void function ( String arg0 ) { this . pdb1 = arg0 ; }
mandatory argument to set the first pdb and optionally chain id to be aligned . concode_field_sep String cacheFilePath concode_elem_sep String saveOutputDir concode_elem_sep boolean printFatCat concode_elem_sep String searchFile concode_elem_sep boolean show3d concode_elem_sep int nrCPU concode_elem_sep boolean isDomainSplit concode_elem_sep String showDBresult concode_elem_sep String alignPairs concode_elem_sep String pdb2 concode_elem_sep boolean printXML concode_elem_sep boolean printCE concode_elem_sep String outFile concode_elem_sep boolean autoFetch concode_elem_sep boolean showMenu concode_elem_sep String pdb1 concode_elem_sep String file2 concode_elem_sep String newline concode_elem_sep String file1 concode_elem_sep boolean printPDB concode_elem_sep String pdbFilePath concode_field_sep boolean isShow3d concode_elem_sep void setSearchFile concode_elem_sep boolean isShowMenu concode_elem_sep void setOutputPDB concode_elem_sep boolean isPrintXML concode_elem_sep String getShowDBresult concode_elem_sep void setPdb2 concode_elem_sep void setShowDBresult concode_elem_sep boolean isOutputPDB concode_elem_sep void setAlignPairs concode_elem_sep void setFile1 concode_elem_sep void setFile2 concode_elem_sep String getCacheFilePath concode_elem_sep String getPdbFilePath concode_elem_sep String getFile1 concode_elem_sep void setOutFile concode_elem_sep String getSaveOutputDir concode_elem_sep void setAutoFetch concode_elem_sep void setCacheFilePath concode_elem_sep boolean isAutoFetch concode_elem_sep String getSearchFile concode_elem_sep boolean isPrintFatCat concode_elem_sep void setPdbDirSplit concode_elem_sep void setPdbFilePath concode_elem_sep void setPrintXML concode_elem_sep void setShowMenu concode_elem_sep boolean isPdbDirSplit concode_elem_sep void setShow3d concode_elem_sep void setSaveOutputDir concode_elem_sep boolean isPrintCE concode_elem_sep void setPrintFatCat concode_elem_sep void setNrCPU concode_elem_sep String getFile2 concode_elem_sep boolean isDomainSplit concode_elem_sep int getNrCPU concode_elem_sep String getAlignPairs concode_elem_sep void setPrintCE concode_elem_sep String getPdb2 concode_elem_sep String getPdb1 concode_elem_sep String toString concode_elem_sep void setDomainSplit concode_elem_sep String getOutFile