public static void main(String[] args){ String file = "/Users/andreas/WORK/PDB/mmCif/a9/1a9n.cif.gz"; //String file = "/Users/andreas/WORK/PDB/MMCIF/1gav.mmcif"; //String file = "/Users/andreas/WORK/PDB/MMCIF/100d.cif"; //String file = "/Users/andreas/WORK/PDB/MMCIF/1a4a.mmcif"; System.out.println("parsing " + file); StructureIOFile pdbreader = new MMCIFFileReader(); try { Structure s = pdbreader.getStructure(file); System.out.println(s); // convert it to a PDB file... System.out.println(s.toPDB()); } catch (IOException e) { e.printStackTrace(); } }
Structure s = null; try { s = reader.getStructure(f); } catch (IOException e){ logger.warn(e.getMessage());
private Structure loadCustomStructure(String userPath2, String userChain2) throws StructureException{ StructureIOFile reader = new PDBFileReader(); Structure s = null; try { s = reader.getStructure(userPath2); } catch (IOException e){ //e.printStackTrace(); throw new StructureException(e); } return StructureTools.getReducedStructure(s, userChain2); }