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AutoDock 4.2.2.1 Release Notes
=============================================================================
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.
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
=============================================================================
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
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.
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
=============================================================================
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
AutoDock Vina 1.0 released!