C ********************************************************************** C READPDB.F ADDED TEMPERATURE MAR 02 ARDEAN LEITH C C ********************************************************************** C=* * C=* This file is part of: SPIDER - Modular Image Processing System. * C=* SPIDER System Authors: Joachim Frank & ArDean Leith * C=* Copyright 1985-2010 Health Research Inc., * C=* Riverview Center, 150 Broadway, Suite 560, Menands, NY 12204. * C=* Email: spider@wadsworth.org * C=* * C=* SPIDER is free software; you can redistribute it and/or * C=* modify it under the terms of the GNU General Public License as * C=* published by the Free Software Foundation; either version 2 of the * C=* License, or (at your option) any later version. * C=* * C=* SPIDER is distributed in the hope that it will be useful, * C=* but WITHOUT ANY WARRANTY; without even the implied warranty of * C=* merchantability or fitness for a particular purpose. See the GNU * C=* General Public License for more details. * C=* You should have received a copy of the GNU General Public License * C=* along with this program. If not, see * C=* * C ********************************************************************** C C READPDM C C PURPOSE: READ PDB FILE, GET COORDINATES, C GENERATE A 3-D SPIDER FORMAT VOLUME C C ********************************************************************** SUBROUTINE READPDB INCLUDE 'CMBLOCK.INC' INCLUDE 'CMLIMIT.INC' REAL, ALLOCATABLE, DIMENSION(:,:,:) :: BUF CHARACTER(LEN=MAXNAM):: PDBFILE,SPIDERFILE,RECLIN CHARACTER(LEN=10):: HEAD*10 CHARACTER(LEN=3):: ATOM*3 CHARACTER(LEN=1):: NULL,CENTER,CTEMP LOGICAL :: ZNUM,TEMP ZNUM = .FALSE. NATOM = 0 TMASS = 0.0 NULL = CHAR(0) LUN1 = 8 LUN2 = 10 XMAX = -1.0E23 XMIN = 1.0E23 YMAX = -1.0E23 YMIN = 1.0E23 ZMAX = -1.0E23 ZMIN = 1.0E23 UX = 0.0 UY = 0.0 UZ = 0.0 C OPEN PDB FILE (WHICH IS READABLE ASCII) AS FORMATTED SEQ. LENREC = 0 CALL OPAUXFILE(.TRUE.,PDBFILE,NULL,LUN1,LENREC,'O', & 'PDB INPUT',.TRUE.,IRTFLG) IF (IRTFLG .NE. 0) RETURN 15 READ(LUN1,20) RECLIN 20 FORMAT(A80) C GET MIN AND MAX OF X,Y,Z AND CALCULATE OFFSET 35 IF (RECLIN(1:4) .EQ. 'ATOM') THEN READ (RECLIN,50) HEAD,ATOM,X,Y,Z,OCCUPANCY,TEMPERATURE IF (OCCUPANCY .GT. 1.0 ) ZNUM = .TRUE. C COORDINATE SYSTEM IS DIFFERENT IN O AND SPIDER W = X X = Y Y = W Z = -Z XMAX=AMAX1(XMAX,X) XMIN=AMIN1(XMIN,X) YMAX=AMAX1(YMAX,Y) YMIN=AMIN1(YMIN,Y) ZMAX=AMAX1(ZMAX,Z) ZMIN=AMIN1(ZMIN,Z) UX=UX+X UY=UY+Y UZ=UZ+Z NATOM=NATOM+1 GOTO 15 ELSEIF (RECLIN(1:3) .NE. 'END') THEN GOTO 15 ENDIF IF (NATOM .LE. 0) THEN CALL ERRT(101,'NO ATOMS IN THE PDB FILE',NE) GOTO 9999 ENDIF C SET CELL DIMENSION SX=(XMAX-XMIN)+3.0 SY=(YMAX-YMIN)+3.0 SZ=(ZMAX-ZMIN)+3.0 WRITE(NOUT,*)' CELL SIZE: ',SX,SY,SZ REWIND LUN1 C INPUT SAMPLE SIZE TEMP = .FALSE. CALL RDPRM(PIXEL,NOT_USED,'PIXEL SIZE [A]') CALL RDPRMC(CENTER,NCHAR,.TRUE.,'CENTER (Y/N)?',NULL,IRTFLG) IF (CENTER .NE. 'Y') THEN UX=0.0 UY=0.0 UZ=0.0 ELSE UX=UX/NATOM UY=UY/NATOM UZ=UZ/NATOM ENDIF CALL RDPRMC(CTEMP,NCHAR,.TRUE., & 'ATOMS OR TEMPERATURE (A/T)?',NULL,IRTFLG) TEMP = (CTEMP .EQ. 'T') NX = NINT(SX/PIXEL)+1 NY = NINT(SY/PIXEL)+1 NZ = NINT(SZ/PIXEL)+1 WRITE(NOUT,506) NX,NY,NZ 506 FORMAT(' Minimum size of the volume: ',3I6) CALL RDPRI3S(NX,NY,NZ,NOT_USED,'VOLUME NX, NY & NZ',IRTFLG) ALLOCATE(BUF(NX,NY,NZ),STAT=IRTFLG) IF (IRTFLG.NE.0) THEN CALL ERRT(46,'CP FROM PDB, BUF',IER) GOTO 9997 ENDIF I=NX/2+1 XOFFSET=PIXEL*I I=NY/2+1 YOFFSET=PIXEL*I I=NZ/2+1 ZOFFSET=PIXEL*I C CHECK IF THE VOLUME IS LARGE ENOUGH TO CONTAIN THE OBJECT IF (XMIN-UX .LT. (-1.*XOFFSET) .OR. YMIN-UY .LT. (-1.*YOFFSET) & .OR. ZMIN-UZ .LT. (-1.*ZOFFSET)) THEN CALL ERRT(101,'VOLUME TOO SMALL TO CONTAIN OBJECT',NE) GOTO 9997 ENDIF TMPX=FLOAT(NX-1)*PIXEL-XOFFSET TMPY=FLOAT(NY-1)*PIXEL-YOFFSET TMPZ=FLOAT(NZ-1)*PIXEL-ZOFFSET IF (XMAX-UX .GT. TMPX .OR. YMAX-UY .GT. TMPY & .OR. ZMAX-UZ .GT. TMPZ) THEN CALL ERRT(101,'VOLUME TOO SMALL TO CONTAIN OBJECT.',NE) GOTO 9997 ENDIF C ZERO WHOLE BUF BUF = 0.0 IFORM = 3 MAXIM = 0 CALL OPFILEC(0,.TRUE.,SPIDERFILE,LUN2,'U',IFORM, & NX,NY,NZ, MAXIM,'SPIDER OUTPUT', .FALSE.,IRTFLG) IF (IRTFLG .EQ. 1) GOTO 9997 C READ IN ATOMS NATOM = 0 TMAX = -100 40 CONTINUE READ(LUN1,20) RECLIN IF (RECLIN(1:4) .EQ. 'ATOM' ) THEN READ(RECLIN,50)HEAD,ATOM,X,Y,Z,OCCUPANCY,TEMPERATURE 50 FORMAT(A6,5X,1X,A3,2X,3X,1X,1X,4X,1X,3X,3F8.3,2F6.2) C WRITE(NOUT,*)'ATOM #',NATOM,' ',ATOM,' AT ',X,Y,Z, C & OCCUPANCY,TEMPERATURE IF (TEMP) THEN VATOM = TEMPERATURE TMAX = MAX(TMAX,TEMPERATURE) ELSEIF (.NOT. ZNUM) THEN IF (ATOM(2:2) .EQ. 'H') THEN VATOM=1.0 ELSEIF (ATOM(2:2) .EQ. 'C') THEN VATOM=6.0 ELSEIF (ATOM(2:2) .EQ. 'N') THEN VATOM=7.0 ELSEIF (ATOM(2:2) .EQ. 'O') THEN VATOM=8.0 ELSEIF (ATOM(2:2) .EQ. 'S') THEN VATOM=16.0 ELSEIF (ATOM(2:2) .EQ. 'P') THEN VATOM=15.0 ELSEIF (ATOM(2:2) .EQ. 'X' .AND. ATOM(1:3) .EQ. 'OXT') & THEN C TRNA THREE PRIME TERMINAL VATOM=8.0 ELSE WRITE(NOUT, *) ' SPECIAL ATOM ENCOUNTERED IN: ' WRITE(NOUT,*) RECLIN GOTO 9997 ENDIF C VATOM = VATOM*OCCUPANCY ELSE VATOM = OCCUPANCY ENDIF C COORDINATE SYSTEM IS DIFFERENT IN O AND SPIDER W = X X = Y Y = W Z = -Z X = X-UX Y = Y-UY Z = Z-UZ C TRILINEAR INTERPOLATION IX = IFIX((X+XOFFSET)/PIXEL) AX = (X+XOFFSET)/PIXEL-FLOAT(IX) IY = IFIX((Y+YOFFSET)/PIXEL) AY = (Y+YOFFSET)/PIXEL-FLOAT(IY) IZ = IFIX((Z+ZOFFSET)/PIXEL) AZ = (Z+ZOFFSET)/PIXEL-FLOAT(IZ) IF (TEMP) THEN BUF(IX,IY,IZ) = VATOM ELSE DO I3=1,0,-1 DO I2=1,0,-1 DO I1=1,0,-1 BUF(IX-I1+1,IY-I2+1,IZ-I3+1) = & BUF(IX-I1+1,IY-I2+1,IZ-I3+1)+ & VATOM*(REAL(I1)-(2*I1-1)*AX)* & (REAL(I2)-(2*I2-1)*AY)*(REAL(I3)-(2*I3-1)*AZ) ENDDO ENDDO ENDDO ENDIF NATOM = NATOM + 1 TMASS = TMASS + VATOM GOTO 40 ELSEIF (RECLIN(1:3) .NE. 'END') THEN GOTO 40 ENDIF DO I=1,NZ DO J=1,NY CALL WRTLIN(LUN2,BUF(1,J,I),NX,(I-1)*NY+J) ENDDO ENDDO IF (TEMP) WRITE(NOUT,*) ' MAX. TEMPERATURE:',TMAX WRITE(NOUT,8701) NATOM,TMASS 8701 FORMAT(' NUMBER OF ATOMS PLACED: ',I8, & ' TOTAL MASS:',1PE10.3) 9997 CLOSE(LUN2) IF (ALLOCATED(BUF)) DEALLOCATE(BUF) 9999 CLOSE(LUN1) END