xlogpdescriptor.java

化学图形处理软件

                                if (getAtomTypeXCount(ac, atomi) == 0 ) {
                                    xlogP += 0.296;
                                    //logger.debug("XLOGP: 34		 0.296");
                                } else {
                                    xlogP -= 0.151;
                                    //logger.debug("XLOGP: 35	C.ar.x	-0.151");
                                }
                            } else {
                                xlogP += 0.337;
                                //logger.debug("XLOGP: 32		 0.337");
                            }
                            //} else if (getAromaticCarbonsCount(ac, atoms[i]) < 2 && getAromaticNitrogensCount(ac, atoms[i]) > 1) {
                        } else if (getAromaticNitrogensCount(ac, atomi) >= 1) {
                            if (hsCount == 0) {
                                if (getAtomTypeXCount(ac, atomi) == 0) {
                                    xlogP += 0.174;
                                    //logger.debug("XLOGP: 36	C.ar.(X)	 0.174");
                                } else {
                                    xlogP += 0.366;
                                    //logger.debug("XLOGP: 37		 0.366");
                                }
                            } else if (getHydrogenCount(ac, atomi) == 1) {
                                xlogP += 0.126;
                                //logger.debug("XLOGP: 33		 0.126");
                            }
                        }
                        //NOT aromatic, but sp2
                    } else {
                        if (hsCount == 0) {
                            if (getAtomTypeXCount(ac, atomi) == 0) {
                                if (getPiSystemsCount(ac, atomi) <= 1) {
                                    xlogP += 0.05;
                                    //logger.debug("XLOGP: 26		 0.05");
                                } else {
                                    xlogP += 0.013;
                                    //logger.debug("XLOGP: 27		 0.013");
                                }
                            }
                            else if (getAtomTypeXCount(ac, atomi) == 1) {
                                if (getPiSystemsCount(ac, atomi) == 0) {
                                    xlogP -= 0.03;
                                    //logger.debug("XLOGP: 28		-0.03");
                                } else {
                                    xlogP -= 0.027;
                                    //logger.debug("XLOGP: 29		-0.027");
                                }
                            }
                            else if (getAtomTypeXCount(ac, atomi) == 2) {
                                if (getPiSystemsCount(ac, atomi) ==0) {
                                    xlogP += 0.005;
                                    //logger.debug("XLOGP: 30		 0.005");
                                } else {
                                    xlogP -= 0.315;
                                    //logger.debug("XLOGP: 31		-0.315");
                                }
                            }
                        }
                        if (hsCount == 1) {
                            if (getAtomTypeXCount(ac, atomi) == 0) {
                                if (getPiSystemsCount(ac, atomi) == 0) {
                                    xlogP += 0.466;
                                    //logger.debug("XLOGP: 22		 0.466");
                                }
                                if (getPiSystemsCount(ac, atomi) == 1) {
                                    xlogP += 0.136;
                                    //logger.debug("XLOGP: 23		 0.136");
                                }
                            } else {
                                if (getPiSystemsCount(ac, atomi) == 0) {
                                    xlogP += 0.001;
                                    //logger.debug("XLOGP: 24		 0.001");
                                }
                                if (getPiSystemsCount(ac, atomi) == 1) {
                                    xlogP -= 0.31;
                                    //logger.debug("XLOGP: 25		-0.31");
                                }
                            }
                        }
                        if (hsCount == 2) {
                            xlogP += 0.42;
                            //logger.debug("XLOGP: 21		 0.42");
                        }
                        if (getIfCarbonIsHydrophobic(ac, atomi)) {
                            xlogP += 0.211;
                            //logger.debug("XLOGP: Hydrophobic Carbon	0.211");
                        }
                    }//sp2 NOT aromatic
                }

                if (bondCount == 4) {
                    // C sp3
                    if (hsCount == 0) {
                        if (getAtomTypeXCount(ac, atomi) == 0) {
                            if (getPiSystemsCount(ac, atomi) == 0) {
                                xlogP -= 0.006;
                                //logger.debug("XLOGP: 16		-0.006");
                            }
                            if (getPiSystemsCount(ac, atomi) == 1) {
                                xlogP -= 0.57;
                                //logger.debug("XLOGP: 17		-0.57");
                            }
                            if (getPiSystemsCount(ac, atomi) >= 2) {
                                xlogP -= 0.317;
                                //logger.debug("XLOGP: 18		-0.317");
                            }
                        } else {
                            if (getPiSystemsCount(ac, atomi) == 0) {
                                xlogP -= 0.316;
                                //logger.debug("XLOGP: 19		-0.316");
                            } else {
                                xlogP -= 0.723;
                                //logger.debug("XLOGP: 20		-0.723");
                            }
                        }
                    }
                    if (hsCount == 1) {
                        if (getAtomTypeXCount(ac, atomi) == 0) {
                            if (getPiSystemsCount(ac, atomi) == 0) {
                                xlogP += 0.127;
                                //logger.debug("XLOGP: 10		 0.127");
                            }
                            if (getPiSystemsCount(ac, atomi) == 1) {
                                xlogP -= 0.243;
                                //logger.debug("XLOGP: 11		-0.243");
                            }
                            if (getPiSystemsCount(ac, atomi) >= 2) {
                                xlogP -= 0.499;
                                //logger.debug("XLOGP: 12		-0.499");
                            }
                        } else {
                            if (getPiSystemsCount(ac, atomi) == 0) {
                                xlogP -= 0.205;
                                //logger.debug("XLOGP: 13		-0.205");
                            }
                            if (getPiSystemsCount(ac, atomi) == 1) {
                                xlogP -= 0.305;
                                //logger.debug("XLOGP: 14		-0.305");
                            }
                            if (getPiSystemsCount(ac, atomi) >= 2) {
                                xlogP -= 0.709;
                                //logger.debug("XLOGP: 15		-0.709");
                            }
                        }
                    }
                    if (hsCount == 2) {
                        if (getAtomTypeXCount(ac, atomi) == 0) {
                            if (getPiSystemsCount(ac, atomi) == 0) {
                                xlogP += 0.358;
                                //logger.debug("XLOGP:  4		 0.358");
                            }
                            if (getPiSystemsCount(ac, atomi) == 1) {
                                xlogP -= 0.008;
                                //logger.debug("XLOGP:  5		-0.008");
                            }
                            if (getPiSystemsCount(ac, atomi) == 2) {
                                xlogP -= 0.185;
                                //logger.debug("XLOGP:  6		-0.185");
                            }
                        } else {
                            if (getPiSystemsCount(ac, atomi) == 0) {
                                xlogP -= 0.137;
                                //logger.debug("XLOGP:  7		-0.137");
                            }
                            if (getPiSystemsCount(ac, atomi) == 1) {
                                xlogP -= 0.303;
                                //logger.debug("XLOGP:  8		-0.303");
                            }
                            if (getPiSystemsCount(ac, atomi) == 2) {
                                xlogP -= 0.815;
                                //logger.debug("XLOGP:  9		-0.815");
                            }
                        }
                    }
                    if (hsCount > 2) {
                        if (getAtomTypeXCount(ac, atomi) == 0) {
                            if (getPiSystemsCount(ac, atomi) == 0) {
                                xlogP += 0.528;
                                //logger.debug("XLOGP:  1		 0.528");
                            }
                            if (getPiSystemsCount(ac, atomi) == 1) {
                                xlogP += 0.267;
                                //logger.debug("XLOGP:  2		 0.267");
                            }
                        }else{
                            //if (getNitrogenOrOxygenCount(ac, atomi) == 1) {
                            xlogP -= 0.032;
                            //logger.debug("XLOGP:  3		-0.032");
                        }
                    }
                    if (getIfCarbonIsHydrophobic(ac, atomi)) {
                        xlogP += 0.211;
                        //logger.debug("XLOGP: Hydrophobic Carbon	0.211");
                    }
                }//csp3


            }//C

            if (symbol.equals("N")) {
                //NO2
                if (ac.getBondOrderSum(atomi) >= 3.0 && getOxygenCount(ac, atomi) >= 2 && maxBondOrder==2) {
                    xlogP += 1.178;
                    //logger.debug("XLOGP: 66		 1.178");
                }
                else {
                    if (getPresenceOfCarbonil(ac, atomi)>=1) {
                        // amidic nitrogen
                        if (hsCount == 0) {
                            if (getAtomTypeXCount(ac, atomi) == 0) {
                                xlogP += 0.078;
                                //logger.debug("XLOGP: 57		 0.078");
                            }
                            if (getAtomTypeXCount(ac, atomi) == 1) {
                                xlogP -= 0.118;
                                //logger.debug("XLOGP: 58		-0.118");
                            }
                        }
                        if (hsCount == 1) {
                            if (getAtomTypeXCount(ac, atomi) == 0) {
                                xlogP -= 0.096;
                                hBondDonors.add(new Integer(i));
                                //logger.debug("XLOGP: 55		-0.096");
                            } else {
                                xlogP -= 0.044;
                                hBondDonors.add(new Integer(i));
                                //logger.debug("XLOGP: 56		-0.044");
                            }
                        }
                        if (hsCount == 2) {
                            xlogP -= 0.646;
                            hBondDonors.add(new Integer(i));
                            //logger.debug("XLOGP: 54		-0.646");
                        }
                    } else {//NO amidic nitrogen
                        if (bondCount == 1) {
                            // -C#N
                            if (getCarbonsCount(ac, atomi) == 1) {
                                xlogP -= 0.566;
                                //logger.debug("XLOGP: 68		-0.566");
                            }
                        }else if (bondCount == 2) {
                            // N sp2
                            if (((Boolean)atomi.getProperty("IS_IN_AROMATIC_RING")).booleanValue()) {
                                xlogP -= 0.493;
                                //logger.debug("XLOGP: 67		-0.493");
                                if (checkAminoAcid!=0){ checkAminoAcid+=1;}
                            } else {
                                if (getDoubleBondedCarbonsCount(ac, atomi) == 0) {
                                    if (getDoubleBondedNitrogenCount(ac, atomi) == 0) {
                                        if (getDoubleBondedOxygenCount(ac, atomi) == 1) {
                                            xlogP += 0.427;
                                            //logger.debug("XLOGP: 65		 0.427");
                                        }
                                    }
                                    if (getDoubleBondedNitrogenCount(ac, atomi) == 1) {
                                        if (getAtomTypeXCount(ac, atomi) == 0) {
                                            xlogP += 0.536;
                                            //logger.debug("XLOGP: 63		 0.536");
                                        }
                                        if (getAtomTypeXCount(ac, atomi) == 1) {
                                            xlogP -= 0.597;
                                            //logger.debug("XLOGP: 64		-0.597");
                                        }
                                    }
                                }else if (getDoubleBondedCarbonsCount(ac, atomi) == 1) {
                                    if (getAtomTypeXCount(ac, atomi) == 0) {
                                        if (getPiSystemsCount(ac, atomi) == 0) {
                                            xlogP += 0.007;
                                            //logger.debug("XLOGP: 59		 0.007");
                                        }
                                        if (getPiSystemsCount(ac, atomi) == 1) {
                                            xlogP -= 0.275;
                                            //logger.debug("XLOGP: 60		-0.275");
                                        }
                                    }else if (getAtomTypeXCount(ac, atomi) == 1) {
                                        if (getPiSystemsCount(ac, atomi) == 0) {
                                            xlogP += 0.366;
                                            //logger.debug("XLOGP: 61		 0.366");
                                        }
                                        if (getPiSystemsCount(ac, atomi) == 1) {
                                            xlogP += 0.251;
                                            //logger.debug("XLOGP: 62		 0.251");
                                        }
                                    }