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/* BBMvtxFilter.m
*
* This format filter does handle read/write of molecules in the
* MoleViewer Text (.mvt) 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: 14.05.1994
*/
#import "BBMvtxFilter.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 ELLIPSEDATATOKEN "ELLIPSE"
#define SINGLEBONDTOKEN "S"
#define DOUBLEBONDTOKEN "D"
#define AROMATICBONDTOKEN "A"
// 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 BBMvtxFilter
- (float)canReadFile:(const char*)filename
{
// Let's see if we can handle the file. Well this is a stupid check.
// Right now we only check the file extention. If its "mvt" we
// will do it.
// Normally we should return (0, 0.5, 1) according to the percentage of
// data we understand. More a fuzzy logic with MAYBE.
id pathString;
id aString;
float answer;
pathString = [MiscString new];
[pathString setPath:filename];
aString = [pathString fileExtension];
if( [aString casecmp:"mvt"] == 0 )
answer = (float)YES;
else answer = (float)NO;
[pathString free];
[aString free];
return answer;
}
- readBeaker:aBeaker fromFile:(const char*)filename
{
// A simple parser for MolViewer Textformat 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.
BOOL goAhead = YES;
id pathString;
id aString;
inStream = fopen( filename, "r" );
if( inStream == NULL ) return self;
// So lets parse the data get one line and do it. We will
// not take care of all the settings! We'll say that the current line
// is already parsed because we want another one to get read.
mol = [BBMolecule new];
pathString = [MiscString new];
[pathString setPath:filename];
aString = [pathString fileBasename];
[(BBMolecule *)mol setName:[aString stringValue]];
[aString free];
[pathString free];
theLine = [MiscString new];
tokenList = nil;
do
{
// Read a new line if no already done. Let the MOString create the
// tokenList. We will only free it.
if( !tokenList )
{
if( !fgets( lineBuffer, MYBUFFERSIZE, inStream )) break;
[theLine setStringValue:lineBuffer];
tokenList = [theLine tokenize:" \t\n\r" into:nil];
}
// Now lets read till we have to stop.
goAhead = [self readNewLine];
}
while( goAhead );
[aBeaker addMolecule:mol];
[theLine free];
fclose( inStream );
return self;
}
- (BOOL)readNewLine
{
// Lets check the tokens..skip empty lines and comments
// theLine and tokenList are already set according to our lineBuffer
// If there is nothing to parse we want to see the next line..
//
// This algorythm is stupid. It only checks for the two-token-line and
// says that this is the line with the atom/bond counts. This will work
// But is not really nice!
// Although we check for ELLIPSE...we don't read the data.
BOOL goAhead = YES;
id token;
int atomCount;
int bondCount;
token = [tokenList objectAt:0];
if( [tokenList count] == 0 )
{
[[tokenList freeObjects] free];
tokenList = nil;
}
else if( [tokenList count] == 2 )
{
// First we'll take the atom count and then we take the bond count.
// If reading atoms was successful we will read the bonds.
// We won't continue after that!
atomCount = [[tokenList objectAt:0] intValue];
bondCount = [[tokenList objectAt:1] intValue];
[[tokenList freeObjects] free];
tokenList = nil;
if( [self readAtomData:atomCount] )
[self readBondData:bondCount];
goAhead = NO;
}
else if( [token compareStr:ELLIPSEDATATOKEN] == 0 )
{
[[tokenList freeObjects] free];
tokenList = nil;
// We should read the ellipse info here.
}
// Currently we do not evaluate every possible token.
// We will simple ingore everything else and just free the tokenList
// if this has not already happened.
else
{
[[tokenList freeObjects] free];
tokenList = nil;
}
return goAhead;
}
- (BOOL)readAtomData:(int)count
{
// Reading the atom data
// Right here we will continue to read lines until count atoms have been
// read. In normal MVTX 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
{
// Leave this place at files end or when there are no more atoms
// to be read.
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 4 elements per line.
token = [tokenList objectAt:0];
if( [tokenList count] < 4 ||
[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 MolViewer atomtype
// settings.
if( [token compareStr:"C*"] == 0 ||
[token compareStr:"CA"] == 0 ||
[token compareStr:"CB"] == 0 ||
[token compareStr:"CC"] == 0 ||
[token compareStr:"CK"] == 0 ||
[token compareStr:"CM"] == 0 ||
[token compareStr:"CN"] == 0 ||
[token compareStr:"CQ"] == 0 ||
[token compareStr:"CR"] == 0 ||
[token compareStr:"CT"] == 0 ||
[token compareStr:"CV"] == 0 ||
[token compareStr:"CW"] == 0)
[token setStringValue:"C"];
else if( [token compareStr:"H2"] == 0 ||
[token compareStr:"H3"] == 0 ||
[token compareStr:"HO"] == 0 ||
[token compareStr:"HS"] == 0 )
[token setStringValue:"H"];
else if( [token compareStr:"NM"] == 0 ||
[token compareStr:"N2"] == 0 ||
[token compareStr:"N3"] == 0 ||
[token compareStr:"N*"] == 0 ||
[token compareStr:"NA"] == 0 ||
[token compareStr:"NB"] == 0 ||
[token compareStr:"NC"] == 0 ||
[token compareStr:"NT"] == 0 )
[token setStringValue:"N"];
else if( [token compareStr:"O2"] == 0 ||
[token compareStr:"OS"] == 0 ||
[token compareStr:"OH"] == 0 )
[token setStringValue:"O"];
else if( [token compareStr:"SH"] == 0 )
[token setStringValue:"S"];
anAtom = [BBAtom new];
basicAtom = [atomLibrary findBasicAtomWithSymbol:[token stringValue]];
[anAtom setMotherAtom:basicAtom];
[anAtom setXPos:[[tokenList objectAt:1] doubleValue]];
[anAtom setYPos:[[tokenList objectAt:2] doubleValue]];
[anAtom setZPos:[[tokenList objectAt:3] doubleValue]];
[mol addAtom:anAtom];
--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;
}
- (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
{
// We will leave this place when there are no more bonds to be read.
// After that left read the new line and quite at files end.
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] < 3 ||
[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:2];
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:0] intValue]];
toAtom = [atomList objectAt:[[tokenList objectAt:1] intValue]];
[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;
}
- 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.
*
* 15.03.94 A basic implementation.
*
*
* Bugs: - We could check the MVTX Magic word instead of relying on the file-
* extension.
*
* - Does not handle Eliptic, charge and labeling info (15.03.94)
*/
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