1 |
gezelter |
828 |
#include <stdlib.h> |
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#include <stdio.h> |
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#include <string.h> |
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mmeineke |
377 |
#include <iostream> |
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#include "MoleculeStamp.hpp" |
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char MoleculeStamp::errMsg[500]; |
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MoleculeStamp::MoleculeStamp(){ |
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n_atoms = 0; |
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n_bonds = 0; |
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n_bends = 0; |
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n_torsions = 0; |
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gezelter |
957 |
n_rigidbodies = 0; |
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gezelter |
1103 |
n_integrable = 0; |
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mmeineke |
377 |
|
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unhandled = NULL; |
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atoms = NULL; |
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bonds = NULL; |
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bends = NULL; |
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torsions = NULL; |
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gezelter |
957 |
rigidBodies = NULL; |
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mmeineke |
377 |
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have_name = 0; |
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have_atoms = 0; |
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have_bonds = 0; |
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have_bends = 0; |
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have_torsions = 0; |
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gezelter |
957 |
have_rigidbodies = 0; |
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mmeineke |
377 |
|
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} |
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MoleculeStamp::~MoleculeStamp(){ |
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int i; |
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if( unhandled != NULL) delete unhandled; |
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gezelter |
957 |
|
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if( rigidBodies != NULL ) { |
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for( i=0; i<n_rigidbodies; i++ ) delete rigidBodies[i]; |
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} |
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mmeineke |
377 |
if( atoms != NULL ){ |
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for( i=0; i<n_atoms; i++ ) delete atoms[i]; |
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} |
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if( bonds != NULL ){ |
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for( i=0; i<n_bonds; i++ ) delete bonds[i]; |
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} |
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if( bends != NULL ){ |
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for( i=0; i<n_bends; i++ ) delete bends[i]; |
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} |
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if( torsions != NULL ){ |
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for( i=0; i<n_torsions; i++ ) delete torsions[i]; |
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} |
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} |
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char* MoleculeStamp::assignString( char* lhs, char* rhs ){ |
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if( !strcmp( lhs, "name" ) ){ |
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strcpy( name, rhs ); |
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have_name = 1; |
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} |
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else{ |
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if( unhandled == NULL ) unhandled = new LinkedAssign( lhs, rhs ); |
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else unhandled->add( lhs, rhs ); |
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have_extras = 1; |
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} |
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return NULL; |
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} |
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char* MoleculeStamp::assignDouble( char* lhs, double rhs ){ |
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int i; |
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if( !strcmp( lhs, "nAtoms" ) ){ |
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n_atoms = (int)rhs; |
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if( have_atoms ){ |
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sprintf( errMsg, |
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"MoleculeStamp error, n_atoms already declared" |
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gezelter |
981 |
" for molecule: %s\n", |
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mmeineke |
377 |
name); |
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return strdup( errMsg ); |
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} |
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have_atoms = 1; |
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atoms = new AtomStamp*[n_atoms]; |
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for( i=0; i<n_atoms; i++ ) atoms[i] = NULL; |
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} |
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else if( !strcmp( lhs, "nBonds" ) ){ |
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n_bonds = (int)rhs; |
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if( have_bonds ){ |
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sprintf( errMsg, |
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"MoleculeStamp error, n_bonds already declared for" |
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" molecule: %s\n", |
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name); |
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return strdup( errMsg ); |
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} |
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have_bonds = 1; |
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bonds = new BondStamp*[n_bonds]; |
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for( i=0; i<n_bonds; i++ ) bonds[i] = NULL; |
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} |
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else if( !strcmp( lhs, "nBends" ) ){ |
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n_bends = (int)rhs; |
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if( have_bends ){ |
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sprintf( errMsg, |
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"MoleculeStamp error, n_bends already declared for" |
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" molecule: %s\n", |
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name); |
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return strdup( errMsg ); |
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} |
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have_bends = 1; |
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bends = new BendStamp*[n_bends]; |
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for( i=0; i<n_bends; i++ ) bends[i] = NULL; |
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} |
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else if( !strcmp( lhs, "nTorsions" ) ){ |
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n_torsions = (int)rhs; |
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if( have_torsions ){ |
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sprintf( errMsg, |
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"MoleculeStamp error, n_torsions already declared for" |
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" molecule: %s\n", |
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name ); |
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return strdup( errMsg ); |
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} |
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have_torsions = 1; |
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torsions = new TorsionStamp*[n_torsions]; |
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for( i=0; i<n_torsions; i++ ) torsions[i] = NULL; |
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} |
138 |
gezelter |
957 |
|
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else if( !strcmp( lhs, "nRigidBodies" ) ){ |
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n_rigidbodies = (int)rhs; |
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if( have_rigidbodies ){ |
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sprintf( errMsg, |
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"MoleculeStamp error, n_rigidbodies already declared for" |
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" molecule: %s\n", |
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name ); |
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return strdup( errMsg ); |
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} |
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have_rigidbodies = 1; |
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rigidBodies = new RigidBodyStamp*[n_rigidbodies]; |
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for( i=0; i<n_rigidbodies; i++ ) rigidBodies[i] = NULL; |
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} |
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mmeineke |
377 |
else{ |
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if( unhandled == NULL ) unhandled = new LinkedAssign( lhs, rhs ); |
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else unhandled->add( lhs, rhs ); |
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have_extras = 1; |
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} |
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return NULL; |
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} |
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char* MoleculeStamp::assignInt( char* lhs, int rhs ){ |
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int i; |
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if( !strcmp( lhs, "nAtoms" ) ){ |
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n_atoms = rhs; |
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if( have_atoms ){ |
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sprintf( errMsg, |
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"MoleculeStamp error, n_atoms already declared for" |
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" molecule: %s\n", |
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name); |
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return strdup( errMsg ); |
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} |
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have_atoms = 1; |
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atoms = new AtomStamp*[n_atoms]; |
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for( i=0; i<n_atoms; i++ ) atoms[i] = NULL; |
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} |
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else if( !strcmp( lhs, "nBonds" ) ){ |
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n_bonds = rhs; |
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if( have_bonds ){ |
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sprintf( errMsg, |
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"MoleculeStamp error, n_bonds already declared for" |
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" molecule: %s\n", |
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name); |
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return strdup( errMsg ); |
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} |
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have_bonds = 1; |
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bonds = new BondStamp*[n_bonds]; |
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for( i=0; i<n_bonds; i++ ) bonds[i] = NULL; |
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} |
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else if( !strcmp( lhs, "nBends" ) ){ |
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n_bends = rhs; |
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if( have_bends ){ |
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sprintf( errMsg, |
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"MoleculeStamp error, n_bends already declared for" |
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" molecule: %s\n", |
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name ); |
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return strdup( errMsg ); |
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} |
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have_bends = 1; |
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bends = new BendStamp*[n_bends]; |
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for( i=0; i<n_bends; i++ ) bends[i] = NULL; |
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} |
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else if( !strcmp( lhs, "nTorsions" ) ){ |
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n_torsions = rhs; |
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if( have_torsions ){ |
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sprintf( errMsg, |
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"MoleculeStamp error, n_torsions already declared for" |
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" molecule: %s\n", |
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name); |
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return strdup( errMsg ); |
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} |
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have_torsions = 1; |
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torsions = new TorsionStamp*[n_torsions]; |
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for( i=0; i<n_torsions; i++ ) torsions[i] = NULL; |
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} |
224 |
gezelter |
957 |
|
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else if( !strcmp( lhs, "nRigidBodies" ) ){ |
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n_rigidbodies = rhs; |
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if( have_rigidbodies ){ |
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sprintf( errMsg, |
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"RigidBodyStamp error, n_rigidbodies already declared for" |
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" molecule: %s\n", |
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name); |
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return strdup( errMsg ); |
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} |
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have_rigidbodies = 1; |
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rigidBodies = new RigidBodyStamp*[n_rigidbodies]; |
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for( i=0; i<n_rigidbodies; i++ ) rigidBodies[i] = NULL; |
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} |
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mmeineke |
377 |
else{ |
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if( unhandled == NULL ) unhandled = new LinkedAssign( lhs, rhs ); |
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else unhandled->add( lhs, rhs ); |
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have_extras = 1; |
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} |
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return NULL; |
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} |
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char* MoleculeStamp::addAtom( AtomStamp* the_atom, int atomIndex ){ |
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if( have_atoms && atomIndex < n_atoms ) atoms[atomIndex] = the_atom; |
250 |
gezelter |
1103 |
else { |
251 |
mmeineke |
377 |
if( have_atoms ){ |
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sprintf( errMsg, "MoleculeStamp error, %d out of nAtoms range", |
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atomIndex ); |
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return strdup( errMsg ); |
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} |
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else return strdup("MoleculeStamp error, nAtoms not given before" |
257 |
gezelter |
981 |
" first atom declaration." ); |
258 |
mmeineke |
377 |
} |
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return NULL; |
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} |
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263 |
gezelter |
957 |
char* MoleculeStamp::addRigidBody( RigidBodyStamp* the_rigidbody, |
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int rigidBodyIndex ){ |
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if( have_rigidbodies && rigidBodyIndex < n_rigidbodies ) |
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rigidBodies[rigidBodyIndex] = the_rigidbody; |
268 |
gezelter |
1103 |
else { |
269 |
gezelter |
957 |
if( have_rigidbodies ){ |
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sprintf( errMsg, "MoleculeStamp error, %d out of nRigidBodies range", |
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rigidBodyIndex ); |
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return strdup( errMsg ); |
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} |
274 |
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else return strdup("MoleculeStamp error, nRigidBodies not given before" |
275 |
gezelter |
981 |
" first rigidBody declaration." ); |
276 |
gezelter |
957 |
} |
277 |
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return NULL; |
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} |
280 |
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281 |
mmeineke |
377 |
char* MoleculeStamp::addBond( BondStamp* the_bond, int bondIndex ){ |
282 |
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283 |
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284 |
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if( have_bonds && bondIndex < n_bonds ) bonds[bondIndex] = the_bond; |
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else{ |
286 |
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if( have_bonds ){ |
287 |
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sprintf( errMsg, "MoleculeStamp error, %d out of nBonds range", |
288 |
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bondIndex ); |
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return strdup( errMsg ); |
290 |
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} |
291 |
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else return strdup("MoleculeStamp error, nBonds not given before" |
292 |
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"first bond declaration." ); |
293 |
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} |
294 |
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295 |
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return NULL; |
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} |
297 |
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298 |
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char* MoleculeStamp::addBend( BendStamp* the_bend, int bendIndex ){ |
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300 |
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301 |
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if( have_bends && bendIndex < n_bends ) bends[bendIndex] = the_bend; |
302 |
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else{ |
303 |
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if( have_bends ){ |
304 |
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sprintf( errMsg, "MoleculeStamp error, %d out of nBends range", |
305 |
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bendIndex ); |
306 |
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return strdup( errMsg ); |
307 |
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} |
308 |
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else return strdup("MoleculeStamp error, nBends not given before" |
309 |
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"first bend declaration." ); |
310 |
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} |
311 |
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312 |
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return NULL; |
313 |
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} |
314 |
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315 |
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char* MoleculeStamp::addTorsion( TorsionStamp* the_torsion, int torsionIndex ){ |
316 |
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317 |
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318 |
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if( have_torsions && torsionIndex < n_torsions ) |
319 |
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torsions[torsionIndex] = the_torsion; |
320 |
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else{ |
321 |
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if( have_torsions ){ |
322 |
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sprintf( errMsg, "MoleculeStamp error, %d out of nTorsions range", |
323 |
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torsionIndex ); |
324 |
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return strdup( errMsg ); |
325 |
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} |
326 |
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else return strdup("MoleculeStamp error, nTorsions not given before" |
327 |
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"first torsion declaration." ); |
328 |
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} |
329 |
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330 |
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return NULL; |
331 |
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} |
332 |
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333 |
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char* MoleculeStamp::checkMe( void ){ |
334 |
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335 |
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int i; |
336 |
gezelter |
957 |
short int no_atom, no_rigidbody; |
337 |
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338 |
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if( !have_name ) return strdup( "MoleculeStamp error. Molecule's name" |
339 |
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" was not given.\n" ); |
340 |
gezelter |
988 |
|
341 |
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if( !have_atoms ){ |
342 |
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return strdup( "MoleculeStamp error. Molecule contains no atoms." ); |
343 |
mmeineke |
377 |
} |
344 |
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|
345 |
gezelter |
957 |
no_rigidbody = 0; |
346 |
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for( i=0; i<n_rigidbodies; i++ ){ |
347 |
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if( rigidBodies[i] == NULL ) no_rigidbody = 1; |
348 |
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} |
349 |
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350 |
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if( no_rigidbody ){ |
351 |
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sprintf( errMsg, |
352 |
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"MoleculeStamp error. Not all of the RigidBodies were" |
353 |
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" declared in molecule \"%s\".\n", name ); |
354 |
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return strdup( errMsg ); |
355 |
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} |
356 |
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|
357 |
mmeineke |
377 |
no_atom = 0; |
358 |
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for( i=0; i<n_atoms; i++ ){ |
359 |
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if( atoms[i] == NULL ) no_atom = 1; |
360 |
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} |
361 |
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362 |
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if( no_atom ){ |
363 |
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sprintf( errMsg, |
364 |
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"MoleculeStamp error. Not all of the atoms were" |
365 |
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" declared in molecule \"%s\".\n", name ); |
366 |
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return strdup( errMsg ); |
367 |
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} |
368 |
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|
369 |
gezelter |
1103 |
|
370 |
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n_integrable = n_atoms; |
371 |
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for (i = 0; i < n_rigidbodies; i++) |
372 |
tim |
1113 |
n_integrable = n_integrable - rigidBodies[i]->getNMembers() + 1; //rigidbody is an integrable object |
373 |
gezelter |
1103 |
|
374 |
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if (n_integrable <= 0 || n_integrable > n_atoms) { |
375 |
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sprintf( errMsg, |
376 |
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"MoleculeStamp error. n_integrable is either <= 0 or" |
377 |
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" greater than n_atoms in molecule \"%s\".\n", name ); |
378 |
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return strdup( errMsg ); |
379 |
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} |
380 |
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|
381 |
mmeineke |
377 |
return NULL; |
382 |
gezelter |
988 |
} |