydrogen names
to be replaced by a digit. Many programs ignore all this and treat the
name as an arbitrary left-justified four-character name. This makes it
difficult to extract the chemical element accurately; most programs
write the '"CA"' for C_alpha in such a way that it actually stands for
a calcium atom. For this reason a special element field has been added
later, but only few files use it. In the absence of an element field,
the code in this module attempts to guess the element using all information
available.
The low-level routines in this module do not try to deal with the atom
name problem; they return and expect four-character atom names
including spaces in the correct positions. The high-level routines use
atom names without leading or trailing spaces, but provide and use the
element field whenever possible. For output, they use the element
field to place the atom name correctly, and for input, they construct
the element field content from the atom name if no explicit element
field is found in the file.
Except where indicated, numerical values use the same units and
conventions as specified in the PDB format description.
Example::
>>>conf = Structure('example.pdb')
>>>print conf
>>>for residue in conf.residues:
>>> for atom in residue:
>>> print atom
@undocumented: atom_format
@undocumented: anisou_format
@undocumented: conect_format
@undocumented: ter_format
@undocumented: model_format
@undocumented: header_format
@undocumented: cryst1_format
@undocumented: scalen_format
@undocumented: mtrixn_format
@undocumented: generic_format
@undocumented: export_filters
@undocumented: DummyChain
"""
from Scientific.IO.TextFile import TextFile
from Scientific.IO.FortranFormat import FortranFormat, FortranLine
from Scientific.Geometry import Vector, Tensor
from Scientific import N
from PDBExportFilters import export_filters
import copy, string
#
# Fortran formats for PDB entries
#
atom_format = FortranFormat('A6,I5,1X,A4,A1,A4,A1,I4,A1,3X,3F8.3,2F6.2,' +
'6X,A4,2A2')
anisou_format = FortranFormat('A6,I5,1X,A4,A1,A4,A1,I4,A1,1X,6I7,2X,A4,2A2')
conect_format = FortranFormat('A6,11I5')
ter_format = FortranFormat('A6,I5,6X,A4,A1,I4,A1')
model_format = FortranFormat('A6,4X,I4')
header_format = FortranFormat('A6,4X,A40,A9,3X,A4')
cryst1_format = FortranFormat('A6,3F9.3,3F7.2,1X,A11,I4')
scalen_format = FortranFormat('A6,4X,3F10.6,5X,F10.5')
mtrixn_format = FortranFormat('A6,1X,I3,3F10.6,5X,F10.5,4X,I1')
generic_format = FortranFormat('A6,A74')
#
# Amino acid and nucleic acid residues
#
amino_acids = ['ALA', 'ARG', 'ASN', 'ASP', 'CYS', 'CYX', 'GLN', 'GLU', 'GLY',
'HIS', 'HID', 'HIE', 'HIP', 'HSD', 'HSE', 'HSP', 'ILE', 'LEU',
'LYS', 'MET', 'PHE', 'PRO', 'SER', 'THR', 'TRP', 'TYR', 'VAL',
'ACE', 'NME', 'NHE']
nucleic_acids = [ 'A', 'C', 'G', 'I', 'T', 'U',
'+A', '+C', '+G', '+I', '+T', '+U',
'RA', 'RC', 'RG', 'RU',
'DA', 'DC', 'DG', 'DT',
'RA5', 'RC5', 'RG5', 'RU5',
'DA5', 'DC5', 'DG5', 'DT5',
'RA3', 'RC3', 'RG3', 'RU3',
'DA3', 'DC3', 'DG3', 'DT3',
'RAN', 'RCN', 'RGN', 'RUN',
'DAN', 'DCN', 'DGN', 'DTN',
]
def defineAminoAcidResidue(symbol):
"""
Make the parser recognize a particular residue type as an amino
acid residue
@param symbol: the three-letter code for an amino acid
@type symbol: C{str}
"""
symbol = symbol.upper()
if symbol not in amino_acids:
amino_acids.append(symbol)
def defineNucleicAcidResidue(symbol):
"""
Make the parser recognize a particular residue type as an nucleic
acid residue
@param symbol: the one-letter code for a nucleic acid
@type symbol: C{str}
"""
symbol = symbol.upper()
if symbol not in nucleic_acids:
nucleic_acids.append(symbol)
#
# Low-level file object. It represents line contents as Python dictionaries.
# For output, there are additional methods that generate sequence numbers
# for everything.
#
class PDBFile:
"""
X{PDB} file with access at the record level
The low-level file access is handled by the module
L{Scientific.IO.TextFile}, therefore compressed files and URLs
(for reading) can be used as well.
"""
def __init__(self, file_or_filename, mode = 'r', subformat = None):
"""
@param file_or_filename: the name of the PDB file, or a file object
@type file_or_filename: C{str} or C{file}
@param mode: the file access mode, 'r' (read) or 'w' (write)
@type mode: C{str}
@param subformat: indicates a specific dialect of the PDB format.
Subformats are defined in
L{Scientific.IO.PDBExportFilters}; they are used
only when writing.
@type subformat: C{str} or C{NoneType}
"""
if isinstance(file_or_filename, basestring):
self.file = TextFile(file_or_filename, mode)
else:
self.file = file_or_filename
self.output = mode[0].lower() == 'w'
self.export_filter = None
if subformat is not None:
export = export_filters.get(subformat, None)
if export is not None:
self.export_filter = export()
self.open = 1
if self.output:
self.data = {'serial_number': 0,
'residue_number': 0,
'chain_id': '',
'segment_id': ''}
self.het_flag = 0
self.chain_number = -1
def readLine(self):
"""
Return the contents of the next non-blank line (= record) The
return value is a tuple whose first element (a string)
contains the record type. For supported record types (HEADER,
CRYST1, SCALEn, MTRIXn, ATOM, HETATM, ANISOU, TERM, MODEL,
CONECT), the items from the remaining fields are put into a
dictionary which is returned as the second tuple element. Most
dictionary elements are strings or numbers; atom positions are
returned as a vector, and anisotropic temperature factors are
returned as a rank-2 tensor, already multiplied by 1.e-4.
White space is stripped from all strings except for atom
names, whose correct interpretation can depend on an initial
space. For unsupported record types, the second tuple element
is a string containing the remaining part of the record.
@returns: the contents of one PDB record
@rtype: C{tuple}
"""
while 1:
line = self.file.readline()
if not line: return ('END','')
if line[-1] == '\n': line = line[:-1]
line = line.strip()
if line: break
line = line.ljust(80)
type = line[:6].strip()
if type == 'ATOM' or type == 'HETATM':
line = FortranLine(line, atom_format)
data = {'serial_number': line[1],
'name': line[2],
'alternate': line[3].strip(),
'residue_name': line[4].strip(),
'chain_id': line[5].strip(),
'residue_number': line[6],
'insertion_code': line[7].strip(),
'position': Vector(line[8:11]),
'occupancy': line[11],
'temperature_factor': line[12],
'segment_id': line[13].strip(),
'element': line[14].strip(),
'charge': line[15].strip()}
return type, data
elif type == 'ANISOU':
line = FortranLine(line, anisou_format)
data = {'serial_number': line[1],
'name': line[2],
'alternate': line[3].strip(),
'residue_name': line[4].strip(),
'chain_id': line[5].strip(),
'residue_number': line[6],
'insertion_code': line[7].strip(),
'u': 1.e-4*Tensor([[line[8], line[11], line[12]],
[line[11], line[9] , line[13]],
[line[12], line[13], line[10]]]),
'segment_id': line[14].strip(),
'element': line[15].strip(),
'charge': line[16].strip()}
return type, data
elif type == 'TER':
line = FortranLine(line, ter_format)
data = {'serial_number': line[1],
'residue_name': line[2].strip(),
'chain_id': line[3].strip(),
'residue_number': line[4],
'insertion_code': line[5].strip()}
return type, data
elif type == 'CONECT':
line = FortranLine(line, conect_format)
data = {'serial_number': line[1],
'bonded': [i for i in line[2:6] if i > 0],
'hydrogen_bonded': [i for i in line[6:10] if i > 0],
'salt_bridged': [i for i in line[10:12] if i > 0]}
return type, data
elif type == 'MODEL':
line = FortranLine(line, model_format)
data = {'serial_number': line[1]}
return type, data
elif type == 'HEADER':
line = FortranLine(line, header_format)
data = {'compound': line[1],
'date': line[2],
'pdb_code': line[3]}
return type, data
elif type == 'CRYST1':
line = FortranLine(line, cryst1_format)
data = {'a': line[1],
'b': line[2],
'c': line[3],
'alpha': line[4],
'beta': line[5],
'gamma': line[6],
'space_group': line[7],
'z': line[8]}
return type, data
elif type[:-1] == 'SCALE':
line = FortranLine(line, scalen_format)
data = {'s1': line[1],
's2': line[2],
's3': line[3],
'u': line[4]}
return type, data
elif type[:-1] == 'MTRIX':
line = FortranLine(line, mtrixn_format)
data = {'serial': line[1],
'm1': line[2],
'm2': line[3],
'm3': line[4],
'v': line[5],
'given': line[6] == 1}
return type, data
else:
return type, line[6:]
def writeLine(self, type, data):
"""
Write a line using record type and data dictionary in the
same format as returned by readLine(). Default values are
provided for non-essential information, so the data dictionary
need not contain all entries.
@param type: PDB record type
@type type: C{str}
@param data: PDB record data
@type data: C{tuple}
"""
if self.export_filter is not None:
type, data = self.export_filter.processLine(type, data)
if type is None:
return
line = [type]
if type == 'ATOM' or type == 'HETATM':
format = atom_format
position = data['position']
line = line + [data.get('serial_number', 1),
data.get('name'),
data.get('alternate', ''),
data.get('residue_name', '').rjust(3),
data.get('chain_id', ''),
data.get('residue_number', 1),
data.get('insertion_code', ''),
position[0], position[1], position[2],
data.get('occupancy', 0.),
data.get('temperature_factor', 0.),
data.get('segment_id', ''),
data.get('element', '').rjust(2),
data.get('charge', '')]
elif type == 'ANISOU':
format = anisou_format
u = 1.e4*data['u']
u = [int(u[0,0]), int(u[1,1]), int(u[2,2]),
int(u[0,1]), int(u[0,2]), int(u[1,2])]
line = line + [data.get('serial_number', 1),
data.get('name'),
data.get('alternate', ''),
data.get('residue_name').rjust(3),
data.get('chain_id', ''),
data.get('residue_number', 1),
data.get('insertion_code', '')] \
+ u \
+ [data.get('segment_id', ''),
data.get('element', '').rjust(2),
data.get('charge', '')]
elif type == 'TER':
format = ter_format
line = line + [data.get('serial_number', 1),
data.get('residue_name').rjust(3),
data.get('chain_id', ''),
data.get('residue_number', 1),
data.get('insertion_code', '')]
elif type == 'CONECT':
format = conect_format
line = line + [data.get('serial_number')]
line = line + (data.get('bonded', [])+4*[None])[:4]
line = line + (data.get('hydrogen_bonded', [])+4*[None])[:4]
line = line + (data.get('salt_bridged', [])+2*[None])[:2]
elif type == 'MODEL':
format = model_format
line = line + [data.get('serial_number')]
elif type == 'CRYST1':
format = cryst1_format
line = line + [data.get('a'), data.get('b'), data.get('c'),
data.get('alpha'), data.get('beta'),
data.get('gamma'),
data.get('space_group'),
data.get('z')]
elif type[:-1] == 'SCALE':
format = scalen_format
line = line + [data.get('s1'), data.get('s2'), data.get('s3'),
data.get('u')]
elif type[:-1] == 'MTRIX':
format = scalen_format
line = line + [data.get('serial'),
data.get('m1'), data.get('m2'), data.get('m3'),
data.get('v'), int(data.get('given'))]
elif type == 'HEADER':
format = header_format
line = line + [data.get('compound', ''), data.get('date', ''),
data.get('pdb_code')]
else:
format = generic_format
line = line + [data]
self.file.write(str(FortranLine(line, format)) + '\n')
def writeComment(self, text):
"""
Write text into one or several comment lines.
Each line of the text is prefixed with 'REMARK' and written
to the file.
@param text: the comment contents
@type text: C{str}
"""
while text:
eol = text.find('\n')
if eol == -1:
eol = len(text)
self.file.write('REMARK %s \n' % text[:eol])
text = text[eol+1:]
def writeAtom(self, name, position, occupancy=0.0, temperature_factor=0.0,
element='', alternate=''):
"""
Write an ATOM or HETATM record using the information supplied.
The residue and chain information is taken from the last calls to
the methods L{nextResidue} and L{nextChain}.
@param name: the atom name
@type name: C{str}
@param position: the atom position
@type position: L{Scientific.Geometry.Vector}
@param occupancy: the occupancy
@type occupancy: C{float}
@param temperature_factor: the temperature factor (B-factor)
@type temperature_factor: C{float}
@param element: the chemical element
@type element: C{str}
@param alternate: the alternate location character
@type element: C{str}
"""
if self.het_flag:
type = 'HETATM'
else:
type = 'ATOM'
name = name.upper()
if element != '' and len(element) == 1 and name and name[0] == element and len(name) < 4:
name = ' ' + name
self.data['name'] = name
self.data['position'] = position
self.data['serial_number'] = (self.data['serial_number'] + 1) % 100000
self.data['alternate'] = alternate
self.data['occupancy'] = occupancy
self.data['temperature_factor'] = temperature_factor
self.data['element'] = element
self.writeLine(type, self.data)
def nextResidue(self, name, number = None, terminus = None):
"""
Signal the beginning of a new residue, starting with the
next call to L{writeAtom}.
@param name: the residue name
@type name: C{str}
@param number: the residue number. If C{None}, the residues
will be numbered sequentially, starting from 1.
@type number: C{int} or C{NoneType}
@param terminus: C{None}, "C", or "N". This information
is passed to export filters that can use this
information in order to use different atom or
residue names in terminal residues.
"""
name = name.upper()
if self.export_filter is not None:
name, number = self.export_filter.processResidue(name, number,
terminus)
self.het_flag = not (name in amino_acids or name in nucleic_acids)
self.data['residue_name'] = name
self.data['residue_number'] = (self.data['residue_number'] + 1) % 10000
self.data['insertion_code'] = ''
if number is not None:
if isinstance(number, int):
if number >= 0:
self.data['residue_number'] = number % 10000
else:
self.data['residue_number'] = -((-number) % 1000)
else:
self.data['residue_number'] = number.number % 10000
self.data['insertion_code'] = number.insertion_code
def nextChain(self, chain_id = None, segment_id = ''):
"""
Signal the beginning of a new chain.
@param chain_id: a chain identifier. If C{None}, consecutive letters
from the alphabet are used.
@type chain_id: C{str} or C{NoneType}
@param segment_id: a chain identifier
@type segment_id: C{str}
"""
if chain_id is None:
self.chain_number = (self.chain_number + 1) % len(self._chain_ids)
chain_id = self._chain_ids[self.chain_number]
if self.export_filter is not None:
chain_id, segment_id = \
self.export_filter.processChain(chain_id, segment_id)
self.data['chain_id'] = (chain_id+' ')[:1]
self.data['segment_id'] = (segment_id+' ')[:4]
self.data['residue_number'] = 0
_chain_ids = 'ABCDEFGHIJKLMNOPQRSTUVWXYZ'
def terminateChain(self):
"""
Signal the end of a chain.
"""
if self.export_filter is not None:
self.export_filter.terminateChain()
self.data['serial_number'] = (self.data['serial_number'] + 1) % 100000
self.writeLine('TER', self.data)
self.data['chain_id'] = ''
self.data['segment_id'] = ''
def close(self):
"""
Close the file. This method B{must} be called for write mode
because otherwise the file will be incomplete.
"""
if self.open:
if self.output:
self.file.write('END\n')
self.file.close()
self.open = 0
def __del__(self):
self.close()
#
# High-level object representation of PDB file contents.
#
#
# Representation of objects.
#
class Atom:
"""
Atom in a PDB structure
"""
def __init__(self, name, position, **properties):
"""
@param name: the atom name
@type name: C{str}
@param position: the atom position
@type position: L{Scientific.Geometry.Vector}
@param properties: any other atom properties as keyword parameters.
These properties are stored in the atom object
and can be accessed by indexing, as for
dictionaries.
"""
self.position = position
self.properties = properties
if self.properties.get('element', '') == '':
if name[0] == ' ' or name[0] in string.digits:
self.properties['element'] = name[1]
elif name[1] in string.digits:
self.properties['element'] = name[0]
else:
self.properties['element'] = name[0:2]
self.name = name.strip()
self.parent = None
def __getitem__(self, item):
"""
@param item: the name of a property, including "name" or "position"
@type item: C{str}
@returns: the property value
"""
try:
return self.properties[item]
except KeyError:
if item == 'name':
return self.name
elif item == 'position':
return self.position
else:
raise KeyError("Undefined atom property: " + repr(item))
def __setitem__(self, item, value):
"""
@param item: the name of an existing or to be defined property
@type item: C{str}
@param value: the new value for the property
"""
self.properties[item] = value
def __str__(self):
return self.__class__.__name__ + ' ' + self.name + \
' at ' + str(self.position)
__repr__ = __str__
def type(self):
"""
@returns: the six-letter record type, ATOM or HETATM
@rtype: C{str}
"""
return 'ATOM '
def writeToFile(self, file):
"""
Write an atom record to a file
@param file: a PDB file object or a filename
@type file: L{PDBFile} or C{str}
"""
close = 0
if type(file) == type(''):
file = PDBFile(file, 'w')
close = 1
file.writeAtom(self.name, self.position,
self.properties.get('occupancy', 0.),
self.properties.get('temperature_factor', 0.),
self.properties.get('element', ''))
if close:
file.close()
class HetAtom(Atom):
"""
HetAtom in a PDB structure
A subclass of Atom, which differs only in the return value
of the method type().
"""
def type(self):
return 'HETATM'
class Group:
"""
Atom group (residue or molecule) in a PDB file
This is an abstract base class. Instances can be created using
one of the subclasses (L{Molecule}, L{AminoAcidResidue},
L{NucleotideResidue}).
Group objects permit iteration over atoms with for-loops,
as well as extraction of atoms by indexing with the
atom name.
"""
def __init__(self, name, atoms = None, number = None):
"""
@param name: the name of the group
@type name: C{str}
@param atoms: a list of atoms (or C{None} for no atoms)
@type atoms: C{list} or C{NoneType}
@param number: the PDB residue number (or C{None})
@type number: C{int} or C{NoneType}
"""
self.name = name
self.number = number
self.atom_list = []
self.atoms = {}
if atoms:
self.atom_list = atoms
for a in atoms:
self.atoms[a.name] = a
def __len__(self):
return len(self.atom_list)
def __getitem__(self, item):
"""
@param item: an integer index or an atom name
@type item: C{int} or C{str}
"""
if isinstance(item, int):
return self.atom_list[item]
else:
return self.atoms[item]
def __str__(self):
s = self.__class__.__name__ + ' ' + self.name + ':\n'
for atom in self.atom_list:
s = s + ' ' + `atom` + '\n'
return s
__repr__ = __str__
def isCompatible(self, residue_data):
return residue_data['residue_name'] == self.name \
and residue_data['residue_number'] == self.number
def addAtom(self, atom):
"""
Add an atom to the group
@param atom: the atom
@type atom: L{Atom}
"""
self.atom_list.append(atom)
self.atoms[atom.name] = atom
atom.parent = self
def deleteAtom(self, atom):
"""
Remove an atom from the group
@param atom: the atom to be removed
@type atom: L{Atom}
@raises KeyError: if the atom is not part of the group
"""
self.atom_list.remove(atom)
del self.atoms[atom.name]
atom.parent = None
def deleteHydrogens(self):
"""
Remove all hydrogen atoms of the group
"""
delete = []
for a in self.atom_list:
if a.name[0] == 'H' or (a.name[0] in string.digits
and a.name[1] == 'H'):
delete.append(a)
for a in delete:
self.deleteAtom(a)
def changeName(self, name):
"""
Set the PDB residue name
@param name: the new name
@type name: C{str}
"""
self.name = name
def writeToFile(self, file):
"""
Write the group to a file
@param file: a PDBFile object or a file name
@type file: L{PDBFile} or C{str}
"""
close = 0
if type(file) == type(''):
file = PDBFile(file, 'w')
close = 1
file.nextResidue(self.name, self.number, None)
for a in self.atom_list:
a.writeToFile(file)
if close:
file.close()
class Molecule(Group):
"""
Molecule in a PDB file
B{Note:} In PDB files, non-chain molecules are treated as residues,
there is no separate molecule definition. This module defines
every residue as a molecule that is not an amino acid residue or a
nucleotide residue.
"""
pass
class Residue(Group):
pass
class AminoAcidResidue(Residue):
"""
Amino acid residue in a PDB file
"""
is_amino_acid = 1
def isCTerminus(self):
"""
@returns: C{True} if the residue is in C-terminal configuration,
i.e. if it has a second oxygen bound to the carbon atom of
the peptide group. C{False} otherwise.
@rtype: C{bool}
"""
return self.name == 'NME' \
or self.atoms.has_key('OXT') \
or self.atoms.has_key('OT2')
def isNTerminus(self):
"""
@returns: C{True} if the residue is in N-terminal configuration,
i.e. if it contains more than one hydrogen bound to be
nitrogen atom of the peptide group. C{False} otherwise.
@rtype: C{bool}
"""
return self.atoms.has_key('1HT') or self.atoms.has_key('2HT') \
or self.atoms.has_key('3HT')
def addAtom(self, atom):
Residue.addAtom(self, atom)
if atom.name == 'CA': # Make sure it's not a calcium
atom.properties['element'] = 'C'
def writeToFile(self, file):
close = 0
if type(file) == type(''):
file = PDBFile(file, 'w')
close = 1
terminus = None
if self.isCTerminus(): terminus = 'C'
if self.isNTerminus(): terminus = 'N'
file.nextResidue(self.name, self.number, terminus)
for a in self.atom_list:
a.writeToFile(file)
if close:
file.close()
class NucleotideResidue(Residue):
"""
Nucleotide residue in a PDB file
"""
is_nucleotide = 1
def __init__(self, name, atoms = None, number = None):
self.pdbname = name
name = name.strip()
if name[0] != 'D' and name[0] != 'R':
name = 'D' + name
Residue.__init__(self, name, atoms, number)
for a in atoms:
if a.name == 'O2*' or a.name == "O2'": # Ribose
self.name = 'R' + self.name[1:]
def isCompatible(self, residue_data):
return (residue_data['residue_name'] == self.name or
residue_data['residue_name'] == self.pdbname) \
and residue_data['residue_number'] == self.number
def addAtom(self, atom):
Residue.addAtom(self, atom)
if atom.name == 'O2*' or atom.name == "O2'": # Ribose
self.name = 'R' + self.name[1:]
def hasRibose(self):
"""
@returns: C{True} if the residue has an atom named O2*
@rtype: C{bool}
"""
return self.atoms.has_key('O2*') or self.atoms.has_key("O2'")
def hasDesoxyribose(self):
"""
@returns: C{True} if the residue has no atom named O2*
@rtype: C{bool}
"""
return not self.hasRibose()
def hasPhosphate(self):
"""
@returns: C{True} if the residue has a phosphate group
@rtype: C{bool}
"""
return self.atoms.has_key('P')
def hasTerminalH(self):
"""
@returns: C{True} if the residue has a 3-terminal H atom
@rtype: C{bool}
"""
return self.atoms.has_key('H3T')
def writeToFile(self, file):
close = 0
if type(file) == type(''):
file = PDBFile(file, 'w')
close = 1
terminus = None
if not self.hasPhosphate(): terminus = '5'
file.nextResidue(self.name[1:], self.number, terminus)
for a in self.atom_list:
a.writeToFile(file)
if close:
file.close()
class Chain:
"""Chain of PDB residues
This is an abstract base class. Instances can be created using
one of the subclasses (L{PeptideChain}, L{NucleotideChain}).
Chain objects respond to len() and return their residues
by indexing with integers.
"""
def __init__(self, residues = None, chain_id = None, segment_id = None):
"""
@param residues: a list of residue objects, or C{None} meaning
that the chain is initially empty
@type residues: C{list} or C{NoneType}
@param chain_id: a one-letter chain identifier or C{None}
@type chain_id: C{str} or C{NoneType}
@param segment_id: a multi-character segment identifier or C{None}
@type segment_id: C{str} or C{NoneType}
"""
if residues is None:
self.residues = []
else:
self.residues = residues
self.chain_id = chain_id
self.segment_id = segment_id
def __len__(self):
"""
@returns: the number of residues in the chain
@rtype: C{int}
"""
return len(self.residues)
def sequence(self):
"""
@returns: the list of residue names
@rtype: C{list} of C{str}
"""
return [r.name for r in self.residues]
def __getitem__(self, index):
"""
@param index: an index into the chain
@type index: C{int}
@returns: the residue corresponding to the index
@rtype: L{AminoAcidResidue} or L{NucleotideResidue}
@raises IndexError: if index exceeds the chain length
"""
return self.residues[index]
def __getslice__(self, i1, i2):
"""
@param i1: in index into the chain
@type i1: C{int}
@param i2: in index into the chain
@type i12 C{int}
@returns: the subchain from i1 to i2
@rtype: L{PeptideChain} or L{NucleotideChain}
"""
return self.__class__(self.residues[i1:i2])
def addResidue(self, residue):
"""
Add a residue at the end of the chain
@param residue: the residue to be added
@type residue: L{AminoAcidResidue} or L{NucleotideResidue}
"""
self.residues.append(residue)
def removeResidues(self, first, last):
"""
Remove residues in a given index range.
@param first: the index of the first residue to be removed
@type first: C{int}
@param last: the index of the first residue to be kept, or C{None}
meaning remove everything to the end of the chain.
@type last: C{int} or C{NoneType}
"""
if last is None:
del self.residues[first:]
else:
del self.residues[first:last]
def deleteHydrogens(self):
"""
Remove all hydrogen atoms in the chain
"""
for r in self.residues:
r.deleteHydrogens()
def writeToFile(self, file):
"""
Write the chain to a file
@param file: a PDBFile object or a file name
@type file: L{PDBFile} or C{str}
"""
close = 0
if type(file) == type(''):
file = PDBFile(file, 'w')
close = 1
file.nextChain(self.chain_id, self.segment_id)
for r in self.residues:
r.writeToFile(file)
file.terminateChain()
if close:
file.close()
class PeptideChain(Chain):
"""
Peptide chain in a PDB file
"""
def isTerminated(self):
"""
@returns: C{True} if the last residue is in C-terminal configuration
@rtype: C{bool}
"""
return self.residues and self.residues[-1].isCTerminus()
def isCompatible(self, chain_data, residue_data):
return chain_data['chain_id'] == self.chain_id and \
chain_data['segment_id'] == self.segment_id and \
residue_data['residue_name'] in amino_acids
class NucleotideChain(Chain):
"""
Nucleotide chain in a PDB file
"""
def isTerminated(self):
"""
@returns: C{True} if the last residue is in 3-terminal configuration
@rtype: C{bool}
@note: There is no way to perform this test with standard PDB files.
The algorithm used works for certain non-standard files only.
"""
return self.residues and \
(self.residues[-1].name[-1] == '3'
or self.residues[-1].hasTerminalH())
def isCompatible(self, chain_data, residue_data):
return chain_data['chain_id'] == self.chain_id and \
chain_data['segment_id'] == self.segment_id and \
residue_data['residue_name'] in nucleic_acids
class DummyChain(Chain):
def __init__(self, structure, chain_id, segment_id):
self.structure = structure
self.chain_id = chain_id
self.segment_id = segment_id
def isTerminated(self):
return 0
def addResidue(self, residue):
self.structure.addMolecule(residue)
def isCompatible(self, chain_data, residue_data):
return chain_data['chain_id'] == self.chain_id and \
chain_data['segment_id'] == self.segment_id and \
residue_data['residue_name'] not in amino_acids and \
residue_data['residue_name'] not in nucleic_acids
#
# Residue number class for dealing with insertion codes
#
class ResidueNumber:
"""
PDB residue number
Most PDB residue numbers are simple integers, but when insertion
codes are used a number can consist of an integer plus a letter.
Such compound residue numbers are represented by this class.
"""
def __init__(self, number, insertion_code):
"""
@param number: the numeric part of the residue number
@type number: C{int}
@param insertion_code: the letter part of the residue number
@type insertion_code: C{str}
"""
self.number = number
self.insertion_code = insertion_code
def __cmp__(self, other):
if isinstance(other, int):
if self.number == other:
return 1
else:
return cmp(self.number, other)
if self.number == other.number:
return cmp(self.insertion_code, other.insertion_code)
else:
return cmp(self.number, other.number)
def __str__(self):
return str(self.number) + self.insertion_code
__repr__ = __str__
#
# The configuration class.
#
class Structure:
"""
A high-level representation of the contents of a PDB file
The components of a structure can be accessed in several ways
('s' is an instance of this class):
- 's.residues' is a list of all PDB residues, in the order in
which they occurred in the file.
- 's.peptide_chains' is a list of PeptideChain objects, containing
all peptide chains in the file in their original order.
- 's.nucleotide_chains' is a list of NucleotideChain objects, containing
all nucleotide chains in the file in their original order.
- 's.molecules' is a list of all PDB residues that are neither
amino acid residues nor nucleotide residues, in their original
order.
- 's.objects' is a list of all high-level objects (peptide chains,
nucleotide chains, and molecules) in their original order.
- 's.to_fractional' is the transformation from real-space coordinates
to fractional coordinates, as read from the SCALEn records.
- 's.from_fractional' is the transformation from fractional coordinates
to real-space coordinates, the inverse of s.to_fractional.
- 's.ncs_transformations' is a list of transformations that
describe non-crystallographic symmetries, as read from the
MTRIXn records.
- if a CRYST1 record exists, 's.a', 's.b', 's.c', 's.alpha',
's.beta', 's.gamma' are the parameters of the unit cell and
's.space_group' is a string indicating the space group.
If no CRYST1 record exists, all those values are None.
Furthermore, 's.cs_transformations' is a list of transformations
that describe crystallographic symmetries. If no CRYST1 record
exists, the list is empty.
An iteration over a Structure instance by a for-loop is equivalent
to an iteration over the residue list.
"""
def __init__(self, file_or_filename, model = 0, alternate_code = 'A'):
"""
@param file_or_filename: the name of the PDB file, or a file object.
Compressed files and URLs are accepted,
as for class L{PDBFile}.
@type file_or_filename: C{str} or C{file}
@param model: the number of the model to read from a multiple-model
file. Only one model can be treated at a time.
@type model: C{int}
@param alternate_code: the version of the positions to be read
from a file with alternate positions.
@type alternate_code: single-letter C{str}
"""
if isinstance(file_or_filename, basestring):
self.filename = file_or_filename
else:
self.filename = ''
self.model = model
self.alternate = alternate_code
self.pdb_code = ''
self.residues = []
self.objects = []
self.peptide_chains = []
self.nucleotide_chains = []
self.molecules = {}
self.to_fractional = self.from_fractional = None
self.ncs_transformations = []
self.cs_transformations = []
self.a = self.b = self.c = None
self.alpha = self.beta = self.gamma = None
self.space_group = None
self.parseFile(PDBFile(file_or_filename))
self.findSpaceGroupTransformations()
peptide_chain_constructor = PeptideChain
nucleotide_chain_constructor = NucleotideChain
molecule_constructor = Molecule
def __len__(self):
return len(self.residues)
def __getitem__(self, item):
return self.residues[item]
def deleteHydrogens(self):
"""
Remove all hydrogen atoms
"""
for r in self.residues:
r.deleteHydrogens()
def splitPeptideChain(self, number, position):
"""
Split a peptide chain into two chains
The two chain fragments remain adjacent in the peptide chain
list, i.e. the numbers of all following chains increase
by one.
@param number: the number of the peptide chain to be split
@type number: C{int}
@param position: the residue index at which the chain is split.
@type position: C{int}
"""
self._splitChain(self.peptide_chain_constructor,
self.peptide_chains, number, position)
def splitNucleotideChain(self, number, position):
"""
Split a nucleotide chain into two chains
The two chain fragments remain adjacent in the nucleotide chain
list, i.e. the numbers of all following chains increase
by one.
@param number: the number of the nucleotide chain to be split
@type number: C{int}
@param position: the residue index at which the chain is split.
@type position: C{int}
"""
self._splitChain(self.nucleotide_chain_constructor,
self.nucleotide_chains, number, position)
def _splitChain(self, constructor, chain_list, number, position):
chain = chain_list[number]
part1 = constructor(chain.residues[:position],
chain.chain_id, chain.segment_id)
part2 = constructor(chain.residues[position:])
chain_list[number:number+1] = [part1, part2]
index = self.objects.index(chain)
self.objects[index:index+1] = [part1, part2]
def joinPeptideChains(self, first, second):
"""
Join two peptide chains into a single one. The new chain occupies
the position of the first chain, the second one is removed from
the peptide chain list.
@param first: the number of the first chain
@type first: C{int}
@param second: the number of the second chain
@type second: C{int}
"""
self._joinChains(self.peptide_chain_constructor,
self.peptide_chains, first, second)
def joinNucleotideChains(self, first, second):
"""
Join two nucleotide chains into a single one. The new chain occupies
the position of the first chain, the second one is removed from
the nucleotide chain list.
@param first: the number of the first chain
@type first: C{int}
@param second: the number of the second chain
@type second: C{int}
"""
self._joinChains(self.nucleotide_chain_constructor,
self.nucleotide_chains, first, second)
def _joinChains(self, constructor, chain_list, first, second):
chain1 = chain_list[first]
chain2 = chain_list[second]
total = constructor(chain1.residues+chain2.residues,
chain1.chain_id, chain1.segment_id)
chain_list[first] = total
del chain_list[second]
index = self.objects.index(chain1)
self.objects[index] = total
index = self.objects.index(chain2)
del self.objects[index]
def addMolecule(self, molecule):
try:
molecule_list = self.molecules[molecule.name]
except KeyError:
molecule_list = []
self.molecules[molecule.name] = molecule_list
molecule_list.append(molecule)
self.objects.append(molecule)
def deleteResidue(self, residue):
self.residues.remove(residue)
delete = None
for type, mlist in self.molecules.items():
try:
mlist.remove(residue)
except ValueError:
pass
if len(mlist) == 0:
delete = type
if delete is not None:
del self.molecules[delete]
delete = None
for chain in self.peptide_chains + self.nucleotide_chains:
try:
chain.residues.remove(residue)
except ValueError:
pass
if len(chain.residues) == 0:
delete = chain
if delete is not None:
try:
self.peptide_chains.remove(chain)
except ValueError:
pass
try:
self.nucleotide_chains.remove(chain)
except ValueError:
pass
try:
self.objects.remove(residue)
except ValueError:
pass
def extractData(self, data):
atom_data = {}
for name in ['serial_number', 'name', 'position',
'occupancy', 'temperature_factor']:
atom_data[name] = data[name]
for name in ['alternate', 'charge']:
value = data[name]
if value:
atom_data[name] = value
element = data['element']
if element != '':
try:
int(element)
except ValueError:
atom_data['element'] = element
residue_data = {'residue_name': data['residue_name']}
number = data['residue_number']
insertion = data['insertion_code']
if insertion == '':
residue_data['residue_number'] = number
else:
residue_data['residue_number'] = ResidueNumber(number, insertion)
chain_data = {}
for name in ['chain_id', 'segment_id']:
chain_data[name] = data[name]
if chain_data['segment_id'] == self.pdb_code:
chain_data['segment_id'] = ''
return atom_data, residue_data, chain_data
def newResidue(self, residue_data):
name = residue_data['residue_name']
residue_number = residue_data['residue_number']
if name in amino_acids:
residue = AminoAcidResidue(name, [], residue_number)
elif name in nucleic_acids:
residue = NucleotideResidue(name, [], residue_number)
else:
residue = self.molecule_constructor(name, [], residue_number)
self.residues.append(residue)
return residue
def newChain(self, residue, chain_data):
if hasattr(residue, 'is_amino_acid'):
chain = self.peptide_chain_constructor([], chain_data['chain_id'],
chain_data['segment_id'])
self.peptide_chains.append(chain)
self.objects.append(chain)
elif hasattr(residue, 'is_nucleotide'):
chain = self.nucleotide_chain_constructor([],
chain_data['chain_id'],
chain_data['segment_id'])
self.nucleotide_chains.append(chain)
self.objects.append(chain)
else:
chain = DummyChain(self, chain_data['chain_id'],
chain_data['segment_id'])
return chain
def parseFile(self, file):
atom = None
residue = None
chain = None
read = self.model == 0
while 1:
type, data = file.readLine()
if type == 'END': break
elif type == 'HEADER':
self.pdb_code = data['pdb_code']
elif type == 'CRYST1':
for name, value in data.items():
setattr(self, name, value)
self.space_group = self.space_group.strip()
elif type[:-1] == 'SCALE':
if not hasattr(self, '_scale_matrix'):
self._scale_matrix = {}
self._scale_matrix[type[-1]] = data
if type[-1] == '3': # last line read
from Scientific.Geometry.Transformation \
import Shear, Translation
l1 = self._scale_matrix['1']
l2 = self._scale_matrix['2']
l3 = self._scale_matrix['3']
s = N.array([[l1['s1'], l1['s2'], l1['s3']],
[l2['s1'], l2['s2'], l2['s3']],
[l3['s1'], l3['s2'], l3['s3']]])
u = Vector(l1['u'], l2['u'], l3['u'])
self.to_fractional = Translation(u)*Shear(s)
self.from_fractional = self.to_fractional.inverse()
del self._scale_matrix
elif type[:-1] == 'MTRIX':
if not hasattr(self, '_ncs_matrix'):
self._ncs_matrix = {}
self._ncs_matrix[type[-1]] = data
if type[-1] == '3': # last line read
from Scientific.Geometry.Transformation \
import Rotation, Translation
l1 = self._ncs_matrix['1']
l2 = self._ncs_matrix['2']
l3 = self._ncs_matrix['3']
m = N.array([[l1['m1'], l1['m2'], l1['m3']],
[l2['m1'], l2['m2'], l2['m3']],
[l3['m1'], l3['m2'], l3['m3']]])
v = Vector(l1['v'], l2['v'], l3['v'])
tr = Translation(v)*Rotation(Tensor(m))
tr.given = data['given']
tr.serial = data['serial']
self.ncs_transformations.append(tr)
del self._ncs_matrix
elif type == 'MODEL':
read = data['serial_number'] == self.model
if self.model == 0 and len(self.residues) == 0:
read = 1
elif type == 'ENDMDL':
read = 0
elif read:
if type == 'ATOM' or type == 'HETATM':
alt = data['alternate']
if alt == '' or alt == self.alternate:
atom_data, residue_data, chain_data = \
self.extractData(data)
if type == 'ATOM':
atom = apply(Atom, (), atom_data)
else:
atom = apply(HetAtom, (), atom_data)
new_chain = chain is None or \
not chain.isCompatible(chain_data,
residue_data)
new_residue = new_chain or residue is None \
or not residue.isCompatible(residue_data)
if new_residue and chain is not None and \
chain.isTerminated():
new_chain = 1
if new_residue:
residue = self.newResidue(residue_data)
if new_chain:
chain = self.newChain(residue, chain_data)
chain.addResidue(residue)
residue.addAtom(atom)
elif type == 'ANISOU':
alt = data['alternate']
if alt == '' or alt == self.alternate:
if atom is None:
raise ValueError("ANISOU record before " +
"ATOM record")
atom['u'] = data['u']
elif type == 'TERM':
if chain is None:
raise ValueError("TERM record before chain")
chain = None
def findSpaceGroupTransformations(self):
if self.space_group is not None and self.to_fractional is not None:
from Scientific.IO.PDBSpaceGroups import \
getSpaceGroupTransformations
try:
trs = getSpaceGroupTransformations(self.space_group)
except KeyError:
return
for tr in trs:
tr = self.from_fractional*tr*self.to_fractional
self.cs_transformations.append(tr)
def renumberAtoms(self):
"""
Renumber all atoms sequentially starting with 1
"""
n = 0
for residue in self.residues:
for atom in residue:
atom['serial_number'] = n
n = n + 1
def __repr__(self):
s = self.__class__.__name__ + "(" + repr(self.filename)
if self.model != 0:
s = s + ", model=" + repr(self.model)
if self.alternate != 'A':
s = s + ", alternate_code = " + repr(self.alternate)
s = s + "):\n"
for name, list in [("Peptide", self.peptide_chains),
("Nucleotide", self.nucleotide_chains)]:
for c in list:
s = s + " " + name + " chain "
if c.segment_id:
s = s + c.segment_id + " "
elif c.chain_id:
s = s + c.chain_id + " "
s = s + "of length " + repr(len(c)) + "\n"
for name, list in self.molecules.items():
s = s + " " + repr(len(list)) + " " + name + " molecule"
if len(list) == 1:
s = s + "\n"
else:
s = s + "s\n"
return s
def writeToFile(self, file):
"""
Write everything to a file
@param file: a PDB file object or a filename
@type file: L{PDBFile} or C{str}
"""
close = 0
if type(file) == type(''):
file = PDBFile(file, 'w')
close = 1
for o in self.objects:
o.writeToFile(file)
if close:
file.close()
if __name__ == '__main__':
if 0:
file = PDBFile('~/3lzt.pdb')
copy = PDBFile('test.pdb', 'w', 'xplor')
while 1:
type, data = file.readLine()
if type == 'END':
break
copy.writeLine(type, data)
copy.close()
if 1:
s = Structure('~/Programs/MMTK/main/MMTK/Database/PDB/insulin.pdb')
print s
|