Tutorial:Measuring distances, angles, dihedrals - Revision history

Dwkulp at 02:55, 10 April 2010

2010-04-10T02:55:29Z

Dwkulp at 02:39, 10 April 2010

2010-04-10T02:39:49Z

Dwkulp at 02:29, 10 April 2010

2010-04-10T02:29:05Z

Dwkulp: Created page with ' Tutorial writing in progress, errors may exist This is an example on how to measure distances, angles and dihedrals (Includes wrapper functions for me…'

2010-04-10T01:40:50Z

Created page with '<font color="red" > Tutorial writing in progress, errors may exist</font> This is an example on how to measure distances, angles and dihedrals (Includes wrapper functions for me…'

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<font color="red" > Tutorial writing in progress, errors may exist</font>

This is an example on how to measure distances, angles and dihedrals (Includes wrapper functions for measuring Phi/Psi/Chi angles).

[http://mslib.svn.sourceforge.net/viewvc/mslib/trunk/examples/example_measurements.cpp?view=markup Complete source of example_measurements.cpp]

=== To compile ===
<source lang="text">
% make bin/example_measurements
</source>

=== To run the program ===
Go to the main directory and run the command ('''note''', the location of the exampleFiles subdirectory needs to be provided as an argument)
<source lang="text">
% bin/example_molecular_measurements exampleFiles
</source>

=== Program description ===

----
'''[[Tutorial|Back to the tutorial page]]'''

[[Category:Tutorial]]

@@ Line 72: / Line 72: @@
 	fprintf(stdout, "%-15s = %8.3f\n","Point Angle",angleDegrees);
 	fprintf(stdout, "%-15s = %8.3f\n","Point Dihedral",dihedralDegrees);
 </source>

← Older revision		Revision as of 02:39, 10 April 2010
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−	~~<font color="red" > Tutorial writing in progress, errors may exist</font>~~
−
	This is an example on how to measure distances, angles and dihedrals (Includes wrapper functions for measuring Phi/Psi/Chi angles).		This is an example on how to measure distances, angles and dihedrals (Includes wrapper functions for measuring Phi/Psi/Chi angles).

← Older revision		Revision as of 02:29, 10 April 2010
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	=== Program description ===		=== Program description ===
		+	<source lang="cpp">
		+	string refFile = "example0005.pdb";
		+	refFile = (string)argv[1] + "/" + refFile;

		+	AtomContainer atoms;
		+	if (!atoms.readPdb(refFile)) {
		+	cerr << endl;
		+	cerr << "File " << refFile << " cannot be found, please speficy the path of the \"exampleFiles\" directory as an argument" << endl;
		+	exit(1);
		+	}
		+
		+
		+	// Distance and Distance Squared bewteen two atoms atoms[0] and atoms[size()-1] (first and last atom)
		+	double distance = atoms[0].distance(atoms[atoms.size()-1]);
		+	double distanceSquared = atoms[0].distance2(atoms[atoms.size()-1]);
		+
		+	// Angle between three atoms ( atoms[0] - atoms[1] - atoms[2] angle)
		+	double angleDegrees = atoms[0].angle(atoms[1],atoms[2]);
		+	double angleRadians = atoms[0].angleRadians(atoms[1],atoms[2]);
		+
		+
		+	// Dihedral between four atoms ( atoms[0] - atoms[1] - atoms[2] - atoms[3] )
		+	double dihedralDegrees = atoms[0].dihedral(atoms[1],atoms[2],atoms[3]);
		+	double dihedralRadians = atoms[0].dihedralRadians(atoms[1],atoms[2],atoms[3]);
		+
		+
		+	// Print out measurements
		+	fprintf(stdout, "%-15s = %8.3f\n","Distance",distance);
		+	fprintf(stdout, "%-15s = %8.3f\n","DistanceSquared",distanceSquared);
		+	fprintf(stdout, "%-15s = %8.3f\n","AngleDegrees",angleDegrees);
		+	fprintf(stdout, "%-15s = %8.3f\n","AngleRadians",angleRadians);
		+	fprintf(stdout, "%-15s = %8.3f\n","DihedralDegrees",dihedralDegrees);
		+	fprintf(stdout, "%-15s = %8.3f\n","DihedralRadians",dihedralRadians);
		+
		+
		+	// Measurement Namespace : CartesianGeometry
		+
		+
		+	// The above Atom-based functions are wrappers to the utility functions in the CartesianGeometry namespace.
		+
		+	CartesianPoint pt1(0.0 , 0.0 , 0.0);
		+	CartesianPoint pt2(1.0 , 0.0 , 0.0);
		+	CartesianPoint pt3(1.0 , 1.0 , 0.0);
		+	CartesianPoint pt4(1.0 , 1.0 , 1.0);
		+
		+	distance = CartesianGeometry::distance(pt1,pt2);
		+	angleDegrees = CartesianGeometry::angle(pt1,pt2,pt3);
		+	dihedralDegrees = CartesianGeometry::dihedral(pt1,pt2,pt3,pt4);
		+
		+	cout << endl;
		+
		+	fprintf(stdout, "%-15s = %8.3f\n","Point Distance",distance);
		+	fprintf(stdout, "%-15s = %8.3f\n","Point Angle",angleDegrees);
		+	fprintf(stdout, "%-15s = %8.3f\n","Point Dihedral",dihedralDegrees);
		+	</source>
		+
		+
		+	}