/*{{{select.c general comments */ /* name: select.c */ /* author: J. Michael Word */ /* date written: 2/20/96 */ /* purpose: parse atom selections */ /*****************************************************************/ /* NOTICE: This is free software and the source code is freely */ /* available. You are free to redistribute or modify under the */ /* conditions that (1) this notice is not removed or modified */ /* in any way and (2) any modified versions of the program are */ /* also available for free. */ /* ** Absolutely no Warranty ** */ /* Copyright (C) 1999 J. Michael Word */ /*****************************************************************/ /*}}}select.c general comments */ /*{{{--includes */ #include /*060902 needs this for strstr() */ #include "select.h" #include "atomprops.h" #include "stdconntable.h" #include "utility.h" /*}}}--includes */ /*{{{getPat() ****************************************************************/ /*select.h includes parse.h, so why is getPat here instead of in parse.c ? */ pattern* getPat(char *line, char *which, int verbose) { pattern *pat; if (!line) return NULL; pat = parseArg(line); /* parse.c/parseArg() */ if (verbose && pat) { fprintf(stderr, "%s: ", which); printPattern(stderr, pat); /* parse.c/printPattern() */ } return pat; } /*}}}getPat() _______________________________________________________________*/ /*{{{declarations ... global AA and Atom properties */ /*{{{AromaticAtomsTbl[] ***/ static ResidueAndAtomPair AromaticAtomsTbl[] = { ":PHE:", ": HD1: HD2: HE1: HE2: HZ : DD1: DD2: DE1: DE2: DZ :", 0, ":HIS:", ": HD1: HD2: HE1: HE2: DD1: DD2: DE1: DE2:", 0, ":TYR:", ": HD1: HD2: HE1: HE2: DD1: DD2: DE1: DE2:", 0, ":TRP:", ": HD1: HE1: HE3: HZ2: HZ3: HH2: DD1: DE1: DE3: DZ2: DZ3: DH2:", 0, ": U:URA:UTP:UDP:UMP: UR:", ": H3 : HN3: H5 : H6 : D3 : DN3: D5 : D6 :", 0, ": T:THY:TTP:TDP:TMP:5MU: DT: TR:", ": H3 : HN3: H6 : D3 : DN3: D6 :", 0, ": A:ADE:ATP:ADP:AMP:1MA:RIA:T6A: DA: AR:", ": H8 : H2 : D8 : D2 :", 0, ": C:CYT:CTP:CDP:CMP:5MC:OMC: DC: CR:", ": H5 : H6 : D5 : D6 :", 0, ": G:GUA:GTP:GDP:GMP:GSP:2MG:M2G:7MG:OMG: DG: GR:", ": H8 : H1 : HN1: D8 : D1 : DN1:", 0, ": YG:1MG:", ": H8 : D8 :", 0, ":PSU:", ": H6 : D6 : H1 : HN1: D1 : DN1: H3 : HN3: D3 : DN3:", 0, ": I: DI:", ": H8 : H2 : H1 : HN1: D8 : D2 : D1 : DN1:", 0, ":PHE:", ": CG : CD1: CD2: CE1: CE2: CZ :", TEST_ACCEPT_ANGLE_PROP, ":HIS:", ": ND1: CD2: CE1: NE2: CG :", 0, ":TYR:", ": CG : CD1: CD2: CE1: CE2: CZ :", TEST_ACCEPT_ANGLE_PROP, // The 5-membered ring is not treated as an aromatic acceptor face, but the 6-membered // ring is. The Nitrogen is not an acceptor because it is protonated. //":TRP:", ": CG : CD1: CD2: NE1: CE2: CE3: CZ2: CZ3: CH2:", TEST_ACCEPT_ANGLE_PROP, ":TRP:", ": CG : CD1: NE1:", 0, ":TRP:", ": CD2: CE2: CE3: CZ2: CZ3: CH2:", TEST_ACCEPT_ANGLE_PROP, ": U:URA:UTP:UDP:UMP:PSU: UR:", ": N1 : C2 : N3 : C4 : C5 : C6 :", TEST_ACCEPT_ANGLE_PROP, ": T:THY:TTP:TDP:TMP:5MU: DT: TR:", ": N1 : C2 : N3 : C4 : C5 : C6 :", TEST_ACCEPT_ANGLE_PROP, ": A:ADE:ATP:ADP:AMP:1MA:RIA:T6A: I: DA: DI: AR:", ": N1 : C2 : N3 : C4 : C5 : C6 : N7 : C8 : N9 :",TEST_ACCEPT_ANGLE_PROP, ": C:CYT:CTP:CDP:CMP:5MC:OMC: DC: CR:", ": N1 : C2 : N3 : C4 : C5 : C6 :", TEST_ACCEPT_ANGLE_PROP, ": G:GUA:GTP:GDP:GMP:GSP:1MG:2MG:M2G:7MG:OMG: DG: GR:", ": N1 : C2 : N3 : C4 : C5 : C6 : N7 : C8 : N9 :",TEST_ACCEPT_ANGLE_PROP, ": YG:", ": N1 : C2 : N3 : C4 : C5 : C6 : N7 : C8 : N9 :\ : N2 : C11: C12:",TEST_ACCEPT_ANGLE_PROP, ":HEM:", ": N A: C1A: C2A: C3A: C4A: N B: C1B: C2B: C3B: C4B:", TEST_ACCEPT_ANGLE_PROP, ":HEM:", ": N C: C1C: C2C: C3C: C4C: N D: C1D: C2D: C3D: C4D:", TEST_ACCEPT_ANGLE_PROP, 0, 0, 0}; /*061018 not allow HIS to accept H-bonds as aromatic ring system ":HIS:", ": ND1: CD2: CE1: NE2: CG :", TEST_ACCEPT_ANGLE_PROP, */ /*}}}AromaticAtomsTbl[] ___________________________________________*/ /*{{{AAList ***/ static char *AAList = ":GLY:ALA:VAL:PHE:PRO:MET:ILE:LEU:ASP:GLU:LYS:ARG:\ SER:THR:TYR:HIS:CYS:ASN:GLN:TRP:ASX:GLX:ACE:FOR:NH2:NME:MSE:AIB:ABU:PCA:"; /*}}}AAList */ /*{{{HphobicAAList ***/ static char *HphobicAAList = ":ALA:VAL:PHE:MET:ILE:LEU:TYR:CYS:TRP:MSE:AIB:ABU:"; /*}}}HphobicAAList */ /*{{{HphilicAAList ***/ static char *HphilicAAList = ":SER:THR:ASN:GLN:"; /*}}}HphilicAAList */ /*{{{AromaticAAList ***/ static char *AromaticAAList = ":PHE:HIS:TYR:TRP:HEM:"; /*}}}AromaticAAList */ /*{{{NAList ***/ static char *NAList = ": C: G: A: T: U:CYT:GUA:ADE:THY:URA:\ CTP:CDP:CMP:GTP:GDP:GMP:ATP:ADP:AMP:TTP:TDP:TMP:UTP:UDP:UMP:\ GSP:H2U:PSU:1MG:2MG:M2G:7MG:5MC:5MU:T6A:1MA:RIA:\ OMC:OMG: YG: I: DA: DT: DC: DG: DI: AR: UR: TR: GR: CR:"; /*}}}NAList */ /*{{{NAbackboneList ***/ static char *NAbackboneList = ": P : O1P: O2P: OP1: OP2: PA : PB : PG :\ : O1A: O2A: O3A: O1B: O2B: O3B: O1G: O2G: O3G: S1G:\ : O5*: C5*: C4*: O4*: C3*: O3*: C2*: O2*: C1*:\ : O5': C5': C4': O4': C3': O3': C2': O2': C1':\ : H1*: H1': H3*: H3': H4*: H4':1H5*:\ :2H5*:*H51:*H52:H5'': H5':1H2*:2H2*:\ : H2*:H2'':2HO*:*HO2: H2': H3T: H5T:\ :3HO*:HO3':*HO3:5HO*:*HO5:HO5':"; /*}}}NAbackboneList */ /*{{{NAbaseGrouping[] **/ /* used to treat similar nucleic acid bases similarly */ static ResidueAndAtomPair NAbaseGrouping[] = { ": U:URA:UTP:UDP:UMP: UR: T:THY:TTP:TDP:TMP:5MU: DT: TR:", "", baseTU, ": A:ADE:ATP:ADP:AMP:1MA:RIA:T6A: DA: AR:", "", baseA, ": C:CYT:CTP:CDP:CMP:5MC:OMC: DC: CR:", "", baseC, ": G:GUA:GTP:GDP:GMP:GSP:1MG:2MG:M2G:7MG:OMG: DG: GR:", "", baseG, ": I: YG:H2U:PSU: DI:", "", baseOther, 0, 0, 0}; /*}}}NAbaseGrouping[] */ /*{{{MethylResList ***/ /* for identifying methyl groups */ static char *MethylResList = ":THR:ALA:MET:LEU:VAL:ILE: T:THY: DT:AIB:ABU:ACE:MSE:NME:HEM:\ :OMG:OMC:1MA:1MG:2MG:M2G:5MU:5MC:7MG: YG:T6A:"; /*}}}MethylResList */ /*{{{MethylAtomsTbl[] ***/ static ResidueAndAtomPair MethylAtomsTbl[] = { /* including xplor names */ ":THR:", ": CG2:1HG2:2HG2:3HG2:HG21:HG22:HG23:", 0, ":ALA:", ": CB :1HB :2HB :3HB : HB1: HB2: HB3:", 0, ":MET:", ": CE :1HE :2HE :3HE : HE1: HE2: HE3:", 0, ":LEU:", ": CD1:1HD1:2HD1:3HD1:HD11:HD12:HD13:\ : CD2:1HD2:2HD2:3HD2:HD21:HD22:HD23:", 0, ":VAL:", ": CG1:1HG1:2HG1:3HG1:HG11:HG12:HG13:\ : CG2:1HG2:2HG2:3HG2:HG21:HG22:HG23:", 0, ":ILE:", ": CG2:1HG2:2HG2:3HG2:HG21:HG22:HG23:\ : CD1:1HD1:2HD1:3HD1:HD11:HD12:HD13:", 0, ": T:", ": C5M:1H5M:2H5M:3H5M:H5M1:H5M2:H5M3:", 0, ":THY:", ": C5A:1H5 :2H5 :3H5 : H51: H52: H53:", 0, ": DT:", ": C7 : H71: H72: H73:", 0, ":AIB:", ": CB1:1HB1:2HB1:3HB1:HB11:HB12:HB13:\ : CB2:1HB2:2HB2:3HB2:HB21:HB22:HB23:", 0, ":ABU:", ": CG :1HG :2HG :3HG : HG1: HG2: HG3:", 0, ":ACE:", ": CH3:1HH3:2HH3:3HH3:HH31:HH32:HH33:", 0, ":MSE:", ": CE :1HE :2HE :3HE : HE1: HE2: HE3:", 0, ":NME:", ": CH3:1HH3:2HH3:3HH3:HH31:HH32:HH33:", 0, ":HEM:", ": CMA:1HMA:2HMA:3HMA:HMA1:HMA2:HMA3:\ : CMB:1HMB:2HMB:3HMB:HMB1:HMB2:HMB3:\ : CMC:1HMC:2HMC:3HMC:HMC1:HMC2:HMC3:\ : CMD:1HMD:2HMD:3HMD:HMD1:HMD2:HMD3:", 0, ":OMG:OMC:", ": CM2:1HM2:2HM2:3HM2:HM22:HM22:HM23:", 0, ":1MA:1MG:", ": CM1:1HM1:2HM1:3HM1:HM12:HM12:HM13: C1A:1H1A:2H1A:3H1A:", 0, ":2MG:M2G:", ": CM1:1HM1:2HM1:3HM1:HM12:HM12:HM13: C1A:1H1A:2H1A:3H1A:\ : CM2:1HM2:2HM2:3HM2:HM22:HM22:HM23: C2A:1H2A:2H2A:3H2A:", 0, ":5MU:5MC:", ": CM5:1HM5:2HM5:3HM5:HM52:HM52:HM53: C5A:1H5A:2H5A:3H5A:", 0, ":7MG:", ": CM7:1HM7:2HM7:3HM7:HM72:HM72:HM73: C7A:1H7A:2H7A:3H7A:", 0, ": YG:", ": C3 :1H3 :2H3 :3H3 : H32: H32: H33:\ : C10:1H10:2H10:3H10:H102:H102:H103:\ : C19:1H19:2H19:3H19:H192:H192:H193:\ : C24:1H24:2H24:3H24:H242:H242:H243:", 0, ":T6A:", ": C15:1H15:2H15:3H15:H152:H152:H153:", 0, 0, 0, 0}; /*}}}MethylAtomsTbl[] */ /*{{{MethyleneResList, protein only ***/ /* for identifying methylene groups on which to find methylene H 20111211dcr*/ static char *MethyleneResList = ":LYS:ILE:ARG:PRO:GLN:GLU:MET:CIS:SER:ASN:ASP:PHE:TYR:TRP:LEU:"; /*}}}MethyleneResList */ /*{{{MethyleneAtomsTbl[] ***/ static ResidueAndAtomPair MethyleneAtomsTbl[] = { ":LYS:", ": HE2: HE3: HD2: HD3: HG2: HG3: HB2: HB3:", 0, ":ILE:", ":HG12:HG13:", 0, ":PRO:", ": HD2: HD3: HG2: HG3: HB2: HB3:", 0, ":ARG:", ": HD2: HD3: HG2: HG3: HB2: HB3:", 0, ":GLN:", ": HG2: HG3: HB2: HB3:", 0, ":GLU:", ": HG2: HG3: HB2: HB3:", 0, ":MET:", ": HG2: HG3: HB2: HB3:", 0, ":CIS:", ": HB2: HB3:", 0, ":SER:", ": HB2: HB3:", 0, ":ASN:", ": HB2: HB3:", 0, ":ASP:", ": HB2: HB3:", 0, ":PHE:", ": HB2: HB3:", 0, ":TYR:", ": HB2: HB3:", 0, ":HIS:", ": HB2: HB3:", 0, ":TRP:", ": HB2: HB3:", 0, ":LEU:", ": HB2: HB3:", 0, 0, 0, 0}; /*}}}MethyleneAtomsTbl[] */ /*{{{ChargedAAList ***/ /* for computing charge state (currently treating HIS as charged) */ static char *ChargedAAList = ":ASP:GLU:LYS:ARG:HIS:HEM:"; /*}}}ChargedAAList */ /*{{{ChargedAAAtomsTbl[] ***/ static ResidueAndAtomPair ChargedAAAtomsTbl[] = { ":ASP:", ": OD1: OD2:", NEGATIVE_PROP, ":GLU:", ": OE1: OE2:", NEGATIVE_PROP, ":LYS:", ":1HZ :2HZ :3HZ :1DZ :2DZ :3DZ : NZ :\ : HZ1: HZ2: HZ3: DZ1: DZ2: DZ3:", POSITIVE_PROP, ":ARG:", ": HE :1HH1:2HH1:1HH2:2HH2:\ : DE :1DH1:2DH1:1DH2:2DH2: NE : NH1: NH2:\ :HH11:HH12:HH21:HH22:\ :DH11:DH12:DH21:DH22:", POSITIVE_PROP, ":HIS:", ": HD1: HE2: DD1: DE2: ND1: NE2:\ : CG : CD2: CE1:", POSITIVE_PROP, ":HEM:", ": O1A: O2A: O1D: O2D:", NEGATIVE_PROP, 0, 0, 0}; /*}}}ChargedAAAtomsTbl[] */ /*{{{AlwaysChargedAtomsList ***/ static char *AlwaysChargedAtomsList = ":1H :2H :3H :1D :2D :3D : HT1: HT2: HT3: DT1: DT2: DT3:\ : NT : OXT:1OXT:2OXT:"; /*}}}AlwaysChargedAtomsList */ /*{{{AmbigChargedAtomsList ***/ static char *AmbigChargedAtomsList = ": O : N :"; /*}}}AmbigChargedAtomsList */ /*{{{ChargedNucAcidAtomsList ***/ static char *ChargedNucAcidAtomsList = ": P : O1P: O2P:\ PA : PB : PG : O1A: O2A: O3A: O1B: O2B: O3B: O1G: O2G: O3G:\ S1G:"; /*}}}ChargedNucAcidAtomsList */ /*{{{WaterList ***/ static char *WaterList = ":HOH:DOD:H2O:WAT:TIP:SOL:MTO:"; /*}}}WaterList */ /*{{{DonorAcceptorAtomTbl[] ***/ static ResidueAndAtomPair DonorAcceptorAtomTbl[] = { ":GLY:ALA:VAL:PHE:PRO:MET:ILE:LEU:ASP:GLU:LYS:ARG:\ :SER:THR:TYR:HIS:CYS:ASN:GLN:TRP:ASX:GLX:NH2:NME:MSE:AIB:ABU:PCA:", ": N : NT : H : HT1: HT2: HT3:1H :2H :3H :\ : HN : D : DT1: DT2: DT3:1D :2D :3D :", DONOR_PROP, ":GLY:ALA:VAL:PHE:PRO:MET:ILE:LEU:ASP:GLU:LYS:ARG:\ :SER:THR:TYR:HIS:CYS:ASN:GLN:TRP:ASX:GLX:ACE:FOR:MSE:AIB:ABU:PCA:", ": O : OXT:1OXT:2OXT:", ACCEPTOR_PROP, ":ASN:ASX:", ": AD1: AD2:", DONOR_PROP|ACCEPTOR_PROP, ":ASN:ASX:", ":1HD1:2HD1:HD11:HD12:\ :1DD1:2DD1:DD11:DD12:", DONOR_PROP, /* if ass backwards */ ":GLN:GLX:", ": AE1: AE2:", DONOR_PROP|ACCEPTOR_PROP, ":GLN:GLX:", ":1HE1:2HE1:HE11:HE12:\ :1DE1:2DE1:DE11:DE12:", DONOR_PROP, /* if ass backwards */ ":ASN:", ": OD1:", ACCEPTOR_PROP, ":ASN:", ": ND2:1HD2:2HD2:HD21:HD22:\ :1DD2:2DD2:DD21:DD22:", DONOR_PROP, ":GLN:", ": OE1:", ACCEPTOR_PROP, ":GLN:", ": NE2:1HE2:2HE2:HE21:HE22:\ :1DE2:2DE2:DE21:DE22:", DONOR_PROP, ":ASP:", ": OD1: OD2:", ACCEPTOR_PROP, ":GLU:", ": OE1: OE2:", ACCEPTOR_PROP, ":LYS:", ": NZ :1HZ :2HZ :3HZ : HZ1: HZ2: HZ3:\ :1DZ :2DZ :3DZ : DZ1: DZ2: DZ3:", DONOR_PROP, ":ARG:", ": NE : NH1: NH2:\ : HE :1HH1:2HH1:1HH2:2HH2:HH11:HH12:HH21:HH22:\ : DE :1DH1:2DH1:1DH2:2DH2:DH11:DH12:DH21:DH22:", DONOR_PROP, // The Nitrogens on Histidine's ring are not marked as acceptors just because of their // status as being on the ring, but they remain acceptors because they might be // unprotonated. ":HIS:", ": ND1: NE2:", DONOR_PROP | ACCEPTOR_PROP, //":HIS:", ": ND1: NE2:", DONOR_PROP, ":HIS:", ": HD1: HE2: DD1: DE2:", DONOR_PROP, ":HIS:", ": HD2: HE1: DD2: DE1:", DONOR_PROP|CH_DONOR_PROP, ":SER:", ": OG :", DONOR_PROP|ACCEPTOR_PROP, ":SER:", ": HG : DG :", DONOR_PROP, ":THR:", ": OG1:", DONOR_PROP|ACCEPTOR_PROP, ":THR:", ": HG1: DG1:", DONOR_PROP, ":TYR:", ": OH :", DONOR_PROP|ACCEPTOR_PROP, ":TYR:", ": HH : DH :", DONOR_PROP, ":CYS:", ": SG :", ACCEPTOR_PROP, /* usually */ ":CYS:", ": HG : DG :", DONOR_PROP, ":TRP:", ": NE1: HE1: DE1:", DONOR_PROP, ":MET:", ": SD :", ACCEPTOR_PROP, ":MSE:", ":SED :", ACCEPTOR_PROP, ":NH2:", ": HN1: HN2:1HN :2HN : DN1: DN2:1DN :2DN :", DONOR_PROP, ": C: G: A: T: U:CYT:GUA:ADE:THY:URA:\ :CTP:CDP:CMP:GTP:GDP:GMP:ATP:ADP:AMP:TTP:TDP:TMP:UTP:UDP:UMP:GSP:\ :H2U:PSU:1MG:2MG:M2G:5MC:5MU:T6A:1MA: YG: I: DA: DT: DC: DG: DI: AR: UR: TR: CR: GR:", ": O2*: O2':", DONOR_PROP|ACCEPTOR_PROP, ": C: G: A: T: U:CYT:GUA:ADE:THY:URA:\ :CTP:CDP:CMP:GTP:GDP:GMP:ATP:ADP:AMP:TTP:TDP:TMP:UTP:UDP:UMP:GSP:\ :H2U:PSU:1MG:2MG:M2G:5MC:5MU:T6A:1MA:RIA:OMC:OMG: YG: I: DA: DT: DC: DG: DI: AR: UR: TR: CR: GR:", ":2HO*:3HO*:5HO*: H3T: H5T:HO3':HO5':\ :2DO*:3DO*:5DO*: D3T: D5T:DO3':DO5':", /* ":2HO*:3HO*:5HO*: H2': H3': H5': H3T: H5T:HO3':HO5':\ RMI removed H2', H3' and H5' 070723 */ /* :2DO*:3DO*:5DO*: D2': D3': D5': D3T: D5T:DO3':DO5':", */ DONOR_PROP, ": C: G: A: T: U:CYT:GUA:ADE:THY:URA:\ :CTP:CDP:CMP:GTP:GDP:GMP:ATP:ADP:AMP:TTP:TDP:TMP:UTP:UDP:UMP:GSP:\ :H2U:PSU:1MG:2MG:M2G:5MC:5MU:T6A:1MA:RIA:OMC:OMG: YG: I: DA: DT: DC: DG: DI: AR: UR: TR: CR: GR:", ": O1P: O2P: OP1: OP2: O1A: O2A: O3A: O1B: O2B: O3B: O1G: O2G: O3G: S1G:\ : O3*: O5*: O3': O5':", ACCEPTOR_PROP, ": U:URA:UTP:UDP:UMP:H2U: DU: UR:",": N3 : H3 : HN3: D3 : DN3:",DONOR_PROP, ":PSU:", ": N1 : H1 : D1 : HN1: DN1:\ : N3 : H3 : D3 : HN3: DN3:", DONOR_PROP, ": U:URA:UTP:UDP:UMP:H2U:PSU: DU: UR:", ": O2 : O4 :", ACCEPTOR_PROP, ": T:THY:TTP:TDP:TMP:5MU: DT: TR:",": N3 : H3 : HN3: D3 : DN3:",DONOR_PROP, ": T:THY:TTP:TDP:TMP:5MU: DT: TR:", ": O2 : O4 :", ACCEPTOR_PROP, ": A:ADE:ATP:ADP:AMP:1MA:RIA: DA: AR:", ": N6 :1H6 :2H6 : H61: H62:1HN6:2HN6:\ :1D6 :2D6 : D61: D62:1DN6:2DN6:", DONOR_PROP, ": A:ADE:ATP:ADP:AMP:RIA: DA: AR:", ": N1 : N3 : N7 :", ACCEPTOR_PROP, ":1MA: I: DI:", ": N3 : N7 :", ACCEPTOR_PROP, ":T6A:", ": N6 : HN6: DN6: N11: HN1: DN1: H14: D14:\ : H11: D11: HO4: DO4:", DONOR_PROP, ":T6A:", ": N1 : N3 : N7 : O10:AO13:BO13: O14:", ACCEPTOR_PROP, ": C:CYT:CTP:CDP:CMP:OMC:5MC: DC: CR:", ": N4 :1H4 :2H4 : H41: H42:1HN4:2HN4:\ :1D4 :2D4 : D41: D42:1DN4:2DN4:", DONOR_PROP, ": C:CYT:CTP:CDP:CMP:OMC:5MC: DC: CR:", ": O2 : N3 :", ACCEPTOR_PROP, ": G:GUA:GTP:GDP:GMP:GSP:OMG:7MG: DG: GR:", ": N1 : N2 : H1 :1H2 :2H2 : H21: H22: HN1:1HN2:2HN2:\ : D1 :1D2 :2D2 : D21: D22: DN1:1DN2:2DN2:",DONOR_PROP, ":2MG:", ": N1 : N2 : H1 : H2 : HN1: HN2:\ : D1 : D2 : DN1: DN2:", DONOR_PROP, ": G:GUA:GTP:GDP:GMP:GSP:OMG:1MG:2MG:M2G: DG: GR:", ": O6 : N3 : N7 :", ACCEPTOR_PROP, ": YG:", ": O6 : N2 : N7 : O17: O17: O22: O23:", ACCEPTOR_PROP, ":1MG:", ": N2 :1H2 :2H2 : H21: H22:1HN2:2HN2:\ :1D2 :2D2 : D21: D22:1DN2:2DN2:", DONOR_PROP, ":M2G:", ": N1 : H1 : HN1: D1 : DN1:", DONOR_PROP, ":7MG:", ": O6 : N3 :", ACCEPTOR_PROP, ": A:ADE:ATP:ADP:AMP:1MA:RIA:T6A: I: DA: DI: AR:", ": H2 : H8 :", DONOR_PROP|CH_DONOR_PROP, ": G:GUA:GTP:GDP:GMP:GSP:OMG:1MG:2MG:M2G:7MG: YG: DG: GR:", ": H8 :", DONOR_PROP|CH_DONOR_PROP, #ifdef EXPLICIT_WATER_ATOM_NAMES ":HOH:DOD:H2O:WAT:TIP:SOL:MTO:", ": O : OH2: OD2: OW :", DONOR_PROP|ACCEPTOR_PROP, ":HOH:DOD:H2O:WAT:TIP:SOL:MTO:", ": H : H1 : H2 :1H :2H : D : D1 : D2 :1D :2D : H? :", DONOR_PROP, #endif /* also, the aromatic heavy atoms are considered H bond acceptors (see setAromaticProp) */ 0, 0, 0}; /*}}}DonorAcceptorAtomTbl[] */ /*}}}declarations */ /*{{{naBaseCategory() ********************************************************/ /* used to assign a category to atoms to allow coloring */ /* dots by base rather than atom type */ /* naBaseCategory() must be called after setProperties() */ int naBaseCategory(atom *a) { ResidueAndAtomPair *pair; if ((a->props & DNA_PROP) && (a->props & SC_PROP)) { if(strstr(NAList, a->r->resname)) { for (pair = NAbaseGrouping; pair->rlist; pair++){ if(strstr(pair->rlist, a->r->resname)) { return pair->bits; /* bits contain the atom type */ } } return baseOther; /* not in table */ } else return baseOther; /* not in list */ } else return nonBase; /* backbone or not recognized as a nucleic acid */ } /*}}}naBaseCategory() _______________________________________________________*/ /*{{{setAromaticProp() *******************************************************/ /* hunt for aromatic atoms and set AROMATIC property & atomHarom */ /* also find aromatic carbon atoms and set atomCarom */ void setAromaticProp(atom *a) { ResidueAndAtomPair *pair; if((strstr(AromaticAAList, a->r->resname)) || (strstr(NAList, a->r->resname))) { for (pair = AromaticAtomsTbl; pair->rlist && pair->alist; pair++){ if((strstr(pair->rlist, a->r->resname)) && (strstr(pair->alist, a->atomname))) { a->props |= AROMATIC_PROP; a->props |= pair->bits; /* selectively set TEST_ACCEPT_ANGLE prop */ if(isHatom(a->elem)) { a->elem = atomHarom; } if(isCatom(a->elem)) { a->elem = atomCarom; } break; } } } } /*}}}setAromaticProp() ______________________________________________________*/ /*{{{setMethylProp() *********************************************************/ /* hunt for Methyl atoms and set METHYL property */ void setMethylProp(atom *a) { ResidueAndAtomPair *pair; if(strstr(MethylResList, a->r->resname)) { for (pair = MethylAtomsTbl; pair->rlist && pair->alist; pair++){ if((strstr(pair->rlist, a->r->resname)) && (strstr(pair->alist, a->atomname))) { a->props |= METHYL_PROP; break; } } } } /*}}}setMethylProp()_________________________________________________________*/ /*{{{setMethyleneProp() ******************************************************/ /* hunt for Methyene atoms and set METHYLENE property */ void setMethyleneProp(atom *a) { ResidueAndAtomPair *pair; if(strstr(MethyleneResList, a->r->resname)) { for(pair = MethyleneAtomsTbl; pair->rlist && pair->alist; pair++) { if( (strstr(pair->rlist, a->r->resname)) && (strstr(pair->alist, a->atomname)) ) { a->props |= METHYLENE_PROP; break; } } } } /*}}}setMethyleneProp()______________________________________________________*/ /*{{{isCarbonylAtom() ********************************************************/ int isCarbonylAtom(atom *a) { /* limitation: this will not handle het groups properly */ return (strstr(AAList, a->r->resname) && (!strcmp(a->atomname, " C "))) ||((strstr(":ASP:ASN:ASX:",a->r->resname))&&(strstr(": CG :",a->atomname))) ||((strstr(":GLU:GLN:GLX:",a->r->resname))&&(strstr(": CD :",a->atomname))); } /*}}}isCarbonylAtom() _______________________________________________________*/ /*{{{setProperties() *********************************************************/ /* set property flags for this atom and return T/F as an indicator */ /* that this atom is important in figuring out if N and O atoms */ /* are in the N or C terminus */ /* later functions can look through a list of these atoms to see if */ /* atoms marked MAYBECHG_PROP are in a terminal residue */ /*060212 Properties as specified in current pdb-format files, */ /*are not logically complete. HETATM records and residue names that are*/ /*known valid protein or nucleic acid names can occur both in regions that */ /*are protein/nucleic chain and regions that are het-chains */ /* The only way to beat this is to accummulate evidence of the type of */ /*region as atoms are read in, then set a new and different flag for region*/ void setProperties(atom *a, int hetflag, int hb2aromaticFace, int chohb) { char *s; ResidueAndAtomPair *pair; int addCharge = FALSE, checkTerminal = FALSE; a->props = 0; setAromaticProp(a); setMethylProp(a); setMethyleneProp(a); /*20111211dcr*/ if (strstr(WaterList, a->r->resname)) { a->props |= WATER_PROP; } else if(hetflag) { /* non water hets */ if (! strstr(":MSE:", a->r->resname)) { /* SelenoMet is not a HET for our purposes here */ a->props |= HET_PROP; } } if(strstr(AAList, a->r->resname)) { /* proteins and peptides */ a->props |= PROT_PROP; if(strstr(HphobicAAList, a->r->resname)){a->props |= RHPHOBIC_PROP;} else if(strstr(HphilicAAList, a->r->resname)){a->props |= RHPHILIC_PROP;} else if(strstr(ChargedAAList, a->r->resname)){a->props |= RCHARGED_PROP;} s = a->atomname; if (a->elem == atomC || isHatom(a->elem)) { if (s[2] == 'A') { if (!strcmp(s, "2HA ")){ a->props |= ALPHA_PROP; } else { a->props |= ALPHA_PROP|MC_PROP; } } else if (s[2] == 'B') { a->props |= BETA_PROP; } else if (!strcmp(s, " C ")) { a->props |= MC_PROP; } else if (!strcmp(s+1, "H ")) { a->props |= MC_PROP; } else if (!strcmp(s+1, "D ")) { a->props |= MC_PROP; } else if (strstr(": HXT: DXT: HN :", s)){ a->props|= MC_PROP; } } else if (!strcmp(s, " N ")) { a->props |= MC_PROP; } else if (!strcmp(s, " O ")) { a->props |= MC_PROP; } else if (strstr(AlwaysChargedAtomsList, s)) { a->props |= MC_PROP; } if (!(a->props & MC_PROP)) { a->props |= SC_PROP;} } else if(strstr(NAList, a->r->resname)) { /* DNA and RNA */ a->props |= DNA_PROP; if (strstr(NAbackboneList, a->atomname)) { a->props |= MC_PROP; } else { a->props |= SC_PROP;} } switch(a->elem) { case atomN: a->props |= N_PROP; break; case atomC: a->props |= C_PROP; break; case atomO: a->props |= O_PROP; break; case atomS: a->props |= S_PROP; break; case atomP: a->props |= P_PROP; break; } if (isHatom(a->elem)) { a->props |= H_PROP; } if (atomHasProp(a->elem, METALIC_ATOM_FLAG)) { a->props |= METAL_PROP; } if (atomHasProp(a->elem, IONIC_ATOM_FLAG)) { a->props |= ION_PROP; }/*dcr041007*/ /* HBond Donor/Acceptor status */ if (hb2aromaticFace && (a->props & TEST_ACCEPT_ANGLE_PROP)) { a->props |= ACCEPTOR_PROP; } if (a->props & WATER_PROP) { /* water O or H */ if (a->elem == atomO) { a->props |= DONOR_PROP|ACCEPTOR_PROP; } else if (isHatom(a->elem)) { a->props |= DONOR_PROP; } } else if ((a->elem == atomN)||(a->elem == atomO)||(a->elem == atomS)||isHatom(a->elem)){ if((strstr(AAList, a->r->resname)) || (strstr(NAList, a->r->resname)) || (strstr(WaterList, a->r->resname))) { for (pair = DonorAcceptorAtomTbl; pair->rlist && pair->alist; pair++){ if((strstr(pair->rlist, a->r->resname)) && (strstr(pair->alist, a->atomname))) { if ((! chohb) && (pair->bits & CH_DONOR_PROP)) { /* do nothing --- not doing CH..O type hbonds */ } else { /* we generally fall in this category */ a->props |= pair->bits; /* set donor/acceptor properties */ } break; } } if ( !( isHatom(a->elem) || (a->props & (ACCEPTOR_PROP|DONOR_PROP)) ) ) { a->props |= ACCEPTOR_PROP; /* default for N,O,S */ } } else if (!isHatom(a->elem)){/* mostly handles het groups we are unsure about */ a->props |= DONOR_PROP|ACCEPTOR_PROP; } } /* note: final H atom DONOR assignment done later in updateHydrogenInfo() */ /* but the above code will set (for selections) most HB donor hydrogens */ /* determining charge state of atoms */ addCharge = FALSE; checkTerminal = FALSE; if (a->props & PROT_PROP) { if(strstr(AmbigChargedAtomsList, a->atomname)) { if (!strcmp(a->atomname, " N ")) { /* *** N+ must be first residue *** */ a->props |= MAYBECHG_PROP; } else if (!strcmp(a->atomname, " O ")) { /* *** O- must be last residue *** */ a->props |= MAYBECHG_PROP; checkTerminal = TRUE; /* O used to indicate end of chain */ } } else if(strstr(AlwaysChargedAtomsList, a->atomname)) { addCharge = TRUE; checkTerminal = TRUE; /* 1H,2H,3H or OXT indicate end of chain */ } else if (strstr(ChargedAAList, a->r->resname)) { for (pair = ChargedAAAtomsTbl; pair->rlist && pair->alist; pair++){ if((strstr(pair->rlist, a->r->resname)) && (strstr(pair->alist, a->atomname))) { /* addCharge = TRUE; */ a->props |= pair->bits; break; } } } } else if ((a->props & DNA_PROP) && (strstr(ChargedNucAcidAtomsList, a->atomname))) { addCharge = TRUE; } else if (a->props & METAL_PROP) { addCharge = TRUE; } else if (a->props & ION_PROP) { addCharge = TRUE; } /*dcr041007*/ if(addCharge) { if (a->props & METAL_PROP) { a->props |= POSITIVE_PROP; } else if (a->props & H_PROP) { a->props |= POSITIVE_PROP; } else { switch(a->elem) { case atomN: a->props |= POSITIVE_PROP; break; case atomO: a->props |= NEGATIVE_PROP; break; case atomS: a->props |= NEGATIVE_PROP; break; case atomP: a->props |= NEGATIVE_PROP; break; /*dcr041007 should O,S,Se be allowed to be acceptors ???? */ /*dcr041007 halides get (NEGATIVE_PROP|ACCEPTOR_PROP) */ case atomF: a->props |= (NEGATIVE_PROP|ACCEPTOR_PROP); break; case atomCl: a->props |= (NEGATIVE_PROP|ACCEPTOR_PROP); break; case atomBr: a->props |= (NEGATIVE_PROP|ACCEPTOR_PROP); break; case atomI: a->props |= (NEGATIVE_PROP|ACCEPTOR_PROP); break; /*dcr041007 halides only need ACCEPTOR_PROP to not clash with polar H*/ } } } if (checkTerminal) { /* now we have to fixup some of the MAYBECHG_PROP atoms elsewhere */ a->props |= CHECK_ENDS_PROP; /* these atoms will help us do that */ } }/*setProperties*/ /*}}}setProperties() ________________________________________________________*/ /*{{{matchPat() ************* only called from probe.c/selectSource() ********/ /* recursive at OR,AND,NOT nodes; TRUE,FALSE nodes allow those logic choices*/ int matchPat(atom *a, pattern *pat) { int lp, rc = FALSE; if (pat) { switch(pat->type) { case OR_NODE: rc = matchPat(a, pat->lhs) ? TRUE : matchPat(a, pat->rhs); break; case AND_NODE: rc = matchPat(a, pat->lhs) ? matchPat(a, pat->rhs) : FALSE; break; case NOT_NODE: rc = !matchPat(a, pat->lhs); break; case FILE_NODE: rc = (a->r->file == pat->val); break; case MODEL_NODE: rc = (a->r->model == pat->val); break; case CHAIN_NODE: lp = strlen(lexString(pat->val)); rc = (strncmp(lexString(pat->val), a->r->chain, lp) == 0); break; case ALT_NODE: rc = (a->altConf == ' ' || a->altConf == pat->val); break; case RES_NODE: rc = (a->r->resid == pat->val); break; case RANGE_NODE: rc = (pat->lhs->val <= a->r->resid && a->r->resid <= pat->rhs->val); break; case RTYPE_NODE: lp = strlen(lexString(pat->val)); rc = (strncmp(lexString(pat->val), a->r->resname, lp) == 0); break; case DIST_NODE: rc = atomWithinDistance(a, pat->fvec); break; case PROP_NODE: rc = (a->props & pat->val); break; case ANAME_NODE: lp = strlen(lexString(pat->val)); rc = (strncmp(lexString(pat->val), a->atomname, lp) == 0); break; case SEGID_NODE: lp = strlen(lexString(pat->val)); rc = (strncmp(lexString(pat->val), a->r->segid, lp) == 0); break; case TRUE_NODE: rc = TRUE; break; case FALSE_NODE: rc = FALSE; break; case OCC_LT_NODE: rc = (a->occ < pat->val/100.0); break; case OCC_GT_NODE: rc = (a->occ > pat->val/100.0); break; case B_LT_NODE: rc = (a->bval < pat->val); break; case B_GT_NODE: rc = (a->bval > pat->val); break; case INS_NODE: rc = (a->r->resInsCode == pat->val); break; /* ignores the insertion code */ case INS_RANGE_NODE: rc = (((pat->lhs->val == AND_NODE) ? pat->lhs->lhs->val : pat->lhs->val) <= a->r->resid && a->r->resid <= ((pat->rhs->val == AND_NODE) ? pat->rhs->lhs->val : pat->rhs->val)); break; default: { char msg[100]; sprintf(msg, "unknown pattern type: %d", pat->type); halt(msg); } }/*switch*/ } return rc; } /*}}}matchPat() _____________________________________________________________*/ /*{{{atomWithinDistance() ****************************************************/ /* is the atom within the specified distance from the given point? */ int atomWithinDistance(atom *a, float *fvec) { double dx = a->loc.x - fvec[1]; double dy = a->loc.y - fvec[2]; double dz = a->loc.z - fvec[3]; return ((dx*dx)+(dy*dy)+(dz*dz)) < (fvec[0]*fvec[0]); } /*}}}atomWithinDistance() ___________________________________________________*/ /*{{{setHydrogenParentName() *************************************************/ /* Set the parent atom name for a hydrogen */ /* if can be determined from the hydrogen name.*/ /* These parent names are used when a hydrogen */ /* has more than one parent close enough to */ /* bond. No such bonding table is currently */ /* setup for non-hydrogens. */ char * setHydrogenParentName(char *rname, char *aname) { return searchForStdBondingPartner(rname, aname, TRUE); } /*}}}setHydrogenParentName() ________________________________________________*/ /*{{{setMainchainBonding() ***************************************************/ /* For heavy atoms, set the name of atoms which would bond with */ /* in standard residues. */ /* This is used only when the -STDBOND flag */ /* is on the command line (UseStdBond == TRUE). */ char * setMainchainBonding(char *rname, char *aname) { return searchForStdBondingPartner(rname, aname, FALSE); } /*}}}setMainchainBonding() __________________________________________________*/