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/* BBAlchemyFilter.m
*
* This format filter does handle read/write of molecules in the
* Alchemy Text (.alchMol or .mol) fileformat.
*
* For interface-info see the header file. The comments in this file mostly
* cover only the real implementation details.
*
* Written by: Thomas Engel
* Created: 15.03.1994 (Copyleft)
* Last modified: 30.10.1994
*/
#import "BBAlchemyFilter.h"
#import "BBFileFilterManager.h"
#import "../BBAppManager.h"
#import "../AtomLibrary.subproj/BBAtomLibraryManager.h"
#import "../BBBeaker.h"
#import "../BBMolecule.h"
#import "../BBAtom.h"
#import "../BBBond.h"
#import <misckit/MiscString.h>
#define MYBUFFERSIZE 500
#define COMMENTTOKEN "#"
#define SINGLEBONDTOKEN "SINGLE"
#define DOUBLEBONDTOKEN "DOUBLE"
#define AROMATICBONDTOKEN "AROMATIC"
// I hate statics but here they might be useful.
// The other variables have been added to the intercase to allow debugging.
static char lineBuffer[MYBUFFERSIZE];
static FILE *inStream;
@implementation BBAlchemyFilter
- (float)canReadFile:(const char*)filename
{
// Let's see if we can handle the file. We will check the extention.
// "alchMol" will be regonized direktly where as the normal "mol"
// extention has to pass so file checking.
id pathString;
id aString;
float answer;
pathString = [MiscString new];
[pathString setPath:filename];
aString = [pathString fileExtension];
if( [aString casecmp:"alchMol"] == 0 )
answer = (float)YES;
else if( [aString casecmp:"mol"] == 0 )
{
// The "mol" extention is not save. We have to check the first line
// for the three magic tokens to see we really have a alchemy file.
inStream = fopen( filename, "r" );
if( inStream == NULL ) return NO;
theLine = [MiscString new];
tokenList = nil;
answer = (float)NO;
if( fgets( lineBuffer, MYBUFFERSIZE, inStream ))
{
[theLine setStringValue:lineBuffer];
tokenList = [theLine tokenize:" \t\n\r" into:nil];
if( [[tokenList objectAt:1] compareStr:"ATOMS,"] == 0 &&
[[tokenList objectAt:3] compareStr:"BONDS,"] == 0 &&
[[tokenList objectAt:5] compareStr:"CHARGES,"] == 0 )
answer = (float)YES;
}
[theLine free];
fclose( inStream );
}
else
answer = (float)NO;
[pathString free];
[aString free];
return answer;
}
- readBeaker:aBeaker fromFile:(const char*)filename
{
// A simple parser for Alchemy molecules.
// The tokenList is only defined as long as its data is not already
// parsed or it contains the parts that have to be parsed. Freeing
// the list is not enough! We have to reset the id to nil to make the
// check work properly.
// Right here we only read the number of data.
id aString;
int atomCount;
int bondCount;
inStream = fopen( filename, "r" );
if( inStream == NULL ) return self;
// We will read the first line and extract all the info in there.
// After that we will read the atoms and bonds.
mol = [BBMolecule new];
theLine = [MiscString new];
tokenList = nil;
if( fgets( lineBuffer, MYBUFFERSIZE, inStream ))
{
[theLine setStringValue:lineBuffer];
tokenList = [theLine tokenize:" \t\n\r" into:nil];
atomCount = [[tokenList objectAt:0] intValue];
bondCount = [[tokenList objectAt:2] intValue];
aString = [theLine substringFromToken:6 toToken:[tokenList count]-1
ofList:tokenList];
[(BBMolecule *)mol setName:[aString stringValue]];
[aString free];
[[tokenList freeObjects] free];
tokenList = nil;
if( [self readAtomData:atomCount] )
[self readBondData:bondCount];
}
[aBeaker addMolecule:mol];
[theLine free];
fclose( inStream );
return self;
}
- (BOOL)readAtomData:(int)count
{
// Reading the atom data
// Right here we will continue to read lines until count atoms have been
// read. In normal Alchemy files the atoms have to follow without a break.
BOOL goAhead = YES;
id anAtom;
id basicAtom;
id atomLibrary;
id token;
atomLibrary = [[NXApp delegate] atomLibrary];
do
{
// Stop after last atom or at files end..
if( count == 0 ) break;
if( !fgets( lineBuffer, MYBUFFERSIZE, inStream ))
{
goAhead = NO;
break;
}
[theLine setStringValue:lineBuffer];
tokenList = [theLine tokenize:" \t\n\r" into:nil];
// Check for comments and blank lines.
// We won't accept less than 6 elements per line.
token = [tokenList objectAt:0];
if( [tokenList count] < 6 ||
[token compareStr:COMMENTTOKEN] == 0 )
{
[[tokenList freeObjects] free];
tokenList = nil;
continue;
}
// Otherwise lets init a new atom from this line:
// We have to find the basicAtom too.
// To find the basic atom we need to convert the Alchemy atomtype
// settings. Therefore we strip of any unwanted character.
token = [tokenList objectAt:1];
[self checkSymbol:token];
anAtom = [BBAtom new];
basicAtom = [atomLibrary findBasicAtomWithSymbol:[token stringValue]];
[anAtom setMotherAtom:basicAtom];
[anAtom setXPos:[[tokenList objectAt:2] doubleValue]];
[anAtom setYPos:[[tokenList objectAt:3] doubleValue]];
[anAtom setZPos:[[tokenList objectAt:4] doubleValue]];
[mol addAtom:anAtom];
--count;
// Lets free the list and make the line as read. We don't need it
// anymore. With count = 0 we have reached the end.
[[tokenList freeObjects] free];
tokenList = nil;
}
while( goAhead );
return goAhead;
}
- (BOOL)readBondData:(int)count
{
// Reading the bond data.
// Right here we will continue to read lines until count bonds are read.
BOOL goAhead = YES;
BBBond * aBond;
id atomList;
id fromAtom;
id toAtom;
id token;
char type;
atomList = [mol atomList];
do
{
// It there are no bonds...let's leave this place..
if( count < 1 ) break;
if( !fgets( lineBuffer, MYBUFFERSIZE, inStream ))
{
goAhead = NO;
break;
}
[theLine setStringValue:lineBuffer];
tokenList = [theLine tokenize:" \t\n\r" into:nil];
// Check for comments, blank lines and new tokens.
// If there are not enough elements we will skip it
token = [tokenList objectAt:0];
if( [tokenList count] < 4 ||
[token compareStr:COMMENTTOKEN] == 0 )
{
[[tokenList freeObjects] free];
tokenList = nil;
continue;
}
// otherwise lets init a new bond from this line:
// We will set the name to some usefull value.
aBond = [BBBond new];
token = [tokenList objectAt:3];
if( [token compareStr:SINGLEBONDTOKEN] == 0 )
type = BOND_SINGLE;
else if( [token compareStr:DOUBLEBONDTOKEN] == 0 )
type = BOND_DOUBLE;
else if( [token compareStr:AROMATICBONDTOKEN] == 0 )
type = BOND_DOUBLE_DELOCATED;
else
type = BOND_SINGLE;
fromAtom = [atomList objectAt:[[tokenList objectAt:1] intValue]-1];
toAtom = [atomList objectAt:[[tokenList objectAt:2] intValue]-1];
[aBond connect:fromAtom to:toAtom with:type];
// We will use the token string object to compose our Bond name.
[token setStringValue:[fromAtom symbol]];
[token catStringValue:"±"];
[token catStringValue:[toAtom symbol]];
[aBond setName:[token stringValue]];
[mol addBond:aBond];
--count;
// Lets free the list and make the line as read. We don't need it
// anymore
[[tokenList freeObjects] free];
tokenList = nil;
}
while( goAhead );
return goAhead;
}
- checkSymbol:symbol
{
// Here we try to simplify a given atom symbol.
// The original symbols have additional information that we might not need
// or can not cope with right now.
// This method will change the original string object.
if( [symbol compareStr:"C2"] == 0 ||
[symbol compareStr:"C3"] == 0 ||
[symbol compareStr:"CAR"] == 0 ||
[symbol compareStr:"CC"] == 0 ||
[symbol compareStr:"CK"] == 0 ||
[symbol compareStr:"CM"] == 0 ||
[symbol compareStr:"CN"] == 0 ||
[symbol compareStr:"CQ"] == 0 ||
[symbol compareStr:"CR"] == 0 ||
[symbol compareStr:"CT"] == 0 ||
[symbol compareStr:"CV"] == 0 ||
[symbol compareStr:"CW"] == 0)
[symbol setStringValue:"C"];
else if( [symbol compareStr:"H2"] == 0 ||
[symbol compareStr:"H3"] == 0 ||
[symbol compareStr:"HO"] == 0 ||
[symbol compareStr:"HS"] == 0 )
[symbol setStringValue:"H"];
else if( [symbol compareStr:"NM"] == 0 ||
[symbol compareStr:"N2"] == 0 ||
[symbol compareStr:"N3"] == 0 ||
[symbol compareStr:"N3+"] == 0 ||
[symbol compareStr:"NPL3"] == 0 ||
[symbol compareStr:"NB"] == 0 ||
[symbol compareStr:"NC"] == 0 ||
[symbol compareStr:"NT"] == 0 )
[symbol setStringValue:"N"];
else if( [symbol compareStr:"O2"] == 0 ||
[symbol compareStr:"O3"] == 0 ||
[symbol compareStr:"OH"] == 0 )
[symbol setStringValue:"O"];
else if( [symbol compareStr:"SH"] == 0 )
[symbol setStringValue:"S"];
else if( [symbol compareStr:"P3D"] == 0 )
[symbol setStringValue:"P"];
return self;
}
- writeBeaker:aBeaker toFile:(const char *)filename
{
return self;
}
@end
/*
* History: 30.10.94 Switched to the MiscString.
*
* 14.05.94 Changes to work with new BB... objects.
*
* 25.03.94 Added checkSymbol.
*
* 15.03.94 A basic implementation.
*
*
* Bugs: - We will watch for '#' comment even they are not defined for that
* data format..
*
* - Does not handle charges and strips extra data from the symbol
* name. These symbolextentions may be automatically typed to our
* symbol addition area..perhaps with some conversion ?? (15.03.94)
*/
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