Toolbox of utilities for Tinker style molecular representation. More...

Static Public Member Functions
static TinkerMolecule	readTinkerIC (String filename) throws DENOPTIMException
	Reads a Tinker INT file. More...

static ArrayList< double[]>	readTinkerXYZ (String filename) throws DENOPTIMException
	Read the tinker XYZ coordinate representation. More...

static void	writeIC (String filename, TinkerMolecule tmol) throws DENOPTIMException
	Write Tinker INT file. More...

static ArrayList< Double >	readPSSROTOutput (String filename) throws DENOPTIMException
	Read the PSSROT output file. More...

static void	readPSSROTParams (String filename, ArrayList< String > initPars, ArrayList< String > restPars) throws DENOPTIMException
	Read the parameter settings to be used by PSSROT. More...

static HashMap< String, Integer >	readTinkerAtomTypes (String filename) throws DENOPTIMException
	Read the Tinker atom mapping from Tinker Force Field. More...

static TinkerMolecule	getICFromIAC (IAtomContainer mol, HashMap< String, Integer > tMap) throws DENOPTIMException
	Convert `IAtomContainer` to `TinkerMolecule`. More...

static void	setTinkerTypes (TinkerMolecule tmol, HashMap< String, Integer > tMap) throws DENOPTIMException
	Conversion to tinker IC may not always have the necessary atom types. More...

static void	ensureOutputExistsOrRelayError (String outputPathName, String logPathName, String taskName) throws TinkerException
	Check for the existence of an output file for a Tinker job and, if the output file is not found, this method throws an exception that contains the error message from Tinker job log. More...

static String	getNameLastCycleFile (String workDir, String fname, String tinkerLog, String pattern) throws DENOPTIMException
	Identifies how many iteration Tinker has done by looking into the log file, searching for a given pattern. More...

Static Private Member Functions
static int	getFirstRefAtomId (int i1, IAtomContainer mol)

static int	getSecondRefAtomId (int i1, int i2, IAtomContainer mol)

static ObjectPair	getThirdRefAtomId (int i1, int i2, int i3, IAtomContainer mol, TinkerMolecule tm) throws DENOPTIMException

static int	countPredefinedNeighbours (int i, IAtom a, IAtomContainer mol)

Static Private Attributes
static final String	NL = System.getProperty("line.separator")

static boolean	debug = false

Detailed Description

Toolbox of utilities for Tinker style molecular representation.

Author: Vishwesh Venkatraman; Marco Foscato

Definition at line 54 of file TinkerUtils.java.

Member Function Documentation

◆ countPredefinedNeighbours()

static int denoptim.integration.tinker.TinkerUtils.countPredefinedNeighbours	(	int	i,
		IAtom	a,
		IAtomContainer	mol
	)

staticprivate

Definition at line 990 of file TinkerUtils.java.

Referenced by denoptim.integration.tinker.TinkerUtils.getThirdRefAtomId().

Here is the caller graph for this function:

◆ ensureOutputExistsOrRelayError()

static void denoptim.integration.tinker.TinkerUtils.ensureOutputExistsOrRelayError	(	String	outputPathName,
		String	logPathName,
		String	taskName
	)		throws TinkerException

static

Check for the existence of an output file for a Tinker job and, if the output file is not found, this method throws an exception that contains the error message from Tinker job log.

Parameters

outputPathName	pathname of the Tinker output file that we expect to exist.
logPathName	pathname to the log of the Tinker job that was supposed to generate the output.
taskName	a string identifying the task that Tinker was supposed to perform.

Exceptions

TinkerException if the output file is not found. This exception will contain the error from Tinker's log.

Definition at line 1063 of file TinkerUtils.java.

References denoptim.integration.tinker.TinkerUtils.NL.

Referenced by denoptim.integration.tinker.ConformationalSearchPSSROT.performPSSROT().

Here is the caller graph for this function:

◆ getFirstRefAtomId()

static int denoptim.integration.tinker.TinkerUtils.getFirstRefAtomId	(	int	i1,
		IAtomContainer	mol
	)

staticprivate

Definition at line 868 of file TinkerUtils.java.

Referenced by denoptim.integration.tinker.TinkerUtils.getICFromIAC().

Here is the caller graph for this function:

◆ getICFromIAC()

static TinkerMolecule denoptim.integration.tinker.TinkerUtils.getICFromIAC	(	IAtomContainer	mol,
		HashMap< String, Integer >	tMap
	)		throws DENOPTIMException

static

Convert IAtomContainer to TinkerMolecule.

Supports only containers where all atoms are reachable following the connectivity and starting from any other atom in the container.

Parameters

mol	the CDK molecule to convert
tMap	the atom type map

Returns: the molecule represented by internal coordinates

Definition at line 730 of file TinkerUtils.java.

Referenced by denoptim.molecularmodeling.MultiMolecularModelBuilder.build3DTree().

Here is the call graph for this function:

Here is the caller graph for this function:

◆ getNameLastCycleFile()

static String denoptim.integration.tinker.TinkerUtils.getNameLastCycleFile	(	String	workDir,
		String	fname,
		String	tinkerLog,
		String	pattern
	)		throws DENOPTIMException

static

Identifies how many iteration Tinker has done by looking into the log file, searching for a given pattern.

The resulting number of iterations is translated in the pathname of the last iteration file. The iteration files have names like
filename.000, filename.001, filename.002. So, if Tinker took 56 iteration, this method will return filename.055.

Parameters

workDir	the directory expected to contain the iteration files.
fname	the basename of the iteration file.
tinkerLog	the log file where we count the iterations by searching the patters.
pattern	the pattern to search in the log file

Returns: the pathname of the last cycle-file.

Exceptions

DENOPTIMException

Definition at line 1121 of file TinkerUtils.java.

References denoptim.molecularmodeling.MMBuilderUtils.countLinesWKeywordInFile(), and denoptim.utils.GeneralUtils.getPaddedString().

Referenced by denoptim.integration.tinker.ConformationalSearchPSSROT.performPSSROT().

Here is the call graph for this function:

Here is the caller graph for this function:

◆ getSecondRefAtomId()

static int denoptim.integration.tinker.TinkerUtils.getSecondRefAtomId	(	int	i1,
		int	i2,
		IAtomContainer	mol
	)

staticprivate

Definition at line 886 of file TinkerUtils.java.

Referenced by denoptim.integration.tinker.TinkerUtils.getICFromIAC().

Here is the caller graph for this function:

◆ getThirdRefAtomId()

static ObjectPair denoptim.integration.tinker.TinkerUtils.getThirdRefAtomId	(	int	i1,
		int	i2,
		int	i3,
		IAtomContainer	mol,
		TinkerMolecule	tm
	)		throws DENOPTIMException

staticprivate

Definition at line 904 of file TinkerUtils.java.

References denoptim.utils.MathUtils.angle(), denoptim.integration.tinker.TinkerUtils.countPredefinedNeighbours(), denoptim.integration.tinker.TinkerUtils.debug, and denoptim.utils.MoleculeUtils.getSymbolOrLabel().

Referenced by denoptim.integration.tinker.TinkerUtils.getICFromIAC().

Here is the call graph for this function:

Here is the caller graph for this function:

◆ readPSSROTOutput()

static ArrayList< Double > denoptim.integration.tinker.TinkerUtils.readPSSROTOutput ( String filename ) throws DENOPTIMException

static

Read the PSSROT output file.

Parameters

filename

Returns: the list of energies

Exceptions

DENOPTIMException

Definition at line 505 of file TinkerUtils.java.

◆ readPSSROTParams()

static void denoptim.integration.tinker.TinkerUtils.readPSSROTParams	(	String	filename,
		ArrayList< String >	initPars,
		ArrayList< String >	restPars
	)		throws DENOPTIMException

static

Read the parameter settings to be used by PSSROT.

Parameters

filename

Returns: list of data

Exceptions

DENOPTIMException

Definition at line 564 of file TinkerUtils.java.

Referenced by denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.processParameters().

Here is the caller graph for this function:

◆ readTinkerAtomTypes()

static HashMap< String, Integer > denoptim.integration.tinker.TinkerUtils.readTinkerAtomTypes ( String filename ) throws DENOPTIMException

static

Read the Tinker atom mapping from Tinker Force Field.

Parameters

filename

Returns: map of atom symbol and Tinker type

Exceptions

DENOPTIMException

Definition at line 637 of file TinkerUtils.java.

References denoptim.integration.tinker.TinkerUtils.NL.

Referenced by denoptim.programs.moldecularmodelbuilder.MMBuilderParameters.processParameters().

Here is the caller graph for this function:

◆ readTinkerIC()

static TinkerMolecule denoptim.integration.tinker.TinkerUtils.readTinkerIC ( String filename ) throws DENOPTIMException

static

Reads a Tinker INT file.

Example of Tinker INT file (i.e., internal coordinates)
8 Ethane
1 C 1
2 C 1 1 1.60000
3 H 5 1 1.10000 2 109.4700
4 H 5 1 1.10000 2 109.4700 3 109.4700 1
5 H 5 1 1.10000 2 109.4700 3 109.4700 -1
6 H 5 2 1.10000 1 109.4700 3 10.0000 0
7 H 5 2 1.10000 1 109.4700 6 109.4700 1
8 H 5 2 1.10000 1 109.4700 6 109.4700 -1

The first line, says that there are eight atoms in the system, and that the name of the molecule is Ethane Second line set the origin of the system, i.e., from which atom start to build the molecule: first atom is atom 1, which is a carbon atom, C, and its atom type for the force field is 1 Third line says that the second atom in the molecule is a carbon atom, C, having atom type 1, bonded to atom 1 placed at a distance of 1.6 Angstroms from the atom 1 Fourth line says that the third atom in the structure is an hydrogen atoms, H, having atom type 5, bonded to atom 1, placed at a distance of 1.1 Angstroms from atom 1 and forming an angle of 109.47 degrees with atom 2 Fifth line says that the fourth atom in the structure is an hydrogen atoms, H, having atom type 5, bonded to atom 1, placed at a distance of 1.1 Angstroms from atom 1, and forming an angle of 109.47 degrees with atom 2 Also, the dihedral angles between the planes defined by atoms 1 2 3 and 2 3 4 is 109.47 degrees The last column indicates the chirality flag The structure of this line is then repeated for all the remain atoms. Atom 1 has no internal coordinates at all. The coordinates of atom 1 are, by definition, Cartesian. Normally, the coordinates of atom 1 are (0,0,0), but can be set to any value desired. Atom 2 must be connected to atom 1 by an interatomic distance only. If atom 1 is not at the origin, then the care must be taken in defining atom 2: if internal coordinates are used, then the connectivity must be given. If the connectivity is not specified, then the coordinate of atom 2 is, by definition, Cartesian. Atom 3 can be connected to atom 1 or 2, and must make an angle with atom 2 or 1 (thus 3-2-1 or 3-1-2); no dihedral is possible for atom 3. For any one atom (i) this consists of an interatomic distance in Angstroms from an already-defined atom (j), an interatomic angle in degrees between atoms i and j and an already defined k, (k and j must be different atoms), and finally a torsional angle in degrees between atoms i, j, k, and an already defined atom l (l cannot be the same as k or j).

Parameters

filename

Definition at line 110 of file TinkerUtils.java.

References denoptim.integration.tinker.TinkerMolecule.setAtoms(), denoptim.integration.tinker.TinkerMolecule.setBondPairs(), and denoptim.integration.tinker.TinkerMolecule.setName().

Referenced by denoptim.integration.tinker.ConformationalSearchPSSROT.performPSSROT().

Here is the call graph for this function:

Here is the caller graph for this function:

◆ readTinkerXYZ()

static ArrayList< double[]> denoptim.integration.tinker.TinkerUtils.readTinkerXYZ ( String filename ) throws DENOPTIMException

static

Read the tinker XYZ coordinate representation.

Parameters

filename

Returns: the 3d coordinates

Exceptions

DENOPTIMException

Definition at line 296 of file TinkerUtils.java.

◆ setTinkerTypes()

static void denoptim.integration.tinker.TinkerUtils.setTinkerTypes	(	TinkerMolecule	tmol,
		HashMap< String, Integer >	tMap
	)		throws DENOPTIMException

static

Conversion to tinker IC may not always have the necessary atom types.

In order to fix this, we add user defined atom types.

Parameters

tmol	The tinker IC representation

Exceptions

DENOPTIMException

Definition at line 1011 of file TinkerUtils.java.

References denoptim.integration.tinker.TinkerUtils.debug, denoptim.integration.tinker.TinkerAtom.getAtomString(), and denoptim.integration.tinker.TinkerAtom.setAtomType().

Referenced by denoptim.molecularmodeling.MultiMolecularModelBuilder.build3DTree(), and denoptim.integration.tinker.TinkerUtils.getICFromIAC().

Here is the call graph for this function:

Here is the caller graph for this function:

◆ writeIC()

static void denoptim.integration.tinker.TinkerUtils.writeIC	(	String	filename,
		TinkerMolecule	tmol
	)		throws DENOPTIMException

static

Write Tinker INT file.

Parameters

filename
tmol

Exceptions

DENOPTIMException

Definition at line 380 of file TinkerUtils.java.

References denoptim.integration.tinker.TinkerAtom.getAtomNeighbours(), denoptim.integration.tinker.TinkerAtom.getAtomString(), denoptim.integration.tinker.TinkerAtom.getAtomType(), denoptim.integration.tinker.TinkerAtom.getDistAngle(), denoptim.integration.tinker.TinkerAtom.getXYZIndex(), and denoptim.integration.tinker.TinkerUtils.NL.

Referenced by denoptim.integration.tinker.ConformationalSearchPSSROT.performPSSROT().

Here is the call graph for this function:

Here is the caller graph for this function:

Member Data Documentation

◆ debug

boolean denoptim.integration.tinker.TinkerUtils.debug = false

staticprivate

Definition at line 57 of file TinkerUtils.java.

Referenced by denoptim.integration.tinker.TinkerUtils.getICFromIAC(), denoptim.integration.tinker.TinkerUtils.getThirdRefAtomId(), and denoptim.integration.tinker.TinkerUtils.setTinkerTypes().

◆ NL

final String denoptim.integration.tinker.TinkerUtils.NL = System.getProperty("line.separator")

staticprivate

Definition at line 56 of file TinkerUtils.java.

Referenced by denoptim.integration.tinker.TinkerUtils.ensureOutputExistsOrRelayError(), denoptim.integration.tinker.TinkerUtils.readTinkerAtomTypes(), and denoptim.integration.tinker.TinkerUtils.writeIC().

The documentation for this class was generated from the following file:

/github/workspace/src/main/java/denoptim/integration/tinker/TinkerUtils.java

Static Public Member Functions

Static Private Member Functions

Static Private Attributes

Detailed Description

Member Function Documentation

◆ countPredefinedNeighbours()

◆ ensureOutputExistsOrRelayError()

◆ getFirstRefAtomId()

◆ getICFromIAC()

◆ getNameLastCycleFile()

◆ getSecondRefAtomId()

◆ getThirdRefAtomId()

◆ readPSSROTOutput()

◆ readPSSROTParams()

◆ readTinkerAtomTypes()

◆ readTinkerIC()

◆ readTinkerXYZ()

◆ setTinkerTypes()

◆ writeIC()

Member Data Documentation

◆ debug

◆ NL