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#include <stdlib.h> |
| 2 |
#include <stdio.h> |
| 3 |
#include <string.h> |
| 4 |
#include <iostream> |
| 5 |
|
| 6 |
#include "MoleculeStamp.hpp" |
| 7 |
|
| 8 |
char MoleculeStamp::errMsg[500]; |
| 9 |
|
| 10 |
MoleculeStamp::MoleculeStamp(){ |
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|
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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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n_rigidbodies = 0; |
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|
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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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rigidBodies = NULL; |
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|
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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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have_rigidbodies = 0; |
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|
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} |
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|
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MoleculeStamp::~MoleculeStamp(){ |
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int i; |
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|
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if( unhandled != NULL) delete unhandled; |
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|
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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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|
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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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|
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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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|
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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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|
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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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} |
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|
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char* MoleculeStamp::assignString( char* lhs, char* rhs ){ |
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|
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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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|
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char* MoleculeStamp::assignDouble( char* lhs, double rhs ){ |
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int i; |
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|
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if( !strcmp( lhs, "nAtoms" ) ){ |
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n_atoms = (int)rhs; |
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|
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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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" for 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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|
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else if( !strcmp( lhs, "nBonds" ) ){ |
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n_bonds = (int)rhs; |
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|
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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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|
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else if( !strcmp( lhs, "nBends" ) ){ |
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n_bends = (int)rhs; |
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|
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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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|
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else if( !strcmp( lhs, "nTorsions" ) ){ |
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n_torsions = (int)rhs; |
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|
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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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} |
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|
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else if( !strcmp( lhs, "nRigidBodies" ) ){ |
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n_rigidbodies = (int)rhs; |
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|
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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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|
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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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|
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char* MoleculeStamp::assignInt( char* lhs, int rhs ){ |
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int i; |
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|
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if( !strcmp( lhs, "nAtoms" ) ){ |
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n_atoms = rhs; |
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|
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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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|
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else if( !strcmp( lhs, "nBonds" ) ){ |
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n_bonds = rhs; |
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|
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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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|
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else if( !strcmp( lhs, "nBends" ) ){ |
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n_bends = rhs; |
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|
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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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|
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else if( !strcmp( lhs, "nTorsions" ) ){ |
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n_torsions = rhs; |
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|
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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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} |
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|
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else if( !strcmp( lhs, "nRigidBodies" ) ){ |
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n_rigidbodies = rhs; |
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|
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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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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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|
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char* MoleculeStamp::addAtom( AtomStamp* the_atom, int atomIndex ){ |
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|
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if( have_atoms && atomIndex < n_atoms ) atoms[atomIndex] = the_atom; |
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else{ |
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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" |
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" first atom declaration." ); |
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} |
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|
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return NULL; |
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} |
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|
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char* MoleculeStamp::addRigidBody( RigidBodyStamp* the_rigidbody, |
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int rigidBodyIndex ){ |
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|
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if( have_rigidbodies && rigidBodyIndex < n_rigidbodies ) |
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rigidBodies[rigidBodyIndex] = the_rigidbody; |
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else{ |
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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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} |
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else return strdup("MoleculeStamp error, nRigidBodies not given before" |
| 274 |
" first rigidBody declaration." ); |
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} |
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|
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return NULL; |
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} |
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|
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char* MoleculeStamp::addBond( BondStamp* the_bond, int bondIndex ){ |
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|
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|
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if( have_bonds && bondIndex < n_bonds ) bonds[bondIndex] = the_bond; |
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else{ |
| 285 |
if( have_bonds ){ |
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sprintf( errMsg, "MoleculeStamp error, %d out of nBonds range", |
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bondIndex ); |
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return strdup( errMsg ); |
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} |
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else return strdup("MoleculeStamp error, nBonds not given before" |
| 291 |
"first bond declaration." ); |
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} |
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|
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return NULL; |
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} |
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|
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char* MoleculeStamp::addBend( BendStamp* the_bend, int bendIndex ){ |
| 298 |
|
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|
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if( have_bends && bendIndex < n_bends ) bends[bendIndex] = the_bend; |
| 301 |
else{ |
| 302 |
if( have_bends ){ |
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sprintf( errMsg, "MoleculeStamp error, %d out of nBends range", |
| 304 |
bendIndex ); |
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return strdup( errMsg ); |
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} |
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else return strdup("MoleculeStamp error, nBends not given before" |
| 308 |
"first bend declaration." ); |
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} |
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|
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return NULL; |
| 312 |
} |
| 313 |
|
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char* MoleculeStamp::addTorsion( TorsionStamp* the_torsion, int torsionIndex ){ |
| 315 |
|
| 316 |
|
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if( have_torsions && torsionIndex < n_torsions ) |
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torsions[torsionIndex] = the_torsion; |
| 319 |
else{ |
| 320 |
if( have_torsions ){ |
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sprintf( errMsg, "MoleculeStamp error, %d out of nTorsions range", |
| 322 |
torsionIndex ); |
| 323 |
return strdup( errMsg ); |
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} |
| 325 |
else return strdup("MoleculeStamp error, nTorsions not given before" |
| 326 |
"first torsion declaration." ); |
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} |
| 328 |
|
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return NULL; |
| 330 |
} |
| 331 |
|
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char* MoleculeStamp::checkMe( void ){ |
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|
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int i; |
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short int no_atom, no_rigidbody; |
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|
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// Fix for Rigid Bodies!!! Molecules may not have any atoms that |
| 338 |
// they know about. They might have only rigid bodies (which then |
| 339 |
// know about the atoms! |
| 340 |
|
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|
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if( !have_name ) return strdup( "MoleculeStamp error. Molecule's name" |
| 343 |
" was not given.\n" ); |
| 344 |
|
| 345 |
if( !have_rigidbodies && !have_atoms ){ |
| 346 |
return strdup( "MoleculeStamp error. Molecule contains no atoms or RigidBodies." ); |
| 347 |
} |
| 348 |
|
| 349 |
no_rigidbody = 0; |
| 350 |
for( i=0; i<n_rigidbodies; i++ ){ |
| 351 |
if( rigidBodies[i] == NULL ) no_rigidbody = 1; |
| 352 |
} |
| 353 |
|
| 354 |
if( no_rigidbody ){ |
| 355 |
sprintf( errMsg, |
| 356 |
"MoleculeStamp error. Not all of the RigidBodies were" |
| 357 |
" declared in molecule \"%s\".\n", name ); |
| 358 |
return strdup( errMsg ); |
| 359 |
} |
| 360 |
|
| 361 |
no_atom = 0; |
| 362 |
for( i=0; i<n_atoms; i++ ){ |
| 363 |
if( atoms[i] == NULL ) no_atom = 1; |
| 364 |
} |
| 365 |
|
| 366 |
if( no_atom ){ |
| 367 |
sprintf( errMsg, |
| 368 |
"MoleculeStamp error. Not all of the atoms were" |
| 369 |
" declared in molecule \"%s\".\n", name ); |
| 370 |
return strdup( errMsg ); |
| 371 |
} |
| 372 |
|
| 373 |
return NULL; |
| 374 |
} |
| 375 |
|
| 376 |
|
| 377 |
int MoleculeStamp::getTotAtoms() { |
| 378 |
int total_atoms; |
| 379 |
int i; |
| 380 |
|
| 381 |
total_atoms = n_atoms; |
| 382 |
|
| 383 |
if( rigidBodies != NULL ) { |
| 384 |
for( i=0; i<n_rigidbodies; i++ ) |
| 385 |
total_atoms += rigidBodies[i]->getNAtoms(); |
| 386 |
} |
| 387 |
|
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return total_atoms; |
| 389 |
} |
| 390 |
|
