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
|
AutoDock RELEASENOTES $Id: RELEASENOTES,v 1.20 2014/07/17 18:09:14 mp Exp $
=============================================================================
AutoDock Release Notes
Release 4.2.6 (July 2014)
=============================================================================
Supported computer platforms in 4.2.6:
Linux2 on Intel i86 (32-bit) and on Intel x86_64 (64-bit).
Linux3 on Intel x86_64 (64-bit).
Macintosh OS X 10.5 (Leopard) on PowerPC (32- and 64-bit),
OS X 10.5-10.9 (Leopard, Snow Leopard, Lion, Mountain Lion,
and Mavericks) on Intel i86 (32-bit) and Intel x86_64 (64-bit).
Solaris 8 (SunOS 5.8) on SPARC.
Windows 5-8.1 on Intel i86.
The executable binaries (autogrid4, autodock4) for Macintosh OS X
are built on Mac OS X 10.5 and tested on up to Mac OS X 10.9.
Each of the two binaries is "universal" and will run on any of
the supported Macs.
The executable binaries for Windows on Intel i86 are built on
Windows 5 (XP) and have been tested on Windows 6, Windows 7, and Windows 8.1.
Windows users do not need to install the CygWin environment,
but they may if they like.
To increase consistency across platforms, all executable programs (both
autogrid and autodock) are compiled using double-precision arithmetic.
The grid maps, as read by AutoDock, are stored internally in single-precision.
Multiple search methods are now possible in a single AutoDock job:
such as 20 runs using Simulated Annealing, 20 runs using the Genetic
Algorithm, and 20 runs using local-search-only. The runs are
done serially and no results "carry over" from one method to another.
However, all results are ranked and clustered together in the
analysis step at the end of the entire job.
You can now use ADT (AutoDock Tools) to visualize results from AutoDock
jobs that use simulated annealing or local-search-only. You must download the
latest build of ADT from http://mgltools.scripps.edu/downloads/latest
Note a limitation in the 4.2.6 release: the "do_local_only" command
runs the pseudo-solis-wets algorithm, even if the solis-wets has been
specified using "set_local sw1". This applies only to "do_local_only":
the "ga_run" command will use whichever local search has been specified.
(We recommend the pseudo-solis-wets for all local searches: "set psw1").
AutoDock calculations are performed as a series of independent
runs. Users will occasionally need to repeat a run. For example,
they might want to repeat a particular run to examine the search space
and convergence of that run. AutoDock now reports the specific random
number seeds used for each run. Any specific run can be repeated
exactly by using the random number seeds reported in the prior calculation.
The docking log file (.dlg) contents have been further standardized:
Regardless of 'outlev' setting, the host name, run date, working directory,
and names of input PDBQT files are reported at the beginning of the AutoDock
job. Each 'run' (GA, LGA, local search, simulated annealing) reports its
initial random number seeds and its ending total energy and state
in a uniform format suitable for automated analysis. At outlev setting
"BASIC" (0) or above, the initial PDBQT ligand (and flexres, if present)
coordinates are reported. At outlev setting "ADT" (1) or above, the
final docked coordinates of each run are reported.
Some advanced autodock users customize the program for
their own specific needs. We've improved and simplified building
AutoDock and AutoGrid from source files. We have documented the
process of compiling new atomic parameter tables into AutoDock and
AutoGrid in the README file included in this distribution.
We continue to improve AutoDock's robustness and stability. AutoDock
now verifies that all its input grid maps are the same size.
If AutoDock's standard input has not been redirected to come from a file
or from a pipe, you must specify a docking parameter file using
"-p <docking parameter file.dpf>". When the docking parameters are
read from standard input (e.g., "autodock4 -l mol.dlg < mol.dpf"),
the docking parameter file now appears in output PDBQT files as "stdin".
Reading and parsing the input PDBQT coordinate files has been made more robust.
Other changes since the 4.2.5.1 release (12/13/2012):
Improved error checking of command-line arguments.
Better checking of the atom numbers that define internal and "flexres" torsions.
Better cross-platform compatibility of the internal random number generator.
Running "autodock4 (or autogrid4) --version" reports compile-time configuration options.
=============================================================================
AutoDock Release Notes
Release 4.2.5.1 (December 13, 2012)
=============================================================================
The changes since the 4.2.5 release (11/02/2012):
#bug fix
4.2.5 incorrectly calculated part of the intermolecular desolvation
energy term; 4.2.5.1 corrects this. All 4.2.5 users should upgrade
to 4.2.5.1 and re-do any runs.
=============================================================================
AutoDock Release Notes
Release 4.2.5 (November 2, 2012)
=============================================================================
Please note that the previous general release was 4.2.3, 29 January 2010.
The 4.2.4 release (7 July 2010) was a specialized release for
"Fight Aids at Home" and other IBM World Community Grid projects.
Supported computer platforms in 4.2.5:
Linux2 on Intel x86 remains supported, as does Solaris 8 on SPARC.
Supported Macintosh platforms are OS X 10.4-10.5 (Tiger and Leopard) on
Intel x86 and PowerPC, and OS X 10.6-10.8 (Snow Leopard, Lion, and
Mountain Lion) on Intel x86. The executable binaries for Windows on
Intel x86 have been built on Windows 5 (XP) and have been tested on Windows 6
but they may if they like.
The changes since the 4.2.3 release (1/29/2010):
#new features
-: new support for specifying output verbosity ranging from low (-2) up to high (8)
with symbolic settings for "outlev" defined in constants.h and used in main.cc
-: new automatic calculation of 'about' as the center of the ligand root group
-: new WIN32 MinGW portability - replacements for times() and getrusage()
-: new desolvation term separate from vdW+Hbond term in epdb
"Per-atom Intermolecular Energy Analysis" table
-: now intelec is on by default; off if "intelec off" in DPF
-: Almost all AutoDock defaults now match defaults supplied by ADT, simplifying PDF files
#code inspection and internal interface self-documentation
-: We thank Steffen Moeller (steffen_moeller@gmx.de) for his enthusiastic
and expert detailed inspection of all function and method calls,
in particular identifying "constant" arguments and verifying
data type compatibiliy.
#improvements
-: improved detailed output of Intermolecular Energy Analysis
-: increased MAX_RUNS from 256 to 2000
-: improved error detection and termination:
replaced exit() by EXIT_SUCCESS/EXIT_FAILURE(win32) or stop(msg)
-: increased precision of energy table
-: implemented EnergyComponent structures
-: integrated call_gs into call_glss
-: improved input checking with ga_run/gals_run
[Added checks to "ga_run/gals_run" for missing "set_ga" and missing "set_psw1" errors]
-: simplified logic so more of the FATAL errors are simply handed to "stop()"
-: now set random number seeds at beginning of simanneal execution; output reduced
-: new compile-time option to print energy terms for each atom [for debugging]
-: AutoDock intramolecular energy smoothing now matches that in AutoGrid
-: Consolidated the "side effects" of trilinterp that record per-atom energy components
and total energy components into two sets of "EnergyComponent" structures instead
of two Real arrays and two pointers to Real.
-: developed substitutes for WIN32 MinGW "times()" and "getpid()"
-: modified mkTorTree.cc to fill in the root atom information
-: Changed 'tlist' declaration to allow space for root atoms at end
#bug fixes
-: corrected energy breakdown report when using flexible residues
-: desolvation energy term is included even for distant pairs (r>nbc)
-: corrected eintcal side effects of "outlev" setting
-: removed support for unused DPF tokens
#autogrid
AutoGrid 4.2.5 has no functional changes from AutoGrid 4.2.3.
The only significant code changes were those required for porting to Windows.o
We added 'copyfilesfromAD', a maintenance script that copies key shared source files
from AutoDock to AutoGrid.
=============================================================================
AutoDock Release Notes
Release 4.2.3 (January 29 2010)
=============================================================================
The changes since the 4.2.2.1 release (9/16/2009):
Corrected printing of atom records whose element names are two characters
long (such as Br). Our thanks to David Lancia for reporting this problem
and working with us on the correction.
Corrected genetic algorithm gene crossover flaw that slowed search progress
for ligands with many torsions. Our thanks to Garrett Morris and Sarnath for
reporting this problem and working with us on the correction.
AutoGrid 4.2.3 differs from AutoGrid 4.2.2 only in the version number.
=============================================================================
AutoDock Release Notes
Release 4.2.2.1 (September 16 2009)
=============================================================================
Please note that the current distribution's executable programs, autogrid and
autodock, were compiled for single precision arithmetic. We believe
compiling with double-precision would increase consistency across platforms.
(See -DUSE_DOUBLE option in Makefile.am)
The changes since the 4.2.2 release (9/9/2009):
Updated printout of unbound system's energy when using "epdb" option
to correctly set unbound internal energy same_as_bound if appropriate.
=============================================================================
AutoDock Release Notes
Release 4.2.2 (September 9 2009)
=============================================================================
The changes since the 4.2.1 release (6/2009):
Makefile.am
-in response to bug 1137 reported by Steffen Moeller@gmx.de added
Wno-write-strings to Makefile.am and strncpy to setflags.cc
calculateEnergies.cc
-added setting the flexible residues internal energies to same_as_bound
(lines 262-265) after conversations with David, Mike and Garrett
eintcal.cc
-replaced missing backslash for newlines
readPDBQT.cc
-fixed bug in flexible residues overcounting number of pieces by changing
code so that ROOTs of all flexible residues are in the same rigid piece
-changed cut-off for nrigid_piece from MAX_TORS to MAX_TORS + nres
to compensate for (unfortunate) fact that each flexible residue has a ROOT
setflags.cc
-repaired copying argv[2] in param_file_fn
-modified lines 183-188 to check for filename length
-in response to bug 1137 reported by Steffen Moeller@gmx.de added
Wno-write-strings to Makefile.am and strncpy to setflags.cc
support.cc
-replaced missing backslash for newlines
=============================================================================
AutoDock Release Notes
Release 4.2.1 (June 9 2009)
=============================================================================
The key changes since the 4.0.1 release (5/2007):
1. Improved overall reliability and detection of input file errors.
2. Improved local search.
----------------------------
AD4.1_bound.dat
AD4_parameters.dat
----------------------------
NEW FEATURE:
-added parameters for G,GA,J and Q atom types used for ring-closure
-added parameters for the covalent atom type, "Z".
CHANGE:
-introduced new "parameter_file" .dat files for AutoDock 4.1 that
have the appropriate coefficients for the bound, compact and extended
models. The previous default parameter file for AutoDock 4.0 was
"AD4_parameters.dat"; the default parameter file for AutoDock 4.2
is "AD4.1_bound.dat".
----------------------------
AUTHORS
----------------------------
CHANGE:
-updated the authors list
----------------------------
INSTALL
----------------------------
CHANGE:
-copied current version from gnu
----------------------------
Makefile.am
----------------------------
CHANGE:
-removed superfluous VERSION_NUM line
-set cygwin stacksize and added possible extension for cygwin...
we don't really understand why the python-driven tests are not
working on cygwin although autodock appears to run ok
-changed version to 4.2.1
-removed command mode
-changed VERSION_NUM strings from 4.0 to 4.02 and from 4.l to 4.1.1
-removed summarizegrids[c,h]
-added check for too many atom types in dpf 'ligand_types' command in
parsetypes.
-added map_declare.h so type of map (float or double) is
independent of 'Real' and not affected by 'USE_DOUBLE' in Makefiles.
-changed the target "check" to "test", since "make check" causes an
error. This means to test, the developer should use "make test", _not_
"make check". Also changed the "-o" argument to "test_autodock4.py",
from "$$outputdir" to "$$outputdir/Tests".
-Added the argument "AD4.1_bound.dat" to the new version of
"paramdat2h.csh" to compile the "default_parameters.h". Also added
two new target, "BUILT_SOURCES", and "CLEANFILES", which depend on
"default_parameters.h".
-Added stack.{cc,h} to the dependencies required to make AutoDock.
-Removed the -DDO_NOT_CROSSOVER_IN_QUAT flags and added -DASSERTQUATOK to "DBUG".
-Changed default parameter file from AD4_parameters.dat to AD4.1_bound.dat,
and added the new AD4.1 parameter files to EXTRA_DIST.
-Rework of Coliny files to use the COLIN 3.0 code.
-Fixed bug reported by Qing Zhong, so that "gs.cc" now uses the same
compiler and flags as everything else except main.cc, i.e. $(CXXCOMPILE).
This means that the option DO_NOT_CROSSOVER_IN_QUAT is now used in gs.cc,
and thus ensures distorted geometries cannot be produced by wayward
quaternions... Now compiles without the spurious "-g -O2" generated by configure.
----------------------------
NEWS
----------------------------
NEW FEATURE:
-added DSG comment on new features
----------------------------
analysis.cc
analysis.h
----------------------------
CHANGE:
-installed Debian compiler-compatibility patches from Stefan Moeller
-Uses calculateBindingEnergies so that if AD4.1_Bound.dat is used,
the internal energy of the unbound state can be set to that of the
docked state. No longer prints the "NEWDPF ndihe" line, since
"ndihe" is deprecated in AutoDock 4.
----------------------------
atom_parameter_manager.cc
----------------------------
CHANGE:
-credit Michael Pique for helping to create this code which
consist of changes to make it more readable.
----------------------------
autocomm.h
----------------------------
CHANGE:
-added a macro-version of assertQuatOK, so that when the assertion
fails, the line number and file of where it failed is output,
not the assertQuatOK function as it was before.
----------------------------
autoglobal.h
----------------------------
CHANGE:
-moved AutoGridHelp into autogrid where it belongs
- introduced initial "Unbound_Default" to detect multiple, inconsistent
settings of ad4_unbound_model
-updated command line arguments including --version
-added a new global, ad4_unbound_model, which can take any of the
enumerated values of Unbound_Model, namely,
{ Unbound_Same_As_Bound=0, Extended=1, Compact=2 }.
----------------------------
banner.cc
----------------------------
CHANGE:
-replaced version number in banner for ADT1.5.2 compatibility with 3 digits
-added -C for copyright notice
-changed format string for version_num, increasing it from 4s to 8s
-updated banner output in the DLG such that the earlier copyright years
matches the header comments (1989 instead of 1991), and the later year
matches the current year (2008 instead of 2007).
-installed Debian compiler-compatibility patches from Stefan Moeller
----------------------------
calculateEnergies.cc
calculateEnergies.h
----------------------------
CHANGE:
-added Unbound_Default case
-Added calculateBindingEnergies() and related functions, to support
the ability to set the internal energy of the unbound state to that
of the docked state.
----------------------------
call_glss.cc
call_gs.cc
gs.cc
mapping.cc
----------------------------
CHANGE:
-correction of when genotype to phenotype mappings are done
-changed so now Individual does mapping of its genotype into its
phenotype and inverse_mapping of its phenotype into its genotype
-changed argument to msort from 3 to 1
-added an argument to the calling signature, "end_of_branch[]",
which can be used to pass in the corresponding branch points for
the new Branch Crossover Mode. Added a call to
"set_eob( end_of_branch )", a method of thisPop, which is a Population.
-added a new integer, "max_numTries", set to 1000, that is used
to prevent the generation of the initial population from getting
stuck in an infinite loop. The code prints a warning if this
maximum number of tries is reached, while trying to create a
population which does not have all energies equal.
----------------------------
cmdmode.cc
cmdmode.h
cmdtokens.h
----------------------------
CHANGE:
-removed command mode
----------------------------
coliny.cc
coliny.h
----------------------------
CHANGE:
-rework of Coliny files to use the COLIN 3.0 code.
-misc change to enable conditional compile of AutoDock with the
new COLIN 3.0 mechanism.
----------------------------
configure.ac
----------------------------
CHANGE:
-changed version to 4.2.1
-pass version_num to setflags
-updated version to 4.1.0.
-fixed bug reported by Qing Zhong, so that "gs.cc" now uses
the same compiler and flags as everything else except main.cc,
i.e. $(CXXCOMPILE). This means that the option
DO_NOT_CROSSOVER_IN_QUAT is now used in gs.cc, and thus ensures
distorted geometries cannot be produced by wayward quaternions...
Now compiles without the spurious "-g -O2" generated by configure.
----------------------------
configure_universal_Darwin8
configure_universal_Darwin9
----------------------------
NEW FEATURE:
-new maintenance and distribution tools
----------------------------
conformation_sampler.cc
----------------------------
CHANGE:
-changed so now Individual does mapping of its genotype
into its phenotype and inverse_mapping of its phenotype
into its genotype
----------------------------
constants.h
----------------------------
CHANGE:
-introduced initial 'Unbound_Default' to be used to detect
multiple, inconsistent settings of ad4_unbound_model
-added a guard, using "#ifndef _UNBOUND_MODEL", around the
definition of the enum "Unbound_Model", to prevent re-definition
errors.
-added "Unbound_Model", an enumerated variable, which can have
the values { Unbound_Same_As_Bound=0, Extended=1, Compact=2 }
----------------------------
dpftoken.h
----------------------------
CHANGE:
-added psw rot scale and tor scale for rho values
-added parsing of autodock_parameter_file version and unbound_model
-made new token for obsolete token quat0 to give better error messages
----------------------------
getInitialState.cc
getInitialState.h
----------------------------
CHANGE:
-Uses calculateBindingEnergies so that if AD4.1_Bound.dat is used,
the internal energy of the unbound state can be set to that of the
docked state.
----------------------------
get_atom_type.cc
----------------------------
CHANGE:
-now allocate storage for message variable
----------------------------
gs.cc
gs.h
----------------------------
NEW FEATURE:
-added a new enum to "Xover_Mode", namely "Branch", and added new
code in the crossover method, to support the new "Branch Crossover
Mode", where only torsion genes (if any) are recombined, and
only those genes that lie within the sub-tree of the torsion
tree affected by the first crossover point. The Global Search
Genetic Algorithm accesses the end_of_branch[] array using the
accessor method get_eob() of the Population object,
"original_population".
-added slerp and alerp to arithmetic crossover to handle
interpolation of rotations and torsion angles gracefully,
and to preserve quaternion-magnitudes of 1.
-added code to handle uniform crossover of the four genes
describing the orientation.
CHANGE:
-changed so now Individual does mapping of its genotype into its
phenotype and inverse_mapping of its phenotype into its genotype
-changed line 1091: now if avg==worst, alloc[i] is set to
1/pop_size; added @@ to debug statements lines 1428,1440
-added <stdlib.h> since MP & GMM added an exit(-1) as a bug check,
to catch genes whose indices are not translation, rotation or
conformation values.
-added several debug statements; made change in translation
alpha value, to make it consistent with slerp and alerp.
-Modified 2-pt and 1-pt crossover to ensure every call does
indeed perform some crossover.
-Fixed uniform crossover such that it will not begin to crossover
within the rotation genes.
-added a "bug check" suggested by MP to catch invalid gene types.
-removed the DO_NOT_CROSSOVER_IN_QUAT blocks.
-added lines to uniform and arithmetic crossover to set the
age of the crossed individuals to 0.
----------------------------
hybrids.h
----------------------------
CHANGE:
-added the argument, "int end_of_branch[MAX_TORS]", to the
prototypes, call_glss() and call_gs().
----------------------------
ls.cc
----------------------------
NEW FEATURE:
-added psw rot scale and tor scale for rho values
CHANGE:
-Changed so now Individual does mapping of its genotype
into its phenotype and inverse_mapping of its phenotype
into its genotype; added use of Boole modified to track
whether mapping needs to be done
----------------------------
ls.h
----------------------------
CHANGE:
-changed return type of SW from void to Boole
----------------------------
main.cc
main.h
----------------------------
NEW FEATURE:
-added psw rot scale and tor scale for rho values
-added code provided by Stefano Forli which improves the warning
message printed to the log file lines ~2108. The new code detects
whether the custom rij+epsij values provided for DPF_INTNBP_REQM_EPS
command are RING CLOSURE values or not
-added named atom pairs to intnb_r_eps and intnb_coeffs to support
ring-closing atom types
-added exit early if number of maps is not equal to the number of
ligand_atom_types plus 2 AND resetting num_maps when fld keyword is
read so two sets of maps can be used
-Added the "int end_of_branch[MAX_TORS]" array, and the parsing code to
detect the new option, "branch", for the "ga_crossover_mode" keyword
(in addition to "onept", "twopt", "uniform", and "arithmetic". This
is to support the new "Branch" crossover mode, which is designed to
exchange only those torsion genes in the sub-tree descending from
the first randomly-chosen torsion gene.
-Modified the function that reads the ligand and flexible residue PDBQT
files, "readPDBQT()", to count the number of non-hydrogen atoms, and
return this value. (Previously, the same argument position that this
count of heavy atoms now occupies, was used to pass in "Htype", but
Htype is no longer used inside "readPDBQT()".)
CHANGE:
-installed Debian compiler-compatibility patches from Stefan Moeller
-updated command line arguments including --version
-updated syntax for unbound options following discussion with DSG
-added reporting of which unbound model is used for each kind of search
-changed interface to setup_parameter_library by adding ad4_unbound_model
-added parsing of autodock_parameter_file version and unbound_model
-pass version_num to setflags
-removed command mode
-added 'exit_if_missing_elecmap_desolvmap_about' method to check that
these keywords have been found and exit if they are not all there
-all filenames are dimensioned to PATH_MAX long, all strings read using
sscanf are dimensioned to LINE_LEN
-made new token for obsolete token quat0 to give better error messages
-Updated the summations for the econf[] array that is used in the
analysis() function, and which is reported in the clustering histogram.
These summations needed to be updated to be able to handle the
"ad4_unbound_model" properly; in this model, the unbound energy must be
updated after each docking has finished, to match the internal energy
at the end of the docking.
-The "epdb" command now uses calculateBindingEnergies so that if
AD4.1_Bound.dat is used, the internal energy of the unbound state can
be set to that of the docked state. * Also, added a check to see if
the number of values specified by the "dihe0" command matches the
number of torsions found in the ligand PDBQT (ntor), and prints a
warning if they do not match.
-Added extra variables and the function call to
"initialise_energy_breakdown()" to the DPF_MOVE-case to re-initialise
key variables before reading in a new ligand. ALSO: changed
version_num to 4.10 (from 4.00) and changed the comment from 4.0 to 4.1 beta.
-Changed sscanf from using %1s to %c, thanks to an email from Alexandre
Lebedev (alexmlebedev@mail.ru); this solves a bug in the simulated
annealing that appeared if the number of rejections, rejs<=255.
-Rework of Coliny files to use the COLIN 3.0 code.
----------------------------
mdist.h
----------------------------
NEW FEATURE:
-Introduced the "set_minmax(a1, a2, min, max)" macro, to set both
the [a1][a2] and [a2][a1] entries in the mindist[][] and maxdist[][]
arrays at the same time. Introduced the constant, "BOND_LENGTH_TOLERANCE",
with a default value of 0.1 Angstrom, to expand the allowed bond length
ranges. Entered an extensive list of values from the "Handbook of
Chemistry and Physics" specifying the lower and upper bounds for
acceptable bond lengths given the atom types of the two potentially-bonding
atoms. This new code is less permissive in creating bonds than the old
AutoDock 3 values, which consisted of 0.9 and 2.1 for most atom type
pairs. This modification was prompted by a compound with a C-bridged
cyclobutane, ZINC01557511, which caused "nonbonds.cc" to try to
access bonded[-1][]...
CHANGE:
-cleaned-up macro; corrected previous incorrect setting of diagonal values; removed 10% of code
-explicitly set values of enum
----------------------------
mkNewState.cc
----------------------------
TODO:
-TODO 5/1/2009: should call slerp to scale down by qtwStep"
----------------------------
mkTorTree.cc
----------------------------
CHANGE:
-moved error message for too many torsions earlier
----------------------------
mkdisttars
----------------------------
NEW FEATURE:
-new maintenance and distribution tools
----------------------------
nonbonds.cc
----------------------------
NEW FEATURE:
-Several changes have been made to improve the bond
and nonbond detection algorithm. Now, atoms that
can potentially form bonds are sorted by distance
first, so that the shortest candidate bonds are added
first. There is now a check to stop adding bonds when
the maximum number of bonds is reached. The bonded[][]
array values are now validated before they are used in
the for-l loop, to make sure they are not less than 0.
There are new debugging print statements that can be
triggered with the "-d" flag. The new algorithm, in
conjunction with the new bond length values in the file
"mdist.h", now correctly handles ZINC01557511, a compound
with a C-bridged cyclobutane that was previously causing
the code to attempt to access bonded[-1][].
----------------------------
paramdat2h.csh
----------------------------
NEW FEATURE:
-compiles and builds both autodock4 and autodock4_0 with
appropriate default parameter libraries. Reports which one is being
used in dlg file.
-changed paramdat2h.csh to now take one argument, the name of the
parameter library.
-changed the default parameter library file from "AD4_parameters.dat"
to "AD4.1_bound.dat".
----------------------------
parameters.h
----------------------------
NEW FEATURE:
-Introduced a new macro, "is_hydrogen_type(t)", that takes a
found_parm->autogrid_type and returns true if the type is a
hydrogen atom type, namely "H", "HD" or "HS".
----------------------------
parse_PDBQT_line.cc
----------------------------
NEW FEATURE:
-added detection of USER records, mapping to PDBQ_NULL.
-now returns PDBQ_UNRECOGNIZED instead of PDBQ_NULL, when
it cannot identify the token.
----------------------------
parse_com_line.cc
parse_com_line.h
----------------------------
DEPRECATED:
-removed command mode
----------------------------
parse_dpf_line.cc
----------------------------
CHANGE:
-removed unnecessary numbering
-added unbound_energy token; removed reminder about NUM_LEXEMES
-added parsing of autodock_parameter_file version and unbound_model
-made new token for obsolete token quat0 to give better error messages
----------------------------
parse_param_line.cc
----------------------------
CHANGE:
-added the new keyword/token pair, {"FE_unbound_model", PAR_UNBOUND},
to the parser.
----------------------------
parsetypes.cc
----------------------------
CHANGE:
-Added check for too many atom types in dpf 'ligand_types' command in
parsetypes. Added map_declare.h so type of map (float or double) is
independent of 'Real' and not affected by 'USE_DOUBLE' in Makefiles.
----------------------------
partokens.h
----------------------------
CHANGE:
-added a new token, PAR_UNBOUND.
----------------------------
printEnergies.cc
----------------------------
CHANGE:
-installed Debian compiler-compatibility patches from Stefan Moeller
-changed printout of receptor internal energy: previously only the
total was reported. Now the moving-fixed and moving-moving components
of the internal energy of the receptor are printed
----------------------------
qmultiply.cc
----------------------------
NEW FEATURE:
-added quatDifferenceToAngle and quatDifferenceToAngleDeg methods;
modified assert line 203 increasing 1 to 1.001
-Introduced a new slerp function adapted from an implementation
by John Ratcliff to replace the previous slerp by Martin Baker;
the previous slerp caused problems with arithmetic-crossover-based
dockings that used typical numbers of energy evaluations, but not
with our "unit" tests which are extremely short dockings. The
slerp based on the implementation from Martin Baker has been renamed
"slerp1".
-Added two new functions, alerp(a,b,fract) and a_range_reduction(a),
which are used to interpolate (torsion) angles, such that the
interpolation gives a if fract=0, b if fract=1, and some fraction
of the smaller difference between a and b (note that the difference
between two range-reduced angles can be either greater than 180 or
less than 180 degrees, and we want to interpolate along the delta
that is smaller than 180 degrees. E.g. the average, i.e. fract=0.5,
of 1 and 359 degrees should be 0 deg, not 180 deg.) There is a test
in one of the added comments, note, of alerp for a wide range of a
and b values.
CHANGE:
-commented out the assertQuatOK function, since the macro version
was introduced in autocomm.h, to permit better reporting of where
the assertion failed. Added a warning for the DEBUG_MUTATION
directive in slerp(), to alert if theta is 180 degrees when the
two quaternions are opposite. Added a comment to clarify that
when fract==0, alerp returns a.
----------------------------
qmultiply.h
----------------------------
NEW FEATURE:
-added quatDifferenceToAngle and quatDifferenceToAngleDeg declarations
-Introduced a new slerp function adapted from an implementation by John
Ratcliff to replace the previous slerp by Martin Baker; the previous
slerp caused problems with arithmetic-crossover-based dockings that
used typical numbers of energy evaluations, but not with our "unit"
tests which are extremely short dockings. The slerp based on the
implementation from Martin Baker has been renamed "slerp1".
CHANGE:
-commented out the prototype for assertQuatOK(). Better to use the
macro version in autocomm.h.
-added prototypes for alerp(a,b,fract) and a_range_reduction(a),
which are for interpolating angles and "mod"-ing angles.
----------------------------
readPDBQT.cc
----------------------------
NEW FEATURE:
-added new code that uses stacks, in particular stack_push(int)
and stack_pop(), to build up the "end_of_branch[]" array, which
is used in the new "Branch Crossover Mode" offered in the GA and
Lamarckian GA search methods. The intention of the branch crossover
mode is to exchange only those torsion genes in the sub-tree
descending from the first crossover point.
-modified the function that reads the ligand and flexible residue PDBQT
files, "readPDBQT()", to count the number of non-hydrogen atoms, and
return this value. (Previously, the same argument position that this
count of heavy atoms now occupies, was used to pass in "Htype", but
Htype is no longer used inside "readPDBQT()".)
other PDBQT_ tokens.
CHANGE:
-increased QTOL from .005 to .05; softened warning message
-corrected ROOT logic for flexible residues
-repaired and clarified detection of end_of_branch entries by
adding a separate array 'branch_last_piece': now the root is
numbered piece one and the rigid pieces moved by torsions are
numbered starting at two; removed 'stack_size' (which should
have been stack_depth anyway) and 'top' from debug statements;
updated DEBUG: indicies; added code to catch error and exit if
parent <0
-added code to check that each of the fields is read correctly in
readPDBQLine. Now checks that each ATOM/HETATM line in the PDBQT
file is at least 78 characters long; if not, the parser now exits
with a fatal error. The warning if an atom type is not found is now
much more informative, now advising the user to check the
"ligand_types" line and to add a "map" line to the DPF. The parser
now explicitly handles all the tokens that can be returned by the
parse_PDBQT_line function. There is now a warning if an unrecognised
token is found in the PDBQT file. The code that handled BEGIN_RES
records has now been mostly moved into a case block, alongside the
----------------------------
read_parameter_library.cc
read_parameter_library.h
----------------------------
CHANGE:
-installed Debian compiler-compatibility patches from Stefan Moeller
-removed unused extern variable
-added warning to PAR_UNBOUND in setup_parameter_library
-added reporting of which unbound model is used for each kind of search
-changed interface to setup_parameter_library by adding ad4_unbound_model
-replaced determining version number using 'strcmp' with
'string_begins_with' to support the new longer version number format: #.#.3
-added a print statement to record the error message in the logFile,
if the FN_parameter_library cannot be opened.
----------------------------
rep.cc
----------------------------
CHANGE:
-added lines to set low and high from init_low and init_high,
supplied in the constructor form ConstrainedRealVector::
ConstrainedRealVector(int num_els, double init_low, double init_high).
----------------------------
rep_constants.h
----------------------------
CHANGE:
-added definitions for Y_TRANSLATION_INDEX, is_first_rotation_index(i)
and is_within_rotation_index(i).
-added a macro to determine if the index of a gene is part of the
conformation, i.e. a torsion gene. (is_conformation_index(i))
----------------------------
setflags.cc
setflags.h
----------------------------
CHANGE:
-added include banner to get to show_warranty and show_copyright
-added -C for copyright notice
-updated command line arguments including --version
-pass version_num to setflags
-removed command mode
-added setlinebuf to ensure output even if program crashes
----------------------------
simanneal.cc
----------------------------
CHANGE:
-updated the summations for the econf[] array that is used in the
analysis() function, and which is reported in the clustering
histogram. These summations needed to be updated to be able to
handle the "ad4_unbound_model" properly; in this model, the
unbound energy must be updated after each docking has finished,
to match the internal energy at the end of the docking.
----------------------------
stack.cc
----------------------------
NEW FEATURE:
-Added new code to handle integer stacks, kindly contributed by
Mike Pique. Added new code to test the stack code.
----------------------------
support.cc
support.h
----------------------------
NEW FEATURE:
-changed so now Individual does mapping of its genotype into
its phenotype and inverse_mapping of its phenotype into its
genotype; in both cases returns a reference to itself;
added a check for self-assignment
-improved bounds checking in heap sort (Population::msort)
-added <stdlib.h> for exit(), which needs to be included on some(?)
systems.
-added "end_of_branch[MAX_TORS]" to the Population class, the
logic being that every Individual in the Population is the same,
so rather than add the overhead to all the Individuals, we added
it to the Population. Also introducted two new methods, set_eob()
and get_eob(), to set the end_of_branch[] array, and get values
given a key torsion number. These changes are to support the
new "Branch Crossover mode".
----------------------------
usage.cc
----------------------------
CHANGE:
-updated command line arguments including --version
----------------------------
version.h
----------------------------
CHANGE:
-pass version_num to setflags
-version numbers changed to match autoconf version numbers.
----------------------------
writePDBQT.cc
----------------------------
CHANGE:
-correction to handling of 2 letter atom names provided by Stefano Forli
-uses calculateBindingEnergies so that if AD4.1_Bound.dat is
used, the internal energy of the unbound state can be set to
that of the docked state.
-to accommodate writing names of atoms with 2 character elements
correctly, increased by one indicies on lines 114: 14->15,
9->10; 132 and 133: 14->15, 9->10;280 and 281:13->14;lines
288 and 289:13->12, 8->9; line 326:14->15; lines 328 and 329:13->14
|