strlib.C File Reference

#include "strlib.h"

Go to the source code of this file.

Functions
int	NAMD_read_line (FILE *fd, char *buf, int bufsize)
void	NAMD_remove_comment (char *str)
void	NAMD_truncate (char *str)
int	NAMD_find_word (const char *source, const char *search)
int	NAMD_blank_string (char *str)
void	NAMD_find_first_word (char *source, char *word)
int	NAMD_read_int (FILE *fd, const char *msg)
void	NAMD_pad (char *str, size_t length)

Function Documentation

NAMD_blank_string()

int NAMD_blank_string

(

char *

str

)

Definition at line 222 of file strlib.C.

Referenced by Molecule::prepare_qm(), Parameters::read_charmm_parameter_file(), Molecule::read_go_file(), Parameters::read_parameter_file(), GroupRestraintParam::SetGroup1AtomFileIndices(), and GroupRestraintParam::SetGroup2AtomFileIndices().

{
        int i;          // Current position in str
        int blank=1;    // Flag 1-> string is blank
        int len;        // length of the string str

        len=strlen(str);

        for (i=0; i<len && blank; i++)
        {
                blank = isspace(str[i]);
        }

        return(blank);
}

NAMD_find_first_word()

void NAMD_find_first_word	(	char *	source,
		char *	word
	)

Definition at line 258 of file strlib.C.

References STRINGNULL.

Referenced by Parameters::read_charmm_parameter_file(), Molecule::read_go_file(), and Parameters::read_parameter_file().

{
        int i=0;        //  Position within source
        int j=0;        //  Position within word

        /*  Skip leading white space                                    */
        while ( (source[i] != STRINGNULL) && isspace(source[i]))
                i++;

        /*  Copy the word                                               */
        while ( (source[i] != STRINGNULL) && !isspace(source[i]))
        {
                word[j]=source[i];
                i++;
                j++;
        }

        word[j]=STRINGNULL;

        return;
}

NAMD_find_word()

int NAMD_find_word	(	const char *	source,
		const char *	search
	)

Definition at line 180 of file strlib.C.

{
        int i=0;                //  Position inside source
        int search_length;      //  Length of string search
        int source_length;      //  Length of string source
        int found=0;            //  Flag 1-> found the value

        search_length=strlen(search);
        source_length=strlen(source);

        /*  While we haven't found it and we haven't readched the      */
        /*  point where our current position plus the length of the    */
        /*  string we are looking for is longer than the string itself,*/
        /*  check the next search_length characters for a match        */
        while (!found && ((i+search_length)<=(source_length)))
        {
                found = (strncasecmp(source+i, search, search_length)==0);

                i++;
        }

        return(found);
}

NAMD_pad()

void NAMD_pad	(	char *	str,
		size_t	length
	)

Definition at line 382 of file strlib.C.

References STRINGNULL.

{
        char tmp_string[128];
        size_t i;

        if (strlen(str) >= length)
                return;

        for (i=0; i<(length-strlen(str)); i++)
        {
                tmp_string[i] = ' ';
        }

        tmp_string[i] = STRINGNULL;

        strcat(str, tmp_string);
}

NAMD_read_int()

int NAMD_read_int	(	FILE *	fd,
		const char *	msg
	)

Definition at line 302 of file strlib.C.

References NAMD_die(), and STRINGNULL.

Referenced by Molecule::read_alch_unpert_angles(), Molecule::read_alch_unpert_bonds(), and Molecule::read_alch_unpert_dihedrals().

{
        int i;                  //  Loop counter
        int c;                  //  Character read in from file
        char tmp_string[11];    //  Temporary string for integer
        int isNeg;
    
        /*  Skip white space                            */
        while ( ((c=fgetc(fd)) == '\n') || isspace(c) )
        {
        }

        /*  Check to make sure we didn't hit EOF        */
        if (c==EOF)
        {
                char err_msg[128];

                sprintf(err_msg, "EOF ENCOUNTERED READING %s FROM PSF FILE", msg);
                NAMD_die(err_msg);
        }

        /*  Now read in the integer itself              */
        i=0;

        /* Modified to read an integer with '-' or '+' sign --Chao Mei */
        isNeg = 0;
        if(c=='-'){
            c = fgetc(fd);
            isNeg = 1;
        }
        if(c=='+')
            c = fgetc(fd);
                

        while (!isspace(c))
        {
                /*  Check to make sure we only get #'s  */
                if (!isdigit(c))
                {
                        char err_msg[128];

                        sprintf(err_msg, "ALPHA CHARCTER ENCOUNTERED WHILE READING %s FROM PSF FILE", msg);
                        NAMD_die(err_msg);
                }

                tmp_string[i] = c;
                i++;

                c=fgetc(fd);

                /*  Check to make sure we didn't hit EOF*/
                if (c==EOF)
                {
                        char err_msg[128];

                        sprintf(err_msg, "EOF ENCOUNTERED WHILE READING %s FROM PSF FILE", msg);
                        NAMD_die(err_msg);
                }
        }

        tmp_string[i]=STRINGNULL;

        /*  Convert the string to an integer and return its value       */
        if(isNeg)
            return(-atoi(tmp_string));
        else
           return(atoi(tmp_string));
}

NAMD_read_line()

int NAMD_read_line	(	FILE *	fd,
		char *	buf,
		int	bufsize
	)

Copyright (c) 1995, 1996, 1997, 1998, 1999, 2000 by The Board of Trustees of the University of Illinois. All rights reserved.

Definition at line 38 of file strlib.C.

References NAMD_die(), and STRINGNULL.

Referenced by Molecule::prepare_qm(), Parameters::read_charmm_parameter_file(), Molecule::read_go_file(), Parameters::read_parameter_file(), GroupRestraintParam::SetGroup1AtomFileIndices(), and GroupRestraintParam::SetGroup2AtomFileIndices().

{
        int i=0;        //  Current position in buf
        int c;          //  Character read in from file

        /*  Loop and read characters until we get either an EOF or a    */
        /*  newline                                                     */
        while ( ((c=fgetc(fd)) != EOF) && (c != '\n') )
        {
                /*  If we encounter a bracketed comment, skip it.  This */
                /*  basically means read EVERYTHING until the next } and*/
                /*  throw it into the big bit bucket                    */
                if (c == '{')
                {
                        while ( ((c=fgetc(fd)) != EOF) && (c!='}') )
                        {
                        }

                        if (c==EOF)
                        {
                                buf[i]=STRINGNULL;
                                char *err_msg = new char[128 + strlen(buf)];
                                sprintf(err_msg, "ABNORMAL EOF FOUND - buffer=*%s*\n", buf);
                                NAMD_die(err_msg);
                        }

                        continue;
                }

                /*  Also, use this little piece of logic to remove      */
                /*  any leading spaces from the line                    */
                if ((i>0) || !isspace(c))
                {
                        buf[i] = c;
                        i++;
                        if ( i == bufsize ) {
                                i--;
                                buf[i]=STRINGNULL;
                                char *err_msg = new char[128 + strlen(buf)];
                                sprintf(err_msg, "BUFFER OVERRUN - buffer=*%s*\n", 
                                   buf);
                                NAMD_die(err_msg);
                        }
                }
        }

        /*  NULL terminate the string                                   */
        buf[i]=STRINGNULL;

        /*  Check for an EOF in the middle of a line                    */
        if ((c==EOF) && (i!=0))
        {
                buf[i]=STRINGNULL;
                char *err_msg = new char[128 + strlen(buf)];
                sprintf(err_msg, "ABNORMAL EOF FOUND - buffer=*%s*\n", buf);
                NAMD_die(err_msg);
        }

        /*  Return the appropriate value                                */
        if (c==EOF)
                return(-1);
        else
                return(0);
}

NAMD_remove_comment()

void NAMD_remove_comment

(

char *

str

)

Definition at line 119 of file strlib.C.

References STRINGNULL.

{
        int i=0;

        while ( (str[i] != STRINGNULL) && (str[i] != '!') )
        {
                i++;
        }

        str[i] = STRINGNULL;
}

NAMD_truncate()

void NAMD_truncate

(

char *

)

Copyright (c) 1995, 1996, 1997, 1998, 1999, 2000 by The Board of Trustees of the University of Illinois. All rights reserved.

Definition at line 145 of file strlib.C.

References STRINGNULL.

{
        int i;          //  Current position in str

        i=strlen(str);

        /*  Loop from the back of the string until we find a non-space  */
        for (i--; i>=0 && isspace(str[i]); i--)
        {
        }
        
        str[i+1]=STRINGNULL;
}