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RxDock
RxDock
Commits
f4e71b1c
Commit
f4e71b1c
authored
Nov 15, 2019
by
Vedran Miletić
Browse files
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Fixed linking of rb* commands with MSVC
parent
4674e3eb
Changes
26
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26 changed files
with
112 additions
and
92 deletions
+112
-92
include/Rbt.h
include/Rbt.h
+9
-9
include/RbtAtom.h
include/RbtAtom.h
+13
-10
include/RbtBaseFileSource.h
include/RbtBaseFileSource.h
+4
-4
include/RbtBaseMolecularFileSink.h
include/RbtBaseMolecularFileSink.h
+2
-1
include/RbtBiMolWorkSpace.h
include/RbtBiMolWorkSpace.h
+1
-1
include/RbtBond.h
include/RbtBond.h
+5
-4
include/RbtCrdFileSink.h
include/RbtCrdFileSink.h
+2
-1
include/RbtDockingSite.h
include/RbtDockingSite.h
+13
-9
include/RbtElementFileSource.h
include/RbtElementFileSource.h
+1
-1
include/RbtFilter.h
include/RbtFilter.h
+6
-6
include/RbtMOEGrid.h
include/RbtMOEGrid.h
+8
-6
include/RbtModel.h
include/RbtModel.h
+11
-11
include/RbtParamHandler.h
include/RbtParamHandler.h
+2
-1
include/RbtParameterFileSource.h
include/RbtParameterFileSource.h
+5
-4
include/RbtPrincipalAxes.h
include/RbtPrincipalAxes.h
+1
-1
include/RbtPsfFileSink.h
include/RbtPsfFileSink.h
+2
-1
include/RbtRand.h
include/RbtRand.h
+2
-2
include/RbtRealGrid.h
include/RbtRealGrid.h
+7
-7
include/RbtSFFactory.h
include/RbtSFFactory.h
+1
-1
include/RbtSiteMapperFactory.h
include/RbtSiteMapperFactory.h
+2
-2
include/RbtTransformFactory.h
include/RbtTransformFactory.h
+1
-1
include/RbtTriposAtomType.h
include/RbtTriposAtomType.h
+4
-4
include/RbtVdwGridSF.h
include/RbtVdwGridSF.h
+3
-0
include/RbtWorkSpace.h
include/RbtWorkSpace.h
+4
-4
src/exe/rbconvgrid.cxx
src/exe/rbconvgrid.cxx
+1
-1
src/lib/RbtVdwGridSF.cxx
src/lib/RbtVdwGridSF.cxx
+2
-0
No files found.
include/Rbt.h
View file @
f4e71b1c
...
...
@@ -50,15 +50,15 @@ std::string GetRbtHome();
// GetCopyright - returns legalese statement
std
::
string
GetCopyright
();
// GetVersion - returns current library version
std
::
string
GetVersion
();
RBTDLL_EXPORT
std
::
string
GetVersion
();
// GetBuildNum - returns current library build number
std
::
string
GetBuild
();
RBTDLL_EXPORT
std
::
string
GetBuild
();
// GetProduct - returns library product name
std
::
string
GetProduct
();
RBTDLL_EXPORT
std
::
string
GetProduct
();
// GetTime - returns current time and date as an RbtString
std
::
string
GetTime
();
// GetCurrentWorkingDirectory - returns current working directory
std
::
string
GetCurrentWorkingDirectory
();
RBTDLL_EXPORT
std
::
string
GetCurrentWorkingDirectory
();
//
////////////////////////////////////////////////////////////////
...
...
@@ -116,9 +116,8 @@ RbtSegmentMap SegmentDiffMap(const RbtSegmentMap &map1,
// DM 30 Mar 1999
// Converts (comma)-delimited string to string list (similar to
// ConvertStringToSegmentMap, but returns list not map)
RbtStringList
ConvertDelimitedStringToList
(
const
std
::
string
&
strValues
,
const
std
::
string
&
strDelimiter
=
","
);
RBTDLL_EXPORT
RbtStringList
ConvertDelimitedStringToList
(
const
std
::
string
&
strValues
,
const
std
::
string
&
strDelimiter
=
","
);
// Converts string list to (comma)-delimited string (inverse of above)
std
::
string
ConvertListToDelimitedString
(
const
RbtStringList
&
listOfValues
,
const
std
::
string
&
strDelimiter
=
","
);
...
...
@@ -148,8 +147,9 @@ PrintStdHeader(std::ostream &s, const std::string &strExecutable = "");
typedef
int
streamsize
;
//#endif
void
WriteWithThrow
(
std
::
ostream
&
ostr
,
const
char
*
p
,
streamsize
n
);
void
ReadWithThrow
(
std
::
istream
&
istr
,
char
*
p
,
streamsize
n
);
RBTDLL_EXPORT
void
WriteWithThrow
(
std
::
ostream
&
ostr
,
const
char
*
p
,
streamsize
n
);
RBTDLL_EXPORT
void
ReadWithThrow
(
std
::
istream
&
istr
,
char
*
p
,
streamsize
n
);
}
// namespace Rbt
...
...
include/RbtAtom.h
View file @
f4e71b1c
...
...
@@ -64,6 +64,7 @@ public:
RBTDLL_EXPORT
RbtAtom
();
// Constructor supplying all 2-D parameters
RBTDLL_EXPORT
RbtAtom
(
int
nAtomId
,
int
nAtomicNo
=
6
,
std
::
string
strAtomName
=
"C"
,
std
::
string
strSubunitId
=
"1"
,
std
::
string
strSubunitName
=
"RES"
,
std
::
string
strSegmentName
=
"SEG1"
,
...
...
@@ -87,7 +88,8 @@ public:
// Insertion operator (primarily for debugging)
// Note: needs to be friend so can access atom private data
// without using the accessor functions
friend
std
::
ostream
&
operator
<<
(
std
::
ostream
&
s
,
const
RbtAtom
&
atom
);
RBTDLL_EXPORT
friend
std
::
ostream
&
operator
<<
(
std
::
ostream
&
s
,
const
RbtAtom
&
atom
);
// Virtual function for dumping atom details to an output stream
// Derived classes (e.g. pseudoatom) can override if required
...
...
@@ -116,8 +118,9 @@ public:
void
SetAtomName
(
const
std
::
string
strAtomName
)
{
m_strAtomName
=
strAtomName
;
}
std
::
string
GetFullAtomName
()
const
;
// Returns composite of segment name,
// subunit id and name, and atom name
RBTDLL_EXPORT
std
::
string
GetFullAtomName
()
const
;
// Returns composite of segment name,
// subunit id and name, and atom name
// SubunitId
std
::
string
GetSubunitId
()
const
{
return
m_strSubunitId
;
}
...
...
@@ -449,7 +452,7 @@ public:
class
isAtomHBondAcceptor
:
public
std
::
unary_function
<
RbtAtom
*
,
bool
>
{
public:
explicit
isAtomHBondAcceptor
()
{}
bool
operator
()(
const
RbtAtom
*
)
const
;
RBTDLL_EXPORT
bool
operator
()(
const
RbtAtom
*
)
const
;
};
// Is atom a H-Bond Donor ?
...
...
@@ -458,7 +461,7 @@ public:
class
isAtomHBondDonor
:
public
std
::
unary_function
<
RbtAtom
*
,
bool
>
{
public:
explicit
isAtomHBondDonor
()
{}
bool
operator
()(
const
RbtAtom
*
)
const
;
RBTDLL_EXPORT
bool
operator
()(
const
RbtAtom
*
)
const
;
};
// Is atom formally charged ?
...
...
@@ -514,7 +517,7 @@ public:
class
isPiAtom
:
public
std
::
unary_function
<
RbtAtom
*
,
bool
>
{
public:
explicit
isPiAtom
()
{}
bool
operator
()(
const
RbtAtom
*
)
const
;
RBTDLL_EXPORT
bool
operator
()(
const
RbtAtom
*
)
const
;
};
// Is atomic number equal to n ?
...
...
@@ -785,8 +788,8 @@ public:
// DM 19 Oct 2001 - extend to all common metals (Na,Mg,K->Zn)
class
isAtomMetal
:
public
std
::
unary_function
<
RbtAtom
*
,
bool
>
{
public:
explicit
isAtomMetal
();
bool
operator
()(
const
RbtAtom
*
pAtom
)
const
;
RBTDLL_EXPORT
explicit
isAtomMetal
();
RBTDLL_EXPORT
bool
operator
()(
const
RbtAtom
*
pAtom
)
const
;
};
// DM 21 Jul 1999 Is atom lipophilic ?
...
...
@@ -804,7 +807,7 @@ class isAtomLipophilic : public std::unary_function<RbtAtom *, bool> {
public:
explicit
isAtomLipophilic
()
:
isSP3
(
RbtAtom
::
SP3
),
isSP2
(
RbtAtom
::
SP2
),
isO
(
8
),
isN
(
7
)
{}
bool
operator
()(
RbtAtom
*
pAtom
)
const
;
RBTDLL_EXPORT
bool
operator
()(
RbtAtom
*
pAtom
)
const
;
};
//////////////////////////////
...
...
@@ -1127,7 +1130,7 @@ RbtAtomList GetBondedAtomList(const RbtBondMap &bondMap);
// above If spAtom can be dynamically_casted to an RbtPseudoAtom, these return
// the constituent atom list for the pseudoatom
unsigned
int
GetNumBondedAtoms
(
const
RbtAtom
*
pAtom
);
RbtAtomList
GetBondedAtomList
(
const
RbtAtom
*
pAtom
);
R
BTDLL_EXPORT
R
btAtomList
GetBondedAtomList
(
const
RbtAtom
*
pAtom
);
// Binary
...
...
include/RbtBaseFileSource.h
View file @
f4e71b1c
...
...
@@ -40,21 +40,21 @@ public:
// Public methods
std
::
string
GetFileName
();
RBTDLL_EXPORT
std
::
string
GetFileName
();
// void SetFileName(const char* fileName);
void
SetFileName
(
const
std
::
string
&
fileName
);
// Status and StatusOK parse the file to check for errors
bool
StatusOK
();
RbtError
Status
();
R
BTDLL_EXPORT
R
btError
Status
();
// FileStatus and FileStatusOK just try and read the file
bool
FileStatusOK
();
RBTDLL_EXPORT
bool
FileStatusOK
();
RbtError
FileStatus
();
// Multi-record methods
bool
isMultiRecordSupported
()
{
return
m_bMultiRec
;
}
void
NextRecord
();
RBTDLL_EXPORT
void
NextRecord
();
void
Rewind
();
protected:
...
...
include/RbtBaseMolecularFileSink.h
View file @
f4e71b1c
...
...
@@ -44,7 +44,8 @@ public:
// DM 21 Apr 1999 - if bUseModelSegmentNames is true, the model segment names
// are rendered if bUseModelSegmentNames is false, incremental numeric segment
// IDs are rendered
void
SetModel
(
RbtModelPtr
spModel
,
bool
bUseModelSegmentNames
=
false
);
RBTDLL_EXPORT
void
SetModel
(
RbtModelPtr
spModel
,
bool
bUseModelSegmentNames
=
false
);
// DM 21 Apr 1999 - change the segment ID counter
// Set to nSegmentId-1 as the counter gets incremented before each Render
...
...
include/RbtBiMolWorkSpace.h
View file @
f4e71b1c
...
...
@@ -42,7 +42,7 @@ public:
RBTDLL_EXPORT
RbtModelPtr
GetReceptor
()
const
;
RBTDLL_EXPORT
RbtModelPtr
GetLigand
()
const
;
RBTDLL_EXPORT
RbtModelList
GetSolvent
()
const
;
bool
hasSolvent
()
const
;
RBTDLL_EXPORT
bool
hasSolvent
()
const
;
RBTDLL_EXPORT
void
SetReceptor
(
RbtModelPtr
spReceptor
);
RBTDLL_EXPORT
void
SetLigand
(
RbtModelPtr
spLigand
);
RBTDLL_EXPORT
void
SetSolvent
(
RbtModelList
solventList
);
...
...
include/RbtBond.h
View file @
f4e71b1c
...
...
@@ -44,7 +44,8 @@ public:
// Insertion operator (primarily for debugging)
// Note: needs to be friend so can access bond private data
// without using the accessor functions
friend
std
::
ostream
&
operator
<<
(
std
::
ostream
&
s
,
const
RbtBond
&
bond
);
RBTDLL_EXPORT
friend
std
::
ostream
&
operator
<<
(
std
::
ostream
&
s
,
const
RbtBond
&
bond
);
////////////////////////////////////////
// Public accessor functions
...
...
@@ -161,14 +162,14 @@ public:
class
isBondToNH3
:
public
RbtBondUnaryPredicate
{
public:
explicit
isBondToNH3
()
{}
bool
operator
()(
RbtBond
*
)
const
;
RBTDLL_EXPORT
bool
operator
()(
RbtBond
*
)
const
;
};
// Is bond to a terminal OH group?
class
isBondToOH
:
public
RbtBondUnaryPredicate
{
public:
explicit
isBondToOH
()
{}
bool
operator
()(
RbtBond
*
pBond
)
const
;
RBTDLL_EXPORT
bool
operator
()(
RbtBond
*
pBond
)
const
;
};
// DM 1 April 1999
...
...
@@ -210,7 +211,7 @@ public:
class
isBondAmide
:
public
RbtBondUnaryPredicate
{
public:
explicit
isBondAmide
()
{}
bool
operator
()(
RbtBond
*
)
const
;
RBTDLL_EXPORT
bool
operator
()(
RbtBond
*
)
const
;
};
////////////////////////////////////////////
...
...
include/RbtCrdFileSink.h
View file @
f4e71b1c
...
...
@@ -22,7 +22,8 @@ public:
////////////////////////////////////////
// Constructors/destructors
// RbtCrdFileSink(const char* fileName, RbtModelPtr spModel);
RbtCrdFileSink
(
const
std
::
string
&
fileName
,
RbtModelPtr
spModel
);
RBTDLL_EXPORT
RbtCrdFileSink
(
const
std
::
string
&
fileName
,
RbtModelPtr
spModel
);
virtual
~
RbtCrdFileSink
();
// Default destructor
...
...
include/RbtDockingSite.h
View file @
f4e71b1c
...
...
@@ -45,42 +45,46 @@ public:
// Class type string
static
std
::
string
_CT
;
RbtDockingSite
(
const
RbtCavityList
&
cavList
,
double
border
);
R
BTDLL_EXPORT
R
btDockingSite
(
const
RbtCavityList
&
cavList
,
double
border
);
RBTDLL_EXPORT
RbtDockingSite
(
std
::
istream
&
istr
);
// Destructor
virtual
~
RbtDockingSite
();
// Insertion operator
friend
std
::
ostream
&
operator
<<
(
std
::
ostream
&
s
,
const
RbtDockingSite
&
site
);
RBTDLL_EXPORT
friend
std
::
ostream
&
operator
<<
(
std
::
ostream
&
s
,
const
RbtDockingSite
&
site
);
// Virtual function for dumping docking site details to an output stream
// Derived classes can override if required
virtual
void
Print
(
std
::
ostream
&
s
)
const
;
// Public methods
void
Read
(
std
::
istream
&
istr
);
// Reads docking site from binary stream
void
Write
(
std
::
ostream
&
ostr
);
// Writes docking site to binary stream
void
Read
(
std
::
istream
&
istr
);
// Reads docking site from binary stream
RBTDLL_EXPORT
void
Write
(
std
::
ostream
&
ostr
);
// Writes docking site to binary stream
RbtRealGridPtr
GetGrid
();
R
BTDLL_EXPORT
R
btRealGridPtr
GetGrid
();
double
GetBorder
()
const
{
return
m_border
;
}
RbtCoord
GetMinCoord
()
const
{
return
m_minCoord
;
}
RbtCoord
GetMaxCoord
()
const
{
return
m_maxCoord
;
}
RbtCavityList
GetCavityList
()
const
{
return
m_cavityList
;
}
int
GetNumCavities
()
const
{
return
m_cavityList
.
size
();
}
double
GetVolume
()
const
;
// returns total volume of all cavities in A^3
RBTDLL_EXPORT
double
GetVolume
()
const
;
// returns total volume of all cavities in A^3
// Returns the combined coord lists of all the cavities
void
GetCoordList
(
RbtCoordList
&
retVal
)
const
;
// Filters an atom list according to distance from the cavity coords
// Only returns atoms within minDist and maxDist from cavity
R
btAtomList
GetAtomList
(
const
RbtAtomList
&
atomList
,
double
minD
ist
,
double
maxDist
);
R
BTDLL_EXPORT
RbtAtomList
GetAtomList
(
const
RbtAtomList
&
atomL
ist
,
double
minDist
,
double
maxDist
);
// Filters an atom list according to distance from the cavity coords
// Only returns atoms within maxDist from cavity
// This version does not require the cavity grid
RbtAtomList
GetAtomList
(
const
RbtAtomList
&
atomList
,
double
maxDist
);
RBTDLL_EXPORT
RbtAtomList
GetAtomList
(
const
RbtAtomList
&
atomList
,
double
maxDist
);
// Returns the count of atoms within minDist and maxDist from cavity
unsigned
int
GetNumAtoms
(
const
RbtAtomList
&
atomList
,
double
minDist
,
double
maxDist
);
...
...
include/RbtElementFileSource.h
View file @
f4e71b1c
...
...
@@ -54,7 +54,7 @@ public:
////////////////////////////////////////
// Public methods
std
::
string
GetTitle
();
RBTDLL_EXPORT
std
::
string
GetTitle
();
std
::
string
GetVersion
();
unsigned
int
GetNumElements
();
RbtStringList
GetElementNameList
();
// List of element names
...
...
include/RbtFilter.h
View file @
f4e71b1c
...
...
@@ -26,7 +26,7 @@ class RbtFilterExpressionVisitor;
class
RbtFilter
:
public
RbtBaseObject
{
public:
static
std
::
string
_CT
;
RbtFilter
(
std
::
string
strfilter
,
bool
filter
=
false
);
R
BTDLL_EXPORT
R
btFilter
(
std
::
string
strfilter
,
bool
filter
=
false
);
///////////////////
// Destructor
//////////////////
...
...
@@ -35,11 +35,11 @@ public:
// Notify observer that subject has changed
virtual
void
Update
(
RbtSubject
*
theChangedSubject
);
void
SetupReceptor
();
// Called by Update when receptor is changed
void
SetupLigand
();
// Called by Update when ligand is changed
void
SetupScore
();
// Called by Update when either model has changed
bool
Write
();
// Output conformation?
bool
Terminate
();
// Finished with ligand?
void
SetupReceptor
();
// Called by Update when receptor is changed
void
SetupLigand
();
// Called by Update when ligand is changed
void
SetupScore
();
// Called by Update when either model has changed
RBTDLL_EXPORT
bool
Write
();
// Output conformation?
RBTDLL_EXPORT
bool
Terminate
();
// Finished with ligand?
RbtModelPtr
GetReceptor
()
const
;
RbtModelPtr
GetLigand
()
const
;
void
SetMaxNRuns
(
int
n
)
{
maxnruns
=
n
;
}
...
...
include/RbtMOEGrid.h
View file @
f4e71b1c
...
...
@@ -48,7 +48,7 @@ class RbtMOEGridPoint {
public:
// default ctor with a 1D gridpoint at 0.0 value 1.0
// see also default ctor for the shape and data vector below
RbtMOEGridPoint
();
R
BTDLL_EXPORT
R
btMOEGridPoint
();
// parametrized ctor when supplying data as a vector + value pair
RbtMOEGridPoint
(
std
::
vector
<
double
>
,
double
);
// parametrized ctor getting coord values from RbtCoord (default 3D
...
...
@@ -87,7 +87,8 @@ public:
// parametrized ctor receives grid as the origin vector, the extent
// vector and stepsize
RbtMOEGridShape
(
std
::
vector
<
double
>
,
std
::
vector
<
double
>
,
double
);
RBTDLL_EXPORT
RbtMOEGridShape
(
std
::
vector
<
double
>
,
std
::
vector
<
double
>
,
double
);
const
std
::
vector
<
double
>
&
GetOrigin
()
{
return
origin
;
}
const
std
::
vector
<
double
>
&
GetExtents
()
{
return
extents
;
}
...
...
@@ -109,7 +110,7 @@ class RbtMOEGrid {
RbtCoord
c_min
,
c_max
;
// current extent min and max coords
public:
// default ctor
RbtMOEGrid
();
R
BTDLL_EXPORT
R
btMOEGrid
();
// parameterised ctor for a single grid
// pass shape, data and outfilename
RbtMOEGrid
(
RbtMOEGridShape
&
,
RbtMOEGridData
&
,
std
::
string
);
...
...
@@ -119,14 +120,15 @@ public:
void
SetData
(
RbtMOEGridData
&
a_data
)
{
myData
=
a_data
;
}
void
SetOutputFileName
(
std
::
string
&
a_filename
)
{
stream_name
=
a_filename
;
}
// methods to calculate grid extents
void
CalculateCommonExtents
(
std
::
vector
<
std
::
string
>
strPrmFiles
);
// for all
void
GetDockingSiteExtents
(
std
::
string
&
a_strPrmFile
);
// for a single
RBTDLL_EXPORT
void
CalculateCommonExtents
(
std
::
vector
<
std
::
string
>
strPrmFiles
);
// for all
void
GetDockingSiteExtents
(
std
::
string
&
a_strPrmFile
);
// for a single
// get methods
RbtCoord
GetMinExtents
()
{
return
min
;
}
RbtCoord
GetMaxExtents
()
{
return
max
;
}
// iofstream methods
long
WriteGrid
(
RBTDLL_EXPORT
long
WriteGrid
(
std
::
ios_base
::
openmode
mode
);
// returns the number of points written
long
ReadGrid
();
// ditto (fields read)
};
...
...
include/RbtModel.h
View file @
f4e71b1c
...
...
@@ -32,11 +32,11 @@ public:
//////////////////////
// Read topology from RbtMolecularFileSource, and coordinates if supported by
// source
RbtModel
(
RbtBaseMolecularFileSource
*
pMolSource
);
R
BTDLL_EXPORT
R
btModel
(
RbtBaseMolecularFileSource
*
pMolSource
);
//(Fairly) temporary constructor taking arbitrary atom and bond lists
// Use with caution
RbtModel
(
RbtAtomList
&
atomList
,
RbtBondList
&
bondList
);
R
BTDLL_EXPORT
R
btModel
(
RbtAtomList
&
atomList
,
RbtBondList
&
bondList
);
// Default destructor
virtual
~
RbtModel
();
...
...
@@ -89,14 +89,14 @@ public:
// Query as to whether a particular data field name is present
bool
isDataFieldPresent
(
const
std
::
string
&
strDataField
)
const
;
// Get a particular data value
RbtVariant
GetDataValue
(
const
std
::
string
&
strDataField
)
const
;
R
BTDLL_EXPORT
R
btVariant
GetDataValue
(
const
std
::
string
&
strDataField
)
const
;
// Set a data value (replaces existing value if field name already exists)
void
SetDataValue
(
const
std
::
string
&
strDataField
,
const
RbtVariant
&
dataValue
);
RBTDLL_EXPORT
void
SetDataValue
(
const
std
::
string
&
strDataField
,
const
RbtVariant
&
dataValue
);
// Removes a data field completely from the data map
void
ClearDataField
(
const
std
::
string
&
strDataField
);
// Removes all data fields starting with a given prefix from the data map
void
ClearAllDataFields
(
const
std
::
string
&
strDataFieldPrefix
);
RBTDLL_EXPORT
void
ClearAllDataFields
(
const
std
::
string
&
strDataFieldPrefix
);
// Removes all data fields from the data map
void
ClearAllDataFields
();
...
...
@@ -143,22 +143,22 @@ public:
void
Rotate
(
const
RbtVector
&
axis
,
double
thetaDeg
,
const
RbtCoord
&
center
);
// Rotate around a given bond by theta degrees (spins both ends of the bond in
// opposite directions)
void
RotateBond
(
RbtBondPtr
spBond
,
double
thetaDeg
);
RBTDLL_EXPORT
void
RotateBond
(
RbtBondPtr
spBond
,
double
thetaDeg
);
// DM 09 Feb 1999 - Rotate around a given bond by theta degrees, keeping the
// given atom fixed (only spins the other end of the bond)
void
RotateBond
(
RbtBondPtr
spBond
,
double
thetaDeg
,
RbtAtomPtr
spFixedAtom
);
// DM 25 Feb 1999 - Rotate around a given bond by theta degrees, only spinning
// one end of the bond If bSwap is false, spins the end bonded to atom2 in the
// bond If bSwap is true, spins the end bonded to atom1 in the bond
void
RotateBond
(
RbtBondPtr
spBond
,
double
thetaDeg
,
bool
bSwap
);
RBTDLL_EXPORT
void
RotateBond
(
RbtBondPtr
spBond
,
double
thetaDeg
,
bool
bSwap
);
// DM 8 Feb 1999
void
SaveCoords
(
const
std
::
string
&
coordName
=
""
);
void
RevertCoords
(
const
std
::
string
&
coordName
=
""
);
RBTDLL_EXPORT
void
RevertCoords
(
const
std
::
string
&
coordName
=
""
);
RbtStringIntMap
GetSavedCoordNames
()
const
{
return
m_coordNames
;
}
int
GetNumSavedCoords
()
const
{
return
m_coordNames
.
size
();
}
int
GetCurrentCoords
()
const
{
return
m_currentCoord
;
}
void
RevertCoords
(
int
);
RBTDLL_EXPORT
void
RevertCoords
(
int
);
// Returns center of mass of model
RbtCoord
GetCenterOfMass
()
const
;
...
...
@@ -167,7 +167,7 @@ public:
// DM 9 Nov 1999
// Returns total atomic mass (molecular weight) for the model
double
GetTotalAtomicMass
()
const
;
RBTDLL_EXPORT
double
GetTotalAtomicMass
()
const
;
// DM 14 Apr 1999 - principal axes methods
// Return principal axes and center of mass for the model
...
...
include/RbtParamHandler.h
View file @
f4e71b1c
...
...
@@ -92,6 +92,7 @@ private:
// Non-member functions
// Insertion operator (primarily for debugging)
std
::
ostream
&
operator
<<
(
std
::
ostream
&
s
,
const
RbtParamHandler
&
ph
);
RBTDLL_EXPORT
std
::
ostream
&
operator
<<
(
std
::
ostream
&
s
,
const
RbtParamHandler
&
ph
);
#endif //_RBTPARAMHANDLER_H_
include/RbtParameterFileSource.h
View file @
f4e71b1c
...
...
@@ -29,7 +29,7 @@ public:
////////////////////////////////////////
// Public methods
std
::
string
GetTitle
();
RBTDLL_EXPORT
std
::
string
GetTitle
();
std
::
string
GetVersion
();
// DM 06 June 2000 - limit #parameters to those in current section
unsigned
int
GetNumParameters
();
...
...
@@ -37,11 +37,12 @@ public:
// RbtStringDoubleMap GetParameterMap();
// DM 12 Feb 1999 - only return the list of parameter names, not their values
// DM 06 Jun 2000 - limits params to those in named section
RbtStringList
GetParameterList
();
R
BTDLL_EXPORT
R
btStringList
GetParameterList
();
// DM 4 Feb 1999 Get a particular named parameter value as a double
double
GetParameterValue
(
const
std
::
string
&
strParamName
);
// DM 12 Feb 1999 Get a particular named parameter value as a string
std
::
string
GetParameterValueAsString
(
const
std
::
string
&
strParamName
);
RBTDLL_EXPORT
std
::
string
GetParameterValueAsString
(
const
std
::
string
&
strParamName
);
// DM 11 Feb 1999 Check if parameter is present
bool
isParameterPresent
(
const
std
::
string
&
strParamName
);
...
...
@@ -55,7 +56,7 @@ public:
int
GetNumSections
();
// Number of named sections
RbtStringList
GetSectionList
();
// List of section names
std
::
string
GetSection
()
const
;
// Get current section name
void
RBTDLL_EXPORT
void
SetSection
(
const
std
::
string
&
strSection
=
""
);
// Set current section name
protected:
...
...
include/RbtPrincipalAxes.h
View file @
f4e71b1c
...
...
@@ -44,7 +44,7 @@ namespace Rbt {
RBTDLL_EXPORT
RbtPrincipalAxes
GetPrincipalAxes
(
const
RbtAtomList
&
atomList
);
// Calculates principal axes and center of mass for the coords in the coord list
// (assumes all masses=1)
RbtPrincipalAxes
GetPrincipalAxes
(
const
RbtCoordList
&
coordList
);
R
BTDLL_EXPORT
R
btPrincipalAxes
GetPrincipalAxes
(
const
RbtCoordList
&
coordList
);
// Special case for water
RbtPrincipalAxes
GetSolventPrincipalAxes
(
const
RbtAtomPtr
&
oAtom
,
const
RbtAtomPtr
&
h1Atom
,
...
...
include/RbtPsfFileSink.h
View file @
f4e71b1c
...
...
@@ -22,7 +22,8 @@ public:
////////////////////////////////////////
// Constructors/destructors
// RbtPsfFileSink(const char* fileName, RbtModelPtr spModel);
RbtPsfFileSink
(
const
std
::
string
&
fileName
,
RbtModelPtr
spModel
);
RBTDLL_EXPORT
RbtPsfFileSink
(
const
std
::
string
&
fileName
,
RbtModelPtr
spModel
);
virtual
~
RbtPsfFileSink
();
// Default destructor
...
...
include/RbtRand.h
View file @
f4e71b1c
...
...
@@ -33,11 +33,11 @@ public:
// Public methods
// Seed the random number generator
void
Seed
(
int
seed
=
0
);
RBTDLL_EXPORT
void
Seed
(
int
seed
=
0
);
// Seed the random number generator from the system clock
void
SeedFromClock
();
// Returns current seed
int
GetSeed
();
RBTDLL_EXPORT
int
GetSeed
();
// Get a random double between 0 and 1 (inlined)
double
GetRandom01
()
{
return
m_rand
.
fdraw
();
}
// Get a random integer between 0 and nMax-1
...
...
include/RbtRealGrid.h
View file @
f4e71b1c
...
...
@@ -25,12 +25,12 @@ public:
////////////////////////////////////////
// Constructors/destructors
// Construct a NXxNYxNZ grid running from gridMin at gridStep resolution
RbtRealGrid
(
const
RbtCoord
&
gridMin
,
const
RbtCoord
&
gridStep
,
unsigned
int
NX
,
unsigned
int
NY
,
unsigned
int
NZ
,
unsigned
int
NPad
=
0
);
R
BTDLL_EXPORT
R
btRealGrid
(
const
RbtCoord
&
gridMin
,
const
RbtCoord
&
gridStep
,
unsigned
int
NX
,
unsigned
int
NY
,
unsigned
int
NZ
,
unsigned
int
NPad
=
0
);
// Constructor reading all params from binary stream
RbtRealGrid
(
std
::
istream
&
istr
);
R
BTDLL_EXPORT
R
btRealGrid
(
std
::
istream
&
istr
);
~
RbtRealGrid
();
// Default destructor
...
...
@@ -85,7 +85,7 @@ public:
// DM 20 Jul 2000 - get values smoothed by trilinear interpolation
// D. Oberlin and H.A. Scheraga, J. Comp. Chem. (1998) 19, 71.
double
GetSmoothedValue
(
const
RbtCoord
&
c
)
const
;
RBTDLL_EXPORT
double
GetSmoothedValue
(
const
RbtCoord
&
c
)
const
;
void
SetValue
(
const
RbtCoord
&
c
,
double
val
)
{
if
(
isValid
(
c
))
...
...
@@ -101,7 +101,7 @@ public:
}
// Set all grid points to the given value
void
SetAllValues
(
double
val
);
RBTDLL_EXPORT
void
SetAllValues
(
double
val
);
// Replaces all grid points with a given value (+/- tolerance) with newVal
void
ReplaceValue
(
double
oldVal
,
double
newVal
)
{
ReplaceValueRange
(
oldVal
-
m_tol
,
oldVal
+
m_tol
,
newVal
);
...
...
@@ -164,7 +164,7 @@ public:
/////////////////////////
// Dump grid in a format readable by Insight
void
PrintInsightGrid
(
std
::
ostream
&
s
)
const
;
RBTDLL_EXPORT
void
PrintInsightGrid
(
std
::
ostream
&
s
)
const
;
protected:
////////////////////////////////////////
...
...
include/RbtSFFactory.h
View file @
f4e71b1c
...
...
@@ -28,7 +28,7 @@ public:
////////////////////////////////////////
// Constructors/destructors
RbtSFFactory
();
// Default constructor
R
BTDLL_EXPORT
R
btSFFactory
();
// Default constructor
virtual
~
RbtSFFactory
();
// Default destructor
...
...
include/RbtSiteMapperFactory.h
View file @
f4e71b1c
...
...
@@ -27,8 +27,8 @@ public:
////////////////////////////////////////
// Constructors/destructors
R
btSiteMapperFactory
();
// Default constructor
virtual
~
RbtSiteMapperFactory
();
// Default destructor
R
BTDLL_EXPORT
RbtSiteMapperFactory
();
// Default constructor
virtual
~
RbtSiteMapperFactory
();
// Default destructor
////////////////////////////////////////
// Public methods
...
...
include/RbtTransformFactory.h
View file @
f4e71b1c
...
...
@@ -29,7 +29,7 @@ public:
////////////////////////////////////////
// Constructors/destructors
RbtTransformFactory
();
// Default constructor
R
BTDLL_EXPORT
R
btTransformFactory
();
// Default constructor
virtual
~
RbtTransformFactory
();
// Default destructor
...
...
include/RbtTriposAtomType.h
View file @
f4e71b1c
...
...
@@ -84,8 +84,8 @@ public:
////////////////////////////////////////
// Constructors/destructors
RbtTriposAtomType
();
virtual
~
RbtTriposAtomType
();
R
BTDLL_EXPORT
R
btTriposAtomType
();
RBTDLL_EXPORT
virtual
~
RbtTriposAtomType
();
////////////////////////////////////////
// Public methods
...
...
@@ -96,13 +96,13 @@ public:
// are used
eType
operator
()(
RbtAtom
*
pAtom
,
bool
useExtendedTypes
=
false
)
const
;
// Converts Tripos type to string
std
::
string
Type2Str
(
eType
)
const
;
RBTDLL_EXPORT
std
::
string
Type2Str
(
eType
)
const
;
// Get hybridisation from Tripos type
int
Type2Hybrid
(
eType
)
const
;
// Get atomic number from Tripos type
int
Type2AtomicNo
(
eType
)
const
;
// Converts string to Tripos type
eType
Str2Type
(
const
std
::
string
&
)
const
;
RBTDLL_EXPORT
eType
Str2Type
(
const
std
::
string
&
)
const
;
protected:
////////////////////////////////////////
...
...
include/RbtVdwGridSF.h
View file @
f4e71b1c
...
...
@@ -22,6 +22,9 @@ class RbtVdwGridSF : public RbtBaseInterSF {
public:
// Class type string
static
std
::
string
_CT
;
RBTDLL_EXPORT
static
std
::
string
&
GetCt
();
// Parameter names
static
std
::
string
_GRID
;
// Suffix for grid filename
static
std
::
string
_SMOOTHED
;
// Controls whether to smooth the grid values
...
...
include/RbtWorkSpace.h
View file @
f4e71b1c
...
...
@@ -51,8 +51,8 @@ public:
////////////////
// Get/set workspace name
std
::
string
GetName
()
const
;
void
SetName
(
const
std
::
string
&
);
RBTDLL_EXPORT
std
::
string
GetName
()
const
;
RBTDLL_EXPORT
void
SetName
(
const
std
::
string
&
);
// Model handling
...
...
@@ -92,7 +92,7 @@ public:
virtual
void
Save
(
bool
bSaveScores
=
true
);
// Get/set the history file sink
RbtMolecularFileSinkPtr
GetHistorySink
()
const
;
void
SetHistorySink
(
RbtMolecularFileSinkPtr
);
RBTDLL_EXPORT
void
SetHistorySink
(
RbtMolecularFileSinkPtr
);
// Saves models to file sink
// If bSaveScores is true, write component scores also
// Base workspace does nothing
...
...
@@ -127,7 +127,7 @@ public:
// BGD 27 Jan 2003 - SetFilter automotically registers the Filter
// with the workspace
RbtFilterPtr
GetFilter
()
const
;
void
SetFilter
(
RbtFilterPtr
spFilter
);
RBTDLL_EXPORT
void
SetFilter
(
RbtFilterPtr
spFilter
);
protected:
////////////////////////////////////////
...
...
src/exe/rbconvgrid.cxx
View file @
f4e71b1c
...
...
@@ -88,7 +88,7 @@ int main(int argc, char *argv[]) {
// Add null character to end of string
header
[
length
]
=
'\0'
;
// Compare title with
bool
match
=
(
RbtVdwGridSF
::
_CT
==
header
);
bool
match
=
(
RbtVdwGridSF
::
GetCt
()
==
header
);
delete
[]
header
;
if
(
!
match
)
{
throw
RbtFileParseError
(
_WHERE_
,
...
...
src/lib/RbtVdwGridSF.cxx
View file @
f4e71b1c
...
...
@@ -19,6 +19,8 @@ std::string RbtVdwGridSF::_CT("RbtVdwGridSF");
std
::
string
RbtVdwGridSF
::
_GRID
(
"GRID"
);
std
::
string
RbtVdwGridSF
::
_SMOOTHED
(
"SMOOTHED"
);
std
::
string
&
RbtVdwGridSF
::
GetCt
()
{
return
_CT
;
}
// NB - Virtual base class constructor (RbtBaseSF) gets called first,
// implicit constructor for RbtBaseInterSF is called second
RbtVdwGridSF
::
RbtVdwGridSF
(
const
std
::
string
&
strName
)
...
...
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