Merge branch 'issue36_orientbias' into fastergrad (4be7517a) · Commits · docking / ocladock

host/inc/getparameters.h

+1 −0

Original line number	Diff line number	Diff line
		@@ -33,6 +33,7 @@ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
		#include "processligand.h"
		#include "processgrid.h"
		#include "miscellaneous.h"
		#include "calcenergy_basic.h"

		typedef struct
		{

host/src/getparameters.cpp

+98 −22

Original line number	Diff line number	Diff line
		@@ -628,6 +628,11 @@ void gen_initpop_and_reflig(Dockpars* mypars,

		int pop_size = mypars->pop_size;

		float u1, u2, u3; // to generate random quaternion
		float qw, qx, qy, qz; // random quaternion
		float x, y, z, s; // convert quaternion to angles
		float phi, theta, rotangle;

		//initial population
		gen_pop = 0;

		@@ -668,29 +673,63 @@ void gen_initpop_and_reflig(Dockpars* mypars,
		//Generating initial population
		if (gen_pop == 1)
		{
		for (entity_id=0; entity_id<pop_size*mypars->num_of_runs; entity_id++)
		for (gene_id=0; gene_id<3; gene_id++)
		for (entity_id=0; entity_id<pop_size*mypars->num_of_runs; entity_id++) {
		for (gene_id=0; gene_id<3; gene_id++) {
		#if defined (REPRO)
		init_populations[entity_id*GENOTYPE_LENGTH_IN_GLOBMEM+gene_id] = 30.1186;
		#else
		init_populations[entity_idGENOTYPE_LENGTH_IN_GLOBMEM+gene_id] = (float) myrand()(mygrid->size_xyz_angstr[gene_id]);
		#endif
		}

		for (entity_id=0; entity_id<pop_size*mypars->num_of_runs; entity_id++)
		for (gene_id=3; gene_id<MAX_NUM_OF_ROTBONDS+6; gene_id++)
		if (gene_id == 4)
		#if defined (REPRO)
		init_populations[entity_id*GENOTYPE_LENGTH_IN_GLOBMEM+gene_id] = 26.0555;
		#else
		init_populations[entity_idGENOTYPE_LENGTH_IN_GLOBMEM+gene_id] = myrand()180;
		#endif
		// generate random quaternion
		u1 = (float) myrand();
		u2 = (float) myrand();
		u3 = (float) myrand();
		qw = sqrt(1.0 - u1) * sin(PI_TIMES_2 * u2);
		qx = sqrt(1.0 - u1) * cos(PI_TIMES_2 * u2);
		qy = sqrt( u1) * sin(PI_TIMES_2 * u3);
		qz = sqrt( u1) * cos(PI_TIMES_2 * u3);

		else
		// convert to angle representation
		rotangle = 2.0 * acos(qw);
		s = sqrt(1.0 - (qw * qw));
		if (s < 0.001){ // rotangle too small
		x = qx;
		y = qy;
		z = qz;
		} else {
		x = qx / s;
		y = qy / s;
		z = qz / s;
		}

		theta = acos(z);
		phi = atan2(y, x);

		init_populations[entity_id*GENOTYPE_LENGTH_IN_GLOBMEM+3] = phi / DEG_TO_RAD;
		init_populations[entity_id*GENOTYPE_LENGTH_IN_GLOBMEM+4] = theta / DEG_TO_RAD;
		init_populations[entity_id*GENOTYPE_LENGTH_IN_GLOBMEM+5] = rotangle / DEG_TO_RAD;

		//printf("angles = %8.2f, %8.2f, %8.2f\n", phi / DEG_TO_RAD, theta / DEG_TO_RAD, rotangle/DEG_TO_RAD);

		/*
		init_populations[entity_idGENOTYPE_LENGTH_IN_GLOBMEM+3] = (float) myrand() 360.0;
		init_populations[entity_idGENOTYPE_LENGTH_IN_GLOBMEM+4] = (float) myrand() 360.0;
		init_populations[entity_idGENOTYPE_LENGTH_IN_GLOBMEM+5] = (float) myrand() 360.0;
		init_populations[entity_idGENOTYPE_LENGTH_IN_GLOBMEM+3] = (float) myrand() 360;
		init_populations[entity_idGENOTYPE_LENGTH_IN_GLOBMEM+4] = (float) myrand() 180;
		init_populations[entity_idGENOTYPE_LENGTH_IN_GLOBMEM+5] = (float) myrand() 360;
		*/

		for (gene_id=6; gene_id<MAX_NUM_OF_ROTBONDS+6; gene_id++) {
		#if defined (REPRO)
		init_populations[entity_id*GENOTYPE_LENGTH_IN_GLOBMEM+gene_id] = 22.0452;
		#else
		init_populations[entity_idGENOTYPE_LENGTH_IN_GLOBMEM+gene_id] = myrand()360;
		#endif
		}
		}

		//generating reference orientation angles
		#if defined (REPRO)
		@@ -698,9 +737,13 @@ void gen_initpop_and_reflig(Dockpars* mypars,
		mypars->ref_ori_angles[1] = 190.279;
		mypars->ref_ori_angles[2] = 190.279;
		#else
		mypars->ref_ori_angles[0] = (float) floor(myrand()360100)/100.0;
		mypars->ref_ori_angles[1] = (float) floor(myrand()/360/180100)/100.0;
		mypars->ref_ori_angles[2] = (float) floor(myrand()360100)/100.0;
		// mypars->ref_ori_angles[0] = (float) floor(myrand()360100)/100.0;
		// mypars->ref_ori_angles[1] = (float) floor(myrand()/360/180100)/100.0;
		// mypars->ref_ori_angles[2] = (float) floor(myrand()360100)/100.0;

		// mypars->ref_ori_angles[0] = 0.0;
		// mypars->ref_ori_angles[1] = 0.0;
		// mypars->ref_ori_angles[2] = 0.0;
		#endif

		//Writing first initial population to initpop.txt
		@@ -758,17 +801,50 @@ void gen_initpop_and_reflig(Dockpars* mypars,
		// Enable only for debugging.
		// These specific values of rotational genes (in axis-angle space)
		// correspond to a quaternion for NO rotation.

		// ref_ori_angles[3*i] = 0.0f;
		// ref_ori_angles[3*i+1] = 0.0f;
		// ref_ori_angles[3*i+2] = 0.0f;

		// Enable for release.
		ref_ori_angles[3i] = (float) (myrand()360.0); //phi
		ref_ori_angles[3i+1] = (float) (myrand()180.0); //theta
		ref_ori_angles[3i+2] = (float) (myrand()360.0); //angle
		// ref_ori_angles[3i] = (float) (myrand()360.0); //phi
		// ref_ori_angles[3i+1] = (float) (myrand()180.0); //theta
		// ref_ori_angles[3i+2] = (float) (myrand()360.0); //angle

		// uniform distr.
		// generate random quaternion
		u1 = (float) myrand();
		u2 = (float) myrand();
		u3 = (float) myrand();
		qw = sqrt(1.0 - u1) * sin(PI_TIMES_2 * u2);
		qx = sqrt(1.0 - u1) * cos(PI_TIMES_2 * u2);
		qy = sqrt( u1) * sin(PI_TIMES_2 * u3);
		qz = sqrt( u1) * cos(PI_TIMES_2 * u3);

		// convert to angle representation
		rotangle = 2.0 * acos(qw);
		s = sqrt(1.0 - (qw * qw));
		if (s < 0.001){ // rotangle too small
		x = qx;
		y = qy;
		z = qz;
		} else {
		x = qx / s;
		y = qy / s;
		z = qz / s;
		}

		theta = acos(z);
		phi = atan2(y, x);

		ref_ori_angles[3*i] = phi / DEG_TO_RAD;
		ref_ori_angles[3*i+1] = theta / DEG_TO_RAD;
		ref_ori_angles[3*i+2] = rotangle / DEG_TO_RAD;

		#endif
		}


		#if 0
		for (i=0; i<mypars->num_of_runs; i++)
		{