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

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

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

static void	writeTinkerINT (String filename, ZMatrix zmat) throws DENOPTIMException
	Write Tinker INT file. More...

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

static void	readPSSROTParams (String filename, List< String > initPars, List< 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 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 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 46 of file TinkerUtils.java.

Member Function Documentation

◆ 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 712 of file TinkerUtils.java.

References denoptim.integration.tinker.TinkerUtils.NL.

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

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◆ 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 770 of file TinkerUtils.java.

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

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

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◆ readPSSROTOutput()

static List< 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 482 of file TinkerUtils.java.

◆ readPSSROTParams()

static void denoptim.integration.tinker.TinkerUtils.readPSSROTParams	(	String	filename,
		List< String >	initPars,
		List< 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 541 of file TinkerUtils.java.

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

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◆ 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 614 of file TinkerUtils.java.

References denoptim.integration.tinker.TinkerUtils.NL.

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

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◆ readTinkerINT()

static ZMatrix denoptim.integration.tinker.TinkerUtils.readTinkerINT ( 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 102 of file TinkerUtils.java.

References denoptim.molecularmodeling.zmatrix.ZMatrix.addAtom(), denoptim.molecularmodeling.zmatrix.ZMatrix.addBond(), denoptim.molecularmodeling.zmatrix.ZMatrix.delBond(), denoptim.molecularmodeling.zmatrix.ZMatrix.getAtom(), and denoptim.molecularmodeling.zmatrix.ZMatrix.setId().

Referenced by denoptim.integration.tinker.ConformationalSearchPSSROT.performPSSROT(), and denoptim.integration.tinker.TinkerUtilsTest.testINTRoundTrip().

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◆ readTinkerXYZ()

static List< 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 264 of file TinkerUtils.java.

◆ writeTinkerINT()

static void denoptim.integration.tinker.TinkerUtils.writeTinkerINT	(	String	filename,
		ZMatrix	zmat
	)		throws DENOPTIMException

static

Write Tinker INT file.

Parameters

filename
zmat

Exceptions

DENOPTIMException

Definition at line 348 of file TinkerUtils.java.

References denoptim.molecularmodeling.zmatrix.ZMatrixAtom.getId(), denoptim.molecularmodeling.zmatrix.ZMatrixAtom.getSymbol(), denoptim.molecularmodeling.zmatrix.ZMatrixAtom.getType(), and denoptim.integration.tinker.TinkerUtils.NL.

Referenced by denoptim.integration.tinker.ConformationalSearchPSSROT.performPSSROT(), denoptim.integration.tinker.TinkerUtilsTest.testINTRoundTrip(), and denoptim.integration.tinker.TinkerUtilsTest.testWriteTinkerINT().

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Member Data Documentation

◆ debug

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

staticprivate

Definition at line 49 of file TinkerUtils.java.

◆ NL

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

staticprivate

Definition at line 48 of file TinkerUtils.java.

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

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 Attributes

Detailed Description

Member Function Documentation

◆ ensureOutputExistsOrRelayError()

◆ getNameLastCycleFile()

◆ readPSSROTOutput()

◆ readPSSROTParams()

◆ readTinkerAtomTypes()

◆ readTinkerINT()

◆ readTinkerXYZ()

◆ writeTinkerINT()

Member Data Documentation

◆ debug

◆ NL