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Add keywords to set default values for PDB occupancy/B-factor columns. (
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#812)

* Add bfacdefault and occdefault keywords for pdb out

* Revision bump for bfacdefault and occdefault keywords.

* Add bfacdefault and occdefault keywords to manual
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@drroe
drroe committed Apr 25, 2020
1 parent 0ab6d6d commit 38b0f8d
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22 changes: 21 additions & 1 deletion doc/cpptraj.lyx
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Expand Up @@ -15120,7 +15120,7 @@ only frames 2, 5, 6, and 7 from input.crd will be written to output.crd.
\begin_layout Subsubsection

\shape italic
Options for pdb format:
Options for pdb format
\end_layout

\begin_layout LyX-Code
Expand All @@ -15139,6 +15139,10 @@ Options for pdb format:
[include_ep] [conect] [keepext] [usecol21]
\end_layout

\begin_layout LyX-Code
[bfacdefault <#>] [occdefault <#>]
\end_layout

\begin_layout LyX-Code
[bfacdata <set>] [occdata <set>] [bfacbyres] [occbyres]
\end_layout
Expand Down Expand Up @@ -15240,6 +15244,22 @@ keepext Keep filename extension; write '<name>.<num>.<ext>' instead (implies
usecol21 Use column 21 for 4-letter residue names.
\end_layout

\begin_layout Description
bfacdefault
\begin_inset space ~
\end_inset

<#> Default value to use in B-factor column (default 0.0).
\end_layout

\begin_layout Description
occdefault
\begin_inset space ~
\end_inset

<#> Default value to use in occupancy column (default 1.0).
\end_layout

\begin_layout Description
bfacdata
\begin_inset space ~
Expand Down
79 changes: 45 additions & 34 deletions src/Traj_PDBfile.cpp
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Expand Up @@ -35,7 +35,9 @@ Traj_PDBfile::Traj_PDBfile() :
occdata_(0),
adpdata_(0),
bfacmax_(99.99),
occmax_(99.99)
occmax_(99.99),
bfacdefault_(0),
occdefault_(-1)
{}

//------------------------------------------------------------------------
Expand Down Expand Up @@ -180,33 +182,35 @@ int Traj_PDBfile::readFrame(int set, Frame& frameIn)
}

void Traj_PDBfile::WriteHelp() {
mprintf("\tdumpq : Write atom charge/GB radius in occupancy/B-factor columns (PQR format).\n"
"\tparse : Write atom charge/PARSE radius in occupancy/B-factor columns (PQR format).\n"
"\tvdw : Write atom charge/VDW radius in occupancy/B-factor columns (PQR format).\n"
"\tpdbres : Use PDB V3 residue names.\n"
"\tpdbatom : Use PDB V3 atom names.\n"
"\tpdbv3 : Use PDB V3 residue/atom names.\n"
"\tteradvance : Increment record (atom) # for TER records (default no).\n"
"\tterbyres : Print TER cards based on residue sequence instead of molecules.\n"
"\tpdbter : Print TER cards according to original PDB TER (if available).\n"
"\tnoter : Do not write TER cards.\n"
"\tmodel : Write to single file separated by MODEL records.\n"
"\tmulti : Write each frame to separate files.\n"
"\tchainid <c> : Write character 'c' in chain ID column.\n"
"\tsg <group> : Space group for CRYST1 record, only if box coordinates written.\n"
"\tinclude_ep : Include extra points.\n"
"\tconect : Write CONECT records using bond information.\n"
"\tkeepext : Keep filename extension; write '<name>.<num>.<ext>' instead (implies 'multi').\n"
"\tusecol21 : Use column 21 for 4-letter residue names.\n"
"\tbfacdata <set> : Use data in <set> for B-factor column.\n"
"\toccdata <set> : Use data in <set> for occupancy column.\n"
"\tbfacbyres : If specified assume X values in B-factor data set are residue numbers.\n"
"\toccbyres : If specified assume X values in occupancy data set are residue numbers.\n"
"\tbfacscale : If specified scale values in B-factor column between 0 and <bfacmax>.\n"
"\toccscale : If specified scale values in occupancy column between 0 and <occmax>.\n"
"\tbfacmax <max> : Max value for bfacscale.\n"
"\toccmax <max> : Max value for occscale.\n"
"\tadpdata <set> : Use data in <set> for anisotropic B-factors.\n"
mprintf("\tdumpq : Write atom charge/GB radius in occupancy/B-factor columns (PQR format).\n"
"\tparse : Write atom charge/PARSE radius in occupancy/B-factor columns (PQR format).\n"
"\tvdw : Write atom charge/VDW radius in occupancy/B-factor columns (PQR format).\n"
"\tpdbres : Use PDB V3 residue names.\n"
"\tpdbatom : Use PDB V3 atom names.\n"
"\tpdbv3 : Use PDB V3 residue/atom names.\n"
"\tteradvance : Increment record (atom) # for TER records (default no).\n"
"\tterbyres : Print TER cards based on residue sequence instead of molecules.\n"
"\tpdbter : Print TER cards according to original PDB TER (if available).\n"
"\tnoter : Do not write TER cards.\n"
"\tmodel : Write to single file separated by MODEL records.\n"
"\tmulti : Write each frame to separate files.\n"
"\tchainid <c> : Write character 'c' in chain ID column.\n"
"\tsg <group> : Space group for CRYST1 record, only if box coordinates written.\n"
"\tinclude_ep : Include extra points.\n"
"\tconect : Write CONECT records using bond information.\n"
"\tkeepext : Keep filename extension; write '<name>.<num>.<ext>' instead (implies 'multi').\n"
"\tusecol21 : Use column 21 for 4-letter residue names.\n"
"\tbfacdefault <#> : Default value to use in B-factor column (default 0).\n"
"\toccdefault <#> : Default value to use in occupancy column (default 1).\n"
"\tbfacdata <set> : Use data in <set> for B-factor column.\n"
"\toccdata <set> : Use data in <set> for occupancy column.\n"
"\tbfacbyres : If specified assume X values in B-factor data set are residue numbers.\n"
"\toccbyres : If specified assume X values in occupancy data set are residue numbers.\n"
"\tbfacscale : If specified scale values in B-factor column between 0 and <bfacmax>.\n"
"\toccscale : If specified scale values in occupancy column between 0 and <occmax>.\n"
"\tbfacmax <max> : Max value for bfacscale.\n"
"\toccmax <max> : Max value for occscale.\n"
"\tadpdata <set> : Use data in <set> for anisotropic B-factors.\n"
);
}

Expand Down Expand Up @@ -288,6 +292,8 @@ int Traj_PDBfile::processWriteArgs(ArgList& argIn, DataSetList const& DSLin) {
if (bfacscale_) bfacmax_ = argIn.getKeyDouble("bfacmax", 99.99);
occscale_ = argIn.hasKey("occscale");
if (occscale_) occmax_ = argIn.getKeyDouble("occmax", 99.99);
bfacdefault_ = argIn.getKeyDouble("bfacdefault", 0.0);
occdefault_ = argIn.getKeyDouble("occdefault", -1.0);
temp = argIn.GetStringKey("adpdata");
if (!temp.empty()) {
adpdata_ = DSLin.GetDataSet( temp );
Expand Down Expand Up @@ -333,10 +339,11 @@ const
}

/** Assign data to specified output array using given input array. */
int Traj_PDBfile::AssignData(Darray& DataOut, DataSet* dataIn, Topology const& topIn, bool byres, const char* desc)
int Traj_PDBfile::AssignData(Darray& DataOut, DataSet* dataIn, Topology const& topIn,
bool byres, const char* desc, double defval)
const
{
DataOut.assign(topIn.Natom(), 0);
DataOut.assign(topIn.Natom(), defval);
if ( dataIn->Size() < 1) {
mprinterr("Error: '%s' set '%s' is empty.\n", desc, dataIn->legend());
return 1;
Expand Down Expand Up @@ -669,7 +676,7 @@ int Traj_PDBfile::setupTrajout(FileName const& fname, Topology* trajParm,
}
Bfactors_.clear();
if (bfacdata_ != 0) {
if (AssignData(Bfactors_, bfacdata_, *trajParm, bfacbyres_, "bfacdata")) return 1;
if (AssignData(Bfactors_, bfacdata_, *trajParm, bfacbyres_, "bfacdata", bfacdefault_)) return 1;
} else if (dumpq_) {
Bfactors_.reserve( trajParm->Natom() );
// Set up radii
Expand All @@ -683,13 +690,17 @@ int Traj_PDBfile::setupTrajout(FileName const& fname, Topology* trajParm,
}
Occupancy_.clear();
if (occdata_ != 0) {
if (AssignData(Occupancy_, occdata_, *trajParm, occbyres_, "occdata")) return 1;
// For backwards compatibility, if no default occupancy make it 0 for data
if (occdefault_ < 0) occdefault_ = 0;
if (AssignData(Occupancy_, occdata_, *trajParm, occbyres_, "occdata", occdefault_)) return 1;
} else if (dumpq_) {
Occupancy_.reserve( trajParm->Natom() );
// Set up charges
for (Topology::atom_iterator atm = trajParm->begin(); atm != trajParm->end(); ++atm)
Occupancy_.push_back( atm->Charge() );
}
// If no default occupancy set it to 1
if (occdefault_ < 0) occdefault_ = 1.0;
if (bfacscale_) ScaleData(Bfactors_, 0.0, bfacmax_);
if (occscale_ ) ScaleData(Occupancy_, 0.0, occmax_);
// If not including extra points, warn if topology has them.
Expand Down Expand Up @@ -765,8 +776,8 @@ int Traj_PDBfile::writeFrame(int set, Frame const& frameOut) {
file_.WriteMODEL(set + 1);

unsigned int adpidx = 0; // Index into adpout_
float Occ = 1.0;
float Bfac = 0.0;
float Occ = (float)occdefault_;
float Bfac = (float)bfacdefault_;
char altLoc = ' ';
int anum = 1; // Actual PDB ATOM record number
const double *Xptr = frameOut.xAddress();
Expand Down
4 changes: 3 additions & 1 deletion src/Traj_PDBfile.h
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Original file line number Diff line number Diff line change
Expand Up @@ -47,7 +47,7 @@ class Traj_PDBfile: public TrajectoryIO {
void WriteDisulfides(Frame const&);
void WriteBonds();
/// Used to set up B-factor/occupancy data from DataSets
int AssignData(Darray&, DataSet*, Topology const&, bool, const char*) const;
int AssignData(Darray&, DataSet*, Topology const&, bool, const char*, double) const;
/// Used to scale Bfactor/occupancy data between set values
void ScaleData(Darray&, double, double) const;

Expand Down Expand Up @@ -91,5 +91,7 @@ class Traj_PDBfile: public TrajectoryIO {
DataSet* adpdata_; ///< Hold anisotropic B-factor data for writing.
double bfacmax_;
double occmax_;
double bfacdefault_;
double occdefault_;
};
#endif
2 changes: 1 addition & 1 deletion src/Version.h
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Expand Up @@ -12,7 +12,7 @@
* Whenever a number that precedes <revision> is incremented, all subsequent
* numbers should be reset to 0.
*/
#define CPPTRAJ_INTERNAL_VERSION "V4.26.0"
#define CPPTRAJ_INTERNAL_VERSION "V4.26.1"
/// PYTRAJ relies on this
#define CPPTRAJ_VERSION_STRING CPPTRAJ_INTERNAL_VERSION
#endif

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