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tjod |
3 |
#define EXTERN extern |
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#include "pcwin.h" |
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#include "pcmod.h" |
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#include "energies.h" |
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#include "substr.h" |
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#include "pdb.h" |
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#include "solv.h" |
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#include "fix.h" |
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#include "atom_k.h" |
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void rdfile(int, int); |
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void rdpcm(int,int); |
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void pcmfin(int,int); |
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void pcmfout(int); |
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void gettoken(void); |
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int make_atom(int,float,float,float,char *); |
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void initialize(void); |
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void make_bond(int,int,int); |
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void message_alert(char *, char *); |
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FILE * fopen_path ( char * , char * , char * ) ; |
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int mm3_mmxtype(int); |
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int mmff_mmxtype(int); |
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int amber_mmxtype(int); |
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int opls_mmxtype(int); |
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void set_atomtype(int,int,int,int,int,int); |
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int FetchRecord(FILE *, char *); |
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void zero_data(void); |
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void read_datafiles(char *); |
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void read_atomtypes(int); |
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void get_atomname(int,char *); |
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void clean_string(char *); |
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void hdel(int); |
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/* COMMON translations */ |
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struct t_pcmfile { |
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char string[200]; |
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int head; |
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char token[20]; |
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int state; |
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unsigned int nocaps; |
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} pcmfile; |
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EXTERN struct t_minim_values { |
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int iprint, ndc, nconst; |
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float dielc; |
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} minim_values; |
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EXTERN struct t_ts_bondorder { |
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float fbnd[15]; |
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} ts_bondorder; |
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EXTERN struct t_files { |
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int nfiles, append, batch, icurrent, ibatno; |
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} files; |
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EXTERN struct t_pistuf { |
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int iuv, ihuck, mult; |
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int norb, nplane, jprint; |
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int *listpi; |
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int nbpi, ntpi, **pibond, **pitor, **piplane ; |
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} pistuf; |
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EXTERN struct t_units { |
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double bndunit, cbnd, qbnd; |
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double angunit, cang, qang, pang, sang, aaunit; |
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double stbnunit, ureyunit, torsunit, storunit, v14scale; |
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double aterm, bterm, cterm, dielec, chgscale; |
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} units; |
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EXTERN struct t_residues { |
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int nchain, ichainstart[10]; |
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int ngroup, iresnum[1000], irestype[1000], istartatom[1000]; |
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} residues; |
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EXTERN int oh2, oh3, oh6; |
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EXTERN int mm3_mmx[]; |
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EXTERN int mmff_mmx[]; |
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EXTERN int amber_mmx[]; |
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EXTERN int opls_mmx[]; |
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// ======================================================== |
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void read_atomtypes(int field) |
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{ |
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char string[20]; |
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if (field == MM3) |
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{ |
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strcpy(string,"mm3.prm"); |
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zero_data(); |
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read_datafiles(string); |
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} else if (field == MMFF94) |
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{ |
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strcpy(string,"mmff94.prm"); |
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zero_data(); |
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read_datafiles(string); |
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} else if (field == AMBER) |
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{ |
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strcpy(string,"amber.prm"); |
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zero_data(); |
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read_datafiles(string); |
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} else if (field == OPLSAA) |
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{ |
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strcpy(string,"oplsaa.prm"); |
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zero_data(); |
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read_datafiles(string); |
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} else if (field == MMX) |
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{ |
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strcpy(string,"mmxconst.prm"); |
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zero_data(); |
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read_datafiles(string); |
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} |
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} |
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// ======================================================== |
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void get_atomname(int type,char *name) |
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{ |
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int i; |
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strcpy(name,""); |
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for (i=1; i <= MAXATOMTYPE; i++) |
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{ |
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if (type == atom_k.type[i]) |
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{ |
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strcpy(name,atom_k.symbol[i]); |
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return; |
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} |
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} |
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} |
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// ======================================================== |
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int mm3_mmxtype(int mm3type) |
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{ |
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int i; |
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if (mm3type < 153) |
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i = mm3_mmx[mm3type-1]; |
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else if (mm3type == 200) |
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i = 60; |
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else |
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i = mm3type; |
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return(i); |
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} |
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// ================================================== |
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int mmff_mmxtype(int mmfftype) |
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{ |
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int i; |
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if (mmfftype < 100) |
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i = mmff_mmx[mmfftype-1]; |
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else |
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i = mmfftype; |
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return(i); |
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} |
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// ================================================== |
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int amber_mmxtype(int ambertype) |
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{ |
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int i; |
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if (ambertype < 43) |
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i = amber_mmx[ambertype-1]; |
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else |
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i = ambertype; |
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return(i); |
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} |
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// ================================================== |
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int opls_mmxtype(int oplstype) |
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{ |
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int i; |
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if (oplstype < 82) |
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i = opls_mmx[oplstype-1]; |
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else |
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i = oplstype; |
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return(i); |
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} |
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// ================================================== |
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void pcmfout(int mode) |
| 172 |
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{ |
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FILE *wfile; |
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int icoord, imetflag, ispin,lps; |
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int i,j,isub,icount, itype; |
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/* Mode = 1 normal packed write operation |
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* Mode = 2 fast no questions asked unpacked write of pcmod.bak |
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* Mode = 3 fast no questions ot file = wfile |
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* mode = 4 start of minim to pcmod.bak but ask questions about pi */ |
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if( mode == 1 ) |
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{ |
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/* assume append is set when we get a filename that exists */ |
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/* put up dialog box with current structure title, pi flags |
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and added constants question */ |
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if( files.append ) |
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wfile = fopen_path(Savebox.path,Savebox.fname,"a"); |
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else |
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wfile = fopen_path(Savebox.path,Savebox.fname,"w"); |
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} |
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else if( mode == 2 || mode == 4 ) |
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{ |
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wfile = fopen_path(pcwindir,"pcmod.bak","w"); |
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} |
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else if( mode == 3 ) |
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{ |
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if( files.append ) |
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wfile = fopen_path(Savebox.path,Savebox.fname,"a"); |
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else |
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wfile = fopen_path(Savebox.path,Savebox.fname,"w"); |
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} |
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if (wfile == NULL) |
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{ |
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message_alert("Error opening file in PCMFOUT. Cannot create file","PCM File"); |
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return; |
| 206 |
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} |
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// remove lone pairs if not writing mmx types |
| 208 |
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lps = FALSE; |
| 209 |
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if (default_outtype != MMX) |
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{ |
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for (i=1; i <= natom; i++) |
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{ |
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if (atom[i].mmx_type == 20) |
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{ |
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lps = TRUE; |
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break; |
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} |
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} |
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} |
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if (lps == TRUE) |
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hdel(1); |
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/* start of file writing */ |
| 224 |
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fprintf(wfile,"{PCM %s\n",Struct_Title); |
| 225 |
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fprintf(wfile,"NA %d\n",natom); |
| 226 |
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/* flags */ |
| 228 |
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fprintf(wfile,"FL "); |
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fprintf(wfile,"EINT%d ",minim_values.ndc); |
| 230 |
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if( units.dielec != 1.5 ) |
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fprintf(wfile,"DIELC%f ",units.dielec); |
| 232 |
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fprintf(wfile,"\n"); |
| 233 |
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// default output filetypes |
| 234 |
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fprintf(wfile,"ATOMTYPES %d\n",default_outtype); |
| 235 |
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/* substructure name information */ |
| 236 |
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icount = 0; |
| 237 |
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for (i=0; i < MAXSS; i++) |
| 238 |
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if ( substr.istract[i] != 0) |
| 239 |
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icount++; |
| 240 |
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for (i=0; i < icount; i++) |
| 241 |
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fprintf(wfile,"SSNAME %s\n",substr.strname[i]); |
| 242 |
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/* box of solvent information */ |
| 243 |
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if (solv.nmols > 0) |
| 244 |
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{ |
| 245 |
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fprintf(wfile,"NMOL %d DENSITY %f BOX %f %f %f\n",solv.nmols,solv.density,solv.boxx, solv.boxy,solv.boxz); |
| 246 |
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} |
| 247 |
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/* |
| 248 |
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if( minim_values.nconst && mode > 1 ) |
| 249 |
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fprintf(wfile,"CO FILE %s\n",constf.cname);*/ |
| 250 |
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/* atoms and bonds lists */ |
| 251 |
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for( i = 1; i <= natom; i++ ) |
| 252 |
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{ |
| 253 |
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if (default_outtype == MMX) |
| 254 |
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{ |
| 255 |
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itype = atom[i].mmx_type; |
| 256 |
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} else if (default_outtype == MM3) |
| 257 |
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{ |
| 258 |
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itype = atom[i].mm3_type; |
| 259 |
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} else if (default_outtype == MMFF94) |
| 260 |
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{ |
| 261 |
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itype = atom[i].mmff_type; |
| 262 |
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} |
| 263 |
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fprintf(wfile,"AT %d %d %8.4f %8.4f %8.4f",i,itype,atom[i].x, |
| 264 |
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atom[i].y, atom[i].z); |
| 265 |
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// bonds |
| 266 |
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fprintf(wfile," B"); |
| 267 |
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for( j = 0; j < MAXIAT; j++ ) |
| 268 |
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{ |
| 269 |
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if( atom[i].iat[j]) |
| 270 |
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{ |
| 271 |
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fprintf(wfile," %d %d",atom[i].iat[j],atom[i].bo[j]); |
| 272 |
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} |
| 273 |
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} |
| 274 |
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if (atom[i].biotype > 0 ) |
| 275 |
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{ |
| 276 |
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fprintf(wfile," D %d",atom[i].biotype); |
| 277 |
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fprintf(wfile," N %d",atom[i].residue); |
| 278 |
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} |
| 279 |
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if( atom[i].substr[0] > 0 ) |
| 280 |
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{ |
| 281 |
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fprintf(wfile," S "); |
| 282 |
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isub = 0; |
| 283 |
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for( j = 0; j < MAXSS; j++ ) |
| 284 |
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{ |
| 285 |
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if( (atom[i].substr[0] & (1L << j) ) && (substr.istract[j]) ) |
| 286 |
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isub = j; |
| 287 |
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} |
| 288 |
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fprintf(wfile,"%d ",isub); |
| 289 |
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} |
| 290 |
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if( atom[i].flags & (1L << HBOND_MASK) ) |
| 291 |
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fprintf(wfile," H "); |
| 292 |
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if( atom[i].flags & (1L << PI_MASK) ) |
| 293 |
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fprintf(wfile," P "); |
| 294 |
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if( atom[i].mmx_type >= 300 ) |
| 295 |
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{ |
| 296 |
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icoord = 0; |
| 297 |
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ispin = -1; |
| 298 |
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imetflag = 0; |
| 299 |
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if( atom[i].flags & (1L << SATMET_MASK) ) |
| 300 |
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imetflag += 2; |
| 301 |
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if( atom[i].flags & (1L << GT18e_MASK) ) |
| 302 |
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imetflag += 1; |
| 303 |
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if( imetflag == 2 ) |
| 304 |
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icoord = 0; |
| 305 |
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if( imetflag == 1 ) |
| 306 |
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icoord = 2; |
| 307 |
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if( imetflag == 3 ) |
| 308 |
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{ |
| 309 |
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icoord = 1; |
| 310 |
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imetflag = 0; |
| 311 |
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if( atom[i].flags & (1L << LOWSPIN_MASK) ) |
| 312 |
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imetflag += 2; |
| 313 |
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if( atom[i].flags & (1L << SQPLAN_MASK) ) |
| 314 |
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imetflag += 1; |
| 315 |
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if( imetflag == 2 ) |
| 316 |
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ispin = 0; |
| 317 |
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if( imetflag == 3 ) |
| 318 |
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ispin = 2; |
| 319 |
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if( imetflag == 1 ) |
| 320 |
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ispin = 1; |
| 321 |
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} |
| 322 |
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if( icoord ) |
| 323 |
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{ |
| 324 |
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fprintf(wfile," M %d",icoord); |
| 325 |
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if( ispin >= 0 ) |
| 326 |
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fprintf(wfile," %d",ispin); |
| 327 |
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} |
| 328 |
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fprintf(wfile," R %g",atom[i].radius); |
| 329 |
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} |
| 330 |
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if( atom[i].charge ) |
| 331 |
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{ |
| 332 |
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fprintf(wfile," C %g",atom[i].charge); |
| 333 |
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} |
| 334 |
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if (solv.nmols > 0) |
| 335 |
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fprintf(wfile," ML %d",atom[i].molecule); |
| 336 |
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fprintf(wfile,"\n"); |
| 337 |
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} |
| 338 |
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if( fxtor.nfxtor == 1 || fxtor.nfxtor == 2 ) |
| 339 |
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{ |
| 340 |
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fprintf(wfile,"DD %d %d %d %d FROM %d TO %d BY %d\n",fxtor.iatom[0][0], |
| 341 |
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fxtor.iatom[0][1], fxtor.iatom[0][2], fxtor.iatom[0][3], fxtor.start_ang[0], |
| 342 |
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fxtor.final_ang[0], fxtor.step[0] ); |
| 343 |
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if( fxtor.nfxtor == 2 ) |
| 344 |
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{ |
| 345 |
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fprintf(wfile,"DD %d %d %d %d FROM %d TO %d BY %d\n",fxtor.iatom[1][0], |
| 346 |
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fxtor.iatom[1][1], fxtor.iatom[1][2], fxtor.iatom[1][3], fxtor.start_ang[1], |
| 347 |
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fxtor.final_ang[1], fxtor.step[1] ); |
| 348 |
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} |
| 349 |
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} |
| 350 |
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if (fixdis.nfxstr) |
| 351 |
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{ |
| 352 |
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for( i = 0; i < fixdis.nfxstr; i++ ) |
| 353 |
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{ |
| 354 |
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fprintf(wfile,"FIX DIS %d %d R %7.3f K %7.3f\n",fixdis.ifxstr[i][0], |
| 355 |
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fixdis.ifxstr[i][1], fixdis.fxstrd[i], fixdis.fxstrc[i] ); |
| 356 |
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} |
| 357 |
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} |
| 358 |
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for (i=0; i < 15; i++) |
| 359 |
|
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{ |
| 360 |
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if (ts_bondorder.fbnd[i] > 0.0F) |
| 361 |
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{ |
| 362 |
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fprintf(wfile,"FBND"); |
| 363 |
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for (j=0; j<15; j++) |
| 364 |
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{ |
| 365 |
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fprintf(wfile," %5.3f",ts_bondorder.fbnd[j]); |
| 366 |
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} |
| 367 |
|
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fprintf(wfile,"\n"); |
| 368 |
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break; |
| 369 |
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} |
| 370 |
|
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} |
| 371 |
|
|
if (residues.ngroup > 0) |
| 372 |
|
|
{ |
| 373 |
|
|
for (i=0; i < residues.ngroup; i++) |
| 374 |
|
|
fprintf(wfile,"Residue %d %d %d\n",residues.iresnum[i], |
| 375 |
|
|
residues.irestype[i],residues.istartatom[i]); |
| 376 |
|
|
} |
| 377 |
|
|
|
| 378 |
|
|
fprintf(wfile,"}\n"); |
| 379 |
|
|
fclose(wfile); |
| 380 |
|
|
} /* end of function */ |
| 381 |
|
|
|
| 382 |
|
|
/* ------------------------------- */ |
| 383 |
|
|
|
| 384 |
|
|
#define NL gettoken(); if (pcmfile.head == 1000) goto L_30; |
| 385 |
|
|
#define ALPHABETIC 2 |
| 386 |
|
|
#define NUMERIC 1 |
| 387 |
|
|
|
| 388 |
|
|
void pcmfin(int nth,int isubred) |
| 389 |
|
|
{ |
| 390 |
|
|
unsigned int substrismin; |
| 391 |
|
|
int newatom, i, ibondcount, ibonded, ibondorder, |
| 392 |
|
|
icoord, imetcount, ioffset, ispin, iprint, |
| 393 |
|
|
isubmap[MAXSS], j, numbonds, niatom, itemp; |
| 394 |
|
|
int newat, newtype, ifile, isMetal, biotype, itype; |
| 395 |
|
|
long int mask; |
| 396 |
|
|
char ianame[3]; |
| 397 |
|
|
float ddcount, xtmp, ytmp, ztmp; |
| 398 |
|
|
FILE *pcminfile; |
| 399 |
|
|
|
| 400 |
|
|
imetcount = 0; |
| 401 |
|
|
isMetal = FALSE; |
| 402 |
|
|
ddcount = 0; |
| 403 |
|
|
substrismin = False; |
| 404 |
|
|
fxtor.nfxtor = 0; |
| 405 |
|
|
pcmfile.nocaps = False; |
| 406 |
|
|
numbonds = 0; |
| 407 |
|
|
ibondcount = 0; |
| 408 |
|
|
units.dielec = 1.5; |
| 409 |
|
|
|
| 410 |
|
|
for (i = 0; i < MAXSS; i++) |
| 411 |
|
|
{ |
| 412 |
|
|
isubmap[i] = 0; |
| 413 |
|
|
} |
| 414 |
|
|
|
| 415 |
|
|
if( isubred == 1 ) |
| 416 |
|
|
{ |
| 417 |
|
|
ioffset = natom; |
| 418 |
|
|
substr.istract[substr.icurstr] = TRUE; |
| 419 |
|
|
} |
| 420 |
|
|
else |
| 421 |
|
|
{ |
| 422 |
|
|
ioffset = 0; |
| 423 |
|
|
} |
| 424 |
|
|
|
| 425 |
|
|
pcminfile = fopen_path(Openbox.path,Openbox.fname,"r"); |
| 426 |
|
|
|
| 427 |
|
|
if (pcminfile == NULL) |
| 428 |
|
|
{ |
| 429 |
|
|
message_alert("Error Opening PCM file","PCM Setup"); |
| 430 |
|
|
fprintf(pcmoutfile,"PCMFIN error opening file %d %s\n",nth,Openbox.fname); |
| 431 |
|
|
return; |
| 432 |
|
|
} |
| 433 |
|
|
|
| 434 |
|
|
ifile = 0; |
| 435 |
|
|
if (nth != 1) |
| 436 |
|
|
{ |
| 437 |
|
|
while ( FetchRecord(pcminfile,pcmfile.string) ) |
| 438 |
|
|
{ |
| 439 |
|
|
if (strncasecmp(pcmfile.string,"{PCM",4) == 0) |
| 440 |
|
|
{ |
| 441 |
|
|
ifile++; |
| 442 |
|
|
if (ifile == nth) |
| 443 |
|
|
break; |
| 444 |
|
|
} |
| 445 |
|
|
} |
| 446 |
|
|
}else |
| 447 |
|
|
{ |
| 448 |
|
|
FetchRecord(pcminfile,pcmfile.string); |
| 449 |
|
|
} |
| 450 |
|
|
|
| 451 |
|
|
/* finished scaning to starting structure now read file */ |
| 452 |
|
|
if (isubred == 0) |
| 453 |
|
|
{ |
| 454 |
|
|
sscanf(pcmfile.string, "{PCM %60c", Struct_Title); |
| 455 |
|
|
clean_string(Struct_Title); |
| 456 |
|
|
strcpy(substr.strname[0]," "); |
| 457 |
|
|
strncpy(substr.strname[0],Struct_Title,20); |
| 458 |
|
|
} else |
| 459 |
|
|
{ |
| 460 |
|
|
if (natom < 1 ) |
| 461 |
|
|
{ |
| 462 |
|
|
sscanf(pcmfile.string, "{PCM %60c", Struct_Title); |
| 463 |
|
|
clean_string(Struct_Title); |
| 464 |
|
|
strcpy(substr.strname[0]," "); |
| 465 |
|
|
strncpy(substr.strname[0],Struct_Title,20); |
| 466 |
|
|
} else |
| 467 |
|
|
{ |
| 468 |
|
|
// read substructure name |
| 469 |
|
|
strcpy(substr.strname[substr.icurstr]," "); |
| 470 |
|
|
sscanf(pcmfile.string,"{PCM %s\n", substr.strname[substr.icurstr]); |
| 471 |
|
|
} |
| 472 |
|
|
} |
| 473 |
|
|
L_30: |
| 474 |
|
|
FetchRecord(pcminfile,pcmfile.string); |
| 475 |
|
|
*(pcmfile.string + strlen(pcmfile.string) ) = '\0'; |
| 476 |
|
|
if (feof(pcminfile)) |
| 477 |
|
|
goto L_170; |
| 478 |
|
|
pcmfile.head = 1; |
| 479 |
|
|
NL; |
| 480 |
|
|
L_40: |
| 481 |
|
|
if (strcmp(pcmfile.token, "NA") == 0) |
| 482 |
|
|
{ |
| 483 |
|
|
gettoken(); |
| 484 |
|
|
if (pcmfile.head == 1000) |
| 485 |
|
|
goto L_30; |
| 486 |
|
|
niatom = atoi(pcmfile.token); |
| 487 |
|
|
if (niatom + ioffset > MAXATOM) |
| 488 |
|
|
{ |
| 489 |
|
|
natom = ioffset; |
| 490 |
|
|
fclose(pcminfile); |
| 491 |
|
|
message_alert(" Maximum number of atoms exceeded in PCMFIN","PCM Setup"); |
| 492 |
|
|
fprintf(pcmoutfile," unable to continue reading, more than Max atoms %d\n",MAXATOM); |
| 493 |
|
|
return; |
| 494 |
|
|
} |
| 495 |
|
|
niatom += ioffset; |
| 496 |
|
|
NL; |
| 497 |
|
|
goto L_30; |
| 498 |
|
|
} else if (strcmp(pcmfile.token,"ATOMTYPES") == 0) |
| 499 |
|
|
{ |
| 500 |
|
|
gettoken(); |
| 501 |
|
|
if (pcmfile.head == 1000) |
| 502 |
|
|
goto L_30; |
| 503 |
|
|
itemp = atoi(pcmfile.token); |
| 504 |
|
|
if (itemp != default_intype) |
| 505 |
|
|
{ |
| 506 |
|
|
default_intype = itemp; |
| 507 |
|
|
read_atomtypes(default_intype); |
| 508 |
|
|
} |
| 509 |
|
|
NL; |
| 510 |
|
|
goto L_30; |
| 511 |
|
|
} else if (strcmp(pcmfile.token,"SSNAME") == 0 && isubred == 0) // substructure name |
| 512 |
|
|
{ |
| 513 |
|
|
gettoken(); |
| 514 |
|
|
if (pcmfile.head == 1000) goto L_30; |
| 515 |
|
|
for (i=0; i < MAXSS; i++) |
| 516 |
|
|
{ |
| 517 |
|
|
if (substr.istract[i] == FALSE) |
| 518 |
|
|
{ |
| 519 |
|
|
substr.istract[i] = TRUE; |
| 520 |
|
|
strcpy(substr.strname[i],pcmfile.token); |
| 521 |
|
|
break; |
| 522 |
|
|
} |
| 523 |
|
|
} |
| 524 |
|
|
} else if (strcmp(pcmfile.token, "NT") == 0) /* This is for Amino Acids */ |
| 525 |
|
|
{ |
| 526 |
|
|
NL; |
| 527 |
|
|
i = atoi(pcmfile.token); /* i is atom number of N terminus */ |
| 528 |
|
|
mask = 1L << NTERM; /* use bit 0 of substr 1 for N terminus*/ |
| 529 |
|
|
atom[i+ioffset].flags |= mask; |
| 530 |
|
|
|
| 531 |
|
|
NL; |
| 532 |
|
|
if (strcmp(pcmfile.token, "CT") == 0) |
| 533 |
|
|
{ |
| 534 |
|
|
NL; |
| 535 |
|
|
i = atoi(pcmfile.token); /* i is atom number of C terminus */ |
| 536 |
|
|
mask = 1L << CNTERM; /* use bit 1 of substr 1 for C terminus */ |
| 537 |
|
|
atom[i+ioffset].flags |= mask; |
| 538 |
|
|
} |
| 539 |
|
|
} else if (strcmp(pcmfile.token, "5PRIME") == 0) /* This is for Nucleic Acids */ |
| 540 |
|
|
{ |
| 541 |
|
|
NL; |
| 542 |
|
|
i = atoi(pcmfile.token); /* i is atom number of 5prime terminus */ |
| 543 |
|
|
mask = 1L << P5; |
| 544 |
|
|
atom[i+ioffset].flags |= mask; |
| 545 |
|
|
}else if (strcmp(pcmfile.token, "3PRIME") == 0) /* This is for Nucleic Acids */ |
| 546 |
|
|
{ |
| 547 |
|
|
NL; |
| 548 |
|
|
i = atoi(pcmfile.token); /* i is atom number of C terminus */ |
| 549 |
|
|
mask = 1L << P3; /* use bit 1 of substr 1 for C terminus */ |
| 550 |
|
|
atom[i+ioffset].flags |= mask; |
| 551 |
|
|
} else if (strcmp(pcmfile.token, "FG") == 0) /* This is for functional groups */ |
| 552 |
|
|
{ |
| 553 |
|
|
NL; |
| 554 |
|
|
i = atoi(pcmfile.token); /* i is atom number of connect point */ |
| 555 |
|
|
mask = 1L << DUMMY; /* use bit 0 of substr 1 for connect*/ |
| 556 |
|
|
atom[i+ioffset].flags |= mask; |
| 557 |
|
|
|
| 558 |
|
|
} else if (strcmp(pcmfile.token, "OT") == 0) /* This is for Sugars */ |
| 559 |
|
|
{ |
| 560 |
|
|
NL; |
| 561 |
|
|
i = atoi(pcmfile.token); /* i is atom number of O terminus */ |
| 562 |
|
|
mask = 1L << NTERM; /* use bit 0 of substr 1 for O terminus*/ |
| 563 |
|
|
atom[i+ioffset].flags |= mask; |
| 564 |
|
|
|
| 565 |
|
|
NL; |
| 566 |
|
|
if (strcmp(pcmfile.token, "CT") == 0) |
| 567 |
|
|
{ |
| 568 |
|
|
NL; |
| 569 |
|
|
i = atoi(pcmfile.token); /* i is atom number of H terminus */ |
| 570 |
|
|
mask = 1L << CNTERM; /* use bit 1 of substr 1 for H terminus */ |
| 571 |
|
|
atom[i+ioffset].flags |= mask; |
| 572 |
|
|
} |
| 573 |
|
|
|
| 574 |
|
|
NL; |
| 575 |
|
|
if (strcmp(pcmfile.token, "OTWO") == 0) |
| 576 |
|
|
{ |
| 577 |
|
|
NL; |
| 578 |
|
|
i = atoi(pcmfile.token); /* i is atom number of H terminus */ |
| 579 |
|
|
oh2 = i+ioffset; |
| 580 |
|
|
} |
| 581 |
|
|
|
| 582 |
|
|
NL; |
| 583 |
|
|
if (strcmp(pcmfile.token, "OTHR") == 0) |
| 584 |
|
|
{ |
| 585 |
|
|
NL; |
| 586 |
|
|
i = atoi(pcmfile.token); /* i is atom number of H terminus */ |
| 587 |
|
|
oh3 = i+ioffset; |
| 588 |
|
|
} |
| 589 |
|
|
|
| 590 |
|
|
NL; |
| 591 |
|
|
if (strcmp(pcmfile.token, "OSIX") == 0) |
| 592 |
|
|
{ |
| 593 |
|
|
NL; |
| 594 |
|
|
i = atoi(pcmfile.token); /* i is atom number of H terminus */ |
| 595 |
|
|
oh6 = i+ioffset; |
| 596 |
|
|
} |
| 597 |
|
|
} else if (strcmp(pcmfile.token,"START") == 0) /* flag for polybuild */ |
| 598 |
|
|
{ |
| 599 |
|
|
NL; |
| 600 |
|
|
i = atoi(pcmfile.token); |
| 601 |
|
|
mask = 1L << DUMMY; |
| 602 |
|
|
atom[i+ioffset].flags |= mask; |
| 603 |
|
|
NL; // END |
| 604 |
|
|
NL; |
| 605 |
|
|
i = atoi(pcmfile.token); |
| 606 |
|
|
mask = 1L << DUMMY; |
| 607 |
|
|
atom[i+ioffset].flags |= mask; |
| 608 |
|
|
} else if (strcmp(pcmfile.token,"NMOL") == 0) |
| 609 |
|
|
{ |
| 610 |
|
|
NL; |
| 611 |
|
|
solv.nmols = atoi(pcmfile.token); |
| 612 |
|
|
NL; |
| 613 |
|
|
NL; |
| 614 |
|
|
solv.density = atof(pcmfile.token); |
| 615 |
|
|
NL; |
| 616 |
|
|
NL; |
| 617 |
|
|
solv.boxx = atof(pcmfile.token); |
| 618 |
|
|
NL; |
| 619 |
|
|
solv.boxy = atof(pcmfile.token); |
| 620 |
|
|
NL; |
| 621 |
|
|
solv.boxz = atof(pcmfile.token); |
| 622 |
|
|
goto L_30; |
| 623 |
|
|
} else if (strcmp(pcmfile.token, "SS") == 0) |
| 624 |
|
|
{ |
| 625 |
|
|
goto L_30; |
| 626 |
|
|
} else if (strcmp(pcmfile.token, "AT") == 0) |
| 627 |
|
|
{ |
| 628 |
|
|
NL; |
| 629 |
|
|
newat = atoi(pcmfile.token); // atom serial number |
| 630 |
|
|
if (newat + ioffset > MAXATOM) |
| 631 |
|
|
{ |
| 632 |
|
|
message_alert(" Maximum number of atoms exceeded in PCMFIN at atom read","PCM Setup"); |
| 633 |
|
|
fprintf(pcmoutfile,"atom read %d %d %d\n",newat,ioffset,natom); |
| 634 |
|
|
natom = ioffset + newat - 1; |
| 635 |
|
|
fclose(pcminfile); |
| 636 |
|
|
exit(0); |
| 637 |
|
|
} |
| 638 |
|
|
newat += ioffset; |
| 639 |
|
|
NL; |
| 640 |
|
|
if (isdigit(*pcmfile.token)) |
| 641 |
|
|
{ |
| 642 |
|
|
newtype = atoi(pcmfile.token); |
| 643 |
|
|
} else // character string for metal atom |
| 644 |
|
|
{ |
| 645 |
|
|
strcpy(ianame,pcmfile.token); |
| 646 |
|
|
isMetal = TRUE; |
| 647 |
|
|
i = strlen(ianame); |
| 648 |
|
|
if ( i == 2) |
| 649 |
|
|
ianame[1] = tolower(ianame[1]); |
| 650 |
|
|
} |
| 651 |
|
|
NL; |
| 652 |
|
|
xtmp = atof(pcmfile.token); |
| 653 |
|
|
NL; |
| 654 |
|
|
ytmp = (atof(pcmfile.token)); |
| 655 |
|
|
NL; |
| 656 |
|
|
ztmp = atof(pcmfile.token); |
| 657 |
|
|
NL; |
| 658 |
|
|
if (isMetal == FALSE) |
| 659 |
|
|
{ |
| 660 |
|
|
itype = newtype; |
| 661 |
|
|
get_atomname(newtype,ianame); |
| 662 |
|
|
if (default_intype == MM3) |
| 663 |
|
|
itype = mm3_mmxtype(newtype); |
| 664 |
|
|
else if (default_intype == MMFF94) |
| 665 |
|
|
itype = mmff_mmxtype(newtype); |
| 666 |
|
|
else if (default_intype == AMBER) |
| 667 |
|
|
itype = amber_mmxtype(newtype); |
| 668 |
|
|
else if (default_intype == OPLSAA) |
| 669 |
|
|
itype = opls_mmxtype(newtype); |
| 670 |
|
|
|
| 671 |
|
|
newatom = make_atom(newtype, xtmp, ytmp, ztmp,ianame); |
| 672 |
|
|
if (default_intype == MM3) |
| 673 |
|
|
set_atomtype(newatom, itype,newtype,0,0,0); |
| 674 |
|
|
else if (default_intype == MMFF94) |
| 675 |
|
|
set_atomtype(newatom, itype,0,newtype,0,0); |
| 676 |
|
|
else if (default_intype == AMBER) |
| 677 |
|
|
set_atomtype(newatom, itype,0,0,newtype,0); |
| 678 |
|
|
else if (default_intype == OPLSAA) |
| 679 |
|
|
set_atomtype(newatom, itype,0,0,0,newtype); |
| 680 |
|
|
}else if (isMetal == TRUE) |
| 681 |
|
|
{ |
| 682 |
|
|
newatom = make_atom(0, xtmp, ytmp, ztmp,ianame); |
| 683 |
|
|
isMetal = FALSE; |
| 684 |
|
|
last_atom = newatom; |
| 685 |
|
|
} |
| 686 |
|
|
if (isubred == 1) |
| 687 |
|
|
{ |
| 688 |
|
|
atom[newatom].substr[0] = 0; |
| 689 |
|
|
atom[newatom].substr[0] |= (1L << substr.icurstr); |
| 690 |
|
|
} |
| 691 |
|
|
|
| 692 |
|
|
L_90: |
| 693 |
|
|
if (strcmp(pcmfile.token, "B") == 0) |
| 694 |
|
|
{ |
| 695 |
|
|
/* Reading bonds now */ |
| 696 |
|
|
NL; |
| 697 |
|
|
j = 0; |
| 698 |
|
|
L_100: |
| 699 |
|
|
j += 1; |
| 700 |
|
|
if (pcmfile.state == NUMERIC) |
| 701 |
|
|
{ |
| 702 |
|
|
ibonded = atoi(pcmfile.token); |
| 703 |
|
|
ibonded += ioffset; |
| 704 |
|
|
} else |
| 705 |
|
|
{ |
| 706 |
|
|
goto L_90; |
| 707 |
|
|
} |
| 708 |
|
|
NL; |
| 709 |
|
|
if (pcmfile.state == NUMERIC) |
| 710 |
|
|
{ |
| 711 |
|
|
ibondorder = atoi(pcmfile.token); |
| 712 |
|
|
} else |
| 713 |
|
|
{ |
| 714 |
|
|
fprintf(stdout, "missing a bondorder, assuming 1\n"); |
| 715 |
|
|
goto L_40; |
| 716 |
|
|
} |
| 717 |
|
|
if (newatom < ibonded) |
| 718 |
|
|
make_bond(newatom, ibonded, ibondorder); |
| 719 |
|
|
if (ibondorder == 9) |
| 720 |
|
|
{ |
| 721 |
|
|
atom[newatom].flags |= (1L << METCOORD_MASK); |
| 722 |
|
|
atom[ibonded].flags |= (1L << METCOORD_MASK); |
| 723 |
|
|
} |
| 724 |
|
|
NL; |
| 725 |
|
|
goto L_100; |
| 726 |
|
|
}else if ( strcmp(pcmfile.token, "P")== 0) |
| 727 |
|
|
{ |
| 728 |
|
|
atom[newatom].flags |= (1L << PI_MASK); |
| 729 |
|
|
NL; |
| 730 |
|
|
goto L_90; |
| 731 |
|
|
}else if (strcmp(pcmfile.token, "D") == 0) // biomolecule marking |
| 732 |
|
|
{ |
| 733 |
|
|
NL; |
| 734 |
|
|
biotype = atoi(pcmfile.token); |
| 735 |
|
|
atom[newatom].biotype = biotype; |
| 736 |
|
|
NL; |
| 737 |
|
|
goto L_90; |
| 738 |
|
|
}else if (strcmp(pcmfile.token, "N") == 0) // residue number |
| 739 |
|
|
{ |
| 740 |
|
|
NL; |
| 741 |
|
|
biotype = atoi(pcmfile.token); |
| 742 |
|
|
atom[newatom].residue = biotype; |
| 743 |
|
|
NL; |
| 744 |
|
|
goto L_90; |
| 745 |
|
|
}else if (strcmp(pcmfile.token,"M")==0) |
| 746 |
|
|
{ |
| 747 |
|
|
NL; |
| 748 |
|
|
icoord = atoi(pcmfile.token); |
| 749 |
|
|
if (icoord == 0) |
| 750 |
|
|
{ |
| 751 |
|
|
atom[newatom].flags |= (1L << SATMET_MASK); |
| 752 |
|
|
} else if (icoord == 2) |
| 753 |
|
|
{ |
| 754 |
|
|
atom[newatom].flags |= (1L << GT18e_MASK); |
| 755 |
|
|
} else{ |
| 756 |
|
|
atom[newatom].flags |= (1L << GT18e_MASK); |
| 757 |
|
|
atom[newatom].flags |= (1L << SATMET_MASK); |
| 758 |
|
|
} |
| 759 |
|
|
NL; |
| 760 |
|
|
if (pcmfile.state != 1) |
| 761 |
|
|
goto L_90; |
| 762 |
|
|
ispin = atoi(pcmfile.token); |
| 763 |
|
|
if (ispin == 0) |
| 764 |
|
|
{ |
| 765 |
|
|
atom[newatom].flags |= (1L << LOWSPIN_MASK); |
| 766 |
|
|
} else if (ispin == 1) |
| 767 |
|
|
{ |
| 768 |
|
|
atom[newatom].flags |= (1L << SQPLAN_MASK); |
| 769 |
|
|
} else |
| 770 |
|
|
{ |
| 771 |
|
|
atom[newatom].flags |= (1L << LOWSPIN_MASK); |
| 772 |
|
|
atom[newatom].flags |= (1L << SQPLAN_MASK); |
| 773 |
|
|
} |
| 774 |
|
|
NL; |
| 775 |
|
|
goto L_90; |
| 776 |
|
|
}else if (strcmp(pcmfile.token,"S")== 0) |
| 777 |
|
|
{ |
| 778 |
|
|
NL; |
| 779 |
|
|
if (pcmfile.state == NUMERIC) |
| 780 |
|
|
{ |
| 781 |
|
|
j = atoi(pcmfile.token); |
| 782 |
|
|
mask = (1L << j); |
| 783 |
|
|
if (isubred == 0) |
| 784 |
|
|
{ |
| 785 |
|
|
atom[newatom].substr[0] |= mask; |
| 786 |
|
|
substr.istract[j] = TRUE; |
| 787 |
|
|
} |
| 788 |
|
|
NL; |
| 789 |
|
|
goto L_90; |
| 790 |
|
|
} else |
| 791 |
|
|
{ |
| 792 |
|
|
goto L_90; |
| 793 |
|
|
} |
| 794 |
|
|
}else if (strcmp(pcmfile.token,"H")== 0) |
| 795 |
|
|
{ |
| 796 |
|
|
atom[newatom].flags |= (1L << HBOND_MASK); |
| 797 |
|
|
NL; |
| 798 |
|
|
goto L_90; |
| 799 |
|
|
}else if (strcmp(pcmfile.token,"C")==0) |
| 800 |
|
|
{ |
| 801 |
|
|
NL; |
| 802 |
|
|
atom[newatom].charge = atof(pcmfile.token); |
| 803 |
|
|
NL; |
| 804 |
|
|
goto L_90; |
| 805 |
|
|
} else if (strcmp(pcmfile.token,"ML") == 0) |
| 806 |
|
|
{ |
| 807 |
|
|
NL; |
| 808 |
|
|
j = atoi(pcmfile.token); |
| 809 |
|
|
atom[newatom].molecule = j; |
| 810 |
|
|
goto L_90; |
| 811 |
|
|
}else if (strcmp(pcmfile.token,"R")== 0) |
| 812 |
|
|
{ |
| 813 |
|
|
NL; |
| 814 |
|
|
atom[newatom].radius = atof(pcmfile.token); |
| 815 |
|
|
NL; |
| 816 |
|
|
goto L_90; |
| 817 |
|
|
} |
| 818 |
|
|
} else if (strncasecmp(pcmfile.token, "}",1) == 0) |
| 819 |
|
|
{ |
| 820 |
|
|
goto L_170; /* end of structure */ |
| 821 |
|
|
} else if (strcmp(pcmfile.token, "FL") == 0) |
| 822 |
|
|
{ |
| 823 |
|
|
NL; |
| 824 |
|
|
L_120: if (strcmp(pcmfile.token, "PRINT") == 0) |
| 825 |
|
|
{ |
| 826 |
|
|
iprint = 1; |
| 827 |
|
|
NL; |
| 828 |
|
|
if (pcmfile.state == ALPHABETIC) |
| 829 |
|
|
goto L_120; |
| 830 |
|
|
iprint = atoi(pcmfile.token); |
| 831 |
|
|
NL; |
| 832 |
|
|
goto L_120; |
| 833 |
|
|
} else if (strcmp(pcmfile.token, "DIELC") == 0) |
| 834 |
|
|
{ |
| 835 |
|
|
NL; |
| 836 |
|
|
if (pcmfile.state != 1) |
| 837 |
|
|
goto L_120; |
| 838 |
|
|
units.dielec = atof(pcmfile.token); |
| 839 |
|
|
NL; |
| 840 |
|
|
goto L_120; |
| 841 |
|
|
} else if (strcmp(pcmfile.token, "UV") == 0) |
| 842 |
|
|
{ |
| 843 |
|
|
NL; |
| 844 |
|
|
if (pcmfile.state != 1) |
| 845 |
|
|
goto L_120; |
| 846 |
|
|
NL; |
| 847 |
|
|
goto L_120; |
| 848 |
|
|
} else if (strcmp(pcmfile.token, "PIPR") == 0) |
| 849 |
|
|
{ |
| 850 |
|
|
NL; |
| 851 |
|
|
if (pcmfile.state != 1) |
| 852 |
|
|
goto L_120; |
| 853 |
|
|
NL; |
| 854 |
|
|
goto L_120; |
| 855 |
|
|
} else if (strcmp(pcmfile.token, "PIPL") == 0) |
| 856 |
|
|
{ |
| 857 |
|
|
NL; |
| 858 |
|
|
if (pcmfile.state != 1) |
| 859 |
|
|
goto L_120; |
| 860 |
|
|
NL; |
| 861 |
|
|
goto L_120; |
| 862 |
|
|
} else if (strcmp(pcmfile.token, "EINT") == 0) |
| 863 |
|
|
{ |
| 864 |
|
|
NL; |
| 865 |
|
|
if (pcmfile.state != 1) |
| 866 |
|
|
goto L_120; |
| 867 |
|
|
minim_values.ndc = atoi(pcmfile.token); |
| 868 |
|
|
NL; |
| 869 |
|
|
goto L_120; |
| 870 |
|
|
} |
| 871 |
|
|
} else if (strcmp(pcmfile.token, "CO") == 0) |
| 872 |
|
|
{ |
| 873 |
|
|
} else if (strcmp(pcmfile.token, "FBND") == 0) |
| 874 |
|
|
{ |
| 875 |
|
|
NL; |
| 876 |
|
|
ts_bondorder.fbnd[0] = atof(pcmfile.token); |
| 877 |
|
|
NL; |
| 878 |
|
|
ts_bondorder.fbnd[1] = atof(pcmfile.token); |
| 879 |
|
|
NL; |
| 880 |
|
|
ts_bondorder.fbnd[2] = atof(pcmfile.token); |
| 881 |
|
|
NL; |
| 882 |
|
|
ts_bondorder.fbnd[3] = atof(pcmfile.token); |
| 883 |
|
|
NL; |
| 884 |
|
|
ts_bondorder.fbnd[4] = atof(pcmfile.token); |
| 885 |
|
|
NL; |
| 886 |
|
|
ts_bondorder.fbnd[5] = atof(pcmfile.token); |
| 887 |
|
|
NL; |
| 888 |
|
|
ts_bondorder.fbnd[6] = atof(pcmfile.token); |
| 889 |
|
|
NL; |
| 890 |
|
|
ts_bondorder.fbnd[7] = atof(pcmfile.token); |
| 891 |
|
|
NL; |
| 892 |
|
|
ts_bondorder.fbnd[8] = atof(pcmfile.token); |
| 893 |
|
|
NL; |
| 894 |
|
|
ts_bondorder.fbnd[9] = atof(pcmfile.token); |
| 895 |
|
|
NL; |
| 896 |
|
|
ts_bondorder.fbnd[10] = atof(pcmfile.token); |
| 897 |
|
|
NL; |
| 898 |
|
|
ts_bondorder.fbnd[11] = atof(pcmfile.token); |
| 899 |
|
|
NL; |
| 900 |
|
|
ts_bondorder.fbnd[12] = atof(pcmfile.token); |
| 901 |
|
|
NL; |
| 902 |
|
|
ts_bondorder.fbnd[13] = atof(pcmfile.token); |
| 903 |
|
|
NL; |
| 904 |
|
|
ts_bondorder.fbnd[14] = atof(pcmfile.token); |
| 905 |
|
|
} else if (strcmp(pcmfile.token, "FIX") == 0) |
| 906 |
|
|
{ |
| 907 |
|
|
NL; |
| 908 |
|
|
if (strcmp(pcmfile.token, "DIS") == 0) |
| 909 |
|
|
{ |
| 910 |
|
|
NL; |
| 911 |
|
|
fixdis.ifxstr[fixdis.nfxstr][0] = atoi(pcmfile.token); |
| 912 |
|
|
NL; |
| 913 |
|
|
fixdis.ifxstr[fixdis.nfxstr][1] = atoi(pcmfile.token); |
| 914 |
|
|
NL; |
| 915 |
|
|
L_1223: if (strcmp(pcmfile.token, "R") == 0) |
| 916 |
|
|
{ |
| 917 |
|
|
NL; |
| 918 |
|
|
fixdis.fxstrd[fixdis.nfxstr] = atof(pcmfile.token); |
| 919 |
|
|
NL; |
| 920 |
|
|
goto L_1223; |
| 921 |
|
|
} else if (strcmp(pcmfile.token, "K") == 0) |
| 922 |
|
|
{ |
| 923 |
|
|
NL; |
| 924 |
|
|
fixdis.fxstrc[fixdis.nfxstr] = atof(pcmfile.token); |
| 925 |
|
|
fixdis.nfxstr +=1; |
| 926 |
|
|
NL; |
| 927 |
|
|
goto L_1223; |
| 928 |
|
|
} |
| 929 |
|
|
} |
| 930 |
|
|
} else if (strcmp(pcmfile.token, "RESIDUE") == 0) |
| 931 |
|
|
{ |
| 932 |
|
|
NL; |
| 933 |
|
|
residues.iresnum[residues.ngroup] = atoi(pcmfile.token); |
| 934 |
|
|
NL; |
| 935 |
|
|
residues.irestype[residues.ngroup] = atoi(pcmfile.token); |
| 936 |
|
|
NL; |
| 937 |
|
|
residues.istartatom[residues.ngroup] = atoi(pcmfile.token); |
| 938 |
|
|
residues.ngroup++; |
| 939 |
|
|
} else if (strcmp(pcmfile.token, "DD") == 0) |
| 940 |
|
|
{ |
| 941 |
|
|
if (isubred == 1) |
| 942 |
|
|
goto L_30; |
| 943 |
|
|
|
| 944 |
|
|
NL; |
| 945 |
|
|
|
| 946 |
|
|
if (pcmfile.state == NUMERIC) |
| 947 |
|
|
{ |
| 948 |
|
|
fxtor.iatom[fxtor.nfxtor][0] = atoi(pcmfile.token); |
| 949 |
|
|
NL; |
| 950 |
|
|
fxtor.iatom[fxtor.nfxtor][1] = atoi(pcmfile.token); |
| 951 |
|
|
NL; |
| 952 |
|
|
fxtor.iatom[fxtor.nfxtor][2] = atoi(pcmfile.token); |
| 953 |
|
|
NL; |
| 954 |
|
|
fxtor.iatom[fxtor.nfxtor][3] = atoi(pcmfile.token); |
| 955 |
|
|
NL; |
| 956 |
|
|
L_150: if (strcmp(pcmfile.token, "FROM") == 0) |
| 957 |
|
|
{ |
| 958 |
|
|
NL; |
| 959 |
|
|
fxtor.start_ang[fxtor.nfxtor] = atoi(pcmfile.token); |
| 960 |
|
|
fxtor.curr_ang[fxtor.nfxtor] = fxtor.start_ang[fxtor.nfxtor]; |
| 961 |
|
|
NL; |
| 962 |
|
|
goto L_150; |
| 963 |
|
|
} else if (strcmp(pcmfile.token, "TO") == 0) |
| 964 |
|
|
{ |
| 965 |
|
|
NL; |
| 966 |
|
|
fxtor.final_ang[fxtor.nfxtor] = atoi(pcmfile.token); |
| 967 |
|
|
NL; |
| 968 |
|
|
goto L_150; |
| 969 |
|
|
} else if (strcmp(pcmfile.token, "BY") == 0) |
| 970 |
|
|
{ |
| 971 |
|
|
NL; |
| 972 |
|
|
fxtor.step[fxtor.nfxtor] = atoi(pcmfile.token); |
| 973 |
|
|
fxtor.nfxtor++; |
| 974 |
|
|
NL; |
| 975 |
|
|
goto L_150; |
| 976 |
|
|
} |
| 977 |
|
|
} |
| 978 |
|
|
} |
| 979 |
|
|
goto L_30; |
| 980 |
|
|
L_170: |
| 981 |
|
|
fclose(pcminfile); |
| 982 |
|
|
for (i=1; i <= natom; i++) |
| 983 |
|
|
{ |
| 984 |
|
|
if (atom[i].mmx_type == 5) |
| 985 |
|
|
{ |
| 986 |
|
|
flags.noh = True; |
| 987 |
|
|
break; |
| 988 |
|
|
} |
| 989 |
|
|
} |
| 990 |
|
|
return; |
| 991 |
|
|
} |
| 992 |
|
|
|
| 993 |
|
|
void gettoken() |
| 994 |
|
|
{ |
| 995 |
|
|
int foundtoken, i; |
| 996 |
|
|
|
| 997 |
|
|
pcmfile.state = 0; |
| 998 |
|
|
foundtoken = -1; |
| 999 |
|
|
strcpy(pcmfile.token, ""); |
| 1000 |
|
|
for (i = pcmfile.head - 1; i <= strlen(pcmfile.string); i++) { |
| 1001 |
|
|
if ((*(pcmfile.string + i) != ':') && |
| 1002 |
|
|
(*(pcmfile.string + i) != ' ') && |
| 1003 |
|
|
(*(pcmfile.string + i) != '\0') && |
| 1004 |
|
|
(*(pcmfile.string + i) != ';') && |
| 1005 |
|
|
(*(pcmfile.string + i) != ',') && |
| 1006 |
|
|
(*(pcmfile.string + i) != '\t')) { |
| 1007 |
|
|
if (foundtoken == -1) { |
| 1008 |
|
|
foundtoken = i; |
| 1009 |
|
|
if (isdigit(*(pcmfile.string + i))) { |
| 1010 |
|
|
/* beginning to read a number */ |
| 1011 |
|
|
pcmfile.state = 1; |
| 1012 |
|
|
} else if ((*(pcmfile.string + i) == '.') || |
| 1013 |
|
|
(*(pcmfile.string + i) == '-')) { |
| 1014 |
|
|
/* period or dash can't yet tell if |
| 1015 |
|
|
* word or number */ |
| 1016 |
|
|
pcmfile.state = 3; |
| 1017 |
|
|
} else { |
| 1018 |
|
|
/* must be a word */ |
| 1019 |
|
|
pcmfile.state = 2; |
| 1020 |
|
|
} |
| 1021 |
|
|
} else { |
| 1022 |
|
|
if ( |
| 1023 |
|
|
( |
| 1024 |
|
|
(pcmfile.state == 2) && |
| 1025 |
|
|
(isdigit(*(pcmfile.string + i))) |
| 1026 |
|
|
) |
| 1027 |
|
|
|| |
| 1028 |
|
|
( |
| 1029 |
|
|
(pcmfile.state == 1) && |
| 1030 |
|
|
(isalpha(*(pcmfile.string + i))) |
| 1031 |
|
|
) |
| 1032 |
|
|
) { |
| 1033 |
|
|
foundtoken = i; |
| 1034 |
|
|
goto L_30; |
| 1035 |
|
|
} else if (pcmfile.state == 3) { |
| 1036 |
|
|
if (isdigit(*(pcmfile.string + i)) || |
| 1037 |
|
|
*(pcmfile.string + i) == '.') { |
| 1038 |
|
|
pcmfile.state = 1; |
| 1039 |
|
|
} else { |
| 1040 |
|
|
pcmfile.state = 2; |
| 1041 |
|
|
} |
| 1042 |
|
|
} |
| 1043 |
|
|
} |
| 1044 |
|
|
strncat(pcmfile.token, pcmfile.string + i, 1); |
| 1045 |
|
|
} else if (foundtoken != -1) { |
| 1046 |
|
|
foundtoken = i; |
| 1047 |
|
|
goto L_30; |
| 1048 |
|
|
} |
| 1049 |
|
|
} |
| 1050 |
|
|
if (foundtoken == -1) { |
| 1051 |
|
|
pcmfile.head = 1000; |
| 1052 |
|
|
return; |
| 1053 |
|
|
} |
| 1054 |
|
|
L_30: |
| 1055 |
|
|
pcmfile.head = foundtoken + 1; |
| 1056 |
|
|
if (pcmfile.state == 2 && !pcmfile.nocaps) |
| 1057 |
|
|
{ |
| 1058 |
|
|
for (i = 0; i < strlen(pcmfile.token); i++) |
| 1059 |
|
|
{ |
| 1060 |
|
|
if (!isupper(*(pcmfile.token + i))) |
| 1061 |
|
|
*(pcmfile.token + i) = toupper(*(pcmfile.token + i)); |
| 1062 |
|
|
} |
| 1063 |
|
|
} |
| 1064 |
|
|
return; |
| 1065 |
|
|
} |
| 1066 |
|
|
/* ============================================================ */ |
| 1067 |
|
|
FILE *pcminfile; |
| 1068 |
|
|
/* ============================================================ */ |
| 1069 |
|
|
void rdfile(int mode, int isub) |
| 1070 |
|
|
{ |
| 1071 |
|
|
if (mode == -1) |
| 1072 |
|
|
fclose(pcminfile); |
| 1073 |
|
|
else if (mode == 0) |
| 1074 |
|
|
{ |
| 1075 |
|
|
pcminfile = fopen_path(Openbox.path,Openbox.fname, "r"); |
| 1076 |
|
|
|
| 1077 |
|
|
if (pcminfile == NULL) |
| 1078 |
|
|
{ |
| 1079 |
|
|
message_alert("Error Opening PCM file","Error"); |
| 1080 |
|
|
return; |
| 1081 |
|
|
} |
| 1082 |
|
|
} else |
| 1083 |
|
|
rdpcm(mode,isub); |
| 1084 |
|
|
} |
| 1085 |
|
|
/* ============================================================ */ |
| 1086 |
|
|
void rdpcm(int nth,int isubred) |
| 1087 |
|
|
{ |
| 1088 |
|
|
unsigned int substrismin; |
| 1089 |
|
|
int i, ibondcount, ibonded, ibondorder,imetcount, ioffset, |
| 1090 |
|
|
isubmap[MAXSS], j, numbonds, niatom; |
| 1091 |
|
|
int newat, newtype, isMetal; |
| 1092 |
|
|
long int mask; |
| 1093 |
|
|
char ianame[3]; |
| 1094 |
|
|
float ddcount, xtmp, ytmp, ztmp; |
| 1095 |
|
|
|
| 1096 |
|
|
imetcount = 0; |
| 1097 |
|
|
isMetal = FALSE; |
| 1098 |
|
|
ddcount = 0; |
| 1099 |
|
|
substrismin = False; |
| 1100 |
|
|
pcmfile.nocaps = False; |
| 1101 |
|
|
numbonds = 0; |
| 1102 |
|
|
ibondcount = 0; |
| 1103 |
|
|
for (i = 0; i < MAXSS; i++) |
| 1104 |
|
|
{ |
| 1105 |
|
|
isubmap[i] = 0; |
| 1106 |
|
|
} |
| 1107 |
|
|
|
| 1108 |
|
|
if( isubred == 1 ) |
| 1109 |
|
|
{ |
| 1110 |
|
|
ioffset = natom; |
| 1111 |
|
|
substr.istract[substr.icurstr] = TRUE; |
| 1112 |
|
|
} |
| 1113 |
|
|
else |
| 1114 |
|
|
{ |
| 1115 |
|
|
ioffset = 0; |
| 1116 |
|
|
} |
| 1117 |
|
|
|
| 1118 |
|
|
|
| 1119 |
|
|
FetchRecord(pcminfile,pcmfile.string); |
| 1120 |
|
|
L_30: |
| 1121 |
|
|
FetchRecord(pcminfile,pcmfile.string); |
| 1122 |
|
|
*(pcmfile.string + strlen(pcmfile.string) ) = '\0'; |
| 1123 |
|
|
if (feof(pcminfile)) |
| 1124 |
|
|
goto L_170; |
| 1125 |
|
|
pcmfile.head = 1; |
| 1126 |
|
|
NL; |
| 1127 |
|
|
L_40: |
| 1128 |
|
|
if (strcmp(pcmfile.token, "NA") == 0) |
| 1129 |
|
|
{ |
| 1130 |
|
|
gettoken(); |
| 1131 |
|
|
if (pcmfile.head == 1000) |
| 1132 |
|
|
goto L_30; |
| 1133 |
|
|
niatom = atoi(pcmfile.token); |
| 1134 |
|
|
niatom += ioffset; |
| 1135 |
|
|
NL; |
| 1136 |
|
|
goto L_30; |
| 1137 |
|
|
} else if (strcmp(pcmfile.token,"ATOMTYPES") == 0) |
| 1138 |
|
|
{ |
| 1139 |
|
|
gettoken(); |
| 1140 |
|
|
if (pcmfile.head == 1000) |
| 1141 |
|
|
goto L_30; |
| 1142 |
|
|
default_intype = atoi(pcmfile.token); |
| 1143 |
|
|
NL; |
| 1144 |
|
|
goto L_30; |
| 1145 |
|
|
} else if (strcmp(pcmfile.token, "NT") == 0) /* This is for Amino Acids */ |
| 1146 |
|
|
{ |
| 1147 |
|
|
NL; |
| 1148 |
|
|
i = atoi(pcmfile.token); /* i is atom number of N terminus */ |
| 1149 |
|
|
mask = 1L << NTERM; /* use bit 0 of substr 1 for N terminus*/ |
| 1150 |
|
|
atom[i+ioffset].flags |= mask; |
| 1151 |
|
|
|
| 1152 |
|
|
NL; |
| 1153 |
|
|
if (strcmp(pcmfile.token, "CT") == 0) |
| 1154 |
|
|
{ |
| 1155 |
|
|
NL; |
| 1156 |
|
|
i = atoi(pcmfile.token); /* i is atom number of C terminus */ |
| 1157 |
|
|
mask = 1L << CNTERM; /* use bit 1 of substr 1 for C terminus */ |
| 1158 |
|
|
atom[i+ioffset].flags |= mask; |
| 1159 |
|
|
} |
| 1160 |
|
|
} else if (strcmp(pcmfile.token, "OT") == 0) /* This is for Sugars */ |
| 1161 |
|
|
{ |
| 1162 |
|
|
NL; |
| 1163 |
|
|
i = atoi(pcmfile.token); /* i is atom number of O terminus */ |
| 1164 |
|
|
mask = 1L << OTERM; /* use bit 0 of substr 1 for O terminus*/ |
| 1165 |
|
|
atom[i+ioffset].flags |= mask; |
| 1166 |
|
|
|
| 1167 |
|
|
NL; |
| 1168 |
|
|
if (strcmp(pcmfile.token, "CT") == 0) |
| 1169 |
|
|
{ |
| 1170 |
|
|
NL; |
| 1171 |
|
|
i = atoi(pcmfile.token); /* i is atom number of H terminus */ |
| 1172 |
|
|
mask = 1L << COTERM; /* use bit 1 of substr 1 for H terminus */ |
| 1173 |
|
|
atom[i+ioffset].flags |= mask; |
| 1174 |
|
|
} |
| 1175 |
|
|
} else if (strcmp(pcmfile.token,"START") == 0) /* flag for polybuild */ |
| 1176 |
|
|
{ |
| 1177 |
|
|
NL; |
| 1178 |
|
|
i = atoi(pcmfile.token); |
| 1179 |
|
|
mask = 1L << DUMMY; |
| 1180 |
|
|
atom[i+ioffset].flags |= mask; |
| 1181 |
|
|
NL; // END |
| 1182 |
|
|
NL; |
| 1183 |
|
|
i = atoi(pcmfile.token); |
| 1184 |
|
|
mask = 1L << DUMMY; |
| 1185 |
|
|
atom[i+ioffset].flags |= mask; |
| 1186 |
|
|
|
| 1187 |
|
|
} else if (strcmp(pcmfile.token, "SS") == 0) |
| 1188 |
|
|
{ |
| 1189 |
|
|
goto L_30; |
| 1190 |
|
|
} else if (strcmp(pcmfile.token, "AT") == 0) |
| 1191 |
|
|
{ |
| 1192 |
|
|
NL; |
| 1193 |
|
|
newat = atoi(pcmfile.token); // atom serial number |
| 1194 |
|
|
if (newat + ioffset > MAXATOM) |
| 1195 |
|
|
{ |
| 1196 |
|
|
message_alert(" Maximum number of atoms exceeded in PCMFIN at atom read","Error"); |
| 1197 |
|
|
fprintf(pcmoutfile,"atom read %d %d %d\n",newat,ioffset,natom); |
| 1198 |
|
|
natom = ioffset + newat - 1; |
| 1199 |
|
|
fclose(pcminfile); |
| 1200 |
|
|
exit(0); |
| 1201 |
|
|
} |
| 1202 |
|
|
newat += ioffset; |
| 1203 |
|
|
NL; |
| 1204 |
|
|
if (isdigit(*pcmfile.token)) |
| 1205 |
|
|
{ |
| 1206 |
|
|
newtype = atoi(pcmfile.token); |
| 1207 |
|
|
} else // character string for metal atom |
| 1208 |
|
|
{ |
| 1209 |
|
|
strcpy(ianame,pcmfile.token); |
| 1210 |
|
|
isMetal = TRUE; |
| 1211 |
|
|
} |
| 1212 |
|
|
NL; |
| 1213 |
|
|
xtmp = atof(pcmfile.token); |
| 1214 |
|
|
NL; |
| 1215 |
|
|
ytmp = (atof(pcmfile.token)); |
| 1216 |
|
|
NL; |
| 1217 |
|
|
ztmp = atof(pcmfile.token); |
| 1218 |
|
|
NL; |
| 1219 |
|
|
atom[newat].x = xtmp; |
| 1220 |
|
|
atom[newat].y = ytmp; |
| 1221 |
|
|
atom[newat].z = ztmp; |
| 1222 |
|
|
|
| 1223 |
|
|
L_90: |
| 1224 |
|
|
if (strcmp(pcmfile.token, "B") == 0) |
| 1225 |
|
|
{ |
| 1226 |
|
|
/* Reading bonds now */ |
| 1227 |
|
|
NL; |
| 1228 |
|
|
j = 0; |
| 1229 |
|
|
L_100: |
| 1230 |
|
|
j += 1; |
| 1231 |
|
|
if (pcmfile.state == NUMERIC) |
| 1232 |
|
|
{ |
| 1233 |
|
|
ibonded = atoi(pcmfile.token); |
| 1234 |
|
|
ibonded += ioffset; |
| 1235 |
|
|
} else |
| 1236 |
|
|
{ |
| 1237 |
|
|
goto L_90; |
| 1238 |
|
|
} |
| 1239 |
|
|
NL; |
| 1240 |
|
|
if (pcmfile.state == NUMERIC) |
| 1241 |
|
|
{ |
| 1242 |
|
|
ibondorder = atoi(pcmfile.token); |
| 1243 |
|
|
} else |
| 1244 |
|
|
{ |
| 1245 |
|
|
fprintf(stdout, "missing a bondorder, assuming 1\n"); |
| 1246 |
|
|
goto L_40; |
| 1247 |
|
|
} |
| 1248 |
|
|
NL; |
| 1249 |
|
|
goto L_100; |
| 1250 |
|
|
}else if ( strcmp(pcmfile.token, "P")== 0) |
| 1251 |
|
|
{ |
| 1252 |
|
|
NL; |
| 1253 |
|
|
goto L_90; |
| 1254 |
|
|
}else if (strcmp(pcmfile.token, "D") == 0) // biomolecule marking |
| 1255 |
|
|
{ |
| 1256 |
|
|
NL; |
| 1257 |
|
|
NL; |
| 1258 |
|
|
goto L_90; |
| 1259 |
|
|
}else if (strcmp(pcmfile.token,"M")==0) |
| 1260 |
|
|
{ |
| 1261 |
|
|
NL; |
| 1262 |
|
|
NL; |
| 1263 |
|
|
if (pcmfile.state != 1) |
| 1264 |
|
|
goto L_90; |
| 1265 |
|
|
NL; |
| 1266 |
|
|
goto L_90; |
| 1267 |
|
|
}else if (strcmp(pcmfile.token,"S")== 0) |
| 1268 |
|
|
{ |
| 1269 |
|
|
NL; |
| 1270 |
|
|
if (pcmfile.state == NUMERIC) |
| 1271 |
|
|
{ |
| 1272 |
|
|
NL; |
| 1273 |
|
|
goto L_90; |
| 1274 |
|
|
} else |
| 1275 |
|
|
{ |
| 1276 |
|
|
goto L_90; |
| 1277 |
|
|
} |
| 1278 |
|
|
}else if (strcmp(pcmfile.token,"H")== 0) |
| 1279 |
|
|
{ |
| 1280 |
|
|
NL; |
| 1281 |
|
|
goto L_90; |
| 1282 |
|
|
}else if (strcmp(pcmfile.token,"C")==0) |
| 1283 |
|
|
{ |
| 1284 |
|
|
NL; |
| 1285 |
|
|
NL; |
| 1286 |
|
|
goto L_90; |
| 1287 |
|
|
}else if (strcmp(pcmfile.token,"R")== 0) |
| 1288 |
|
|
{ |
| 1289 |
|
|
NL; |
| 1290 |
|
|
NL; |
| 1291 |
|
|
goto L_90; |
| 1292 |
|
|
} |
| 1293 |
|
|
} else if (strncmp(pcmfile.token, "}",1) == 0) |
| 1294 |
|
|
{ |
| 1295 |
|
|
goto L_170; /* end of structure */ |
| 1296 |
|
|
} else if (strcmp(pcmfile.token, "FL") == 0) |
| 1297 |
|
|
{ |
| 1298 |
|
|
NL; |
| 1299 |
|
|
L_120: if (strcmp(pcmfile.token, "PRINT") == 0) |
| 1300 |
|
|
{ |
| 1301 |
|
|
NL; |
| 1302 |
|
|
if (pcmfile.state == ALPHABETIC) |
| 1303 |
|
|
goto L_120; |
| 1304 |
|
|
NL; |
| 1305 |
|
|
goto L_120; |
| 1306 |
|
|
} else if (strcmp(pcmfile.token, "DIELC") == 0) |
| 1307 |
|
|
{ |
| 1308 |
|
|
NL; |
| 1309 |
|
|
if (pcmfile.state != 1) |
| 1310 |
|
|
goto L_120; |
| 1311 |
|
|
NL; |
| 1312 |
|
|
goto L_120; |
| 1313 |
|
|
} else if (strcmp(pcmfile.token, "UV") == 0) |
| 1314 |
|
|
{ |
| 1315 |
|
|
NL; |
| 1316 |
|
|
if (pcmfile.state != 1) |
| 1317 |
|
|
goto L_120; |
| 1318 |
|
|
NL; |
| 1319 |
|
|
goto L_120; |
| 1320 |
|
|
} else if (strcmp(pcmfile.token, "PIPR") == 0) |
| 1321 |
|
|
{ |
| 1322 |
|
|
NL; |
| 1323 |
|
|
if (pcmfile.state != 1) |
| 1324 |
|
|
goto L_120; |
| 1325 |
|
|
NL; |
| 1326 |
|
|
goto L_120; |
| 1327 |
|
|
} else if (strcmp(pcmfile.token, "PIPL") == 0) |
| 1328 |
|
|
{ |
| 1329 |
|
|
NL; |
| 1330 |
|
|
if (pcmfile.state != 1) |
| 1331 |
|
|
goto L_120; |
| 1332 |
|
|
NL; |
| 1333 |
|
|
goto L_120; |
| 1334 |
|
|
} else if (strcmp(pcmfile.token, "EINT") == 0) |
| 1335 |
|
|
{ |
| 1336 |
|
|
NL; |
| 1337 |
|
|
if (pcmfile.state != 1) |
| 1338 |
|
|
goto L_120; |
| 1339 |
|
|
NL; |
| 1340 |
|
|
goto L_120; |
| 1341 |
|
|
} |
| 1342 |
|
|
} else if (strcmp(pcmfile.token, "CO") == 0) |
| 1343 |
|
|
{ |
| 1344 |
|
|
} else if (strcmp(pcmfile.token, "FBND") == 0) |
| 1345 |
|
|
{ |
| 1346 |
|
|
NL; |
| 1347 |
|
|
NL; |
| 1348 |
|
|
NL; |
| 1349 |
|
|
NL; |
| 1350 |
|
|
NL; |
| 1351 |
|
|
NL; |
| 1352 |
|
|
NL; |
| 1353 |
|
|
NL; |
| 1354 |
|
|
NL; |
| 1355 |
|
|
NL; |
| 1356 |
|
|
NL; |
| 1357 |
|
|
NL; |
| 1358 |
|
|
NL; |
| 1359 |
|
|
NL; |
| 1360 |
|
|
NL; |
| 1361 |
|
|
goto L_30; // get another line |
| 1362 |
|
|
} else if (strcmp(pcmfile.token, "FIX") == 0) |
| 1363 |
|
|
{ |
| 1364 |
|
|
NL; |
| 1365 |
|
|
if (strcmp(pcmfile.token, "DIS") == 0) |
| 1366 |
|
|
{ |
| 1367 |
|
|
NL; |
| 1368 |
|
|
NL; |
| 1369 |
|
|
NL; |
| 1370 |
|
|
L_1223: if (strcmp(pcmfile.token, "R") == 0) |
| 1371 |
|
|
{ |
| 1372 |
|
|
NL; |
| 1373 |
|
|
NL; |
| 1374 |
|
|
goto L_1223; |
| 1375 |
|
|
} else if (strcmp(pcmfile.token, "K") == 0) |
| 1376 |
|
|
{ |
| 1377 |
|
|
NL; |
| 1378 |
|
|
NL; |
| 1379 |
|
|
goto L_1223; |
| 1380 |
|
|
} |
| 1381 |
|
|
} |
| 1382 |
|
|
} else if (strcmp(pcmfile.token, "DD") == 0) |
| 1383 |
|
|
{ |
| 1384 |
|
|
if (isubred == 1) |
| 1385 |
|
|
goto L_30; |
| 1386 |
|
|
|
| 1387 |
|
|
NL; |
| 1388 |
|
|
|
| 1389 |
|
|
if (pcmfile.state == NUMERIC) |
| 1390 |
|
|
{ |
| 1391 |
|
|
NL; |
| 1392 |
|
|
NL; |
| 1393 |
|
|
NL; |
| 1394 |
|
|
NL; |
| 1395 |
|
|
L_150: if (strcmp(pcmfile.token, "FROM") == 0) |
| 1396 |
|
|
{ |
| 1397 |
|
|
NL; |
| 1398 |
|
|
NL; |
| 1399 |
|
|
goto L_150; |
| 1400 |
|
|
} else if (strcmp(pcmfile.token, "TO") == 0) |
| 1401 |
|
|
{ |
| 1402 |
|
|
NL; |
| 1403 |
|
|
NL; |
| 1404 |
|
|
goto L_150; |
| 1405 |
|
|
} else if (strcmp(pcmfile.token, "BY") == 0) |
| 1406 |
|
|
{ |
| 1407 |
|
|
NL; |
| 1408 |
|
|
NL; |
| 1409 |
|
|
goto L_150; |
| 1410 |
|
|
} |
| 1411 |
|
|
} |
| 1412 |
|
|
} |
| 1413 |
|
|
goto L_30; |
| 1414 |
|
|
L_170: |
| 1415 |
|
|
return; |
| 1416 |
|
|
} |
